During early neural development, the most anterior neural plate is segmented into three subregions: telencephalon, eye field and diencephalon (Diacou et al., 2022, Prog Retin Eye Res. 91:101093; Giger & Houart, 2018, Front Neurosci 12:87). The eye field, located at the medial portion of the anterior neural plate, is defined by the expression of a group of eye field transcription factors (EFTFs) that include PAX6, RAX, OTX2, LHX2, SIX3 and SIX6 (Zuber et al. 2003, Development 130:5155-5167). The EFTFs are not uniquely expressed in eye field cells and many of them are also expressed by cells in the telencephalon and diencephalon regions (adjunctive subregion) (Maden, 2002, Nat Rev Neurosci 3:843-853; Niehrs, 2004, Nat Rev Genet 5:425-434; Mason, 2007, Nat Rev Neurosci 8:583-596; Bielen & Houart, 2014, Dev Neurobiol 74:772-780); for instance, PAX6, OTX2, LHX2 and SIX3 expression is found in the prospective telencephalon while OTX2, LHX2, SIX3, RAX and SIX6 are expressed in the prospective diencephalon (Lagutin et al., 2003, Genes Dev 17:368-379; Ando et al., 2005, Dev Biol 287:456-468; Georgala et al., 2011, Dev Neurobiol 71:690-709; Hoch et al., 2015, Cell Rep 12:482-494; Matsuo et al., 1995, Genes Dev 9:2646-2658; Orquera et al. 2016, Dev Biol 416:212-224; Jean et al., 1999, Mech Dev 84:31-40). The regulatory mechanisms of EFTFs by morphogens that delineate the eye field from neighboring regions remain elusive.
Eye field formation accompanies regional patterning along the anterior-posterior axis in the neural plate. Inhibitors of the Wnt pathway are present in both telencephalon and eye field subregions in the anterior neural plate to repress posterization (Niehrs et al., 2001, Int J Dev Biol 45:237-240; Houart et al., 2002, Neuron 35:255-265; Tendeng. & Houart, 2006, Gene Expr Patterns 6:761-771). It remains unknown how the eye field and telencephalic regions are further subdivided (Esteve & Bovolenta, 2006, Curr Opin Neurobiol 16:13-19). Due to the challenges in accessing those subregions within the neural plate at such an early stage, there have been only limited studies investigating the signals specifying eye field formation. Studies in a Xenopus frog model have suggested that fibroblast growth factor (FGF) and ephrin signaling pathways regulate cell movements to the eye field (Moore et al., 2004, Dev Cell 6:55-67) while the non-canonical WNT pathway promotes cell coherence within the eye field and represses the Wnt/beta-catenin pathway (Cavodeassi et al., 2005, Neuron 47:43-56). Rostral paraxial mesoderm has been shown to inhibit normal eye development through BMPs in chicken embryo (Teraoka et al., 2009, Dev Biol 330, 389-398). A zebrafish study demonstrated that BMP pathway acts as a repressor of the eye field fate by inhibiting Rx3 (RAX homolog) hence preventing the telencephalon from acquiring the eye identity (Bielen & Houart, 2012, Dev Cell 23:812-822), suggesting the negative role of BMP in the eye field formation. However, these findings have not been validated in other vertebrates including humans due to technical difficulties in distinguishing cell movement during gastrulation. Consequently, the molecular pathways and their interactions that underlie the specification of the eye-field or retinal cells from the prospective telencephalic cells in humans remains unclear.
Human pluripotent stem cells (hPSCs) have the potential to be used as an advantageous model to reveal aspects of early development, including eye-field/retinal specification. They may also be promising source for generating retinal cells to treat retina diseases. Given the neuroectodermal origin of retinas, most of the current methods to generate retinal cells have involved guiding hPSCs to neuroepithelia through embryoid body formation followed by spontaneous differentiation to retinal cells in the form of optic cup-like structures in a suspension culture which are then manually selected (Zhao et al., 2017, Development 144:1368-1381; Zhong et al., 2014, Nat Commun 5:4047; Capowski et al., 2019, Development 146; Gonzalez-Cordero et al., 2017, Stem Cell Reports 9:820-837). However, such approaches are inefficient, primarily due to the lack of understanding how the early neuroepithelia are specified to the eye field cells and subsequent retina progenitors.
There remains a need in this art for methods to produce retinal cells for treating retina degenerative diseases, as well as methods for using such cells for these treatments and isolated populations of retinal cells for such uses.
Disclosed herein are methods for generating pure retinal progenitor cells (RPCs) and their progenies, and isolated populations of such cells produced thereby. Elucidated herein is a previously unappreciated role of BMP in specifying early (primitive) neuroepithelia to the eye-field/retinal fate through identification of differential molecular pathways in neuroepithelial and retinal scRNA-Seq datasets, followed by serial molecular interventions during the neuroepithelia-to-retina transition. Generation of pure retinal progenitor cells (RPCs) and their progenies using chemically defined conditions without any need for manual selection is a consequence of this understanding of molecular pathways underlying the transition from neuroepithelia to eye field-like cells disclosed herein. Further disclosed is the use of EFTFs, including PAX6 wherein expression thereof is mediated by BMP.
Also provided herein are methods for producing neuroectoderm cells from human pluripotent stem cells (hPSCs) comprising the steps of treating hPSCs in cell culture in vitro with inhibitors of BMP or TGF-beta, alone or in combinations thereof.
The RPCs produced by the methods disclosed herein are advantageously derived from neuroectoderm cells produced from human pluripotent stem cells (hPSCs). Accordingly, provided herein are methods for producing primitive neuroectoderm cells (PNCs) from human pluripotent stem cells (hPSCs).
Also provided herein are methods for producing RPCs from PNCs comprising the steps of treating the PNCs in cell culture in vitro with BMP2, BMP4, or BMP7.
Also provided herein are methods for producing RPCs from human pluripotent stem cells (hPSCs) comprising the steps of treating hPSCs in cell culture with a TGF-beta inhibitor for 5 days followed by treatment with BMP activator from day 6 to day 20.
Also provided herein are compositions of retinal progenitor cells, including cell populations comprising 50-100% RPCs, produced by the disclosed methods.
These and other features, objects, and advantages of the present invention will become better understood from the description that follows. In the description, reference is made to the accompanying drawings, which form a part hereof and in which there is shown by way of illustration, not limitation, embodiments of the invention. The description of preferred embodiments is not intended to limit the invention to cover all modifications, equivalents, and alternatives. Reference should therefore be made to the claims recited herein for interpreting the scope of the invention.
The disclosure will be better understood and features, aspects, and advantages other than those set forth above will become apparent when consideration is given to the following detailed description thereof. Such detailed description refers to the following figures.
For the purposes of explicating and understanding the principles of this disclosure, reference is made to embodiments and specific language used to describe the same. The skilled artisan will nevertheless understand that no limitation of the scope of the disclosure is thereby intended, such alteration and further modifications of the disclosure as illustrated herein, being contemplated as would be understood by one skilled in the art to which the disclosure relates.
As used herein, articles “a” and “an” are intended to refer to one or to more than one (i.e., at least one) of the grammatical object of the article. By way of example, “an element” means at least one element and can include more than one element.
“About” is used to provide flexibility to a numerical range endpoint by providing that a given value can be “slightly above” or “slightly below” the endpoint without affecting the therapeutically beneficial result. The term “about” in association with a numerical value means that the numerical value can vary by plus or minus 5% or less of the numerical value.
Throughout this specification, unless the context requires otherwise, the word “comprise” and “include” and variations (e.g., “comprises,” “comprising,” “includes,” “including”) will be understood to imply the inclusion of a stated component, feature, element, or step or group of components, features, elements, or steps but not the exclusion of any other integer or step or group of integers or steps.
As used herein, “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations where interpreted in the alternative (“or”).
Recitation of ranges of values herein are merely intended to serve as a succinct method of referring individually to each separate value falling within the range, unless otherwise indicated herein. Furthermore, each separate value is incorporated into the specification as if it were individually recited herein. For example, if a range is stated as 1 to 50, it is intended that values such as 2 to 4, 10 to 30, or 1 to 3, etc., are expressly enumerated in this disclosure. These are only examples of what is specifically intended, and all possible combinations of numerical values between and including the lowest value and the highest value enumerated are to be considered to be expressly stated in this disclosure.
Unless otherwise defined, all technical terms used herein have the same meaning as commonly understood by a person of ordinary skill in the art to which this disclosure belongs.
The terms “express” or “expression” refer to transcription and translation of a nucleic acid coding sequence resulting in production of the encoded polypeptide. “Express” or “expression” also refers to antigens that are expressed on cell surfaces.
As used herein, the term “subject” refers to both human and nonhuman animals. The term “nonhuman animals” of the disclosure includes all vertebrates, e.g., mammals and non-mammals, such as nonhuman primates, sheep, dog, cat, horse, cow, chickens, amphibians, reptiles, and the like. The subject also and specifically can be a human patient that is at risk for, or suffering from, one or more retinal diseases or disorders. The human subject can be of any age (e.g., an infant, child, or adult).
The term “construct” refers to an artificially designed segment of DNA that can be used to incorporate genetic material into a target cell.
The term “sequence identity” refers to the number of identical or similar nucleotide bases on a comparison between a test and reference oligonucleotide or nucleotide sequence. Sequence identity can be determined by sequence alignment of a first nucleic acid sequence to identify regions of similarity or identity to second nucleic acid sequence. As described herein, sequence identity is generally determined by alignment to identify identical residues. Matches, mismatches, and gaps can be identified between compared sequences by techniques known in the art. Alternatively, sequence identity can be determined without taking into account gaps as the number of identical positions/lengths of the total aligned sequence×100. In one embodiment, the term “at least 90% sequence identity to” refers to percent identities from 90 to 100%, relative to the reference nucleotide sequence. Identity at a level of 90% or more is indicative of the fact that, assuming for exemplary purposes a test and reference polynucleotide sequence length of 100 nucleotides are compared, no more than 10% (i.e., 10 out of 100) of the nucleotides in the test oligonucleotide differ from those of the reference oligonucleotide. Differences are defined as nucleic acid substitutions, insertions, or deletions.
The term “media” or “medium,” as used herein, refers to a gel or liquid that contains nutrients sufficient to facilitate growth of one or more cells, particularly human cells and specifically human iPSCs and differentiated species produced therefrom as disclosed herein.
The term “chemically defined,” as used herein related to growth media, refers to a growth medium suitable for in vitro cell culture, wherein all components and concentrations thereof in the medium are known.
The term “progenitor cells,” as used herein, refers to cells descending from stem cells that can be further differentiated, e.g., retinal progenitor cells as disclosed herein.
The term “stem cell” as used herein is a cell which is undifferentiated. Such a cell can undergo differentiation when submitted to one or more stimuli. The stimuli might be physical, mechanical, electrical, chemical, biochemical, biological or a combination of any of the latter. By stem cell, it is to be understood here either pluripotent or multipotent cells, and either embryonic or induced.
As used herein, the term “pluripotent stem cells” appropriate for use according to a method of the invention are cells having the capacity to differentiate into cells of all three germ layers. Pluripotent stem cells (PSCs) suitable for the differentiation methods disclosed herein include, but are not limited to, human embryonic stem cells (hESCs), human induced pluripotent stem cells (hiPSCs) non-human primate embryonic stein cells (nhpESCs), non-human primate induced pluripotent stem cells (nhpiPSCs). As used herein, “embryonic stem cells” or “ESCs” mean a pluripotent cell or population of pluripotent cells derived from an inner cell mass of a blastocyst.
As used herein, the term “human pluripotent stem cell” will be understood to include cells derived from human embryonic stem cells (hESCs) or induced pluripotent stem cells (iPSCs), in particular such cells that are mammalian cells and particularly human cells.
As used herein, the term “induced pluripotent stem cells” or “iPS cells” or “iPSCs” mean a pluripotent cell or population of pluripotent cells that may vary with respect to their differentiated somatic cell of origin, that may vary with respect to a specific set of potency-determining factors and that may vary with respect to culture conditions used to isolate them, but nonetheless are substantially genetically identical to their respective differentiated somatic cell of origin and display characteristics similar to pluripotent stem cells, such as ESCs, as described herein. Induced pluripotent stem cells, however, are not immediately derived from embryos. As used herein, “not immediately derived from embryos” means that the starting cell type for producing iPS cells is a non-embryonic, non-pluripotent cell, such as a multipotent cell or terminally differentiated cell, such as somatic cells obtained from a post-natal individual.
As used herein, the term “retinal progenitors” or “retinal progenitor cells” (RPCs) relates to cells presenting at least one of (i) retinal multipotency (ii) the expression of various retinal progenitor markers, (iii) a mitotic capacity.
As used herein, the term “early neuroectoderm cells” or “primitive neuroectoderm cells” refer to an early or primitive neuroepithelial stage in the first week that express PAX6 but not SOX1.
As used herein, the term “late neuroectoderm cells” or “definitive neuroectoderm cells” refer to a late or definitive neuroepithelial stage in the second week that express PAX6 and SOX1 in an embryoid body culture system. Definitive neuroectoderm cells are the cells that form the neural tube in vivo.
The terms “pure” and “purity,” as used herein, refer to the proportion of desired cells from the final isolated cells.
The term “composition,” as used herein, refers to a mixture of one or more types of cells.
The term “enriched,” as used herein, when used regarding genes identified in metabolic or developmental pathways, refers to the pathways or gene ontologies are overrepresented in a group of genes more than would be expected at random.
The term “enriched population,” as used herein, refers to increased percentage of the target cell types in a population.
The term “low cell quality,” as used herein, refers to low detection of RNA, the presence of dead cells, or potential doublets. The standard quality control used refers to selecting single cells with more than 300 unique genes (nFeature) and less than 15% or 20% mitochondrial gene reads (percent.mt) for follow-up analysis. Additional procedures were used to exclude low quality cells and doublets in each sample (nFeature<6,000 and nCount<20,000).
In some embodiments, human pluripotent stem cells (hPSCs) are treated with inhibitors of cellular gene expression for certain developmentally relevant genes.
In some embodiments, the inhibitors are BMP or TGF-beta.
In some embodiments, the BMP inhibitor is DMH1.
In further embodiments, neuroectoderm cells treated with the BMP inhibitor produce definitive neuroectoderm cells.
In even further embodiments, treatment with the BMP inhibitor induces PAX6 and SOX1 expression which is characteristic for definitive neuroectoderm cells.
In some embodiments, the TGF-beta inhibitor is chosen from, but not limited to, A 77-01, A 83-01, AZ 12799734, D 4476, disitertide, galunisertib, GW 788388, IN 1130, LY 2109761, R 268712, RepSox, SB 431542, SB 505124, SB 525334, SD 208, or SM 16 (Bio-techne Corporation), or any other suitable TGF-beta inhibitor.
In some embodiments, the TGF-beta inhibitor is SB 431542.
As used herein, the skilled worker will understand the terms set forth below to have their corresponding meanings, wherein BMP is bone morphogenic protein, and BMP2, BMP4, and BMP7 are variant species of BMP; see, Reddi & Reddi, 2009, “Bone morphogenetic proteins (BMPs): from morphogens to metabologens.” Cytokine & Growth Factor Reviews 20:341-2; Human Gene Name Committee (HUGO) reference HGNC 1067.
DMH1 is a BMP (ALK2) inhibitor that is commercially available from Stem Cell Technologies (Cat. No. 73632) having the structure:
TGF-beta is transforming growth factor beta, identified by OMIM 190180 and UniProt P01137; Human Gene Name Committee (HUGO) reference HGNC 11766.
TGF-beta inhibitors as set forth herein are identified as follows: A 77-01 is a TGF-beta inhibitor commercially available from MedChem Express (Cat. No. 6712) having the structure:
A 83-01 is a TGF-beta inhibitor commercially available from Stem Cell Technologies (Cat. No. 100-1041) having the structure:
AZ 12799734 is a TGF-beta inhibitor commercially available from biotechne tocris (Cat. No. 6870) having the structure:
D 4476 is a TGF-beta (ALK-5) inhibitor commercially available from Selleckchem Cat. No. 301836-43-1) having the structure:
Disitertide is a peptidic TGF-beta inhibitor commercially available from MedChemExpres (Cat. No. HY-P0118).
Galunisertib is an experimental TGF-beta inhibitor developed by Eli Lilly & Co. having the structure:
GW 788388 is a TGF-beta (ALK-5) inhibitor commercially available from ApexBio (Cat. No. A8301) having the structure:
IN 1130 is a TGF-beta (ALK-5) inhibitor commercially available from MedChemExpress (Cat. No. HY-18758) having the structure:
LY 2109761 is a TGF-beta (ALK-5) inhibitor commercially available from Selleckchem Cat. No. S2704) having the structure:
R 268712 is a TGF-beta (ALK-5) inhibitor commercially available from MedChemExpress (Cat. No. HY-12953) having the structure:
RepSox is a TGF-beta (ALK-5) inhibitor commercially available from Selleckchem Cat. No. S7223) having the structure:
SB 431542 is a TGF-beta (ALK-5) inhibitor commercially available from ApexBio (Cat. No. A8249) having the structure:
SB 505124 is a TGF-beta (ALK-4, ALK-5) inhibitor commercially available from Selleckchem Cat. No. S2186) having the structure:
SB 525334 is a TGF-beta (ALK-5) inhibitor commercially available from Selleckchem Cat. No. S1476) having the structure:
SD 208 is a TGF-beta (ALK-5) inhibitor commercially available from ApexBio (Cat. No. A3808) having the structure:
SM 16 is a TGF-beta (ALK-5/ALK-4) inhibitor commercially available from MedChemExpress (Cat. No. HY-111482) having the structure:
In further embodiments, neuroectoderm cells treated with the TGF-beta inhibitor produce definitive primitive cells (PNCs).
In even further embodiments, treatment with the TGF-beta inhibitor induces PAX6 and SOX1 expression.
In some embodiments PNCs express PAX6, but not SOX1 expression.
In some embodiments, the hPSCs and inhibitors were incubated in chemically defined media for up to 6 days.
In some embodiments, hPSCs are treated simultaneously with a BMP inhibitor and a TGF-beta inhibitor.
In some embodiments, PNCs are treated in cell culture in vitro with BMP2, BMP4, or BMP7 for about 20 days. Treating PNCs with BMP2, BMP4, or BMP7 is effective for producing retinal progenitor cells.
In some embodiments, hPSCs are treated with BMP and TGF-beta for 5 to 6 days. In some embodiments, PNCs are produced by treating the cells with BMP2.
In some embodiments, BMP2 is administered in a concentration of 2-10 ng/ml.
In some embodiments, PNCs are treated with BMP2 after day 4 and before day 7 of cell culture.
In some embodiments, retinal progenitor cells are produced from hPSCs treated with a TGF-beta inhibitor for 5 days followed by treatment with BMP activator from day 6 to day 20.
In some embodiments, the BMP activator is BMP2.
In some embodiments, the concentration of BMP2 is 10 ng/mL.
In some embodiments, the composition of retinal progenitor cells are at least 50% pure.
The retina originates from the eye field that is situated between the prospective telencephalon and diencephalon at the most anterior neural plate. How the eye-field cells are specified from the early neuroectoderm remains an enigma, though BMP inhibition was proposed as a driving force from animal studies (Teraoka et al., 2009, Dev Biol 330, 389-398; Bielen & Houart, 2012, Dev Cell 23:812-822). As disclosed herein, informatics analysis comparing the human retinal vs. cerebral cortical progenitors revealed active expression of the BMP pathway genes in retinal progenitors but not in cortical progenitors, suggesting a need of BMP activation for retinal (eye field) specification from the early neuroectoderm instead. Indeed, blockade of BMP signaling committed the early ectodermal cells to the definitive neuroectoderm fate while removal of BMP inhibition endowed the early (primitive) neuroectoderm cells for retinal differentiation. Further BMP activation converted the primitive neuroepithelia to eye-field-like cells and then RPCs. This was achieved through cross regulation between the BMP pathway and the EFTFs at multiple stages. The findings set forth herein renewed the concept on human eye field specification and subsequent RPC differentiation, which led to the establishment of a novel system to generate pure RPCs.
Neuroectoderm induction during gastrulation is orchestrated by inhibition of the TGF-beta/BMP and WNT pathways and activation of the FGF signaling in a temporal-spatial manner (Hemmati-Brivanlou, A et al., 1997, Cell 88, 13-17; Munoz-Sanjuan, et al., 2002, Nat Rev Neurosci 3, 271-280; Harland, R., 2000, Curr Opin Genet Dev 10, 357-362; Heeg-Truesdell, E. et al., 2006, Dev Biol 298, 71-86; Delaune, E., et al., 2005, Development 132, 299-310; Linker, C. et al., 2004, Development 131, 5671-5681). Provided herein also is the evidence that induction of neuroepithelia from hPSCs undergoes two identifiable stages, an early or primitive neuroepithelial stage in the first week that express PAX6 but not SOX1 and a late or definitive neuroepithelial stage in the second week that express PAX6 and SOX1 in an embryoid body culture system (Li, X. J. et al., 2005, Nat.Biotechnol. 23, 215-221; Pankratz, M. T. et al., 2007, Stem Cells 25, 1511-1520; Zhang, X. et al., 2010, Cell Stem Cell 7, 90-100). The result set forth herein confirmed that two-stage neural induction using a monolayer culture platform under TGF-beta inhibition. Results further showed that additional inhibition of the BMP pathway committed the primitive neuroectoderm cells to the definitive neuroectoderm cells, consistent with previous observation (Chambers, S. M. et al., 2009, Nat.Biotechnol. 27, 275-280), which further explained why “dual-smad inhibition” blocked RPC specification. This finding contradicted hypotheses in the prior art that BMP inhibition is required to remove repressive signaling on Rx3 (RAX homolog) expression in the prospective eye field cells (Bielen & Houart, 2012, Dev Cell 23:812-822). Cellular and scRNA-Seq analysis on the differentiating cells demonstrated that BMP inhibition was not required for inducing early primitive neuroepithelia nor eye field cells. In fact, BMP inhibition hindered the specification of RPCs from the primitive neuroepithelia due to the progression to the dorsal telencephalon cells, as indicated by the expression of GLI3, LHX2, PAX6, SIX3 and OTX2 but not RAX. Such a phenomenon suggested a need of a signal to trigger the eye field cells and/or RPC specification from the primitive neuroepithelia. As disclosed herein, treatment with multiple BMP ligands converted the early neuroepithelia to RPCs, as indicated by expression of RAX, PAX6, SIX6, VSX2 and MITF. This was similar to an observation in mice that knocking out BMP receptors conditionally in developing retina cells by Six3Cre resulted in reduced growth of embryonic retina (Murali, D. et al., 2005, Development 132, 913-923) and in hPSC differentiation that a transient high dose of BMP enhances the generation of retinal cells (Capowski et al., 2019, Development 146; Kuwahara, A. et al., 2015, Nat Commun 6, 6286; Harkin, J. et al., 2024, Proc Natl Acad Sci USA 121, e2317285121), although when and how BMPs work in these studies was not documented. The results set forth herein further showed that the effects of BMP treatment occurred only on the primitive neuroepithelia but not before (day 4) or after (day 7). These results further showed that during early development, TGF-beta inhibition allowed specification of the primitive neuroectoderm, which is conducive for specification of both the definitive neuroectoderm and the eye field in the anterior neural plate. Blockade of BMP committed the primitive neuroectoderm to the definitive neuroectoderm whereas activation of BMP permits or triggered the specification of the eye field to generate RPCs.
It is well established in animals (Hogan, B. L., et al., 1988, Development 103 Suppl, 115-119; Hill, R. E. et al., 1991, Nature 354, 522-525; Grindley, J. C., et al., 1995, Development 121, 1433-1442; Hogan, B. L. et al., 1986, J Embryol Exp Morphol 97, 95-110) and hPSCs (Tao et al., 2020, EMBO reports 21) that EFTFs, especially PAX6, are required for neuroretina development. Indeed, knock-out of PAX6, either the PAX6AB KO, retina specific D isoform (PAX6D KO), or both blocked the generation of RPCs despite treatment with BMPs, demonstrating the necessity of PAX6 in mediating the effect of BMPs. Furthermore, PAX6 modulated BMP signaling by regulating BMPR1B transcription during retina specification, as indicated by ChIP-Seq analysis, validating direct targeting of BMPR1B by both PAX6A and PAX6D. These findings suggested a cross signaling between BMPs and PAX6 in regulating eye field or RPC specification. Considering the differential roles of PAX6 isoforms in neuroectoderm and neuroretina specification as well as the spatio-temporal effects of BMPs in these processes, such cross-talks can ensure generation of accurate cell types in these neighboring areas.
Developmental principles are the guideline for hPSC differentiation (Tao, Y. & Zhang, S.C., 2016, Cell Stem Cell 19:573-586). Without the knowledge of how the (early) neuroectoderm is converted into the eye-field cells, current retina differentiation technology employs the embryoid body method to generate the retina lineage cells (Meyer, J. S. et al., 2009, Proc Natl Acad Sci USA 106, 16698-16703; Zhang, S. C., et al., 2001, Nat Biotechnol 19, 1129-1133 (2001), which relies on spontaneous differentiation and yields heterogeneous populations comprising of large populations of cerebral cells besides retinal cells. Hence, manual selection is often necessary to separate the retinal cells from the telencephalic cells thanks to the characteristic optic cup-like morphology (Zhao et al., 2017, Development 144:1368-1381; Zhong et al., 2014, Nat Commun 5:4047; Capowski et al., 2019, Development 146; Gonzalez-Cordero et al., 2017, Stem Cell Reports 9:820-837).
The identification of differential BMP effects in the process of eye-field formation as set forth herein provides a robust system to generate RPCs through generation of the primitive neuroepithelia by TGF-β inhibition followed by eye-field specification and RPC differentiation by BMP activation. This method enables generation of a nearly pure population of RPCs and their differentiated progenies in either a monolayer or 3D culture platform, validated by scRNA-Seq. It is superior to many existing protocols (Harkin, J. et al., 2024, Proc Natl Acad Sci USA 121, e2317285121; Meyer, J. S. et al., 2009, P Natl Acad Sci USA 106, 16698-16703; Mellough, C. B. et al., 2012, Stem Cells 30, 673-686, Nakano, T. et al., 2012, Cell Stem Cell 10, 771-785; Reichman, S. et al., 2014, Proc Natl Acad Sci USA 111, 8518-8523; Zhong, X. F. et al., 2014, Nat Commun 5; Kuwahara, A. et al., 2015, Nat Commun 6) thanks to the directed differentiation with defined conditions that is built upon the well characterized underlying molecular pathway (Table 1). Such a system will facilitate research on the development and pathogenesis of the retinas as well as developing therapeutics for retinal diseases.
Provided herein are therapeutic compositions and methods for producing neuroectoderm and retinal progenitor cells from pluripotent stem cells. Retinal progenitors are known in the art to be capable of giving rise to multiple retina progenies (final differentiated cells) such as ganglion cells and photoreceptor cells. Progenitor cells can be used to treat eye diseases because the cells have the potential to become effective cells, wherein later stage progenies fare desirable for treating degenerative retinal diseases such as glaucoma, age-related macular degeneration (AMD) and retinitis pigmentosa.
Various exemplary embodiments of compositions and methods according to this invention are now described in the following non-limiting Examples. The Examples are offered for illustrative purposes only and are not intended to limit the scope of the present invention in any way. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and the following examples and fall within the scope of the appended claims.
The Examples set forth herein incorporate and rely on certain experimental and preparatory methods and techniques preformed as exemplified herein.
hPSC Culture and Retina Differentiation
hPSCs (H9, IMR-90-4 and WC30) were maintained under E8/feeder-free culture condition and passaged at 1:20 ratio with Rock inhibitor. After each new passage, the cells were fed with E8 medium for another 1˜2 days to reach 30-40% confluence. To initiate retina differentiation, culture medium was replaced with Retina Induction Medium (RIM) containing Neural induction medium (NIM) comprising DMEM/F12 media containing 1% N2 and 1× nonessential amino acids (NEAA) supplemented with 10 μM SB431542 (TGF inhibitor, Stemgent, 04-0010-10); this new passage day was counted as day 0 (DO) of retina differentiation. Cells were then fed daily with RIM, or every other day based on the cell density. On day 4, the cells were dissociated by ReLeSR (STEM CELL) or EDTA and re-suspended in the fresh RIM containing 0.5 micromolar (μM) Rock inhibitor. Cell clusters were thereafter transferred to a cell culture flask and cultured in suspension. On day 5, the resulting cell spheres were fed with RIM without SB431542. On day 6, the cell spheres were fed with Retina Specification Medium (RSM) containing NIM supplemented with 10 ng/ml BMP2 (R&D SYSTEMS, 355-BM) every other day till day 20. Typical optical cup structures can be observed as early as day 15; BMP2 can be replaced by BMP4 or BMP7. At day 20, the spheres were cultured in Transition medium (DMEM/F12: Neurobasal (1:1) with 1% N2, 2% B27, 1×NEAA and 1×Glutamax) until analysis.
Differentiating cells at multiple time points (day 0-day 12) indicated below were digested and collected for nucleus isolation and library construction (Tao et al., 2024, Nat. Biotech. 12:1404-1416; https://doi.org/10.1038/s41587-023-01977-4). All libraries prepared in this way were processed by NovaSeq. Alignment of raw sequencing reads, and generation of feature barcode matrices were performed using Cellranger (7.1.0). Seurat (4.1.3) was used to process feature barcode matrices and analyze snRNA-Seq data32. All samples were processed under standard quality control metrics. Single cells with more than 300 unique genes (nFeature) and less than 15% or 20% mitochondrial gene reads (percent.mt) were selected for follow-up analysis. Additional procedures were used to exclude low quality cells and doublets in each sample (nFeature<6,000 and nCount<20,000). In day 30 retina organoid samples, retinoic acid (RA) was used to accelerate retinogenesis from day 20. Early exposure to RA can caudalize progenitors towards the spinal cord region of the neural tube. Cells were filtered by removing HOXB3- and HOXB4-expressing cells to exclude possible caudalized cells in this sample. After quality control, all snRNA-Seq data were normalized using the SCTransform (v2) function in Seurat with mitochondria genes regressed out (Choudhary, S. et al., 2022, Genome Biol 23, 27). PCA and UMAP reduction, gene feature plots were done by using Seurat as well.
Bulk RNA-Seq was performed as previously described (Tao et al., 2020, EMBO reports 21: e50000). RNA-Seq data were processed following quality control, mapping, and analysis of transcripts using FastQC, Trimmomatic, HISAT2, FeatureCount, and DESeq2 pipelines in R. All gene ontology and pathway related analysis were performed using ToppGene (https://toppgene.cchmc.org/). Heatmap and hierarchical clustering of differentially regulated genes in wildtype, PAX6 KO, PAX6AB KO and PAX6D KO were processed by Morpheus (https://software.broadinstitute.org/morpheus/). Gene overlapping was analyzed by Venny 2.1 (https://bioinfogp.cnb.csic.es/tools/venny/)
qPCR Analysis
Total RNA was isolated with the RNeasy Plus Mini Kit according to the manufacturer's instructions. For quantitative PCR (qPCR), cDNA was synthesized using PrimeScript RT Reagent Kit (Takara). qPCR was performed using iTaq Universal SYBR Green Supermix (Bio-Rad). GAPDH gene was used as an internal control to equalize cDNA.
Immunocytochemistry was performed as described previously (Huang et al., 2016, Sci Rep 6:32600; Tao et al., 2021, Nat Med 27:632-639). In brief, cells on coverslips were fixed in 4% neutral-buffered paraformaldehyde (PFA) for 10 min at room temperature. Following rinsing with phosphate-buffered saline (PBS), coverslips were incubated in 0.2% Triton X-100 (in PBS) for 10 min followed by incubation in a solution of 10% donkey serum (in PBS) at room temperature for 1 h. Coverslips were then incubated with primary antibodies diluted in 5% donkey serum in 0.1% Triton X-100 (in PBS) at 4° C. overnight, followed by incubation with fluorescently conjugated secondary antibodies at room temperature for 30 min. Nuclei were stained with Hoechst stain. Images were collected with a Nikon A1 laser-scanning confocal microscope.
Flow cytometry was performed following manufacturer's instruction using Transcription Factor Buffer Set which is designed for transcription factor staining. Briefly, single cells were prepared using TrypLE Express Enzyme and fixed in the fixation buffer provided in the kit at 2-8° C. for 45 min. After 3 washings with the permeable buffer, the primary antibodies were added to cells for 45 min at 2-8° C. in a light-tight box. The cells were washed 3 times before incubation with fluorescently conjugated secondary antibodies for 45 mins at 2-8° C. in a light-tight box. After 3 times of washing, cells were suspended in the washing buffer and analyzed by flow cytometry (BD LSR or BD LSRII). Data analysis was performed using FlowJo.
Antibodies used were: SOX2 (R&D Systems AF2018), SOX1 (R&D Systems AF3369), PAX6 Alexa Fluor 488 (BD Biosciences Cat #561664), SOX2-V450 (BD Biosciences Cat #561610), SOX1-PE (BD Biosciences Cat #561592), PAX6 (Covance Cat #PRB-278P), VSX2 (Exalpha, Cat #X1180P), CRX (Abnova, Cat #H00001406-M02), OPSIN (MilliporeSigma, Cat #AB5407).
Data were presented as mean±SEM unless specified in the legends. Statistical analyses were performed using GraphPad Prism 5 or Microsoft Office Excel. The methods used to assess the significance were specified in the figure legends.
The raw snRNA-seq datasets are available at the Gene Expression Omnibus with accession number GSE250547 (GSM7981367, GSM7981368, GSM7981369, GSM7981370, GSM7981371, GSM7981372). The raw data for RNA-Seq and ChIP-Seq are from GSE128141.
BMP Pathway Genes were Differentially Expressed in Cortical and Retinal Progenitors
The eye field and telencephalon are adjacent in the most anterior neural plate (
Integration of cortical and retinal progenitors by Seurat (Stuart, T. et al., 2019, Cell 177:1888-1902) revealed that progenitors from the retina and the cortex organoid merged in multiple clusters, indicating very similar gene expression profiles (
Analysis of molecular functions of the up-regulated genes revealed enrichment in “SMAD binding,” “R-SMAD binding,” and “transcription factor binding.” Pathway analysis using MSigDB C2 BIOCARTA (v7.5.1) showed that “TGF-beta receptor signaling” was highly enriched in retinal cells (
In order to understand whether activation of the BMP pathway was required for switching the neuro/ectoderm to their retinal fate (because inhibition of TFG-beta, BMP, and/or WNT promotes neuroectoderm specification from hPSCs), the next step was to find how regulation of these pathways affected retinal specification. H9 human embryonic stem cells (hESCs) were differentiated to neuroepithelia by culture in chemically defined media as disclosed above and then treated with inhibitors against BMP (DMH1), TGF-beta (SB-431542, SB), or WNT (IWR1) pathways separately for 6 days during the neural induction process (
Due to the lack of retinal differentiation resulting from BMP inhibition, expression of retina genes was examined at multiple time points in SB and SB plus dorsomorphin homolog 1 (SB+DMH1), which was a well-established dual-SMAD inhibition condition for neural conversion (Chambers, S. M. et al., 2009, Nat Biotechnol 27:275-280). Retinal progenitor specific marker VSX2 was completely blocked by BMP inhibition when compared to the SB condition (
Regulation of retinal differentiation by the BMP pathway was also assessed. Single nucleus RNA-seq (snRNA-Seq) assays were performed to profile and compare the differentiating cells under the SB or SB+DMH1 conditions (
To verify this observation, cells were differentiated with only SB for the first 6 days to generate primitive neuroepithelial cells and then how the BMP pathway regulated retinal differentiation was investigated by treating the cells with or without DMH1 at day 6 (
The retina originates from the eye field that is situated between the prospective telencephalon and diencephalon at the most anterior neural plate. The informatics analysis comparing the human retinal vs. cerebral cortical progenitors revealed an active expression of the BMP pathway genes in retinal progenitors but not in cortical progenitors, suggesting a need of BMP activation for retinal (eye field) specification from the early neuroectoderm instead. Indeed, blockade of BMP signaling commits the early ectodermal cells to the definitive neuroectoderm fate while removal of BMP inhibition endows the early (primitive) neuroectoderm cells for retinal differentiation. Further BMP activation converts the primitive neuroepithelia to eye-field-like cells and then RPCs. This is achieved through cross regulation between the BMP pathway and the EFTFs at multiple stages. These findings provided a pathway for establishing a novel system to generate pure RPCs.
BMP Specified the Neural Retinal Fate from Primitive Neuroepithelial Cells
The finding that BMP inhibition blocked EFTF expression raised the question of whether BMP was sufficient for retinal differentiation. To determine whether this was the case, cells were treated with BMP2 (2 ng/ml) on day 6 and collected on day 12 (
Next, these cells were treated for 4 days with BMP2 starting from day 4, 5, 6 or 7 and retinal gene expression examined at day 12 to determine whether BMP specified retinal fate. Treating these cells with BMP2 at day 4 was found to inhibit generation of retinal cells, which was indicated by low expression levels of VSX2. This is likely due to impairment of neuroectoderm or ectoderm induction processes, because the BMP pathway was necessary for neuroectoderm differentiation in this early stage (Tao, Y. & Zhang, S.C., 2016, Cell Stem Cell 19:573-586), which was also indicated by low expression levels for SOX1 (
Analysis of the dose effect in these experiments indicated that VSX2 and PAX6 expression levels increased with higher doses of BMP2. BMP2 administration (10 ng/ml) induced maximum levels of VSX2 and PAX6 expression while reducing expression of the definitive neuroepithelial marker SOX1 (
Cellular and scRNA-Seq analysis on the differentiating cells demonstrated that BMP inhibition is not required for inducing early primitive neuroepithelia nor the eye field cells. BMP inhibition hinders the specification of RPCs from the primitive neuroepithelia due to the progression to the dorsal telencephalon cells, as indicated by the expression of GLI3, LHX2, PAX6, SIX3 and OTX2 but not RAX. Treatment with multiple BMP ligands converts the early neuroepithelia to RPCs, as indicated by expression of RAX, PAX6, SIX6, VSX2 and MITF. These results further showed that the BMP effect occurred only on the primitive neuroepithelia but not before (day 4) or after (day 7).
To further illuminate how BMP2 regulated retina specification at a single cell level, snRNA-Seq was performed to profile the differentiating cells under treatment with BMP2 (10 ng/ml) at day 12 (
Retina development is tightly regulated by the intrinsic factors such as EFTFs. Results set forth herein demonstrated that BMP signaling was necessary for RPC specification by regulating EFTFs such as RAX, PAX6 and SIX6. In particular, one of the EFTFs, PAX6, was also found to be essential for retinal development at multiple stages (Shaham, O., et al., 2012, Prog Retin Eye Res 31:351-376). How EFTFs interacted with the BMP signaling pathway to regulate retinal differentiation was investigated by the disclosed methods (SB→BMP) to determine whether PAX6 mediated the effects of BMP by differentiating hPSCs without all PAX6 isoforms (PAX6 KO) (Tao, Y. et al., 2020, EMBO reports 21). No VSX2 expression was found in PAX6 KO hPSC-differentiated progenitors (
To further elucidate how PAX6 regulated the BMP signal pathway and which PAX6 isoform(s) were required (because PAX6 has multiple isoforms expressed in retina cells; Tao, Y. et al., 2020, EMBO reports 21), joint bulk RNA-Seq analysis was performed with RNA-Seq datasets of day 20 progenitors generated from PAX6 KO, PAX6D KO (an isoform uniquely expressed in retina lineage cells) (Tao, Y. et al., 2020, EMBO reports 21) and another PAX6 isoform A&B knockout (PAX6AB KO) (Chen, Y. et al., 2015, Cell Stem Cell 17:233-244) cell lines (
To further examine whether PAX6 isoforms directly regulated BMPR1B transcription, ChIP-Seq data was revisited to investigate both PAX6A and PAX6D targets during the retina specification process (Tao, Y. et al., 2020, EMBO reports 21). PAX6A and PAX6D shared 1283 target genes in the process of retina differentiation. Consistent with an essential role of each isoform in BMPR1B expression, BMPR1B was found to be one of the common downstream targets regulated by both PAX6A and PAX6D (
Treatment of the primitive neuroepithelia with BMPs up-regulated PAX6 expression, which can be the consequence of retina specification or the direct regulation by BMPs. Knock-out of PAX6, either the A&B, D isoform, or both blocks the generation of RPCs despite the treatment with BMPs, demonstrating the necessity of PAX6 in mediating the effect of BMPs. Furthermore, PAX6 modulates the BMP signaling by regulating BMPR1B transcription during retina specification, as indicated by ChIP-Seq analysis validating the direct targeting of BMPR1B by both PAX6A and PAX6D.
The Examples set forth above resulted in an effective retinal differentiation method performed by sequentially treating hPSCs with SB (day 0-day 5), induction of primitive neuroepithelia and BMP2 (day 6-day 20, 10 ng/ml, specification of eye-field cells and subsequent retinal differentiation) (
To further validate the identity of retina progenitors specified by sequential treatment of SB and BMP2 (
Mapping the snRNA-Seq dataset (day 30) to the scRNA-Seq datasets from human fetal retina (day 59, GSM4231316) (Sridhar, A. et al., 2020, Cell Rep 30:1644-1659) revealed that all major retinal cells in these cultures merged well with their in vivo counterparts in DCX positive clusters (
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, and patent application was specifically and individually indicated to be incorporated by reference.
While some embodiments have been illustrated and described in detail in the appended drawings and the foregoing description, such illustration and description are to be considered illustrative and not restrictive. Other variations to the disclosed embodiments can be understood and effected in practicing the claims, from a study of the drawings the disclosure, and the appended claims. The mere fact that certain measures or features are recited in mutually different dependent claims does not indicate that the combination of these measures or features cannot be used. Any reference signs in the claims should not be construed as limiting the scope.
Table 1 shows the percentage of cells expressing the gene in retina cells (Pct. 1), the percentage of cells expressing the gene in cortical cells (Pct.2), and the fold change (FC) for the expression levels of the gene in retina versus cortical cells. P_val is p-value; avg_log 2FC is the log fold-change of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first group. P_val_adjust is the adjusted p-value, based on boneferroni correction using all genes in the dataset.
This invention was made with government support under National Institute of Child Health and Human Development (NICHD) (U54 HD090256 and HD106197). The government has certain rights in the invention.
Number | Date | Country | |
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63596926 | Nov 2023 | US |