Patent Application
20240010704
The instant application contains a Sequence Listing that has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Mar. 10, 2023, is named LNK_246US_SL.txt and is 147,818 bytes in size.
The present invention provides chimeric polypeptides that are useful in identifying modulators of adhesion G protein-coupled receptors and Polycystin-1/Polycystin-1-like proteins. The invention further provides screening methods using the novel polypeptides.
Adhesion G protein-coupled receptors (aGPCRs) and Polycystin-1/Polycystin-1-like (PC1/PC1-like) proteins are involved in physiological cell and organ functions. Genetic aberrations and the resulting functional impairments in these molecules play a role in human diseases.1-7 aGPCRs and PC1/PC1-like molecules form two classes of cell membrane receptors with 7 and 1/11 transmembrane segments, respectively (
The physical dissociation of aGPCRs and PC1/PC1-like molecules (
NTF-CTF separation is predicted to expose a short β-sheet motif C-terminal of the GPS4, 17 This motif has been previously shown to harbour receptor stimulating activity by acting as a tethered agonist (TA)18, 19. aGPCR activation results in the stimulation of canonical intracellular second messenger cascades and thereby cell-autonomously governs biochemical and cell biological states (reviewed in ref.7) Presence and principal utility of TAs has since been demonstrated for numerous aGPCRs and Polycystin-1 (reviewed in refs.6, 20, 36) (
Based on these observations, it appears critical to detect GAIN domain proteolysis and NTF-CTF separation as initiating steps for aGPCR and PC1/PC1-like molecule activation (
To date, the family of adhesion G protein-coupled receptors (aGPCRs) consists of 33 members in humans. Many reports have demonstrated critical functions for members of this family in organogenesis, neurodevelopment, myelination, angiogenesis, and cancer progression. Importantly, mutations in several aGPCRs have been linked to human diseases. Furthermore, overexpression in cancer cells of aGPCRs has been reported. Yet, there are no approved drugs specifically targeting these proteins.
To date, there are no screening methods for identifying molecules that affect GAIN domain proteolysis and/or NTF-CTF separation, in particular in a high-throughput format.
WO 2019/099689 A1 discloses chimeric polypeptides containing a force sensor cleavage domain and methods of use thereof. WO 2019/099689 A1 defines the term “force sensor cleavage domain” as referring to a polypeptide domain of a force sensitive protein that, upon the application of force, is cleavable, e.g., by a protease. This contrasts with the GAIN domain of aGPCRs and PC1/PC1-like molecules, which is cleaved at a GPS site within the GAIN domain first and then disjoins upon force transmission acting on the NTF (N-terminal fragment), overcoming the non-covalent interactions holding together the NTF/CTF heterodimer. Furthermore, in contrast to the chimeric polypeptide defined in WO 2019/099689 A1 the aGPCR/PC1/PC1-like GAIN domain facilitates autocatalytic cleavage and hence constitutes both enzyme and substrate in one structure.
Importantly, WO 2019/099689 A1 does not disclose chimeric polypeptides comprising a GAIN domain or even mention a GAIN domain. According to WO 2019/099689 A1 one possible force sensor cleavage domain, among a list of possibilities, is an “adhesion-GPCR cleavage domain”, which may be derived from an aGPCR protein (e.g. Drosophila Flamingo protein) or a homolog thereof (i.e. CELSR1, CELSR2 and CELSR3). These aGPCR are large, e.g. about 3000 amino acid long proteins, which may comprise a GAIN domain, but also multiple other protease cleavage sites16, 40-46.
WO 2019/099689 A1 does not further define “adhesion-GPCR cleavage domain” but gives with SEQ ID NO: 272-274 a number of examples for amino acid sequences of such an “adhesion-GPCR cleavage domain”. These sequences are far too short to constitute a complete GAIN domain and even if comprising part of a GAIN domain sequence they would not be expected to properly fold into a GAIN domain and would consequently not be able function as the “adhesion-GPCR cleavage domain”.
In light of all the above, there is a need for a screening method as outlined above, in particular for a method to identify inhibitors of GAIN domain proteolysis and/or NTF-CTF separation.
The inventors surprisingly found that GAIN domain proteolysis and/or NTF-CTF separation can be detected using a chimeric sensor protein comprising the extracellular region of an aGPCR, a Notch transmembrane domain, and an intracellular reporter moiety. The sensor protein of the present invention allows the identification of compounds that modulate the activation of aGPCR molecules or PC1/PC1-like molecules, e.g. by affecting GAIN domain proteolysis and/or NTF-CTF separation.
The present invention therefore relates to the subject matter defined in the following items [1] to [34]:
[1] A polypeptide comprising (i) a first sequence comprising a GPCR autoproteolysis-inducing (GAIN) domain of an adhesion GPCR or of a PC1/PC1-like protein, (ii) a second sequence comprising the transmembrane region of a Notch receptor, and (iii) a third sequence comprising a transcription factor moiety.
[2] The polypeptide of item [1], wherein the first sequence comprises or consists of a fragment of the extracellular region (ECR) of the aGPCR or PC1/PC1-like protein, wherein said fragment comprises said GAIN domain.
[3] The polypeptide of item [2], wherein said fragment does not comprise the N-terminal end of said aGPCR or PC1/PC1-like protein; and/or wherein said fragment does not comprise the full amino acid sequence that N-terminally precedes the GAIN domain of said aGPCR or PC1/PC1-like protein.
[4] The polypeptide of item [2] or [3], wherein said fragment has the structure X-G-Y, wherein G is the GAIN domain, X is an amino acid sequence adjacent to the N-terminal end of the GAIN domain in said aGPCR or PC1/PC1-like protein, and Y is absent or an amino acid sequence adjacent to the C-terminal end of the GAIN domain in said aGPCR or PC1/PC1-like protein.
[5] The polypeptide of item [4], wherein X consists of 1 to 7,000, or 10 to 6,000, or 100 to 5,000, or 200 to 4,000, or 300 to 3,000, or 400 to 2,000, or 500 to 1,000 amino acids.
[6] The polypeptide of item [4] or [5], wherein Y consists of 1 to 30 amino acids, or 2 to 20 amino acids, or 3 to 10 amino acids.
[7] The polypeptide of item [1], wherein the first sequence comprises or consists of the N-terminal part of the aGPCR or PC1/PC1-like protein, from the N-terminal amino acid of the aGPCR or PC1/PC1-like protein to the C-terminal end of the GAIN domain of the aGPCR or PC1/PC1-like protein.
[8] The polypeptide of item [1] or [7], wherein the first sequence comprises or consists essentially of the complete extracellular region (ECR) of said aGPCR or said PC1/PC1-like protein, such that the first sequence of the polypeptide ends before the start of the transmembrane (TM) domain of the aGPCR or the PC1/PC1-like protein.
[9] The polypeptide of any one of the preceding items, wherein the aGPCR is selected from the group of aGPCRs listed in Table 1 hereinbelow.
[10] The polypeptide of item [1], [7], [8] or [9], wherein the first sequence comprises or consists of the extracellular region of an aGPCR selected from the group of aGPCRs listed in Table 1 hereinbelow.
[11] The polypeptide of any one of items [1] to [8], wherein the PC1/PC1-like protein is selected from the group of PC1/PC1-like proteins listed in Table 2 hereinbelow.
[12] The polypeptide of any one of items [1], [7], [8] or [11], wherein the first sequence comprises or consists of the extracellular region of an PC1/PC1-like protein selected from the group of PC1/PC1-like proteins listed in Table 2 hereinbelow.
[13] The polypeptide of any one of the preceding items, wherein the GAIN domain comprises or consists of (i) an amino acid sequence selected from the group consisting of SEQ ID NOs:1-37; or (ii) an amino acid sequence having a sequence identity of at least 90% to any one of SEQ ID NOs:1-37.
[14] The polypeptide of any one of the preceding items, wherein the GAIN domain comprises or consists of an amino acid sequence selected from the group consisting of SEQ ID NOs:1-32.
[15] The polypeptide of any one of items [1] to [13], wherein the GAIN domain comprises or consists of an amino acid sequence selected from the group consisting of SEQ ID NOs:33-37.
[16] The polypeptide of any one of the preceding items, wherein the second sequence comprises the S2 cleavage site of a Notch receptor.
[17] The polypeptide of any one of the preceding items, wherein the second sequence comprises the S3 cleavage site and optionally the S4 cleavage site of the Notch receptor.
[18] The polypeptide of any one of the preceding items, wherein the second sequence comprises or consists essentially of a fragment of the Notch receptor comprising the S2 and the S3 cleavage sites, and optionally the S4 cleavage site.
[19] The polypeptide of any one of the preceding items, wherein the second sequence consists essentially of the iuxtamembrane segment and the transmembrane region of the Notch receptor.
[20] The polypeptide of any one of the preceding items, wherein the second sequence comprises or consists essentially of (i) an amino acid sequence selected from the group consisting of SEQ ID NOs:52-56, (ii) an amino acid sequence having a sequence identity of at least 90% to any one of SEQ ID NOs:52-56, (iii) an amino acid sequence which differs from any one of SEQ ID NOs:52-56 in less than 10, or less than 7, or less than 5, or less than 3 amino acids, e.g. in one or two amino acids, or (iv) a fragment of (i), (ii) or (iii) comprising the S2 and the S3 cleavage sites.
[21] The polypeptide of any one of the preceding items, wherein the transcription factor moiety is selected from the group consisting of LexA from E. coli, GAL4 from S. cerevisiae, QF, QF2 and QF2w derived from N. crassa.
[22] The polypeptide of any one of the preceding items, wherein the transcription factor moiety, upon separation from the second sequence, is capable of activating transcription of a reporter gene.
[23] The polypeptide of any one of the preceding items, wherein release of an N-terminal portion of the first sequence induces cleavage of the second sequence at one or more proteolytic cleavage sites, thereby releasing the transcription factor moiety.
[24] The polypeptide of any one of the preceding claims, which is a sensor protein suitable for detecting the release of its N-terminal fragment and/or proteolytic cleavage within the GAIN domain.
[25] The polypeptide of item [1], having or consisting essentially of the amino acid sequence as shown in SEQ ID NO:59.
[26] The polypeptide of any one of the preceding items, which is embedded in a biological membrane, e.g. in a cell membrane.
[27] The polypeptide of any one of the preceding items, which is integrated in the membrane of a cell, wherein the first sequence extends to the extracellular/luminal space, the transmembrane region is located within the membrane, and the transcription factor moiety extends to the intracellular/cytoplasmic space.
[28] A nucleic acid encoding the polypeptide of any one of the preceding items.
[29] A plasmid or vector comprising the nucleic acid of item [28].
[30] A cell comprising the polypeptide of any one of items [1] to [27], the nucleic acid of item [28], or the plasmid or vector of item [29].
[31] The cell of item [30], further comprising a nucleic acid capable of binding to the transcription factor moiety, operably linked to a nucleic acid encoding a reporter.
[32] A non-human transgenic animal comprising the polypeptide of any one of items [1] to [27], the nucleic acid of item [28], the plasmid or vector of item [29], or the cell of item [30] or [31].
[33] A non-human transgenic animal expressing the polypeptide of any one of items [1] to [27].
[34] A screening method comprising the following steps
The present invention relates to a polypeptide comprising (i) a first sequence comprising a GAIN domain of an adhesion GPCR or of a PC1/PC1-like protein (ii) a second sequence comprising the transmembrane region of a Notch receptor, and (iii) a third sequence comprising a transcription activator.
The polypeptide of the invention is a chimeric transmembrane protein comprising a single-pass transmembrane domain.
The term “adhesion GPCR” or “aGPCR” refers to a G-protein coupled receptor protein of class B subfamily 237 characterized by a 7 transmembrane domain and an extracellular region (ECR) with a GAIN domain. It does not necessarily need to but can additionally contain one or more adhesion domains within its ECR.
The term “adhesion domain” refers to autonomously folding protein subunits that permit interactions with ligands contained within the extracellular matrix, mounted on the same (cis) or neighbouring (trans) cell surfaces. Adhesion domains mediate but are not limited to one or more of the following functions: adhesive cell anchoring, formation of cell junctions, cell migration, cell polarisation, tissue polarisation, interaction with fixed or soluble ligands, transmission of mechanical signals onto expressing cells.
The terms “GPCR autoproteolysis-inducing domain” and “GAIN domain”, as used herein, refer to a region within the ECR of an aGPCR or PC1/PC1-like protein composed of an N-terminal subdomain A and a C-terminal subdomain B (see refs. 9, 38 and 39). Subdomain A of the GAIN domain is composed of 3 to 6 α-helices. Subdomain B of the GAIN domain is composed of 13 β-strands and can additionally contain several small α-helices. Subdomain B typically forms a twisted β-sandwich structure and contains the GPCR Proteolysis Site (GPS). Based on primary protein sequences these properties can be predicted by publicly available software tools such as Phyre2 (http://www.sbg.bio.ic.ac.uk/˜phyre2), Psipred (http://bioinf.cs.ucl.ac.uk/psipred/) and DALI (http://ekhidna2.biocenter.helsinki.fi/dali/). Primary sequence identity between orthologous GAIN domains can be as low as 10%, but the Root Mean Square Deviation (RMSD) of atomic positions of the folded GAIN domain is <5 Å.
For example, the GAIN domain of rat CL1 (UniProtKB—O88917/AGRL1_RAT) extends from Thr533-Ile849 of the amino acid sequence of the receptor. Using structure-based searches such as DALI and BLAST one can determine for other aGPCRs or PC1/PC1-like proteins which amino acids constitute the GAIN domain. For example, the GAIN domains of several human aGPCRs are shown in SEQ ID NOs:1-32 (see also Table 1 below), and the GAIN domains of several human PC1/PC1-like proteins are shown in SEQ ID NOs:33-37 (see also Table 2 below). The GAIN domain may or may not induce autoproteolysis in the polypeptide of the invention. The term “GAIN” domain includes domains which do not exert autoproteolytic activity, but are classified as GAIN domains on the basis of alignments and/or sequence similarity to other proteins known to have a GAIN domain. Some adhesion GPCRs and PC1 molecules contain autoproteolytic domains in addition to the GAIN domain, some are processed by other endogenous proteases. All three modes of cleavage (through the GAIN domain, through non-GAIN domains of the receptors, through endogenous proteases) can be detected using the polypeptide of the invention and are encompassed by the present invention.
The aGPCRs in the sense of the present invention include, but are not limited to, human aGPCRs and non-human orthologs thereof (e.g. from mammalians such as mouse, rat, Macaca mulatta or Macaca fascicularis, other vertebrates such as Xenopus tropicalis and Danio rerio, and invertebrates such as Drosophila melanogaster or Caenorhabditis elegans). Preferably, the aGPCR is a human aGPCR. More preferably, the aGPCR is selected from the aGPCRs listed in Table 1.
The term “PC1/PC1-like protein” as used herein refers to polypeptides comprising a 1 or 11 transmembrane domain and an extracellular region with a GAIN domain, PKD domains and adhesion domains. Preferably the PC1/PC1-like protein in accordance with this invention is a human PC1/PC1-like protein. In another preferred embodiment the PC1/PC1-like protein is selected from the group consisting of human Polycystin-1 (hPC1; also known as hPKD1), hPC1L1 (also known as hPKDL1), hPC1L2 (also known as hPKDL2), hPC1L3 (also known as hPKDL3), hPKDREJ and non-human orthologs thereof (e.g. from mammalians such as mouse, rat, Macaca mulatta or Macaca fascicularis).
The full length of the polypeptide of the invention may range from about 200 to about 10,000 amino acids, preferably from about 500 to about 8,000 amino acids, or from about 1,000 to about 6,000 amino acids.
The first sequence of the polypeptide of the invention typically has a length from about 150 to about 7,000 amino acids, preferably from about 200 to about 6,000 amino acids, or from about 300 to about 5,000 amino acids, or from 400 to 4,000 amino acids. The first sequence may comprise at least two adhesion domains, preferably at least three or at least four or at least five adhesion domains.
In one embodiment the first sequence comprises, or consists of, a fragment of the extracellular region (ECR) of the aGPCR or PC1/PC1-like protein, wherein said fragment comprises said GAIN domain. In certain embodiments the fragment does not comprise the full amino acid sequence that N-terminally precedes the GAIN domain of said aGPCR or PC1/PC1-like protein. In other embodiments the fragment does not comprise the N-terminal end of said aGPCR or PC1/PC1-like protein. In another embodiment, the first sequence comprises or consists of the N-terminal amino acid sequence of an aGPCR extending from the N-terminus of the aGPCR to the C-terminus of the GAIN domain. In another embodiment the first sequence comprises or consists essentially of the complete ECR of the aGPCR, i.e. the first sequence of the polypeptide ends before the start of the TM domain of the aGPCR. In yet other embodiments the first sequence comprises or consists essentially of the N-terminal amino acid sequence of a PC1/PC1-like protein from the N-terminus to the C-terminus of the GAIN domain. In another embodiment the first sequence comprises or consists essentially of the complete ECR of the PC1/PC1-like protein, i.e. the first sequence of the polypeptide ends before the start of the TM domain of the PC1/PC1-like protein.
In a specific embodiment, the first sequence comprises or consists essentially of (a) an amino acid sequence selected from the group consisting of SEQ ID NOs:1-37, (b) an amino acid which has a sequence identity of at least 90% to any one of SEQ ID NOs:1-37, or (c) an amino acid sequence which differs from an amino acid sequence as shown in any one of SEQ ID NOs:1-37 in less than 50, or less than 25, or less than 10, or less than 5, or less than 3 amino acids.
In another embodiment, the first sequence comprises or consists essentially of (a) an amino acid sequence selected from the group consisting of SEQ ID NOs:1-32, (b) an amino acid which has a sequence identity of at least 90% to any one of SEQ ID NOs:1-32, or (c) an amino acid sequence which differs from an amino acid sequence as shown in any one of SEQ ID NOs:1-32 in less than 50, or less than 25, or less than 10, or less than 5, or less than 3 amino acids.
In yet another embodiment, the first sequence comprises or consists essentially of (a) an amino acid sequence selected from the group consisting of SEQ ID NOs:33-37, (b) an amino acid which has a sequence identity of at least 90% to any one of SEQ ID NOs:33-37, or (c) an amino acid sequence which differs from an amino acid sequence as shown in any one of SEQ ID NOs:33-37 in less than 50, or less than 25, or less than 10, or less than 5, or less than 3 amino acids.
The difference in amino acid sequence may be a substitution, deletion and/or insertion relative to the reference sequence. The comparison of sequences and determination of percent identity between two amino acid sequences can be accomplished using any suitable program, e.g. the program “BLAST 2 SEQUENCES (blastp)” (Tatusova et al. (1999) FEMS Microbiol. Lett. 174, 247-250) with the following parameters: Matrix BLOSUM62; Open gap 11 and extension gap 1 penalties; gap x_dropoff50; expect 10.0 word size 3; Filter: none.
In another preferred embodiment the first sequence comprises one of the amino acid sequences shown in
In other embodiments, the first sequence comprises or consists of the GAIN domain of one of the following aGPCRs:
mGPR133, rGPR128, rGPR126, rGPR116, mGPR110, rGPR64, mCELSR3, rCELS, mGPR125, mGPR124, rCD97, rEMR1, mEMR4, mGPR97, rGPR114, rETL1, mGPR115, mGPR111, mVLGR1, rGPR113, rBA11, rBAI2, and rCL1. These GAIN domain sequences are disclosed in Supplementary Table 3 of Arac et al. EMBO J 31, 1364-1378 (2012), which sequences are incorporated herein by reference.
In yet other embodiments, the first sequence comprises or consists of the GAIN domain of one of the following aGPCRs: TT89292280, TT89298346, DM48958429, TT89296699, CE115532418, MB16753744x7, MB167524088, MB238058440, TA195996857, DD66815909, TA196016767, CE35396740, TA196004662, and DM19527793. These GAIN domain sequences are disclosed in Supplementary Table 2 of Arac et al. EMBO J31, 1364-1378 (2012), which sequences are incorporated herein by reference.
The GAIN domain in accordance with this invention includes splice variants, isoforms, human single nucleotide polymorphisms (SNPs) and pathophysiologically relevant human mutations of any one of the GAIN domains mentioned above.
The second sequence comprises the transmembrane region of a Notch receptor. The Notch receptor can be a human Notch receptor. In one embodiment the Notch receptor is selected from the group consisting of Notch1, Notch2, Notch3, and Notch4. The amino acid sequence of human Notch1 can be found in UniProtKB—P46531. The amino acid sequence of human Notch2 is described in UniProtKB—004721. The amino acid sequence of human Notch3 is described in UniProtKB—Q9UM47. The amino acid sequence of human Notch4 is described in UniProtKB—Q99466. In other embodiments the Notch receptor is a mammalian orthologue of one of the human Notch proteins mention above.
The length of the second sequence may range from about 40 amino acids to about 100 amino acids, preferably from about 45 to about 75 amino acids, or from about 50 to about 60 amino acids.
The second sequence typically includes the S2 cleavage site which is located in the extracellular part of the Notch protein, adjacent to the TM domain. The S2 cleavage site can be cleaved by the matrix metalloprotease of the Kuzbanian/ADAM (a disintegrin and metalloprotease domain) family. The short segment from the amino acids constituting the S2 cleavage site of a Notch receptor to the C-terminal end of the extracellular region of the Notch receptor is referred to as iuxtamembrane segment herein. For the avoidance of doubt, the iuxtamembrane segment includes the S2 cleavage site, but it does not include amino acids of the transmembrane region of the Notch receptor. Thus, the second sequence typically comprises or consists essentially of the iuxtamembrane segment and the transmembrane region of a Notch receptor. For example, the iuxtamembrane segment of human Notch 1 includes amino acids 25-42 of SEQ ID NO:52. The structure and function of Notch receptors is reviewed in ref.24
The second sequence usually further comprises the S3 cleavage site, which is located within the TM portion of Notch. In yet another embodiment the second sequence further comprises the S4 cleavage site, which is located within the TM portion of Notch.
In a preferred embodiment the second sequence comprises or consists essentially of (i) an amino acid sequence selected from the group consisting of SEQ ID NOs:52-56, (ii) an amino acid sequence having a sequence identity of at least 90% to any one of SEQ ID NOs:52-56, (iii) an amino acid sequence which differs from any one of SEQ ID NOs:52-56 in less than 10, or less than 7, or less than 5, or less than 3 amino acids, e.g. in one or two amino acids, or (iv) a fragment of (i), (ii) or (iii) comprising the S2 and the S3 cleavage sites. The fragment may have an N-terminal truncation of any one of SEQ ID NOs:52-56, by 1-25 amino acids, by 1-24 amino acids, by 1-23 amino acids, by 1-22 amino acids, by 1-21 amino acids, or by 1-20 amino acids. The fragment may have a C-terminal truncation of any one of SEQ ID NOs:52-56, by 1, 2, 3, 4 or 5 amino acids. The embodiments concerning the N-terminal truncation and the C-terminal truncation can be combined.
The polypeptide of the invention further comprises, at the C-terminal end, a transcription factor moiety.
The length of the third sequence may range from about 50 amino acids to about 1,500 amino acids, or from about 100 to about 1,000 amino acids.
Upon release from the second sequence, e.g. by proteolytic cleavage, the transcription factor moiety can bind to a DNA target sequence, thereby inducing transcription of a reporter gene. The type of the reporter gene is not particularly limited, provided that it encodes an expression product that can be detected, or which provides a detectable signal. Suitable transcription factors include, but are not limited to, LexA from Escherichia coli21, GAL4 from Saccharomyces cerevisiae22, and QF, QF2 and QF2w derived from Neurospora crassa23, for which corresponding transcription factor DNA binding motifs for the construction of reporter transgenes are known.
Optionally, there can be a spacer between the first sequence and the second sequence, and/or between the second and the third sequence. The spacer does not affect the functionality of the chimeric polypeptide. The length of the spacer may range from about 1 to about 10 amino acids. The sequence of the spacer may be heterologous to the adjacent sequences. Preferably, no spacer is present between the first sequence and the second sequence. In another embodiment, no spacer is present between the second and the third sequence. In yet another embodiment, no spacer is present between the first sequence and the second sequence, nor between the second and the third sequence. In a specific embodiment, no spacer is present between the first sequence and the second sequence, and a spacer is present between the second and the third sequence.
In other optional embodiments, the polypeptide of the invention comprises at its N-terminal end an amino acid sequence that is heterologous to the aGPCR sequence or PC1/PC1-like sequence that is present in the first sequence. Examples of such heterologous sequences include tag sequences, signal peptides and the like.
In other optional embodiments, the polypeptide of the invention comprises at its C-terminal end an amino acid sequence that is heterologous to the transcription factor sequence of that is present in the third sequence. Examples of such heterologous sequences include tag sequences and the like.
The present invention further relates to a nucleic acid encoding the polypeptide of the invention. The nucleic acid sequences encoding various aGPCRs and Notch proteins are known. Similarly, the nucleic acid sequences encoding various transcription factor moieties are known. Based on the teaching of the present application the skilled person is able to design and prepare suitable nucleic acid constructs encoding the polypeptide described herein.
The invention further pertains to a plasmid or vector comprising a nucleic acid of the invention. The vector is preferably an expression vector. Typical expression vectors contain promoters that direct the synthesis of large amounts of mRNA corresponding to the inserted nucleic acid in the plasmid-bearing cells. They may also include an origin of replication sequence allowing for their autonomous replication within the host organism, and sequences that increase the efficiency with which the synthesized mRNA is translated. Stable long-term vectors may be maintained as freely replicating entities by using regulatory elements of, for example, viruses (e.g., the OriP sequences from the Epstein Barr Virus genome). Cell lines may also be produced that have integrated the vector into the genomic DNA, and in this manner the gene product is produced on a continuous basis.
The present invention further relates to a cell comprising the polypeptide of the present invention. The invention further pertains to a cell comprising the nucleic acid of the present invention. The invention further pertains to a cell comprising the plasmid or vector of the present invention. The invention further pertains to a cell expressing the polypeptide of the present invention. The cell of the invention is obtainable by a process comprising the steps of introducing a nucleic acid encoding the polypeptide of the invention into a host cell, and culturing the cells so obtained under conditions that allow expression of the polypeptide.
Any cell can be chosen as long as the polypeptide as expressed is functional. In one embodiment, the expression of the polypeptide is stable, optionally inducible. Alternatively, the expression of the polypeptide is transient. Preferably, the cell is a eukaryotic cell. More preferably, the cell is an insect or a mammalian cell. Even more preferably, the mammalian cell is a human cell. Examples of mammalian cells are HEK293, HEK293T, MDCK, CHO, COS, NIH3T3, Swiss3T3, BHK, and A549. Even more preferably, the cell is a mammalian cell such as HEK293.
Depending on the type of expression system chosen, the skilled person may possibly adapt the culture conditions to obtain a most favorable expression level of the polypeptide. In the case of an inducible expression system, the skilled person may also possibly optimize an inducing condition. The time period of induction of the expression and the temperature during induction of the expression could also possibly be optimized.
Typically, the cells to be provided are obtained by introducing the nucleic acid encoding a polypeptide of the invention into host cells, e.g. mammalian host cells. Typically, the host cell is transfected with a suitable plasmid or nucleic acid, or transduced with a suitable vector, e.g. a viral vector.
The cell of the invention preferably includes a heterologous nucleic acid sequence which is capable of binding to the transcription factor moiety comprised in the third sequence. Suitable transcription factor binding DNA sequences include, but are not limited to, QUAS (for binding to transcription activators of the Q system, such as QF or QF2), UAS (for binding to transcription activators such as Gal4) and LexAop (for binding to transcription activators such as LexA).
It is further preferred that the cell of the invention comprises a heterologous nucleic acid sequence encoding a reporter. Suitable reporters include, e.g., fluorescent proteins; enzymes that catalyze a reaction that generates a detectable signal as a product, and the like.
Suitable fluorescent proteins are described in Shaner et al. (2005) Nat. Methods 2:905-909) and Matz et al. (1999) Nature Biotechnol. 17:969-973, the content of which is incorporated herein.
Suitable enzymes include, but are not limited to, horse radish peroxidase (HRP), alkaline phosphatase (AP), beta-galactosidase (GAL), glucose-6-phosphate dehydrogenase, beta-N-acetylglucosaminidase, Xanthine Oxidase, firefly luciferase, glucose oxidase (GO), and the like.
Preferred reporters are firefly luciferase, green fluorescent protein and red fluorescent proteins such as mCherry. The nucleic acid sequences encoding reporters are known, as well as suitable promoters to be operably linked to the nucleic acid encoding the reporter.
Such cells are obtained by additionally introducing a nucleic acid encoding the reporter into the cell.
The invention further pertains to a non-human transgenic animal comprising the polypeptide of the invention, the nucleic acid of the invention, the plasmid or vector of the invention, or the cell of the invention. The invention further relates to a non-human transgenic animal expressing the polypeptide of the present invention.
The transgenic non-human animal may be a transgenic non-human vertebrate animal, preferably a mammal, preferably a rodent, such as a mouse. Suitable animals are available, or easily generated, using conventional methods, in a variety of genera, including rodents (e.g., rats), rabbits, guinea pigs, dogs, goats, sheep, cows, horses, pigs, llamas, camels or the like. Preferably, the non-human transgenic animal is a transgenic mouse.
The invention further provides a transgenic gamete, including a transgenic ovum or sperm cell, a transgenic embryo, and any other type of transgenic cell or cluster of cells, whether haploid, diploid, or of higher zygosity comprising a nucleic acid of the present invention.
As used herein, the term “embryo” includes a fertilized ovum or egg (i.e., a zygote) as well as later multicellular developmental stages of the organism.
Also included herein are progeny of the transgenic animal that preferably comprises a nucleic acid of the invention.
The transgenic animal may be sterile although, preferably, it is fertile. The present invention further includes a cell line derived from a transgenic embryo or other transgenic cell of the invention, which comprises the nucleic acid of the invention and/or expresses the polypeptide of the invention. Methods of isolating such cells and propagating them are known to those of skill in the art.
Techniques for the generation of non-human transgenic animals are generally known to the skilled person (see, e.g. Pinkert, Transgenic Animal Technology: A Laboratory Handbook, ISBN-13: 978-0124104907). The transgenic non-human animals of the invention can be produced by introducing recombinant nucleic acids into the germline of the non-human animal. Embryonal target cells at various developmental stages are used to introduce the nucleic acids or vectors of the invention. Different methods are used depending on the stage of development of the embryonal target cell(s). Such methods include, but are not limited to, microinjection of zygotes, viral integration, and transformation of embryonic stem cells.
The invention further relates to methods for identifying compound that are capable of modulating aGPCR activity. The method may be a screening method. The method typically comprises the following steps
“Determining the level” can be a quantitative determination or a qualitative determination (e.g. determining whether or not a reporter or signal can be detected).
The method may further comprise one or more of the following steps
The above embodiments described for a cellular assay can be applied to methods using non-human transgenic animals mutatis mutandis.
The invention further pertains to the use of the polypeptide of the invention, of the nucleic acid of the invention, of the plasmid or vector of the invention, or of the cell of the invention, or of the transgenic animal of the invention for identifying a modulator, preferably an inhibitor, of an adhesion GPCR or of a PC1/PC1-like protein.
Modulators of an adhesion GPCR or of a PC1/PC1-like protein can be activators or inhibitors. Modulators further include agonists and antagonists. Preferably, the modulator is an inhibitor of an adhesion GPCR or of a PC1/PC1-like protein.
The invention further pertains to the use of the polypeptide of the invention for screening for agonistic ligands of an adhesion GPCR or of a PC1/PC1-like protein. In another embodiment the invention pertains to the use of the polypeptide of the invention for screening for antagonistic ligands of an adhesion GPCR or of a PC1/PC1-like protein. In another embodiment the invention pertains to the use of the polypeptide of the invention for screening for agonistic modulators of an adhesion GPCR or of a PC1/PC1-like protein. In another embodiment the invention pertains to the use of the polypeptide of the invention for screening for modulators of non-GAIN domain proteolysis of the ECR. The N-terminal fragments cleaved off from the polypeptide of the present invention can be isolated and/or collected and subsequently be used in various ways. For example, the N-terminal fragments can be used as antigens for generating antibodies. The N-terminal fragments can further be used for generating a protein library. In one aspect the invention therefore relates to a protein library comprising multiple different N-terminal fragments obtained by cleavage from the polypeptide of the invention. The library can be used to screen for binding partners, e.g. by mass spectrometry. In another aspect the invention therefore relates to the use of the protein library in a screening method, e.g. in a screening method to identify binding partner of a aGPCR or PC1/PC1-like protein.
The present disclosure provides a kit for carrying out a method described herein.
In some cases, a subject kit comprises an expression vector comprising a nucleotide sequence encoding a polypeptide of the present invention.
In some cases, a subject kit comprises a chimeric polypeptide of the present invention.
In some cases, a subject kit comprises a cell that is genetically modified with a nucleic acid comprising a nucleotide sequence encoding a chimeric polypeptide of the present invention.
In some cases, the kit comprises a cell that is genetically modified with a recombinant expression vector comprising a nucleotide sequence encoding the polypeptide of the present invention. Kit components can be in the same container, or in separate containers.
Any of the above-described kits can further include one or more additional reagents, where such additional reagents can be selected from: a dilution buffer; a reconstitution solution; a wash buffer; a control reagent; a control expression vector; a negative control polypeptide (e.g., a chimeric polypeptide that lacks the one or more proteolytic cleavage sites); a positive control polypeptide; a reagent for in vitro production of the chimeric polypeptide, and the like.
In addition to above-mentioned components, a subject kit can further include instructions for using the components of the kit to practice the subject methods. The instructions for practicing the subject methods are generally recorded on a suitable recording medium. For example, the instructions may be printed on a substrate, such as paper or plastic. As such, the instructions may be present in the kits as a package insert, in the labeling of the container of the kit or components thereof. In other embodiments, the instructions are present as an electronic file present on a suitable computer readable storage medium. In yet other embodiments, the actual instructions are not present in the kit, but means for obtaining the instructions from a remote source, e.g. via the internet, are provided. An example of this embodiment is a kit that includes a web address where the instructions can be viewed and/or from which the instructions can be downloaded. As with the instructions, this means for obtaining the instructions is recorded on a suitable substrate.
Operating Principle of the NRS for Adhesion GPCRs and PC1/PC1-Like Molecules
We have harnessed the regulated intramembrane proteolysis (RIP) principle employed in Notch receptor activation for the NRS. Notch is the key element in an evolutionarily highly conserved pathway that controls binary developmental decisions and plays essential roles in the determination of cell lineages (reviewed in ref.24). Briefly, Notch is activated through one of its ligands Delta or Serrate, which are transmembrane proteins mounted in cis and in trans to the receptor protein. Ligand endocytosis in trans transmits mechanical force onto the Notch ECR (extracellular region) causing the exposure of a iuxtamembrane receptor region25,26, which during signal inactivity is shielded by the NRR (negative regulatory region). Consequently, the iuxtamembrane S2 site becomes accessible to the matrix metalloprotease Kuzbanian/ADAM (a disintegrin and metalloprotease domain), which cleaves the receptor protein outside the plasma membrane leading to shedding of a large part of the Notch ECR. The working principle of the NRS (
In the naturally occurring setting for Notch signaling its S2 proteolysis site is protected by multiple EGF domain repeats, which mediate physiological ligand interactions, and the NNR (Notch-1 negative regulatory) region of the receptor's extracellular part of the receptor (reviewed in ref.27). EGF repeats and the NRR can be entirely replaced by heterologous domains while still protecting the signal-initiating S2 site from Kuz/ADAM engagement28 (
NTF-CTF separation within the NRS is made possible through posttranslational GAIN domain autoproteolysis and subsequent covalent stabilisation of the ensuing NTF-CTF heterodimer or similar autoproteolytic events in other extracellular domains of aGPCRs/PC1/PC1-like proteins. NTF-CTF separation is induced spontaneously, through ligand binding, mechanical stimulation or a combination of the aforementioned processes (
Proteolytic Processing of Iuxta- and Transmembrane Segment of NRS
S2 proteolytic processing of the NRS occurs through ADAM-like matrix metalloproteinases present in the test cell (
Intracellular Release of Transcription Factor Moiety
The Notch intracellular domain (NICD) was replaced with a heterologous transcription factor, (LexA::VP16 cassette), so that NRS activation upon NTF release results in the liberation of the TF from the intracellular face of the membrane (
In order to conceptually establish the approach to fuse heterologous ECRs to the NotchITS to suppress its proteolytic activation, a sensor protein containing 4 immunoglobulin (Ig) domains of the human CD4 receptor fused to the NotchITS was engineered28 (
A tri- or hexarepeat of the highly selective TEV (Tobacco etch virus) protease cleavage site (TEVs) was introduced between CD4 repeats and ITS (CD4-3TEVs-NRS-LexA, CD4-6TEVs-NRS-LexA) in order to conditionally sever artificial ECR and NotchITS of the sensor and expose the extracellular S2 site by TEV protease expression. Upon co-expression of a secreted version of TEV (secTEVp), but not when TEV was expressed intracellularly (intraTEVp) or not at all, strong activation of both CD4-3/6TEVs-NRS-LexA reporters were observed in S2 cells by a commercially available firefly luciferase lexAop-FLuc reporter (
Replacement of a critical Valin residue in the S3 site of NotchITS by Lysine29 (
Next, the extracellular CD4 repeats of the sensor protein were replaced with the ECR of an aGPCR, the Latrophilin/ADGRL-homolog CIRL/CG8639 (calcium independent receptor of α-latrotoxin) to enable the NRS to detect the physical dissociation of the NTF-CTF complex within the GAIN domain when appended to the NotchITS. Thus, the entire ECR of CIRL (including the GAIN domain, GPS, tethered agonist segment and predicted linker to the 7TM domain) was N-terminally fused to the NRS core (CIRL-NRS-LexA;
To test the utility of the NRS sensor principle in vivo, an existing genomic engineering platform13,35 was used to encode NRS sensors in alleles of the adhesion GPCR cirl/CG8639 of Drosophila melanogaster. This places CIRL-NRS expression under the endogenous regulatory control of the cirl locus (
Western blot analysis of fly head homogenates expressing CIRL-NRS-LexA and CIRL-NRSS3-LexA confirmed that S3 proteolytic processing of CIRL-NRS-LexA is quenched by the mutation (
Next, the functionality of CIRL-NRS was further studied in anatomical expression analyses. Expression of cirl-NRS-LexA in thirs instar larvae showed that the CIRL-NRS-LexA is activated only in Cirl+ neurons in the peripheral nervous system, the ventral nerve cord (VNC) and the brain hemispheres such as previously through a transcriptional cirlp-Gal4 reporter35 (data not shown). In adult animals cirl-NRS-LexA expression recapitulates endogenous cirl expression35 with strong expression in the eye, proboscis and leg neurons (
Disabling GAIN domain proteolysis and thus potential NTF release of CIRL through replacement of a critical Histidin residue at position −2 to the GPS of the CIRL-NRS-LexA protein (CIRLH>A-NRS-LexA) abrogated NRS activation apparent through loss of the mCherry reporter induction in all organs and tissues (
To control for potential misexpression inherent to the LexA transcriptional reporter, additional cirl-NRS transgenes alternatively terminating in Ga/4 or QF2 transcription factor cassettes were generated an analysed. A comparison of expression patterns controlled by cirl-NRS-LexA (
Amino acid sequences:
SEQ ID NO:59. Full-length NTF release sensor for dmCIRL
SEQ ID NO:60 Full-length NTF release sensor for dmCIRL (GPS cleavage site mutated)
SEQ ID NO:61 Full-length NTF release sensor for dmCIRL (S3 cleavage site mutated)
SEQ ID NO:62 NTF release sensor positive control
SEQ ID NO:63 NTF release sensor negative control
For transfection, mini- or midi-prepped plasmid DNA (Qiagen) for each construct was adjusted to a stock concentration 100 ng/μl using a nanophotometer (Implen). For individual transfections a total amount of 200 ng DNA per 96-well plate well was used and always contained 30 ng of lexAop>FLuc2 (test construct reporter) and Act5.1Cp>RLuc (transfection control reporter), respectively. Test constructs (X-NRS-LexA) and TEV protease plasmids were added at 1:1 ratio (equimolarly adjusted to lexAop>FLuc2) to the DNA mixes; each DNA mix was supplemented with empty pBSK-SK+ vector (Stratagene) to 200 ng. S2 cells were cultured in Schneider's Drosophila medium (Invitrogen, Cat. no. 21720-024). Cultures were maintained in an air incubator at 25° C. S2 cells were split and plated into individual wells of a 96-well plate at a concentration of 5×105/well on day 0. 24 hours after plating (day 1), cells were transfected with Lipofectamine 2000 (Invitrogen, #11668019) with the suitable 1:1 plasmid/reagent mixture according to manufacturer's instructions and incubated for 48 hours. When induction of the metallothionein-promoter was required, CuSO4 stock medium was added in each well of the experiment to a final concentration of 0.5 mM CuSO4 24 hrs after transfection (day 2).
Cells were lysed on day 3 (48 hrs after transfection) and luciferase measurements with the Dual-Glo luciferase assay system (Promega) were performed according to the manufacturer's protocol. In brief, the supernatant was removed from each well by aspiration and cells were incubated with 200 μl passive lysis buffer on a shaker at room temperature for 30 min. Lysates were analyzed in 96-well plates with a Victor2 plate reader luminometer (PerkinElmer). Firefly and Renilla luciferase luminescence signals were collected for 10 s. Relative luciferase activities were calculated for each sample individually as principally described in Potter et al. (ref. 23) according to the following formula:
RLA
x=(Fx/Rx)/(
where
(
where n=number of control samples; F=Firefly luciferase luminescence signal; R=Renilla luciferase luminescence signal; Empty=lexAop>FLuc2+Ac5.1p>RLuc+BSK-SK+. Each condition was executed at least in triplicate, the average and SEM were determined for each condition, and statistical significance was evaluated using Student's t test. Plasmids used for transfection in S2 cells were: NECN-LexA, NEGF-LexA, ChiN-Test, pChiN1, pChiN2, pChiN3, lexAop-FLuc2, Ac5.1-RLuc, secTEVp, intraTEVp, pBSK-SK+.
Fly heads were collected into 0.5 ml Eppi and immediately frozen in liquid nitrogen. Next, heads were mechanically crushed in 40 μl SDS (2%, supplemented with protease Inhibitor Cocktail, Sigma-Aldrich; 1:1000) using a glass stirrer. Samples were incubated on ice for 10 min before the addition of 4 μl Triton-X100 (10%). Next, SDS-based sample buffer (Li-cor) was supplemented with β-Mercaptoethanol and was added to final dilution of 1×. Samples were centrifuged for 30 min at 14000 rpm (4° C.) and supernatant was collected. Centrifugation step was repeated, supernatant collected in fresh tube and subjected to electrophoresis on 6% or 4-12% Tris-Glycin SDS gel (Novex-Wedge-Well; Invitrogen) and blotted onto nitrocellulose membrane (0.2 μm pore size). The membrane was blocked for 1 hour (RT) using Odyssey Blocking buffer (Li-cor) diluted 1:2 with 1×PBS.
Blots were probed with primary antisera at the indicated concentrations overnight at 4° C.: rabbit-α-HA (1:1000, RRID: AB_10693385), mouse-α-V5 (1:500; RRID:AB_2556564), mouse-α-tubulinβ (1:5000, RRID:AB_528499), rabbit-α-tubulinα (1:500, RRID:AB_25541125). After rinsing twice and 3-10 min washing steps, membranes were incubated with IRDye 680RD goat-α-rabbit (RRID:AB_2721181) and goat-α-mouse (RRID:AB_2651128) as well as 800CW goat-α-mouse (1:15000; RRID:AB_2687825) and goat-α-rabbit (1:15000; RRID:AB_2651127) for 1 hour at RT, and again rinsed twice and washed 3-10 min. Blots were imaged with an OdysseyFc 2800 (Li-cor).
| Number | Date | Country | Kind |
|---|---|---|---|
| 20198501.7 | Sep 2020 | EP | regional |
The instant application corresponds to the U.S. National phase of International Application No. PCT/EP2021/076234, filed Sep. 23, 2021, which, in turn, claims priority to European Patent Application No. 20198501.7.3 filed Sep. 25, 2020, the contents of which are incorporated by reference herein in their entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2021/076234 | 9/23/2021 | WO |
