Patent Application
20240294890
The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. The xml copy, created on May 3, 2024, is named 753652_083474-015DV_ST26.xml and is 950,786 bytes in size.
The subject matter disclosed herein is generally related to systems, methods, and compositions for RNA-guided RNA-targeting CRISPR effectors for the treatment of diseases and diagnostics.
RNA targeting tools for genetic engineering are important to study RNA biology and develop RNA therapeutics. These tools can regulate intracellular and intercellular target-gene functions and expressions and manipulate specific target-genomic information. In contrast to DNA targeting tools, only a few RNA targeting tools for CRISPR applications have been developed, and these RNA specific tools present challenges. For instance, protein complexes for CRISPR RNA editing can have a weak activity in mammalian cells and present collateral effects which can be toxic in some cell types. Also, the size of the RNA editing tools can be a significant barrier to their use, as technologies such as programmable activation cannot be delivered in mouse models using common methods such as adeno-associated vectors (AAV). Development of effective gene and cell therapies requires genome editing tools and delivery technologies that can meet the demands for cell type specificity, large payload sizes, and efficient integration of diverse and large sequences. Many applications, including single-vector homology directed repair (HDR), CRISPR base editing, gene activation, and large gene delivery, are limited by AAV size restrictions. Thus, there remains a need for more effective tools for gene correction and delivery.
The present invention is directed to systems, methods, and compositions for RNA-guided RNA-targeting CRISPR effectors for the treatment of diseases and diagnostics. It also pertains to nucleotide deaminase functionalized CRISPR systems for RNA editing RNA knockdown, viral resistance, splicing modulation, RNA tracking, translation modulation, and epi-transcriptomic modifications.
In one aspect, a composition that cleaves an RNA target is discussed, which comprises a guide RNA that specifically hybridizes to the RNA target, and a polypeptide comprising an amino acid sequence 85% identical to an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-32 and 632. The amino acid sequence can be SEQ ID NO: 1. The polypeptide can comprise a glutamate at a position corresponding to position 70 of SEQ ID NO:1, an aspartate at a position corresponding to position 429 of SEQ ID NO:1, an aspartate at a position corresponding to position 487 of SEQ ID NO:1, and/or an aspartate at a position corresponding to position 654 of SEQ ID NO:1. If desired, the polypeptide can comprise an amino acid sequence 90% identical to the amino acid sequence of SEQ ID NO:1. If desired, the polypeptide can comprise an amino acid sequence 95% identical to the amino acid sequence of SEQ ID NO:1. If desired, the polypeptide can comprise an amino acid sequence 99% identical to the amino acid sequence of SEQ ID NO:1. If desired, the polypeptide can be the amino acid sequence of SEQ ID NO:1.
Yet in another aspect, the guide RNA comprises a mismatch distance that is 20-65% of the length of the guide. If desired, the guide RNA can comprise a mismatch that is about 20 to about 30 nucleotides from the non-pairing C of the guide RNA. If desired, the guide RNA can have a sequence with a length of from about 20 to about 53 nucleotides (nt), preferably from about 25 to about 53 nt, more preferably from about 29 to about 53 nt or from about 40 to about 50 nt. If desired, the guide RNA can be a pre-crRNA. If desired, the guide RNA can be a mature crRNA.
Yet in another aspect, the RNA target can be a single-strand RNA (ssRNA). If desired, the RNA target can be in a cell. The cell can be a prokaryotic cell. The cell can be a eukaryotic cell. The eukaryotic cell can be a mammalian cell. The mammalian cell can be a human cell.
Yet in another aspect, the polypeptide can comprise a deaminase domain. The deaminase can be selected from the group consisting of an adenosine deaminase, a cytidine deaminase, and a catalytic domain thereof. If desired, the deaminase can be an adenosine deaminase. If desired, the deaminase domain can comprise an amino acid sequence 85% identical to an amino acid sequence selected from the group consisting of SEQ ID NOs: 25-31. If desired, the deaminase domain can comprise an amino acid sequence 85% identical to an amino acid sequence selected from the group consisting of SEQ ID NOs: 32-42.
Yet in another aspect, a nucleic acid molecule encoding the polypeptide is discussed. The nucleic acid molecule can encode the guide RNA.
Yet in another aspect, a vector comprising the nucleic acid molecule is discussed.
Yet in another aspect, a cell comprising the composition, the nucleic acid molecule or the vector is discussed. If desired, the cell can be a prokaryotic cell. If desired, the cell can be a eukaryotic cell. The eukaryotic cell can be a mammalian cell. The mammalian cell can be a human cell.
Yet in another aspect, a method of cleaving an RNA target in a cell is discussed, which comprises providing to the cell the composition, the nucleic acid molecule or the vector. If desired, the RNA target can be an ssRNA.
Yet in another aspect, a method of stabilizing an RNA target in a cell is discussed, which comprises providing to the cell the composition, the nucleic acid molecule or the vector. If desired, the RNA target can be an ssRNA.
Yet in another aspect, a method of affecting translation of an RNA target in a cell is discussed, which comprises providing to the cell the composition, the nucleic acid molecule or the vector. If desired, the RNA target can be an ssRNA.
Yet in another aspect, a method of treating a genetically inherited disease in a subject in need thereof is discussed, which comprises administering to the subject an effective amount of the composition, the nucleic acid molecule or the vector, wherein the genetically inherited disease involves a guanosine to adenosine change in the genome of the subject. The genetically inherited disease can be selected from the group consisting of Meier-Gorlin syndrome; Seckel syndrome 4; Joubert syndrome 5; Leber congenital amaurosis 10; Charcot-Marie-Tooth disease, type 2; leukoencephalopathy; Usher syndrome, type 2C; spinocerebellar ataxia 28; glycogen storage disease type III; primary hyperoxaluria, type I; long QT syndrome 2; Sjögren-Larsson syndrome; hereditary fructosuria; neuroblastoma; amyotrophic lateral sclerosis type 9; Kallmann syndrome 1; limb-girdle muscular dystrophy, type 2L; familial adenomatous polyposis 1; familial type 3 hyperlipoproteinemia; Alzheimer's disease, type 1; metachromatic leukodystrophy; and cancer.
Yet in another aspect, a method of treating a genetically inherited disease in a subject in need thereof is discussed, which comprises administering to the subject an effective amount of the composition, the nucleic acid molecule or the vector, wherein the genetically inherited disease is a pre-termination disease.
Yet in another aspect, a method of altering splicing of a pre-mRNA in a cell is discussed, which comprises administering to the cell an effective amount of the composition, the nucleic acid molecule or the vector.
Yet in another aspect, a method of changing microRNA targets in a subject in need is discussed, which comprises administering to the subject an effective amount of the composition, the nucleic acid molecule or the vector.
Yet in another aspect, a method of increasing RNA stability in a cell is discussed, which comprises administering to the cell an effective amount of the composition, the nucleic acid molecule or the vector.
Yet in another aspect, a method of modulating translation in a cell is discussed, which comprises administering to the cell an effective amount of the composition, the nucleic acid molecule or the vector.
Yet in another aspect, a method of detecting a bacterium or derivative thereof in a sample is discussed, the method comprises adding to the sample an effective amount of the composition, the nucleic acid molecule or the vector, and detecting a reporter specific to the bacterium or derivative thereof.
Yet in another aspect, a method of detecting a virus or derivative thereof in a sample is discussed, the method comprises adding to the sample an effective amount of the composition, the nucleic acid molecule or the vector, and detecting a reporter specific to the virus or derivative thereof.
These and other aspects of the applicants' teaching are set forth herein.
Aspects, features, benefits and advantages of the embodiments described herein will be apparent with regard to the following description, appended claims, and accompanying drawings where:
It will be appreciated that for clarity, the following discussion will describe various aspects of embodiments of the applicant's teachings. It should be noted that the specific embodiments are not intended as an exhaustive description or as a limitation to the broader aspects discussed herein. One aspect described in conjunction with a particular embodiment is not necessarily limited to that embodiment and can be practiced with any other embodiment(s). Reference throughout this specification to “one embodiment”, “an embodiment,” “an example embodiment,” means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present invention. Thus, appearances of the phrases “in one embodiment,” “in an embodiment,” or “an example embodiment” in various places throughout this specification are not necessarily all referring to the same embodiment, but may. Furthermore, the particular features, structures or characteristics may be combined in any suitable manner, as would be apparent to a person skilled in the art from this disclosure, in one or more embodiments. Furthermore, while some embodiments described herein include some but not other features included in other embodiments, combinations of features of different embodiments are meant to be within the scope of the invention. For example, in the appended claims, any of the claimed embodiments can be used in any combination.
Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure pertains. Definitions of common terms and techniques in molecular biology may be found in Molecular Cloning: A Laboratory Manual, 2nd edition (1989) (Sambrook, Fritsch, and Maniatis); Molecular Cloning: A Laboratory Manual, 4th edition (2012) (Green and Sambrook); Current Protocols in Molecular Biology (1987) (F. M. Ausubel et al. eds.); the series Methods in Enzymology (Academic Press, Inc.): PCR 2: A Practical Approach (1995) (M. J. MacPherson, B. D. Hames, and G. R. Taylor eds.): Antibodies, A Laboratory Manual (1988) (Harlow and Lane, eds.): Antibodies A Laboratory Manual, 2nd edition 2013 (E. A. Greenfield ed.); Animal Cell Culture (1987) (R. I. Freshney, ed.); Benjamin Lewin, Genes IX, published by Jones and Bartlet, 2008 (ISBN 0763752223); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0632021829); Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 9780471185710); Singleton et al., Dictionary of Microbiology and Molecular Biology 2nd ed., J. Wiley & Sons (New York, N.Y. 1994), March, Advanced Organic Chemistry Reactions, Mechanisms and Structure 4th ed., John Wiley & Sons (New York, N. Y. 1992); and Marten H. Hofker and Jan van Deursen, Transgenic Mouse Methods and Protocols, 2nd edition (2011).
As used herein, the singular forms “a”, “an,” and “the” include both singular and plural referents unless the context clearly dictates otherwise.
The term “optional” or “optionally” means that the subsequent described event, circumstance or substituent may or may not occur, and that the description includes instances where the event or circumstance occurs and instances where it does not.
The recitation of numerical ranges by endpoints includes all numbers and fractions subsumed within the respective ranges, as well as the recited endpoints.
The terms “about” or “approximately” as used herein when referring to a measurable value such as a parameter, an amount, a temporal duration, and the like, are meant to encompass variations of and from the specified value, such as variations of +/−10% or less, +/−5% or less, +/−1% or less, +/−0.5% or less, and +/−0.1% or less of and from the specified value, insofar such variations are appropriate to perform in the disclosed invention. It is to be understood that the value to which the modifier “about” or “approximately” refers is itself also specifically, and preferably, disclosed.
The embodiments disclosed herein provide (non-naturally occurring or engineered) constructs, compositions, systems, and methods for site-directed RNA editing of RNA molecules. For example, the present invention provides (non-naturally occurring or engineered) methods for inhibiting intra and inter-cellular signaling pathways by modification of post-translational modification sites on select target RNA molecules. In certain example embodiments, the present invention provides (non-naturally occurring or engineered) methods for inhibiting intracellular phosphorylation of serine, threonine and tyrosine residues by editing the genetic codon of these amino acids by means of site-directed RNA editing or RNA molecules. Embodiments disclosed herein further provide methods of inhibiting pathological activation of cell signaling mediated by post-translational modifications, such as phosphorylation, which are involved in many diseases, including cancer, immunodeficiency, infectious diseases, inflammatory disorders and neurodegenerative disorders. The RNA-editing modification may be aimed at a single post-translational modification site of a single gene, but can also be multiplexed by targeting multiple sites on the same or different genes to increase efficacy. These approaches may be further combined with other treatments such as radiation, chemotherapy, targeted therapy based on antibodies or small molecules, and immunotherapy, which may have a synergistic effect.
The embodiments disclosed herein provide (non-naturally occurring or engineered) systems, constructs, and methods for targeted base editing. In general, the systems disclosed herein comprise a targeting component and a base editing component. The targeting component may function to specifically target the base editing component to a target nucleotide sequence in which one or more nucleotides are to be edited. The base editing component may then catalyze a chemical reaction to convert a first nucleotide in the target sequence to a second nucleotide. For example, the base editor may catalyze conversion of an adenine such that it is read as guanine by a cell's transcription or translation machinery, or vice versa. Likewise, the base editing component may catalyze conversion of cytidine to an uracil, or vice versa. In certain example embodiments, the base editor may be derived by starting with a known base editor, such as an adenine deaminase or cytidine deaminase, and modified using methods such as directed evolution to derive new functionalities. Directed evolution techniques are known in the art and may include those described in WO 2015/184016 “High-Throughput Assembly of Genetic Permutations.”
The present disclosure provides (non-naturally occurring or engineered) systems for editing a nucleic acid such as a gene or a product thereof (e.g., the encoded RNA or protein). In some embodiments, the systems may be an engineered, non-naturally occurring system suitable for modifying post-translational modification sites on proteins encoded by a target nucleic acid sequence. In certain cases, the target nucleic acid sequence is RNA, e.g., mRNA or a fragment thereof. In certain cases, the target nucleic acid sequence is DNA, e.g., a gene or a fragment thereof. In general, the system may comprise one or more of a catalytic inactive (dead) Cas protein (e.g., dead Cas7-11), a nucleotide deaminase protein or catalytic domain thereof, and a guide molecule. In certain examples, the nucleotide deaminase protein may be an adenosine deaminase. In certain examples, the nucleotide deaminase protein may be a cytidine deaminase. The guide sequence may be designed to have a degree of complementarity with a target sequence at one or more codons comprising an adenine or cytidine and that is post-translationally modified.
Some embodiments disclosed herein are directed to CRISPR-Cas (clustered regularly interspaced short palindromic repeats associated proteins) systems. In the conflict between bacterial hosts and their associated viruses, CRISPR-Cas systems provide an adaptive defense mechanism that utilizes programmed immune memory. CRISPR-Cas systems provide their defense through three stages: adaptation, the integration of short nucleic acid sequences into the CRISPR array that serves as memory of past infections; expression, the transcription of the CRISPR array into a pre-crRNA (CRISPR RNA) transcript and processing of the pre-crRNA into functional crRNA species targeting foreign nucleic acids; and interference, the programming of CRISPR effectors by crRNA to cleave nucleic acid of foreign threats. Across all CRISPR-Cas systems, these fundamental stages display enormous variation, including the identity of the target nucleic acid (either RNA, DNA, or both) and the diverse domains and proteins involved in the effector ribonucleoprotein complex of the system.
CRISPR-Cas systems can be broadly split into two classes based on the architecture of the effector modules involved in pre-crRNA processing and interference. Class 1 systems have multi-subunit effector complexes composed of many proteins, whereas Class 2 systems rely on single-effector proteins with multi-domain capabilities for crRNA binding and interference; Class 2 effectors often provide pre-crRNA processing activity as well. Class 1 systems contain 3 types (type I, III, and IV) and 33 subtypes, including the RNA and DNA targeting type III-systems. Class 2 CRISPR families encompass 3 types (type II, V, and VI) and 17 subtypes of systems, including the RNA-guided DNases Cas9 and Cas12 and the RNA-guided RNase Cas13. Continual sequencing of novel bacterial genomes and metagenomes uncovers new diversity of CRISPR-Cas systems and their evolutionary relationships, necessitating experimental work that reveals the function of these systems and develops them into new tools.
Among the currently known CRISPR-Cas systems, only the type III and type VI systems have been demonstrated to bind and target RNA, and these two systems have substantially different properties, the most distinguishing being their membership in Class 1 and Class 2, respectively. Characterized subtypes of type III, which span type III-A, B, and C systems, target both RNA and DNA species through an effector complex containing multiple Cas7 (Csm3/5 or Cmr1/4/6) RNA nuclease units in association with a single Cas10 (Csm1 or Cmr2) DNA nuclease. The RNA nuclease activity of Cas7 is mediated through acidic residues in the repeat-associated mysterious proteins (RAMP) domains, which cut at stereotyped intervals in the guide:target duplex. Type III systems also have a target restriction, and cannot efficiently target protospacers in vivo if there is extended homology between the 5′ “tag” of the crRNA and the “anti-tag” 3′ of the protospacer in the target, although this binding does not block RNA cleavage in vitro. In type III systems, pre-crRNA processing is carried out by either host factors or the associated Cas6 family protein, which can physically complex with the effector machinery.
In contrast to type III systems, type VI systems contain a single CRISPR effector Cas13 that can only effect RNA interference, mediated through basic catalytic residues of dual HEPN domains. This interference requires a protospacer flanking sequence (PFS), although the influence of the PFS varies between orthologs and families. Importantly, the RNA cleavage activity of Cas13, once triggered by crRNA:target duplex formation, is indiscriminate, and activated Cas13 enzymes will cleave other RNA species in vitro, in bacterial hosts, and mammalian cells. This activity, termed the collateral effect, has been applied to CRISPR-based nucleic acid detection technologies. In addition to the RNA interference activity, the Cas13 family members contain pre-crRNA processing activity. Just as single-effector DNA targeting systems have given rise to numerous genome editing applications, Cas13 family members have been applied to a suite of RNA-targeting technologies in both bacterial and eukaryotic cells, including RNA knockdown, RNA editing, RNA tracking, epitranscriptome editing, translational upregulation, epi-transcriptomic reading and writing via N6-Methyladenosine, and isoform modulation.
The novel type III-E system was recently identified from genomes of 8 bacterial species and is characterized as a fusion of several Cas7 proteins and a putative Cas11 (Csm2)-like small subunit. The domain composition suggests the fusion of multiple type III effector module domains involved in crRNA binding into a single protein effector that is predicted to process pre-crRNA given its homology with Cas5 (Csm4) and conserved aspartates. The lack of other putative effector nucleases in these CRISPR loci raise the additional possibility that this fusion protein is capable of crRNA-directed RNA cleavage. If so, this system would blur the distinction of Class 1 and Class 2 systems, as it would have domains homologous to other Class 1 systems, but possess a single effector module characteristic of Class 2 systems. Beyond the single effector module present in all subtype III-E loci, a majority of type III-E family members contain a putative ancillary gene with a CHAT domain, which is a caspase family protease associated with programmed cell death (PCD), suggesting involvement of PCD-mediated antiviral strategies, as has been observed with type III and VI systems.
Type III-E system associated effector, interchangeably termed Cas15 and Cas7-11 herein, is a programmable RNase (
Cas7-11 differs substantially from Cas13, in terms of both domain organization and activity (
Regulation of interference by accessory proteins has been observed in both type III and type VI systems, and other proteins in the D. ishimotonii type III-E locus can regulate activity of DisCas7-11a. Notably, TPR-CHAT had a strong inhibitory effect on DisCas7-11a phage interference, raising the possibility that unrestricted DisCas7-11a activity could be detrimental for the host. Alternatively, as TPR-CHAT is a caspase family protease associated with programmed cell death (PCD), it is possible that TPR-CHAT is activated by DisCas7-11a and leads to host death, which could mimic death due to phage in these assays. TPR-CHAT caspase activity could be activated by DisCas7-11a and cause PCD through general proteolysis, analogous to PCD triggered by Cas13 collateral activity.
Similar to Class 2 CRISPR effectors such as Cas9, Cas12, and Cas13, Cas7-11 is highly active in mammalian cells, with substantial knockdown activity on both reporter and endogenous transcripts. Moreover, via inactivation of active sites through mutagenesis, the catalytically inactive dCas7-11 enzyme can be used to recruit ADAR2DD for efficient site-specific A-to-I editing on transcripts. These applications establish Cas7-11 as the basis for an RNA-targeting toolbox that has several benefits compared to Cas13, including the lack of sequence preferences and collateral activity, the latter of which has been shown to induce toxicity in certain cell types. A Cas7-11 toolbox may serve as the basis for multiple RNA technologies, including RNA knockdown, RNA editing, translation modulation, RNA recruitment, RNA tracking, splicing control, RNA stabilization, and potentially even diagnostics.
In some embodiments, the systems may be AD-functionalized CRISPR system. The term “AD-functionalized CRISPR system” as used here refers to a nucleic acid targeting and editing system comprising (a) a CRISPR-Cas protein, more particularly a Cas7-11 protein which is catalytically active or inactive; (b) a guide molecule which comprises a guide sequence; and (c) an adenosine deaminase (AD) protein or catalytic domain thereof; wherein the adenosine deaminase protein or catalytic domain thereof is covalently or non-covalently linked to the CRISPR-Cas protein or the guide molecule or is adapted to link thereto after delivery; wherein the guide sequence is substantially complementary to the target sequence but comprises a non-pairing C corresponding to the A being targeted for deamination, resulting in an A-C mismatch in an RNA duplex formed by the guide sequence and the target sequence. In some embodiments, the CRISPR-Cas protein and/or the adenosine deaminase comprise one or more heterologous nuclear export signal(s) (NES(s)) or nuclear localization signal(s) (NLS(s)). For application in eukaryotic cells, the CRISPR-Cas protein and/or the adenosine deaminase can be NES-tagged or NLS-tagged.
One skilled in the art would appreciate that the components (a), (b) and (c) can be delivered to the cell as a ribonucleoprotein complex. The ribonucleoprotein complex can be delivered via one or more lipid nanoparticles. One skilled in the art would appreciate that the components (a), (b) and (c) can be delivered to the cell as one or more RNA molecules, such as one or more guide RNAs and one or more mRNA molecules encoding the CRISPR-Cas protein, the adenosine deaminase protein, and optionally the adaptor protein. The RNA molecules can be delivered via one or more lipid nanoparticles. One skilled in the art would appreciate that the components (a), (b) and (c) can be delivered to the cell as one or more DNA molecules. The one or more DNA molecules can be comprised within one or more vectors such as viral vectors (e.g., AAV). The one or more DNA molecules can comprise one or more regulatory elements operably configured to express the CRISPR-Cas protein, the guide molecule, and the adenosine deaminase protein or catalytic domain thereof, optionally wherein the one or more regulatory elements comprise inducible promoters.
In some embodiments, the CRISPR-Cas protein is a dead Cas7-11. In some embodiments, the dead Cas7-11 comprises one or more mutations in the Cas7-like domains, including D429A and D654A as well as many other mutations (see table 1).
In some embodiments, the guide molecule is capable of hybridizing with a target sequence comprising the Adenine to be deaminated within an RNA sequence to form an RNA duplex which comprises a non-pairing Cytosine opposite to said Adenine. Upon RNA duplex formation, the guide molecule forms a complex with the Cas7-11 protein and directs the complex to bind the RNA polynucleotide at the target RNA sequence of interest. Details on the aspect of the guide of the AD-functionalized CRISPR-Cas system are provided herein below.
In at least a first design, the AD-functionalized CRISPR system comprises: (a) an adenosine deaminase fused or linked to a CRISPR-Cas protein, wherein the CRISPR-Cas protein is catalytically inactive; and (b) a guide molecule comprising a guide sequence designed to introduce an A-C mismatch in an RNA duplex formed between the guide sequence and the target sequence. In some embodiments, the CRISPR-Cas protein and/or the adenosine deaminase can be NLS-tagged on either the N- or C-terminus or both.
In at least a second design, the AD-functionalized CRISPR system comprises: (a) a CRISPR-Cas protein that is catalytically inactive; (b) a guide molecule comprising a guide sequence designed to introduce an A-C mismatch in an RNA duplex formed between the guide sequence and the target sequence, and an aptamer sequence (e.g., MS2 RNA motif or PP7 RNA motif) capable of binding to an adaptor protein (e.g., MS2 coating protein or PP7 coat protein); and (c) an adenosine deaminase fused or linked to an adaptor protein, wherein the binding of the aptamer and the adaptor protein recruits the adenosine deaminase to the RNA duplex formed between the guide sequence and the target sequence for targeted deamination at the A of the A-C mismatch. In some embodiments, the adaptor protein and/or the adenosine deaminase can be NLS-tagged, on either the N- or C-terminus or both. The CRISPR-Cas protein can also be NLS-tagged. The CRISPR-Cas protein can also be NLS-tagged.
The use of different aptamers and corresponding adaptor proteins also allows orthogonal gene editing to be implemented. In one example in which adenosine deaminase are used in combination with cytidine deaminase for orthogonal gene editing/deamination, sgRNA targeting different loci are modified with distinct RNA loops in order to recruit MS2-adenosine deaminase and PP7-cytidine deaminase (or PP7-adenosine deaminase and MS2-cytidine deaminase), respectively, resulting in orthogonal deamination of A or C at the target loci of interested, respectively. PP7 is the RNA-binding coat protein of the bacteriophage Pseudomonas. Like MS2, it binds a specific RNA sequence and secondary structure. The PP7 RNA-recognition motif is distinct from that of MS2. Consequently, PP7 and MS2 can be multiplexed to mediate distinct effects at different genomic loci simultaneously. For example, an sgRNA targeting locus A can be modified with MS2 loops, recruiting MS2-adenosine deaminase, while another sgRNA targeting locus B can be modified with PP7 loops, recruiting PP7-cytidine deaminase. In the same cell, orthogonal, locus-specific modifications are thus realized. This principle can be extended to incorporate other orthogonal RNA-binding proteins.
In at least a third design, the AD-functionalized CRISPR system comprises: (a) an adenosine deaminase inserted into an internal loop or unstructured region of a CRISPR-Cas protein, wherein the CRISPR-Cas protein is catalytically inactive or a nickase; and (b) a guide molecule comprising a guide sequence designed to introduce an A-C mismatch in an RNA duplex formed between the guide sequence and the target sequence.
The AD-functionalized CRISPR system described herein can be used to target a specific Adenine within an RNA polynucleotide sequence for deamination. For example, the guide molecule can form a complex with the CRISPR-Cas protein and directs the complex to bind a target RNA sequence in the RNA polynucleotide of interest. Because the guide sequence is designed to have a non-pairing C, the RNA duplex formed between the guide sequence and the target sequence comprises an A-C mismatch, which directs the adenosine deaminase to contact and deaminate the A opposite to the non-pairing C, converting it to an Inosine (I). Since Inosine (I) base pairs with C and functions like G in cellular processes, the targeted deamination of A described herein are useful for correction of undesirable G-A and C-T mutations, as well as for obtaining desirable A-G and T-C mutations.
In some embodiments, the AD-functionalized CRISPR system is used for targeted deamination in an RNA polynucleotide molecule in vitro. In some embodiments, the AD-functionalized CRISPR system is used for targeted deamination in a DNA molecule and/or RNA molecule within a cell. The cell can be an eukaryotic cell such as a bacteria or cyanobacteria. The cell can be a eukaryotic cell, such as an animal cell, a mammalian cell, a human, or a plant cell.
The invention also relates to a (non-naturally occurring or engineered) method for treating or preventing a disease by the targeted deamination using the AD-functionalized CRISPR system, wherein the deamination of the A, which remedies a disease caused by transcripts containing a pathogenic G→A or C→T point mutation. Examples of disease that can be treated or prevented with the present invention include cancer, Meier-Gorlin syndrome, Seckel syndrome 4, Joubert syndrome 5, Leber congenital amaurosis 10; Charcot-Marie-Tooth disease, type 2; Charcot-Marie-Tooth disease, type 2; Usher syndrome, type 2C; Spinocerebellar ataxia 28; Spinocerebellar ataxia 28; Spinocerebellar ataxia 28; Long QT syndrome 2; Sjogren-Larsson syndrome; Hereditary fructosuria; Hereditary fructosuria; Neuroblastoma; Neuroblastoma; Kallmann syndrome 1; Kallmann syndrome 1; Kallmann syndrome 1; Metachromatic leukodystrophy.
AD-functionalized CRISPR system for RNA editing can be used for translation upregulation or downregulation, improving RNA stability and diagnostics. For example, for application in diagnostics, TPR-Chat is an accessory protein that interacts with Cas7-11 interference. Cas7-11 can activate TPR-Chat caspase activity which can then activate a reporter. While this can be used for inducing cell death based on RNA detection (e.g., in cancer cells), it also can be useful for general RNA diagnostics (i.e. molecular diagnostics for bacteria, viruses, and derivatives thereof) in samples. Furthermore, Cas7-11 can re-constitute a split protein like GFP on a specific transcript.
AD-functionalized CRISPR system for RNA editing can be used to treat or prevent premature termination diseases. Pre-termination diseases are characterized by mutations in early stop codons, either through single nucleotide polymorphisms that introduce termination, indels that change the translational frame of the protein and generate new stop codons, or alternative splicing that preferentially introduces exons that have early termination. By removing stop codons generated in these ways via A to I editing, RNA editing with ADAR could rescue diseases involving premature termination. In cases where SNPs are not G to A, but generate nonsense mutations, clinical benefit could be derived from changing nonsense mutations into missense mutations.
AD-functionalized CRISPR system for RNA editing can be used to change fertility mutations without germline editing. One advantage of RNA editing over DNA editing is in cases of SNPs affecting fertility, where correction with genome editing would necessarily result in germline editing, with potential ethical or safety implications. RNA editing could correct these mutations without permanent effects on the genome, thereby circumventing these issues.
AD-functionalized CRISPR system for RNA editing can be used for splicing alteration. Pre-mRNA requires specific splice donor and acceptor sequences in order to undergo processing by the spliceosome. Splice acceptor sites contain an invariant AG sequence that is necessary for acceptance of the attack by the splice donor sequence and intron removal. By targeting Cas7-11-ADAR fusions to pre-mRNA and editing AG splice acceptor sites to IG, it can be possible to inactivate the splice acceptor site, resulting in skipping of the downstream exon. This approach to splicing alteration has advantages over the current method of exon skipping with chemically modified anti-sense oligos. Cas7-11-ADAR can be genetically encoded, allowing for long-term exon skipping. Additionally, Cas7-11-ADAR creates a mutation to promote skipping, which can be more robust than masking of the splice donor/acceptor site by a double stranded RNA, as is done with anti-sense oligos.
AD-functionalized CRISPR system for RNA editing can be used to alter neoantigens. Neoantigens in cancer are novel antigens that are expressed in tumor cells due to mutations that arise because of defective mismatch repair. Engineering T cells against neoantigens is advantageous because the T cells will have no off-target activity and thus toxicity since the antigens are only expressed in the tumor cells. With RNA base editors, the Cas7-11-ADAR fusions can be targeted to cancer cells to introduce mutations in transcripts that would introduce amino acid changes and new antigens that can be targeted using chimeric antigen receptor T cells. This approach is better than DNA base editors because it is transient and thus the risk of editing non-tumor cells permanently due to off-target delivery is minimal.
AD-functionalized CRISPR system for RNA editing can be used to change microRNA targets for tumor suppressors. ADAR naturally edits mRNA to generate or remove microRNA targets, thereby modulating expression. Programmable RNA editing can be used to up- or down-regulate microRNA targets via altering of targeting regions. Additionally, microRNAs themselves are natural substrates for ADAR, and programmable RNA editing of micoRNAs can reduce or enhance the function on their corresponding targets.
AD-functionalized CRISPR system for RNA editing can be used to make multiple edits along a region. The Cas7-11-ADAR fusions can be precisely targeted to edit specific adenosines by introducing a mismatch in the guide region across from the desired adenosine target and creating a bubble that is favorable for A-to-I editing. By introducing multiple of these mismatches across different adenosine sites in the guide/target duplex, it can be possible to introduce multiple mutations at once.
AD-functionalized CRISPR system for RNA editing can be used for the reversal of TAA (double A to G) for PTC. Many diseases that involve pretermination codon changes involve a TAA stop codon, which would require A-to-I changes to correct rather than the TAG or TGA stop codons which only need one A-to-I edit. Two approaches can be used to reverse the TAA stop codon. (1) As described in the previous section, two mismatches can be introduced in the guide against the two adenosines in the TAA codon. (2) A two-guide array can be used to convert each of the adenosines to inosine sequentially. The first guide in the array can contain a mutation against the first adenosine and the second guide can then have complementarity to this change and have a mismatch against the second adenosine in the stop codon.
AD-functionalized CRISPR system for RNA editing can be used to treat or prevent cancer (GOF, LOF mutation reversal). Many oncogenic changes in cancer involve G to A mutations that introduce gain of function or loss of function phenotypes to the mutated proteins. The RNA base editors are well positioned to correct these changes and reduce oncogenesis.
RNA editing with ADAR can be used for the design of new base preferences. Current ADAR1/2 proteins have been found to have surrounding base preferences for catalytic activity, which may pose constraints for certain applications. Rational mutagenesis or directed evolution of ADAR variants with altered or relaxed base preferences can increase the versatility of programmable RNA editing.
AD-functionalized CRISPR system for RNA editing can comprise ADAR mutants with increased activity in human cells. Although ADAR mutants with altered activity in vitro or in yeast have been previously reported, screening or rational design of mutants with increased activity in the context of human cells can improve the efficiency or specificity of ADAR-based programmable RNA editing constructs.
AD-functionalized CRISPR system for RNA editing can be used in biological applications of inosine generation. The RNA editing with ADAR generates inosine, which, when occurring multiple times in a transcript, can interact with endogenous biological pathways to increase inflammation in cells and tissues. Generation of multiple inosine bases can increase inflammation, especially in cells where inflammation can lead to clearance. Additional inosine generation could also be used to destabilize transcripts.
AD-functionalized CRISPR system for RNA editing can be used in removing upstream start codons to promote protein expression of downstream ORF (ATG mutation). Anti-sense oligos have been used for blocking upstream start codon sites to promote protein expression at downstream start codons. This allows the boosting of endogenous protein levels for therapeutic purposes. Cas7-11-ADAR fusions could accomplish a similar effect by converting ATG sites to ITG (GTG) sites and thus remove upstream codons in endogenous transcripts and thus boost protein translation. So far, most therapeutic applications discussed have been for correcting G to A mutations or removing pre-termination sites. This would be an application that allows for boosting gene expression. A good example is boosting fetal hemoglobin levels in sickle cell disease and thalassemias.
AD-functionalized CRISPR system for RNA editing can comprise the mutagenesis of ADAR for C to U or any transition. It is possible through rational mutagenesis or directed evolution that the ADARs listed in the ortholog section could be made into C to U editors or editors of any base transition.
In particular embodiments, the compositions described herein can be used in therapy. This implies that the methods can be performed in vivo, ex vivo or in vitro. In particular embodiments, the methods can be not methods of treatment of the animal or human body or a method for modifying the germ line genetic identity of a human cell. In particular embodiments, when carrying out the method, the target RNA can be not comprised within a human or animal cell. In particular embodiments, when the target is a human or animal target, the method can be carried out ex vivo or in vitro.
In some embodiments, the system comprises one or more components of a CRISPR-Cas system. For example, the system may comprise a Cas protein, a guide molecule, or a combination thereof.
In the methods and systems of the present invention use is made of a CRISPR-Cas protein and corresponding guide molecule. More particularly, the CRISPR-Cas protein is a class 2 CRISPR-Cas protein. In certain embodiments, said CRISPR-Cas protein is a Cas7-11. The Cas7-11 may be Cas7-11a, Cas7-11b, Cas7-11c, or Cas7-11d. The CRISPR-Cas system does not require the generation of customized proteins to target specific sequences but rather a single Cas protein can be programmed by guide molecule to recognize a specific nucleic acid target, in other words the Cas enzyme protein can be recruited to a specific nucleic acid target locus of interest using said guide molecule.
In some embodiments, the systems may comprise a CRISPR-Cas protein. In certain examples, the CRISPR-Cas protein may be a catalytically inactive (dead) Cas protein. The catalytically inactive (dead) Cas protein may have impaired (e.g., reduced or no) nuclease activity. In some cases, the dead Cas protein may have nickase activity. In some cases, the dead Cas protein may be dead Cas 15 protein. For example, the dead Cas 15 may be dead Cas7-11a, dead Cas7-11b, dead Cas7-11c, or dead Cas7-11d. In some embodiments, the system may comprise a nucleotide sequence encoding the dead Cas protein.
In its unmodified form, a CRISPR-Cas protein is a catalytically active protein. This implies that upon formation of a nucleic acid-targeting complex (comprising a guide RNA hybridized to a target sequence) one or both DNA strands in or near (e.g., within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or more base pairs from) the target sequence is modified (e.g., cleaved). As used herein the term “sequence(s) associated with a target locus of interest” refers to sequences near the vicinity of the target sequence (e.g., within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or more base pairs from the target sequence, wherein the target sequence is comprised within a target locus of interest). The unmodified catalytically active Cas7-11 protein generates a staggered cut, whereby the cut sites are typically within the target sequence. More particularly, the staggered cut is typically 13-23 nucleotides distal to the PAM. In particular embodiments, the cut on the non-target strand is 17 nucleotides downstream of the PAM (i.e., between nucleotide 17 and 18 downstream of the PAM), while the cut on the target strand (i.e. strand hybridizing with the guide sequence) occurs a further 4 nucleotides further from the sequence complementary to the PAM (this is 21 nucleotides upstream of the complement of the PAM on the 3′ strand or between nucleotide 21 and 22 upstream of the complement of the PAM).
In the methods according to the present invention, the CRISPR-Cas protein is preferably mutated with respect to a corresponding wild-type enzyme such that the mutated CRISPR-Cas protein lacks the ability to cleave one or both DNA strands of a target locus containing a target sequence. In particular embodiments, one or more catalytic domains of the Cas7-11 protein are mutated to produce a mutated Cas protein which cleaves only one DNA strand of a target sequence.
In particular embodiments, the CRISPR-Cas protein may be mutated with respect to a corresponding wild-type enzyme such that the mutated CRISPR-Cas protein lacks substantially all DNA cleavage activity. In some embodiments, a CRISPR-Cas protein may be considered to substantially lack all DNA and/or RNA cleavage activity when the cleavage activity of the mutated enzyme is about no more than 25%, 10%, 5%, 1%, 0.1%, 0.01%, or less of the nucleic acid cleavage activity of the non-mutated form of the enzyme; an example can be when the nucleic acid cleavage activity of the mutated form is nil or negligible as compared with the non-mutated form.
In certain embodiments of the methods provided herein the CRISPR-Cas protein is a mutated CRISPR-Cas protein which cleaves only one DNA strand, i.e., a nickase. More particularly, in the context of the present invention, the nickase ensures cleavage within the non-target sequence, i.e., the sequence which is on the opposite DNA strand of the target sequence and which is 3′ of the PAM sequence.
In some embodiments, a CRISPR-Cas protein is considered to substantially lack all DNA cleavage activity when the DNA cleavage activity of the mutated enzyme is about no more than 25%, 10%, 5%, 1%, 0.1%, 0.01%, or less of the DNA cleavage activity of the non-mutated form of the enzyme; an example can be when the DNA cleavage activity of the mutated form is nil or negligible as compared with the non-mutated form. In these embodiments, the CRISPR-Cas protein is used as a generic DNA binding protein. The mutations may be artificially introduced mutations or gain- or loss-of-function mutations.
In addition to the mutations described above, the CRISPR-Cas protein may be additionally modified. As used herein, the term “modified” with regard to a CRISPR-Cas protein generally refers to a CRISPR-Cas protein having one or more modifications or mutations (including point mutations, truncations, insertions, deletions, chimeras, fusion proteins, etc.) compared to the wild type Cas protein from which it is derived. By derived is meant that the derived enzyme is largely based, in the sense of having a high degree of sequence homology with, a wildtype enzyme, but that it has been mutated (modified) in some way as known in the art or as described herein. The modification can be fusions of effectors like fluorophore, proteins involved in translation modulation (e.g., eIF4E, eIF4A, and eIF4G) and proteins involved with epitranscriptomic modulation (e.g. pseudouridine synthase and m6a writer/readers), and splicing factors involved with changing splicing. Cas7-11 could also be used for sensing RNA for diagnostic purposes. In some embodiments, the C-terminus of the Cas7-11 effector can be truncated. For example, at least 20 amino acids, at least 40 amino acids, at least 50 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 150 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 250 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas 13 effector. For example, up to 120 amino acids, up to 140 amino acids, up to 160 amino acids, up to 180 amino acids, up to 200 amino acids, up to 250 amino acids, up to 300 amino acids, up to 350 amino acids, or up to 400 amino acids may be truncated at the C-terminus of the Cas 15 effector.
In some embodiments, the N-terminus of the Cas7-11 effector protein may be truncated. For example, at least 20 amino acids, at least 40 amino acids, at least 50 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 150 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 250 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For examples, up to 120 amino acids, up to 140 amino acids, up to 160 amino acids, up to 180 amino acids, up to 200 amino acids, up to 250 amino acids, up to 300 amino acids, up to 350 amino acids, up to 400 amino acids may be truncated at the N-terminus of the Cas7-11 effector.
In some embodiments, both the N- and the C-termini of the Cas7-11 effector protein may be truncated. For example, at least 20 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 40 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 60 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 80 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 100 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 120 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 140 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 160 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 180 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 200 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 220 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 240 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 260 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 280 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 300 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector. For example, at least 20 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 40 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 60 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 80 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 100 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 120 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 140 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 160 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 180 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 200 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 220 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 240 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 260 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 280 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 300 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector. For example, at least 350 amino acids may be truncated at the N-terminus of the Cas7-11 effector, and at least 20 amino acids, at least 40 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 120 amino acids, at least 140 amino acids, at least 160 amino acids, at least 180 amino acids, at least 200 amino acids, at least 220 amino acids, at least 240 amino acids, at least 260 amino acids, at least 300 amino acids, or at least 350 amino acids may be truncated at the C-terminus of the Cas7-11 effector.
The additional modifications of the CRISPR-Cas protein may or may not cause an altered functionality. By means of example, and in particular with reference to CRISPR-Cas protein, modifications which do not result in an altered functionality include for instance codon optimization for expression into a particular host, or providing the nuclease with a particular marker (e.g., for visualization). Modifications with may result in altered functionality may also include mutations, including point mutations, insertions, deletions, truncations (including split nucleases), etc. Fusion proteins may without limitation include for instance fusions with heterologous domains or functional domains (e.g., localization signals, catalytic domains, etc.). In certain embodiments, various modifications may be combined (e.g., a mutated nuclease which is catalytically inactive and which further is fused to a functional domain, such as for instance to induce DNA methylation or another nucleic acid modification, such as including without limitation a break (e.g. by a different nuclease (domain)), a mutation, a deletion, an insertion, a replacement, a ligation, a digestion, a break or a recombination). As used herein, “altered functionality” includes without limitation an altered specificity (e.g., altered target recognition, increased (e.g. “enhanced” Cas proteins) or decreased specificity, or altered PAM recognition), altered activity (e.g. increased or decreased catalytic activity, including catalytically inactive nucleases or nickases), and/or altered stability (e.g. fusions with destabilization domains). Suitable heterologous domains include without limitation a nuclease, a ligase, a repair protein, a methyltransferase, (viral) integrase, a recombinase, a transposase, an argonaute, a cytidine deaminase, a retron, a group II intron, a phosphatase, a phosphorylase, a sulpfurylase, a kinase, a polymerase, an exonuclease, etc. Examples of all these modifications are known in the art. It will be understood that a “modified” nuclease as referred to herein, and in particular a “modified” Cas or “modified” CRISPR-Cas system or complex preferably still has the capacity to interact with or bind to the polynucleic acid (e.g., in complex with the guide molecule). Such modified Cas protein can be combined with the deaminase protein or active domain thereof as described herein.
In certain embodiments, CRISPR-Cas protein may comprise one or more modifications resulting in enhanced activity and/or specificity, such as including mutating residues that stabilize the targeted or non-targeted strand (e.g., eCas9; “Rationally engineered Cas9 nucleases with improved specificity”, Slaymaker et al. (2016), Science, 351(6268):84-88, incorporated herewith in its entirety by reference). In certain embodiments, the altered or modified activity of the engineered CRISPR protein comprises increased targeting efficiency or decreased off-target binding. In certain embodiments, the altered activity of the engineered CRISPR protein comprises modified cleavage activity. In certain embodiments, the altered activity comprises increased cleavage activity as to the target polynucleotide loci. In certain embodiments, the altered activity comprises decreased cleavage activity as to the target polynucleotide loci. In certain embodiments, the altered activity comprises decreased cleavage activity as to off-target polynucleotide loci. In certain embodiments, the altered or modified activity of the modified nuclease comprises altered helicase kinetics. In certain embodiments, the modified nuclease comprises a modification that alters association of the protein with the nucleic acid molecule comprising RNA (in the case of a Cas protein), or a strand of the target polynucleotide loci, or a strand of off-target polynucleotide loci. In an aspect of the invention, the engineered CRISPR protein comprises a modification that alters formation of the CRISPR complex. In certain embodiments, the altered activity comprises increased cleavage activity as to off-target polynucleotide loci. Accordingly, in certain embodiments, there is increased specificity for target polynucleotide loci as compared to off-target polynucleotide loci. In other embodiments, there is reduced specificity for target polynucleotide loci as compared to off-target polynucleotide loci. In certain embodiments, the mutations result in decreased off-target effects (e.g., cleavage or binding properties, activity, or kinetics), such as in case for Cas proteins for instance resulting in a lower tolerance for mismatches between target and guide RNA. Other mutations may lead to increased off-target effects (e.g., cleavage or binding properties, activity, or kinetics). Other mutations may lead to increased or decreased on-target effects (e.g., cleavage or binding properties, activity, or kinetics). In certain embodiments, the mutations result in altered (e.g., increased or decreased) helicase activity, association or formation of the functional nuclease complex (e.g. CRISPR-Cas complex). In certain embodiments, as described above, the mutations result in an altered PAM recognition, i.e., a different PAM may be (in addition or in the alternative) be recognized, compared to the unmodified Cas protein. Particularly preferred mutations include positively charged residues and/or (evolutionary) conserved residues, such as conserved positively charged residues, in order to enhance specificity. In certain embodiments, such residues may be mutated to uncharged residues, such as alanine.
The application describes methods using Type-III CRISPR-Cas proteins. This is exemplified herein with Cas7-11, whereby a number of orthologs or homologs have been identified. It will be apparent to the skilled person that further orthologs or homologs can be identified and that any of the functionalities described herein may be engineered into other orthologs, including chimeric enzymes comprising fragments from multiple orthologs.
Computational methods of identifying novel CRISPR-Cas loci are described in EP3009511 or US2016208243 and may comprise the following steps: detecting all contigs encoding the Cas1 protein; identifying all predicted protein coding genes within 20 KB of the casl gene; comparing the identified genes with Cas protein-specific profiles and predicting CRISPR arrays; selecting unclassified candidate CRISPR-Cas loci containing proteins larger than 500 amino acids (>500 aa); analyzing selected candidates using methods such as PSI-BLAST and HHPred to screen for known protein domains, thereby identifying novel Class 2 CRISPR-Cas loci (see also Schmakov et al. 2015, Mol Cell. 60(3):385-97). In addition to the above-mentioned steps, additional analysis of the candidates may be conducted by searching metagenomics databases for additional homologs. Additionally or alternatively, to expand the search to non-autonomous CRISPR-Cas systems, the same procedure can be performed with the CRISPR array used as the seed.
In one aspect the detecting all contigs encoding the Cas1 protein is performed by GenemarkS, a gene prediction program as further described in “GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.” John Besemer, Alexandre Lomsadze and Mark Borodovsky, Nucleic Acids Research (2001) 29, pp 2607-2618, herein incorporated by reference.
In one aspect the identifying all predicted protein coding genes is carried out by comparing the identified genes with Cas protein-specific profiles and annotating them according to NCBI Conserved Domain Database (CDD) which is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins. These are available as position-specific score matrices (PSSMs) for fast identification of conserved domains in protein sequences via RPS-BLAST. CDD content includes NCBI-curated domains, which use 3D-structure information to explicitly define domain boundaries and provide insights into sequence/structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, PRK, TIGRFAM). In a further aspect, CRISPR arrays were predicted using a PILER-CR program which is a public domain software for finding CRISPR repeats as described in “PILER-CR: fast and accurate identification of CRISPR repeats,” Edgar, R. C., BMC Bioinformatics, January 20; 8:18(2007), herein incorporated by reference.
In a further aspect, the case by case analysis is performed using PSI-BLAST (Position-Specific Iterative Basic Local Alignment Search Tool). PSI-BLAST derives a position-specific scoring matrix (PSSM) or profile from the multiple sequence alignment of sequences detected above a given score threshold using protein-protein BLAST. This PSSM is used to further search the database for new matches, and is updated for subsequent iterations with these newly detected sequences. Thus, PSI-BLAST provides a means of detecting distant relationships between proteins.
In another aspect, the case by case analysis is performed using HHpred, a method for sequence database searching and structure prediction that is as easy to use as BLAST or PSI-BLAST and that is at the same time much more sensitive in finding remote homologs. In fact, HHpred's sensitivity is competitive with the most powerful servers for structure prediction currently available. HHpred is the first server that is based on the pairwise comparison of profile hidden Markov models (HMMs). Whereas most conventional sequence search methods search sequence databases such as UniProt or the NR, HHpred searches alignment databases, like Pfam or SMART. This greatly simplifies the list of hits to a number of sequence families instead of a clutter of single sequences. All major publicly available profile and alignment databases are available through HHpred. HHpred accepts a single query sequence or a multiple alignment as input. Within only a few minutes it returns the search results in an easy-to-read format similar to that of PSI-BLAST. Search options include local or global alignment and scoring secondary structure similarity. HHpred can produce pairwise query-template sequence alignments, merged query-template multiple alignments (e.g. for transitive searches), as well as 3D structural models calculated by the MODELLER software from HHpred alignments.
Where the Cas7-11 protein has nuclease activity, the Cas7-11 protein may be modified to have diminished nuclease activity e.g., nuclease inactivation of at least 70%, at least 80%, at least 90%, at least 95%, at least 97%, or 100% as compared with the wild type enzyme; or to put in another way, a Cas7-11 enzyme having advantageously about 0% of the nuclease activity of the non-mutated or wild type Cas7-11 enzyme or CRISPR-Cas protein, or no more than about 3% or about 5% or about 10% of the nuclease activity of the non-mutated or wild type Cas7-11 enzyme.
In particular embodiments, it is of interest to make use of an engineered Cas7-11 protein as defined herein, such as Cas7-11, wherein the protein complexes with a nucleic acid molecule comprising RNA to form a CRISPR complex, wherein when in the CRISPR complex, the nucleic acid molecule targets one or more target polynucleotide loci, the protein comprises at least one modification compared to unmodified Cas7-11 protein, and wherein the CRISPR complex comprising the modified protein has altered activity as compared to the complex comprising the unmodified Cas7-11 protein. It is to be understood that when referring herein to CRISPR “protein,” the Cas7-11 protein is an unmodified or modified CRISPR-Cas protein (e.g. having increased or decreased or the same (or no) enzymatic activity, such as without limitation including Cas7-11. The term “CRISPR protein” may be used interchangeably with “CRISPR-Cas protein”, irrespective of whether the CRISPR protein has altered, such as increased or decreased (or no) enzymatic activity, compared to the wild type CRISPR protein.
Computational analysis of the primary structure of Cas7-11 nucleases reveals 5 distinct domain regions.
Based on the above information, mutants can be generated which lead to inactivation of the enzyme or which modify the double strand nuclease to nickase activity. In alternative embodiments, this information is used to develop enzymes with reduced off-target effects.
In certain of the above-described Cas7-11 enzymes, the enzyme is modified by mutation of one or more residues (in the Cas7-like domains as well as the small subunit) including but not limited to positions listed in table 1.
The terms “orthologue” (also referred to as “ortholog” herein) and “homologue” (also referred to as “homolog” herein) are well known in the art. By means of further guidance, a “homologue” of a protein as used herein is a protein of the same species which performs the same or a similar function as the protein it is a homologue of. Homologous proteins may but need not be structurally related, or are only partially structurally related. An “orthologue” of a protein as used herein is a protein of a different species which performs the same or a similar function as the protein it is an orthologue of. Orthologous proteins may but need not be structurally related, or are only partially structurally related. Homologs and orthologs may be identified by homology modelling (see, e.g., Greer, Science vol. 228 (1985) 1055, and Blundell et al. Eur J Biochem vol 172 (1988), 513) or “structural BLAST” (Dey F, Cliff Zhang Q, Petrey D, Honig B. Toward a “structural BLAST”: using structural relationships to infer function. Protein Sci. 2013 April; 22(4):359-66. doi: 10.1002/pro.2225). See also Shmakov et al. (2015) for application in the field of CRISPR-Cas loci. Homologous proteins may but need not be structurally related, or are only partially structurally related.
The present invention encompasses the use of a Cas7-11 effector protein, derived from a Cas7-11 locus denoted as subtype III-E. Herein such effector proteins are also referred to as “Cas7-11p”, e.g., a Cas7-11 protein (and such effector protein or Cas7-11 protein or protein derived from a Cas7-11 locus is also called “CRISPR-Cas protein”).
In particular embodiments, the effector protein is a Cas7-11 effector protein from an organism from a genus comprising Candidatus Jettenia caeni, Candidatus Scalindua brodae, Desulfobacteraceae, Candidatus Magnetomorum, Desulfonema Ishimotonii, Candidatus Brocadia, Deltaproteobacteria, Syntrophorhabdaceae, or Nitrospirae.
In certain example embodiments, the CRISPR effector protein is a Cas7-11 type III-D/III-E ortholog selected from Table 1 and
The system may comprise a guide molecule. The guide molecule may comprise a guide sequence. In certain cases, the guide sequence may be linked to a direct repeat sequence. In some cases, the system may comprise a nucleotide sequence encoding the guide molecule. The guide molecule may form a complex with the dead Cas7-11 protein and directs the complex to bind the target RNA sequence at one or more codons encoding an amino acid that is post-translationally modified. The guide sequence may be capable of hybridizing with a target RNA sequence comprising an Adenine or Cytidine encoding said amino acid to form an RNA duplex, wherein said guide sequence comprises a non-pairing nucleotide at a position corresponding to said Adenine or Cytidine resulting in a mismatch in the RNA duplex formed. The guide sequence may comprise one or more mismatch corresponding to different adenosine sites in the target sequence. In certain cases, guide sequence may comprise multiple mismatches corresponding to different adenosine sites in the target sequence. In cases where two guide molecules are used, the guide sequence of each of the guide molecules may comprise a mismatch corresponding to a different adenosine sites in the target sequence.
In general, a CRISPR system is characterized by elements that promote the formation of a CRISPR complex at the site of a target sequence. In the context of formation of a CRISPR complex, “target sequence” refers to a sequence to which a guide sequence is designed to have complementarity, where hybridization between a target DNA sequence and a guide sequence promotes the formation of a CRISPR complex.
In certain embodiments, the target sequence should be associated with a PAM (protospacer adjacent motif) or PFS (protospacer flanking sequence or site); that is, a short sequence recognized by the CRISPR complex. Depending on the nature of the CRISPR-Cas protein, the target sequence should be selected such that its complementary sequence in the DNA duplex (also referred to herein as the non-target sequence) is upstream or downstream of the PAM. The precise sequence and length requirements for the PAM differ depending on the Cas7-11 protein used, but PAMs are typically 2-8 base pair sequences adjacent the protospacer (that is, the target sequence). Examples of the natural PAM sequences for different Cas7-11 orthologues are provided herein below and the skilled person will be able to identify further PAM sequences for use with a given Cas7-11 protein. In certain embodiments, the Cas7-11 protein has been modified to recognize a non-natural PAM, such as recognizing a PAM having a sequence or comprising a sequence YCN, YCV, AYV, TYV, RYN, RCN, TGYV, NTTN, TTN, TRTN, TYTV, TYCT, TYCN, TRTN, NTTN, TACT, TYCC, TRTC, TATV, NTTV, TTV, TSTG, TVTS, TYYS, TCYS, TBYS, TCYS, TNYS, TYYS, TNTN, TSTG, TTCC, TCCC, TATC, TGTG, TCTG, TYCV, or TCTC.
The terms “guide molecule” and “guide RNA” are used interchangeably herein to refer to RNA-based molecules that are capable of forming a complex with a CRISPR-Cas protein and comprises a guide sequence having sufficient complementarity with a target nucleic acid sequence to hybridize with the target nucleic acid sequence and direct sequence-specific binding of the complex to the target nucleic acid sequence. The guide molecule or guide RNA specifically encompasses RNA-based molecules having one or more chemically modifications (e.g., by chemical linking two ribonucleotides or by replacement of one or more ribonucleotides with one or more deoxyribonucleotides), as described herein.
As used herein, the term “guide sequence” in the context of a CRISPR-Cas system, comprises any polynucleotide sequence having sufficient complementarity with a target nucleic acid sequence to hybridize with the target nucleic acid sequence and direct sequence-specific binding of a nucleic acid-targeting complex to the target nucleic acid sequence. In the context of the present invention the target nucleic acid sequence or target sequence is the sequence comprising the target adenosine to be deaminated also referred to herein as the “target adenosine”. In some embodiments, except for the intended dA-C mismatch, the degree of complementarity, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more.
Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences, non-limiting example of which include the Smith-Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler Transform (e.g., the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies; available at www.novocraft.com), ELAND (Illumina, San Diego, CA), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net). The ability of a guide sequence (within a nucleic acid-targeting guide RNA) to direct sequence-specific binding of a nucleic acid-targeting complex to a target nucleic acid sequence may be assessed by any suitable assay. For example, the components of a nucleic acid-targeting CRISPR system sufficient to form a nucleic acid-targeting complex, including the guide sequence to be tested, may be provided to a host cell having the corresponding target nucleic acid sequence, such as by transfection with vectors encoding the components of the nucleic acid-targeting complex, followed by an assessment of preferential targeting (e.g., cleavage) within the target nucleic acid sequence, such as by Surveyor assay as described herein. Similarly, cleavage of a target nucleic acid sequence (or a sequence in the vicinity thereof) may be evaluated in a test tube by providing the target nucleic acid sequence, components of a nucleic acid-targeting complex, including the guide sequence to be tested and a control guide sequence different from the test guide sequence, and comparing binding or rate of cleavage at or in the vicinity of the target sequence between the test and control guide sequence reactions. Other assays are possible, and will occur to those skilled in the art. A guide sequence, and hence a nucleic acid-targeting guide RNA may be selected to target any target nucleic acid sequence.
In some embodiments, the guide molecule comprises a guide sequence that is designed to have at least one mismatch with the target sequence, such that an RNA duplex formed between the guide sequence and the target sequence comprises a non-pairing C in the guide sequence opposite to the target A for deamination on the target sequence. In some embodiments, aside from this A-C mismatch, the degree of complementarity, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. In some cases, the distance between the non-pairing C and the 5′ end of the guide sequence is from about 10 to about 50, e.g., from about 10 to about 20, from about 15 to about 25, from about 20 to about 30, from about 25 to about 35, from about 30 to about 40, from about 35 to about 45, or from about 40 to about 50 nucleotides (nt) in length. In certain example. In some cases, the distance between the non-pairing C and the 3′ end of the guide sequence is from about 10 to about 50, e.g., from about 10 to about 20, from about 15 to about 25, from about 20 to about 30, from about 25 to about 35, from about 30 to about 40, from about 35 to about 45, or from about 40 to about 50 nucleotides (nt) in length. In one example, the distance between the non-pairing C and the 5′ end of said guide sequence is from about 20 to about 30 nucleotides.
In certain embodiments, the guide sequence or spacer length of the guide molecules is from 15 to 50 nt. In certain embodiments, the spacer length of the guide RNA is at least 15 nucleotides. In certain embodiments, the spacer length is from 15 to 17 nt, e.g., 15, 16, or 17 nt, from 17 to 20 nt, e.g., 17, 18, 19, or 20 nt, from 20 to 24 nt, e.g., 20, 21, 22, 23, or 24 nt, from 23 to 25 nt, e.g., 23, 24, or 25 nt, from 24 to 27 nt, e.g., 24, 25, 26, or 27 nt, from 27-30 nt, e.g., 27, 28, 29, or 30 nt, from 30-35 nt, e.g., 30, 31, 32, 33, 34, or 35 nt, or 35 nt or longer. In certain example embodiment, the guide sequence is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 40, 41, 42, 43, 44, 45, 46, 47 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 nt.
In some embodiments, the guide sequence has a length from about 10 to about 100, e.g., from about 20 to about 60, from about 20 to about 55, from about 20 to about 53, from about 25 to about 53, from about 29 to about 53, from about 20 to about 30, from about 25 to about 35, from about 30 to about 40, from about 35 to about 45, from about 40 to about 50, from about 45 to about 55, from about 50 to about 60, from about 55 to about 65, from about 60 to about 70, from about 70 to about 80, from about 80 to about 90, or from about 90 to about 100 nucleotides (nt) long that is capable of forming an RNA duplex with a target sequence. In certain example, the guide sequence has a length from about 20 to about 53 nt capable of forming said RNA duplex with said target sequence. In certain example, the guide sequence has a length from about 25 to about 53 nt capable of forming said RNA duplex with said target sequence. In certain example, the guide sequence has a length from about 29 to about 53 nt capable of forming said RNA duplex with said target sequence. In certain example, the guide sequence has a length from about 40 to about 50 nt capable of forming said RNA duplex with said target sequence. In some examples, the guide sequence comprises a non-pairing Cytosine at a position corresponding to said Adenine resulting in an A-C mismatch in the RNA duplex formed. The guide sequence is selected so as to ensure that it hybridizes to the target sequence comprising the adenosine to be deaminated.
In some embodiments, the guide sequence is about 10 nt to about 100 nt long and hybridizes to the target DNA strand to form an almost perfectly matched duplex, except for having a dA-C mismatch at the target adenosine site. Particularly, in some embodiments, the dA-C mismatch is located close to the center of the target sequence (and thus the center of the duplex upon hybridization of the guide sequence to the target sequence), thereby restricting the nucleotide deaminase to a narrow editing window (e.g., about 4 bp wide). In some embodiments, the target sequence may comprise more than one target adenosine to be deaminated. In further embodiments, the target sequence may further comprise one or more dA-C mismatch 3′ to the target adenosine site. In some embodiments, to avoid off-target editing at an unintended Adenine site in the target sequence, the guide sequence can be designed to comprise a non-pairing Guanine at a position corresponding to said unintended Adenine to introduce a dA-G mismatch, which is catalytically unfavorable for certain nucleotide deaminases such as ADAR1 and ADAR2. Sec Wong et al., RNA 7:846-858 (2001), which is incorporated herein by reference in its entirety.
In some embodiments, the sequence of the guide molecule (direct repeat and/or spacer) is selected to reduce the degree secondary structure within the guide molecule. In some embodiments, about or less than about 75%, 50%, 40%, 30%, 25%, 20%, 15%, 10%, 5%), 1%), or fewer of the nucleotides of the nucleic acid-targeting guide RNA participate in self-complementary base pairing when optimally folded. Optimal folding may be determined by any suitable polynucleotide folding algorithm. Some programs are based on calculating the minimal Gibbs free energy. An example of one such algorithm is mFold, as described by Zuker and Stiegler (Nucleic Acids Res. 9 (1981), 133-148). Another example folding algorithm is the online webserver RNAfold, developed at Institute for Theoretical Chemistry at the University of Vienna, using the centroid structure prediction algorithm (see e.g., A. R. Gruber et al., 2008, Cell 106(1): 23-24; and P A Carr and G M Church, 2009, Nature Biotechnology 27(12): 1151-62).
In some embodiments, it is of interest to reduce the susceptibility of the guide molecule to RNA cleavage, such as to cleavage by Cas7-11. Accordingly, in particular embodiments, the guide molecule is adjusted to avoid cleavage by Cas7-11 or other RNA-cleaving enzymes.
In some embodiments, the guide molecule is modified, e.g., by one or more aptamer(s) designed to improve guide molecule delivery, including delivery across the cellular membrane, to intracellular compartments, or into the nucleus. Such a structure can include, either in addition to the one or more aptamer(s) or without such one or more aptamer(s), moiety(ies) so as to render the guide molecule deliverable, inducible or responsive to a selected effector. The invention accordingly comprehends a guide molecule that responds to normal or pathological physiological conditions, including without limitation pH, hypoxia, O2 concentration, temperature, protein concentration, enzymatic concentration, lipid structure, light exposure, mechanical disruption (e.g. ultrasound waves), magnetic fields, electric fields, or electromagnetic radiation.
The system may further comprise an adenosine deaminase or catalytic domain thereof. The adenosine deaminase protein or catalytic domain thereof deaminates an Adenine or Cytidine at the one or more codons thereby changing the codon to encode for an amino acid that is not post-translationally modified. The term “adenosine deaminase” or “adenosine deaminase protein” as used herein refers to a protein, a polypeptide, or one or more functional domain(s) of a protein or a polypeptide that is capable of catalyzing a hydrolytic deamination reaction that converts an adenine (or an adenine moiety of a molecule) to a hypoxanthine (or a hypoxanthine moiety of a molecule), as shown below. In some embodiments, the adenine-containing molecule is an adenosine (A), and the hypoxanthine-containing molecule is an inosine (I). The adenine-containing molecule can be deoxyribonucleic acid (DNA) or ribonucleic acid (RNA).
According to the present disclosure, adenosine deaminases that can be used in connection with the present disclosure include, but are not limited to, members of the enzyme family known as adenosine deaminases that act on RNA (ADARs), members of the enzyme family known as adenosine deaminases that act on tRNA (ADATs), and other adenosine deaminase domain-containing (AD AD) family members. According to the present disclosure, the adenosine deaminase is capable of targeting adenine in a RNA/DNA and RNA duplexes. Indeed, Zheng et al. (Nucleic Acids Res. 2017, 45(6): 3369-3377) demonstrate that ADARs can carry out adenosine to inosine editing reactions on RNA/DNA and RNA/RNA duplexes. The adenosine deaminase can be modified to increase its ability to edit DNA in a RNA/DNAn RNA duplex.
In some embodiments, the adenosine deaminase is derived from one or more metazoa species, including but not limited to, mammals, birds, frogs, squids, fish, flies and worms. In some embodiments, the adenosine deaminase is a human, cephalopod (e.g., squid) or Drosophila adenosine deaminase. In certain examples, the adenosine deaminase is a human adenosine deaminase. In certain examples, the adenosine deaminase is a cephalopod adenosine deaminase. In certain examples, the adenosine deaminase is a Drosophila adenosine deaminase.
The term “cytidine deaminase” or “cytidine deaminase protein” as used herein refers to a protein, a polypeptide, or one or more functional domain(s) of a protein or a polypeptide that is capable of catalyzing a hydrolytic deamination reaction that converts a cytosine (or a cytosine moiety of a molecule) to an uracil (or an uracil moiety of a molecule), as shown below. In some embodiments, the cytosine-containing molecule is a cytidine (C), and the uracil-containing molecule is an uridine (U). The cytosine-containing molecule can be deoxyribonucleic acid (DNA) or ribonucleic acid (RNA).
According to the present disclosure, cytidine deaminases that can be used in connection with the present disclosure include, but are not limited to, members of the enzyme family known as apolipoprotein B mRNA-editing complex (APOBEC) family deaminase, an activation-induced deaminase (AID), or a cytidine deaminase 1 (CDA1). In particular embodiments, the deaminase in an APOBEC 1 deaminase, an APOBEC2 deaminase, an APOBEC3A deaminase, an APOBEC3B deaminase, an APOBEC3C deaminase, and APOBEC3D deaminase, an APOBEC3E deaminase, an APOBEC3F deaminase an APOBEC3G deaminase, an APOBEC3H deaminase, or an APOBEC4 deaminase. The cytidine deaminase can be modified to increase its ability to edit DNA in a RNA/DNAn RNA duplex.
In some embodiments, the cytidine deaminase is derived from one or more metazoa species, including but not limited to, mammals, birds, frogs, squids, fish, flies and worms. In some embodiments, the cytidine deaminase is a human, primate, cow, dog, rat or mouse cytidine deaminase.
CD (cytidine deaminase)-functionalized CRISPR system for RNA editing can be used for C to U conversions. In some embodiments, the cytidine deaminase protein or catalytic domain thereof is a human, rat or lamprey cytidine deaminase protein or catalytic domain thereof. In some embodiments, the cytidine deaminase protein or catalytic domain thereof is an apolipoprotein B mRNA-editing complex (APOBEC) family deaminase, an activation-induced deaminase (AID), or a cytidine deaminase 1 (CDA1). In some embodiments, the cytidine deaminase protein or catalytic domain thereof is an APOBEC1 deaminase comprising one or more mutations corresponding to W90A, W90Y, R118A, H121R, H122R, R126A, R126E, or R132E in rat APOBEC1, or an APOBEC3G deaminase comprising one or more mutations corresponding to W285A, W285Y, R313A, D316R, D317R, R320A, R320E, or R326E in human APOBEC3G. In some embodiments, the cytidine deaminase protein or catalytic domain thereof is delivered together with an uracil glycosylase inhibitor (UGI), where said UGI is covalently linked to said cytidine deaminase protein or catalytic domain thereof and/or said catalytically inactive Cas7-11 protein.
Cas7-11-APOBEC fusions can perform C-to-U editing of RNA. APOBEC substrates are ssRNA and the Cas7-11-APOBEC can therefore target regions of the RNA around the guide/target duplex. Cas7-11-APOBEC fusions can perform C to U knockdown via stop codon introduction. In addition to correcting pathogenic U to C mutations that arise during the cellular life cycle, Cas7-11-APOBEC fusions can lead to the introduction of stop codons by converting a CAA, CGA, or CAG to TAA, TGA, or TAG, respectively. APOBEC orthologs in fusion with Cas7-11 can increase the efficiency of C-to-U editing, or can allow for additional types of base conversions. Mutating the APOBEC from the Cas7-11-APOBEC can lead to fusions with specific dsRNA activity, base flip activity and increased activity.
In certain example embodiments, the deaminase is selected from Table 2.
While several experimental Examples are contemplated, these Examples are intended non-limiting.
Table 3 below shows examples of bacterial plasmids.
Table 4 below shows examples of bacterial spacers.
Table 5 below shows examples of targets and pre-crRNA.
Table 6 below shows examples of crRNA for in vitro assays.
Table 7 below shows examples of mammalian plasmids.
Table 8 below shows examples of Cas7-11 guides for mammalian.
Table 9 shows the representative Cas7-11 orthologs of
Table 10 shows the representative Cas7-11 orthologs of
Table 11 shows the representative Cas7-11 orthologs of
Table 12 shows the representative Cas7-11 orthologs of
Table 13 shows the representative Cas7-11 orthologs of
Table 14 shows the representative Cas7-11 orthologs of
Table 15 shows sequence alignments of cas nucleases.
While several experimental Examples are contemplated, these Examples are intended non-limiting.
New Cas7-11 family members were mined from bacterial and metagenomic data downloaded from NCBI, JGI, and ENA repositories. CDS were extracted using MetaGeneMark (Besemer and Borodovsky 1999; Zhu et al. 2010), and used to build BLAST databases (Camacho et al. 2009). Existing Cas7-11 family members (Makarova et al. 2019) were used as seeds to find putative orthologs. In parallel CRISPR arrays were identified using both CRISPRCasFinder (Couvin et al. 2018) and PILER-CR (Edgar 2007), and putative orthologs were filtered for proximity to CRISPR arrays.
Cas7-11 family members were computationally identified and expressed. The Cas7-11 family is summarized in the trees presented in
By screening a database of bacterial genomic and metagenomic sequences from diverse sources containing more than ˜11.6 billion protein sequences, the set of subtype III-E systems was expended to 17 loci from various bacteria and metagenomes (
Examination of the extended set of type III-E systems confirmed that almost all III-E loci (15 of the 17) contained the TPR-CHAT protein (Csx29), and a majority encompassed uncharacterized proteins denoted Csx30 (10/17) and Csx31 (9/17) as well as the alternative sigma factor RpoE (8/17) (
The RNA-guided RNA-targeting Cas7-11 was demonstrated to be capable of defense against ssRNA MS2 phage and RNA knockdown in bacteria.
The CRISPR array screen of all crRNAs targeting the MS2 genome was performed (
The enrichment of DisCas7-11 crRNAs in the phage targeting condition denotes the survival of bacteria and enhanced representation of specific active crRNAs. The results of the MS plaque dilution assay are shown in
The number of DisCas7-11a spacers that display survival enrichment over a threshold of 1.7 across different phage dilution conditions are shown in
The quantification of resistance conferred by two MS2-targeting DisCas7-11 spacers compared against a panel of 6 non-targeting spacers is shown in
The RFP knockdown assay containing a DisCas7-11 and spacers expression vector co-transformed with an RFP-expressing vector is illustrated in
The DisCas7-11a full locus with TPR-CHAT nearby and DisCas7-11a effector expressed alone with TPR-CHAT are illustrated in
The DisCas7-11 programmable RNA cleavage activity was biochemically characterized. The CRISPR array processing assay for DisCas7-11 is illustrated in
The catalytic residues in DisCas7-11 were identified.
The protein domains of DisCas7-11 with putative catalytic residues highlighted in Cas7-like domains 3 and 4 are illustrated in
The DisCas7-11:crRNA complex binding to a complementary MS2 ssRNA target is determined by electrophoretic mobility shift assay (EMSA) and illustrated in
DisCas7-11 cleavage sites were characterized. The DisCas7-11 guides targeting multiple sites on a synthetic 100 nt EGFP ssRNA target are illustrated in
The CRISPR processing and RNA cleavage activity were demonstrated for different DisCas7-11 orthologs.
The schematics of three Cas7-11 orthologs (GwCas7-11, CjcCas7-11, and DisCas7-11) chosen for additional characterization are shown in
The activity of the GwCas7-11 orthologs at concentrations between 2 uM to 125 nM was assessed. The activity of Cas7-11 from Candidatus Jettenia caeni (CjcCas7-11) shows robust processing of CRISPR arrays specific to the CjcCas7-11 locus (
The knockdown of RNA in mammalian cells by DisCas7-11 was evaluated. The schematic of a luciferase reporter assay for RNA knockdown using a vector expressing human codon-optimized DisCas7-11 and guide RNA is shown in
RNA A-to-I editing of Cypridina luciferase (Cluc) mRNA W85X mutation in mammalian cells by dead DisCas7-11a-NES-ADAR2 was investigated. Guides were designed with mismatch distances between 2-50 nt. Editing was measured by two methods: 1) restoration of Cluc luciferase activity that is normalized to the non-targeting guide condition (
The RFP knockdown by DisCas7-11 or LwaCas13a in E. coli bacteria was assessed (
Given that DisCas7-11 lacked collateral activity in vitro or in vivo, the efficiency and effects of targeting with DisCas7-11, multiple Cas13 family members, and RNA interference through small hairpin RNA (shRNA) was compared. The activity in HEK293 FT cells was assessed, for which no detectable growth impact from Cas13a targeting has been reported. Comparing Gluc knockdown between DisCas7-11, LwaCas13a, PspCas13b, RfxCas13d, and shRNA, comparable knockdown efficiencies was found for the different systems, with the exception of LwaCas13a, which could only reach ˜35% knockdown (
The heterologous expression of the Desulfonema ishimotonii Type III-E CRISPR-Cas system and associated CRISPR array were performed. The Desulfonema ishimotonii Type III-E full locus matures crRNAs (
Dilution assays with DisCas7-11 and different spacers were performed. The DisCas7-11 assays for MS2 targeting spacers, non-targeting spacers and RFP targeting spacers were performed with dilution of phage up to 1e-1 (
The effects of genes in the Desulfonema ishimotonii type III-E CRISPR-Cas locus on MS2 interference were analyzed. The Type III-E locus of the Desulfonema ishimotonii is illustrated in
The robustness of DisCas7-11 pre-crRNA processing to DR mutations was evaluated. The in vitro transcription of pre-crRNA and processing by DisCas7-11 is illustrated in
The effects of ions on pre-crRNA processing and ions, complex concentrations, and incubation time on target cleavage was analyzed. The in vitro transcription and 5′ end labeling of pre-crRNA and processing by DisCas7-11 were assessed. Pre-crRNA was processed by DisCas7-11 in the presence of different ions or chelating agents (
The effects of DR length, spacer length, and DR mutations on in vitro target cleavage by DisCas7-11 were evaluated. A schematic of the sequence of DisCas7-11 crRNA 5 targeting the ssRNA target is shown in
The in vivo collateral activity of DisCas7-11 was evaluated. The results from the three-hour end point fluorescence of RnaseAlert reporter incubated with either DisCas7-11 or LwaCas13a targeting and non-targeting guides against MS2 ssRNA target are shown in
The cleavage activity of DisCas7-11 catalytic mutants on MS2 RNA target was evaluated. A schematic showing the positions of DisCas7-11 crRNA 1 and crRNA 2 targeting the MS2 target is shown in
The DisCas7-11 catalytic mutants that were assessed are presented in Table 16 below.
Electrophoretic mobility shift assays (EMSA) for crRNA-target interactions and quantification of EMSA intensities were performed (
The characterization of DisCas7-11 cleavage sites on ssRNA targets was performed.
DisCas7-11 was incubated with a panel of crRNAs targeting either MS2 ssRNA or ssRNA target 2, two targets of equivalent length (153 nt) (
A schematic of the position of the tested crRNAs along the SARS-CoV-2 ssRNA is shown in
DisCas7-11a was incubated with a crRNA targeting a crRNA site flanked by different sequences (
Biochemical characterization of DisCas7-11 programmable RNA cleavage activity on various length EGFP ssRNA substrates was performed. A schematic of the position of the tested crRNAs along the 100 nt EGFP ssRNA target is shown in
The heterologous expression of the Candidatus Jettenia caeni Type III-E CRISPR-Cas system and associated CRISPR array in E. coli was performed. The schematic of Candidatus Jettenia caeni locus (minus Cas1) in E. coli is shown in
The processing of Cas7-11 orthologs was found to be specific to the cognate pre-cRNAs and to do not occur on other synthetic RNAs. The DisCas7-11 pre-cRNA processing is specific to the DisCas7-11 array and does not occur on the MS2 ssRNA target as illustrated in
The correction of Cluc W85X mRNA by dDisCas7-11 was measured. A schematic of the DisCas7-11 guide design for RNA editing of Cluc W85A target mRNA is shown in
To extract total RNA, freeze-dried Desulfonema ishimotonii cultures (DSMZ 9680) were resuspended in TRIzol (R2051, Zymo), homogenized by bead beating with zirconia/silica beads, and processed with the Direct-Zol RNA miniprep protocol (R2051, Zymo). Purified RNA samples were treated with T4 Polynucleotide Kinase (M0201S, New England Biolabs), both with and without ATP to allow for the enrichment of 3′-P and 5′-OH ends. Samples has ribosomal RNA depleted using the Ribo Minus Kit (K155004, Thermo Fisher Scientific) before being processed for next-generation sequencing with the NEBNext Small RNA Library Prep Set for Illumina sequencing (E7330S, New England Biolabs). Notably, the PCR extension step was increased to 1 minute to allow for longer templates to be included in the library. Libraries were sequenced on an MiSeq (Illumina) to sufficient depth and analyzed using the alignment tool BWA (Li and Durbin 2009). Paired-end alignments were used to extract entire transcript sequences using Galaxy tools (https://usegalaxy.org/), and these sequences were analyzed using Geneious 8.1.5 (Biomatters, Auckland, New Zealand) and custom scripts (https://github.com/abugoot-lab).
To clone DisCas7-11 constructs, genomic DNA from D. ishimotonii cultures (DSMZ 9680) was extracted using the Blood & Cell Culture DNA Mini Kit (13323, Qiagen). The Type III-E D. ishimotonii CRISPR locus was PCR amplified and cloned into a pACYC184 backbone with chloramphenicol resistance using Gibson cloning. For the Cas7-11 only construct, DisCas7-11a was cloned with a J23119 promoter and B0015 terminator. Removal or addition of other genes in the CRISPR locus was cloned using Gibson cloning; when adding genes to the Cas7-11-only construct, expression of these genes was driven by a pLac promoter. In order to facilitate simple cloning of spacers, a minimal spacer construct with two flanking direct repeats (DR) surrounding a Golden Gate acceptor site was used as a backbone for Golden Gate cloning (Engler and Marillonnet 2014). To clone the CjcCas7-11b locus, DNA corresponding to the locus was synthesized by GeneArt (Thermo Scientific). Unless otherwise noted, all clonings were transformed into Stbl3 cells (C737303, Thermo Fisher Scientific) made competent with the Mix and Go kit (T3001, Zymo Research), all colonies were picked into Terrific Broth (TB) (24 g/L Yeast Extract, 12 g/L Tryptone, 9.4 g/L K2HPO4, 2.2 g/L KH2PO4, pH 7.2) supplemented with the appropriate antibiotic (chloramphenicol, 25 μg/mL; ampicillin, 100 μg/mL) and all plasmids were isolated using the QiaPrep Spin Miniprep kit (27104, Qiagen) protocol and verified by next generation sequencing on a MiSeq (Illumina). All bacterial plasmids used are listed in Table 3.
To design the MS2 library for screening, all possible spacers targeting the MS2 genome were computationally extracted, and synthesized as a library by Twist Biosciences. This library was Golden Gate cloned into the minimal CRISPR array containing the Golden Gate acceptor site on the DisCas7-11a-only backbone and transformed into Endura Duo electro-competent cells (60240-1, Lucigen) and plated on chloramphenicol-supplemented Bioassay agar plates. 16 hours post transformation, libraries were harvested by scraping and purified using a NucleoBond Xtra MaxiPrep EF (740424.10, Takara Bio).
To transform the MS2 spacer library, 400 uL NovaBlue(DE3) Gigasingle competent cells (71227-3, EMD Millipore) were transformed with a total of 2 ug of the spacer library. Cells were recovered in SOC while shaking at 37° C. for 1 hour. After recovery, cells were split into two biological replicates and used to inoculate 8 mL of Luria Broth (LB) (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl) supplemented with chloramphenicol. Cells were further incubated in LB-chlor while shaking at 37° C. for 4 hours, after which the volume was brought to a total of 12 mL for each biological replicate. Replicates were split into 6 2 mL tubes, and phages of different dilutions were added to each tube. Cells were incubated with phage while shaking at 37° C. for 3 hours, after which they were plated on Bioassay plates with LB-agar supplemented chloramphenicol. After 16 hours of growth, all colonies were harvested by scraping and scraped and plasmid DNA was extracted with the NucleoBond Xtra MaxiPrep EF (740424.10, Takara Bio). Spacer sequences were PCR amplified from extracted plasmids and sequenced using a MiSeq (Illumina) with a paired-end 150 cycle kit.
Plasmid libraries for PFS screens were cloned from synthesized oligonucleotides (IDT) consisting of 7 randomized nucleotides either upstream or downstream of the spacer 1 target. To generate dsDNA fragments for cloning, the ssDNA oligonucleotides were annealed to a short primer for second strand synthesis by large Klenow fragment (M0210S, New England Biolabs). dsDNA fragments were Gibson cloned into digested pUC19, either at the 5′-end of the beta-lactamase (Ampicillin resistance) transcript (RNA targeting library), or in a non-transcribed region of pUC19 (DNA targeting library). Gibson clonings were electroporated into Endura Duo electro-competent cells (60240-1, Lucigen) and plated on Bioassay plates with LB-agar supplemented with ampicillin. After 16 hours of growth, all colonies were harvested by scraping and scraped and plasmid DNA was extracted with the NucleoBond Xtra MaxiPrep EF (740424.10, Takara Bio).
To screen libraries, we co-transformed 50 ng of the pooled ampicillin library and an equimolar amount of the Cas7-11 locus plasmid or pACYC184 plasmid control intoNovaBluc(DE3) Gigasingle competent cells (71227-3, EMD Millipore). After transformation, cells were plated on ampicillin and chloramphenicol to select for both plasmids. After 16 hours of growth, all colonies were harvested by scraping and scraped and plasmid DNA was extracted with the NucleoBond Xtra MaxiPrep EF (740424.10, Takara Bio). The target PFS region was PCR amplified and sequenced using a MiSeq (Illumina) with a single-end 150 cycle kit.
To determine enriched spacers from the bacteriophage interference screens, sequenced spacer regions were counted and normalized to total reads for each sample. For enriched spacers, enrichment was measured as the log 2 ratio compared to no phage dilution controls, with a pseudocount adjustment. PFS regions (both at 5′ and 3) from spacers above a 1.7 log 2 enrichment threshold in both biological replicates were used to generate sequence logos for the phage dilution samples.
For transcribed/non-transcribed (beta-lactamase) pUC19 PFS screens, PFS regions were extracted and computationally collapsed to 5 nt to have broader coverage. Collapsed PFS were counted and normalized to total reads for each sample. For a given PFS region, enrichment was measured as the log ratio compared to control (pACYC184 control), with a 0.01 pseudocount adjustment. PFSs above a 6 depletion threshold that were enriched in both biological replicates were collected and used to generate sequence logos (Crooks et al. 2004).
To test individual spacers for MS2 interference with drop plaque assays, complementary oligonucleotides encoding the spacer sequences (see Table 4) flanked by overhangs corresponding to the Cas7-11a Golden Gate acceptor sites were ordered from IDT. Oligonucleotides (final concentration 10M) were annealed in T4 ligase buffer (B0202S, New England Biolabs) supplemented with 5 units of T4 Polynucleotide Kinase (M0201S, New England Biolabs). The oligonucleotides were phosphorylated at 37° C. for 30 minutes and annealed by heating to 95° C. for 5 minutes followed by a 5° C./minute cool to 25° C. Annealed oligos were then cloned into the locus backbone by Golden Gate cloning. After verification by sequencing, clonal plasmids were transformed into NovaBlue(DE3) GigaSingle competent cells (71227-3, EMD Millipore) made competent with the Mix and Go kit (T3001, Zymo Research). Transformed GigaSingle cells were seeded from an overnight culture grown to OD600 of ˜2, at which point they were diluted 1:6 in Top Agar (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, 7 g/L agar) and poured onto warm LB-chloramphenicol plates. Dilutions of MS2 phage in phosphate buffered saline were then spotted on the plates with a multichannel pipette, and plaque formation was recorded after overnight incubation.
Spacers (see Table 4) targeting RFP mRNA were Golden Gate cloned into the DisCas7-11a-only construct (as described above). After verification by sequencing, clonal plasmids were co-transformed with a tetracycline-inducible RFP plasmid on the pBR322 backbone (Addgene 79157). Colonies were picked into TB supplemented with ampicillin, chloramphenicol, and 50 ng/mL anhydrotetracycline final (631310, Takara Bio) and grown to saturation by shaking at 37° C. overnight. Cells were separated by centrifugation through a 40 μm filter plate (MANMN4010, EMD Millipore) and analyzed by flow cytometry on a FACSCanto II Cell Analyzer (BD Biosciences). Knockdown efficiency was quantified as the percent of RFP positive cells compared to a non-targeting spacer control.
The E. coli codon-optimized genes for DisCas7-11a and GwCas7-11c, and the human codon-optimized gene for CjcCas7-11b were synthesized by Twist Biosciences, PCR amplified, and Gibson into a Twin-Strep-tag and SUMO tag bacterial expression vector (Addgene 90097). Sequence verified clonal Cas7-11 expression constructs were transformed into either T7 Express lysY Competent E. coli cells (C3010I, New England Biolabs), for DisCas7-11a and GwCas7-11c, or Rosetta(DE3)pLysS Competent Cells (70956-3, EMD Millipore), for CjcCas7-11b. Colonies were picked and grown overnight in TB supplemented with ampicillin. 10 ml of overnight culture was used to inoculate 1 L of TB supplemented with ampicillin, and the culture was grown by shaking at 37° C. until the OD600 reached 1. At this point, cultures were cooled at 4° C. for 30 minutes, and induced with IPTG (16758, Sigma) to a final concentration of 500 uM. Induced cultures were grown overnight (16-24 hours) by shaking at 18° C. After growth, Cells were harvested by centrifuged at 17,700×g for 15 min at 4° C., and the cell pellet was frozen at −80° C. for later purification.
Frozen cell paste was crushed and resuspended to a final concentration of 250 mg/mL in lysis Buffer (20 mM Tris-HCl, 500 mM NaCl, 1 mM DTT, pH 8.0) supplemented with Complete Ultra EDTA-free protease inhibitor tablets (5892953001, Sigma), 1 mg/mL lysozyme (L6876, Sigma) and 1U/mL Benzonase nuclease (E1014, Sigma). Resuspension was performed by spinning for 30 minutes at 4° C. After resuspension, the solution was sonicated on ice with a 600W Ultrasonic Homogenizer (U.S. Solid) for 15 minutes with a 50% duty cycle. Sonicated lysate was cleared by centrifugation at 38,400×g for 1 hour at 4° C. The supernatant was supplemented with 1 mL of Strep-Tactin XT superflow high capacity resin (2-4030-010, IBA Life Sciences) and incubated with rotation for 1 hour at 4° C. Bound resin was loaded onto a glass Econo-Column (7371507, Bio-Rad) and washed with three column volumes of lysis buffer supplemented with Complete Ultra EDTA-free protease inhibitor tablets. To cleave protein off of bead-bound Twin-Strep-tag and SUMO tag, the resin was resuspended in 3 mL of SUMO digest buffer (30 mM Tris-HCl, 500 mM NaCl, 1 mM DTT, 0.15% NP-40, pH 8.0) supplemented with 100 ug of SUMO protease (purified in-house). Cleavage occurred on-column overnight at 4° C. with rotation, after which supernatant was drained from the column by gravity filtration and concentrated to a volume of 1 mL with a 100 kDa centrifugal filter (UFC810024, Sigma). Concentrated protein was loaded onto a gel filtration column (Superdex 200 Increase 10/300 GL, GE Healthcare Life Sciences) via an ÄKTA pure FPLC machine. The resulting fractions from gel filtration were analyzed by SDS-PAGE Stain-Free gels (4568096, Bio-Rad), and fractions containing protein were pooled, buffer exchanged into Storage Buffer (600 mM NaCl, 50 mM Tris-HCl pH 7.5, 5% glycerol, 2 mM DTT), quantified via comparison SDS-PAGE with a Bovine Serum Albumin (BSA) ladder, aliquoted, and frozen at −80° C. for storage.
RNA targets for testing cleavage and pre-crRNA targets were synthesized by in vitro transcription. Single stranded DNA oligonucleotide templates with a T7 RNA polymerase promoter appended at the 5′ end were synthesized by IDT, and converted to dsDNA by PCR and gel extraction. Gel extracted dsDNA products (˜1 μg/reaction) were used as input for the HiScribe T7 Quick High Yield RNA Synthesis kit (E2050S, New England Biolabs), with the 30 uL reaction size recommended for transcripts <300 nt. Transcription occurred overnight at 30° C., after which targets were purified with RNA Clean and Concentrator columns (R1017, Zymo Research). Labeling was performed with the 3′ EndTag End Labeling System (MB-9002, Vector Laboratories) and 5′ EndTag End Labeling System (MB-9001, Vector Laboratories), per the manufacturer's instructions, which was followed by incubation with 100× molar ratio of Cyanine5.5 maleimide (17080, Lumiprobe) at 65° C. for 30 minutes. We confirmed that this labeling was not 5′ or 3′ specific, but rather body labeling, via Rnase H gel assays (fig. S21), likely due to the intercalating or groove-binding properties of Cyanine5.5 (Biver et al. 2005). After labeling, RNA was purified with RNA Clean and Concentrator columns (R1017, Zymo Research). All targets used for in vitro cleavage are listed in supplemental Table 5.
crRNA designs were ordered from IDT as reverse complement DNA oligonucleotide templates with a T7 RNA polymerase promoter appended at the 5′ end. These templates were annealed with a T7 promoter oligonucleotide, generating a dsDNA promoter region. Annealing occurred in Taq Buffer (B9014S, New England Biolabs) with both oligonucleotides at 10 μM. 1 uL of the anneal reaction was used as input for the HiScribe T7 Quick High Yield RNA Synthesis kit (E2050S, New England Biolabs), with the 30 uL reaction size recommended for transcripts <300 nt. Transcription occurred overnight at 37° C., after which targets were purified with RNAClean XP beads (A63987, Beckman Coulter); beads were used at 3.3× volume ratio and supplemented with 3× volume of isopropanol. All crRNA used for in vitro cleavage are listed in supplemental Table 6.
Unless otherwise indicated, in vitro nuclease assays were performed with 233 nM purified Cas7-11, 30 nM of labeled ssRNA target and 200 nM crRNA in nuclease assay buffer (40 mM Tris-HCl, 60 mM NaCl, 6 mM MgCl2, pH 7.5) supplemented with 4U of RNase Inhibitor, Murine (M0314S, New England Biolabs). For pre-crRNA processing reactions, crRNA was omitted and pre-crRNA was used in place of labeled ssRNA target. Reactions were incubated for 1 hour at 37° C. (unless otherwise indicated) and then quenched with addition of proteinase K, EDTA, and urea (final concentrations 1 mg/mL proteinase K, 6 mM EDTA, and 400 uM Urea) for 15 minutes at 50° C. To prepare for gel electrophoresis, reactions were denatured with 4.5M urea denaturing buffer at 95° C. for 5 minutes and loaded onto a 10% Novex PAGE TBE-Urea gel (EC6885BOX, Invitrogen), which was run at 235V for 25 minutes at 60° C. Gels were imaged using an Odyssey scanner (LI-COR Biosciences).
In vitro PFS screens were reverse transcribed with a target specific primer using the qScript cDNA SuperMix (95048-025, Quanta Bio) and, the target PFS region was PCR amplified and sequenced using a MiSeq (Illumina) with a single-end 150 cycle kit. PFS regions were computationally extracted and collapsed to 5 nt to have broader coverage, and collapsed PFS were counted and normalized to total reads for each sample. For a given PFS region, enrichment was measured as the log ratio compared to non-targeting control, with a 0.01 pseudocount adjustment. PFSs above a 5 depletion threshold that were enriched in both experimental replicates were collected and used to generate sequence logos
In vitro collateral activity assays were performed with 233 nM purified Cas7-11 or LwaCas13a, 10 nM of unlabeled ssRNA target and 200 nM crRNA in nuclease assay buffer (40 mM Tris-HCl, 60 mM NaCl, 6 mM MgCl2, pH 7.5) supplemented with 4U of RNase Inhibitor, Murine (M0314S, New England Biolabs) and 250 nM final concentration RnaseAlert V2 (4479768, Thermo Fisher Scientific). Reactions were incubated at 37° C. and activity was read continuously in the FAM channel of a Synergy Neo2 plate reader (BioTek).
EMSA reactions were performed with dilutions of Cas7-11-crRNA complex with 10 nM of labeled ssRNA target in EMSA buffer (5 mM EDTA, 2.5% glycerol, 20 mM Tris, 5 μg/mL heparin, pH 7.5) supplemented with 4U of RNase Inhibitor, Murine (M0314S, New England Biolabs). Binding occurred by incubation at 37° C. for 20 minutes, after which reactions were mixed with 2× loading buffer (0.5× TBE buffer, 10% Ficoll, 18 mM EDTA) and run on a 6% Novex PAGE TBE gel (EC6265BOX, Thermo Fisher Scientific) at 180V for 30 min at 4° C. Gels were imaged using an Odyssey scanner (LI-COR Biosciences).
In vitro nuclease assays were performed and samples were quenched as described above using unlabeled ssRNA targets. After quenching, samples were treated with alkaline phosphatase (EF0651, Thermo Fisher Scientific) and purified with RNA Clean and Concentrator columns (R1017, Zymo Research). Libraries were then treated with the same small RNA sequencing pipeline applied to in vivo crRNA species, with the RiboMinus depletion step omitted.
To generate vectors for testing DisCas7-11a in mammalian cells, a mammalian codon optimized DisCas7-11a sequence was ordered from Twist Biosciences, PCR amplified, and cloned into a mammalian expression vector containing combinations of modifications, including with and without NLS tags or N- or C-terminal msfGFP fusions, all under the control of a CMV promoter.
The dual luciferase reporter was cloned by PCR amplifying Gaussia and Cypridinia luciferase coding DNA, the EF1alpha and CMV promoters and assembled using the NEB Gibson Assembly (E2611S, New England Biolabs).
For mammalian DisCas7-11a guide expression, we synthesized both the full-length and mature DR sequences and cloned with golden-gate acceptor sites under U6 expression via restriction digest cloning. Individual guides were then cloned into the corresponding expression backbones for DisCas7-11a by golden-gate cloning. All mammalian DisCas7-11 plasmids are listed in Table 7. All DisCas7-11a guide sequences for knockdown or RNA editing experiments are listed in Table 8.
All mammalian experiments were performed using the HEK293 FT cell line (American Type Culture Collection (ATCC)). HEK293 FT cells were grown in Dulbecco's Modified Eagle Medium with high glucose, sodium pyruvate, and GlutaMAX (Thermo Fisher Scientific), additionally supplemented with 1× penicillin-streptomycin (Thermo Fisher Scientific) and 10% fetal bovine serum (VWR Seradigm). We maintained cells below a confluency of 80%.
Transfections were performed using Lipofectamine 2000 (Thermo Fisher Scientific) in 96-well plates coated with poly-D-lysine (BD Biocoat). For transfections, cells were plated 16 hours prior to transfection at seeding densities of ˜20,000-30,000 cells per well, allowing cells to reach 90% confluency by transfection. For each well on the plate, transfection plasmids were combined with Opti-MEM I Reduced Serum Medium (Thermo Fisher) to a total of 25 μl. Separately, 24.5 μl of Opti-MEM was combined with 0.5 μl of Lipofectamine 2000. Plasmid and Lipofectamine solutions were then combined and incubated for 5-10 minutes, after which they were pipetted onto cells.
To assess RNA knockdown in mammalian cells with reporter constructs, 100 ng of DisCas7-11a expression vector was co-transfected with 150 ng of guide expression plasmid and 40 ng of the knockdown reporter construct. After 48 hours, we harvested media containing secreted luciferase and measured luciferase activity using the Gaussia Luciferase Assay reagent (GAR-2B) (Targeting Systems) and Cypridina (Vargula) luciferase assay reagent (VLAR-2) (Targeting Systems) kits. Assays were performed in white 96 well plates on a plate reader (Biotek Synergy Neo 2) with an injection protocol. All replicates performed are biological replicates. Luciferase measurements were normalized by dividing the Gluc values by the Cluc values, thus normalizing for variation from well to well.
For targeting of endogenous genes, 100 ng of DisCas7-11a expression vector was co-transfected with 150 ng of guide expression plasmid. After 48 hours, we lysed cells and harvested RNA using a method previously described (Joung et al. 2017) with a gene-specific reverse transcription primers. Using Fast Advanced Master Mix (Thermo Fisher Scientific), we measured gene expression using the cDNA via qPCR and TaqMan qPCR probes for the KRAS, PPIB, CXCR4, and MALAT1 transcripts (Thermo Fisher Scientific) as well as the GAPDH control probe (Thermo Fisher Scientific). qPCR reactions were read out on a Bio-Rad CFX384 Touch Real-Time PCR Detection System, with four 5 μl technical replicates in 384-well format.
To assess dDisCas7-11a-ADAR2dd editing activity in mammalian cells, we transfected 100 ng of dDisCas7-11a-ADAR2dd expression vector, 150 ng of guide expression plasmid, and 25 ng of the RNA editing reporter. After 48 hours, we harvested media from the cells, which should contain the secreted Gluc (normalization control) and Cluc (protein targeted for correction of W85X) proteins. If planning to sequence the RNA for the precise RNA editing levels, we also harvested RNA using a method previously described (Joung et al. 2017) with a gene-specific reverse transcription primer.
For luciferase measurements, we used undiluted media and the Gaussia Luciferase Assay reagent (GAR-2B) (Targeting Systems) and Cypridina (Vargula) luciferase assay reagent (VLAR-2) (Targeting Systems) kits. Assays were performed in white 96 well plates on a plate reader (Biotek Synergy Neo 2) with an injection protocol. All replicates performed are biological replicates. Luciferase measurements were normalized by dividing the Cluc values by the Gluc values, thus normalizing for variation from well to well. This ratio measurement could further be normalized by dividing by the non-targeting guide ratios.
For sequencing of RNA editing rates, we performed two rounds of PCR (NEBNext High-Fidelity 2×PCR Master Mix from New England Biolabs) using the extracted cDNA to add Illumina adaptors and sample barcodes. Illumina next generating sequencing was used to sequence editing rates in our prepared libraries on a MiSeq instrument. RNA editing rates were evaluated at the targeted adenosine in the W85X pre-termination codon.
DisCas7-11-mediated RNA-guided RNA interference against MS2 phage and RNA knockdown in E. coli was investigated. The potential role of PFS in the function of the III-E systems was assessed by performing randomized PFS screens on both a DNA-only target and an expressed target at the 5′ end of an ampicillin gene. It was found that there was no signal on the DNA-only target on either side of the protospacer (
The regulation of DisCas7-11 interference activity by accessory proteins was assessed. Whether accessory proteins in the D. ishimotonii subtype III-E CRISPR locus could modulate RNA interference activity was investigated (
The mapping of the DisCas7-11a cleavage mechanism via in vitro cleavage of ssRNA of a 31 nt target was investigated. The DisCas7-11a cleavage of synthetic 31 nt MS2 ssRNA with a 31 nt crRNA completely duplexed to the target shows two cleavage fragments that are generated in the targeting condition when protein is generated (indicated by triangles) (
The effects of DisCas7-11a-mediated knockdown of mRNA in mammalian cells by guide variants or inactivating mutations was measured. The knockdown of Gaussia luciferase (Gluc) mRNA in mammalian cells by DisCas7-11a unmodified or with N-/C-terminal msfGFP fusions, with guides containing the full DR sequence was assessed. The guides are designed to be tiled across the Gluc transcript. The knockdown of Gluc mRNA in mammalian cells by DisCas7-11a unmodified or with N-/C-terminal msfGFP fusion, with guides containing the mature DR sequence was assessed. Guides are designed to be tiled across the Gluc transcript. The comparison of knockdown activity of Gluc mRNA in mammalian cells between active DisCas7-11a, catalytically inactive D429A/D654A DisCas7-11a, and GFP is illustrated in
The RNA editing efficiency with active and inactive DisCas7-11a-NES-ADAR2 constructs was measured. The RNA A-to-I editing of Cypridinia luciferase (cluc) mRNA W85X mutation in mammalian cells by active DisCas7-11a-NES-ADAR2 or dead DisCas7-11a-NES-ADAR2 is shown in
The RNase H cleavage of target showing body labeling was investigated. Cleavage of 3′ (
The mechanism of the programmable RNA cleavage activity of DisCas7-11 was assessed. The type III-E system from D. ishimotonii and corresponding effector DisCas7-11 were chosen, as a representative of type III-E systems to characterize in detail. The small RNA from D. ishimotonii were harvested and sequenced. Mature crRNA species indicative of pre-crRNA processing were identified (
One skilled in the art will appreciate further features and advantages of the invention based on the above-described embodiments. Accordingly, the invention is not to be limited by what has been particularly shown and described, except as indicated by the appended claims. All publications and references cited herein are expressly incorporated herein by reference in their entirety.
This application is a divisional of U.S. patent application Ser. No. 17/365,777, filed Jul. 1, 2021, and claims priority to U.S. Provisional Application Nos. 63/073,898, filed Sep. 2, 2020, and 63/208,606, filed Jun. 9, 2021, the entire contents of which are hereby incorporated by reference in their entirety.
This invention was made with government support under Grant No. R21 AI149694 awarded by the National Institutes of Health (NIH). The government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 63208606 | Jun 2021 | US | |
| 63073898 | Sep 2020 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 17365777 | Jul 2021 | US |
| Child | 18649077 | US |
