MHC-independent tumor-associated antigens
10987413 · 2021-04-27
Assignee
Inventors
- Dirk Schadendorf (Essen, DE)
- Annette Paschen (Essen, DE)
- Silke Lübcke (Munich, DE)
- Martina Fatho (Woerrstadt, DE)
- Daniela Eberts (Gau-Algesheim, DE)
- Hakim Echchannaoui (Mainz, DE)
- Volker Lennerz (Ober-Olm, DE)
- Catherine Woelfel (Mainz, DE)
- Thomas Woelfel (Mainz, DE)
Cpc classification
A61K39/001156
HUMAN NECESSITIES
A61K35/17
HUMAN NECESSITIES
A61K39/001118
HUMAN NECESSITIES
A61P35/00
HUMAN NECESSITIES
International classification
A61K39/00
HUMAN NECESSITIES
C07K14/715
CHEMISTRY; METALLURGY
G01N33/50
PHYSICS
A61K35/17
HUMAN NECESSITIES
Abstract
The present invention relates to novel tumor-associated antigens, which elicit independently from a presentation via MHC a CD8-positive T-cell response. GM-CSF-Receptor alpha chain (CSF2RA) and Tyrosinase-related protein 2 (TRP-2) were found to be targets of CD8-positive T-cell clones which could detect the proteins on the surface of HLA I negative melanoma cells. Thus, the invention provides proteins, protein fragments and polypeptides of the novel antigens for use in medicine, for example for the treatment, diagnosis and prevention of a tumor disease. Furthermore provided are nucleic acids expressing the antigens of the invention, binding agents specific for the antigens of the invention, such as T-cell receptor chains and isolated T cells which are reactive against the antigens of the invention or which express the T-cell receptors of the invention. The invention further pertains to pharmaceutical compositions, especially vaccine compositions, comprising the antigens, nucleic acids, binding agents or T cells in accordance with the invention, and methods for the generation of T cells, which are specifically reactive to the antigens of the invention in an MHC-independent manner.
Claims
1. A binding agent that is a T cell receptor, comprising (i) a) T cell receptor alpha chain, or a binding fragment thereof, comprising SEQ ID NO 9, 10 and 11; and b) a T cell receptor beta chain, or a binding fragment thereof, comprising SEQ ID NO: 12, 13 and 14; (ii) a) a T cell receptor alpha chain, or a binding fragment thereof, comprising SEQ ID NO: 15, 16 and 17; and b) a T cell receptor beta chain, or a binding fragment thereof, comprising SEQ ID NO: 18, 19 and 20, or (iii) a) a T cell receptor alpha chain, or a binding fragment thereof, comprising SEQ ID NO: 21, 22, and 23; and b) a T cell receptor beta chain, or a binding fragment thereof, comprising SEQ ID NO: 24, 25 and 26.
2. The binding agent according to claim 1, comprising a sequence according to SEQ ID NO: 3, 7, or 5.
3. The binding agent according to claim 1, comprising a sequence according to SEQ ID NO: 4, 8, or 6.
4. The binding agent according to claim 1, which is a chimeric T cell receptor comprising a murinized constant region and a human variable region.
5. An isolated T cell, comprising a T-cell receptor (TCR) that binds to a protein, protein fragment or polypeptide comprising at least 8 contiguous amino acids from the amino add sequence of GM-CSF-Receptor alpha chain (CSF2RA) (SEQ ID NO: 1), and wherein the TCR comprises: (i) T cell receptor alpha chain, or a binding fragment thereof, comprising SEQ ID NO: 9, 10 and 11; and b) a T cell receptor beta chain, or a binding fragment thereof, comprising SEQ ID NO: 12, 13 and 14; (iii) a) a T cell receptor alpha chain, or a binding fragment thereof, comprising SEQ ID NO: 15, 16 and 17; and b) a T cell receptor beta chain, or a binding fragment thereof, comprising SEQ ID NO: 18, 19 and 20, or (iii) a) a T cell receptor alpha chain, or a binding fragment thereof, comprising SEQ ID NO: 21, 22, and 23; and b) a T cell receptor beta chain, or a binding fragment thereof, comprising SEQ ID NO: 24, 25 and 26.
6. A pharmaceutical composition, comprising an isolated T cell according to claim 5 and a pharmaceutically acceptable carrier or diluent.
Description
(1) The present invention will now be further described in the following examples with reference to the accompanying figures and sequences, nevertheless, without being limited thereto. For the purposes of the present invention, all references as cited herein are incorporated by reference in their entireties. In the Figures and Sequences:
(2)
(3)
(4)
(5)
(6)
(7)
(8)
(9)
(10)
(11)
(12)
(13)
(14)
(15) SEQ ID NO: 1 shows the amino acid sequence of CSF2RA:
(16) TABLE-US-00002 MLLLVTSLLLCELPHPAFLLIPEKSDLRTVAPASSLNVRFDSRTMNLSWD CQENTTFSKCFLTDKKNRVVEPRLSNNECSCTFREICLHEGVTFEVHVNT SQRGFQQKLLYPNSGREGTAAQNFSCFIYNADLMNCTWARGPTAPRDVQY FLYIRNSKRRREIRCPYYIQDSGTHVGCHLDNLSGLTSRNYFLVNGTSRE IGIQFFDSLLDTKKIERFNPPSNVTVRCNTTHCLVRWKQPRTYQKLSYLD FQYQLDVHRKNTQPGTENLLINVSGDLENRYNFPSSEPRAKHSVKIRAAD VRILNWSSWSEAIEFGSDDGNLGSVYIYVLLIVGTLVCGIVLGFLFKRFL RIQRLFPPVPQIKDKLNDNHEVEDEIIWEEFTPEEGKGYREEVLTVKEIT
(17) SEQ ID NO: 2 shows the amino acid sequence of TRP-2 (isoform 1)
(18) TABLE-US-00003 MSPLWWGFLLSCLGCKILPGAQGQFPRVCMTVDSLVNKECCPRLGAESA NVCGSQQGRGQCTEVRADTRPWSGPYILRNQDDRELWPRKFFHRTCKCT GNFAGYNCGDCKFGWTGPNCERKKPPVIRQNIHSLSPQEREQFLGALDL AKKRVHPDYVITTQHWLGLLGPNGTQPQFANCSVYDFFVWLHYYSVRDT LLGPGRPYRAIDFSHQGPAFVTWHRYHLLCLERDLQRLIGNESFALPYW NFATGRNECDVCTDQLFGAARPDDPTLISRNSRFSSWETVCDSLDDYNH LVTLCNGTYEGLLRRNQMGRNSMKLPTLKDIRDCLSLQKFDNPPFFQNS TFSFRNALEGFDKADGILDSQVMSLHNLVHSFLNGTNALPHSAANDPIF VVLHSFTDAIFDEWMKRFNPPADAWPQELAPIGHNRMYNMVPFFPPVTN EELFLTSDQLGYSYAIDLPVSVEETPGWPTTLLVVMGTLVALVGLFVLL AFLQYRRLRKGYTPLMETHLSSKRYTEEA
(19) SEQ ID NO: 3 shows the TCR alpha chain sequence of CTL 1A.1/506
(20) TABLE-US-00004 METTIGPLILWLQLQWVSSKQEVTQIPAALSVPEGENLVLNCSFTDSAI YNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAA SQSGDSATYLCAVGGNDYKLSFGAGTIVTVRANIQNSDPAVYQLRDSKS SDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWS NKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDMILNFQNL SVIGFRILLLKVAGFNLLMTIALWSS
(21) SEQ ID NO: 4 shows the TCR beta chain sequence of clone CTL 1A.1/506
(22) TABLE-US-00005 MGTRLFFYVALCLLWTGHMDAGITQSPRHKVTETGTPVTLRCHQTENHR YMYWYRQDPGHGLRLIHYSYGVKDTDKGEVSDGYSVSRSKTEDFLLTLE SATSSQTSVYFCAISEKLAGAYEQYFGPGIRLTVTEDLKNVFPPEVAVF EPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPL KEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQD RAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYAV LVSALVLMAMVKRKDSRG
(23) SEQ ID NO: 5 shows the TCR alpha chain sequence of clone CTL 2C/417
(24) TABLE-US-00006 MASAPISMLAMLFTLSGLRAQSVAQPEDQVNVAEGNPLTVKCTYSVSGN PYLFWYVQYPNRGLQFLLKYITGDNLVKGSYGFEAEINKSQTSFELKKP SALVSDSALYFCAVRDMIEGGGNKLTFGTGTQLKVELNIQNPDPAVYQL RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNS AVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNL NFQNLSVIGFRILLLKVAGFNLLMTLRLWSS
(25) SEQ ID NO: 6 shows the TCR beta chain sequence of clone CTL 2C/417
(26) TABLE-US-00007 MGIRLLCRVAFCFLAVGLVDVKVTQSSRYLVKRTGEKVFLECVQDMDHE NMFWYRQDPGLGLRLIYFSYDVKMKEKGDIPEGYSVSREKKERFSLILE SASTNQTSMYLCASSRQGAVGQPQHFGDGTRLSILEDLNKVFPPEVAVF EPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPL KEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQD RAKPVTQIVSAEAWGRADCGFTSVSYQQGVLSATILYEILLGKATLYAV LVSALVLMAMVKRKDF
(27) SEQ ID NO: 7 shows the TCR alpha chain sequence of clone CTL 1A3/46
(28) TABLE-US-00008 MSLSSLLKVVTASLWLGPGIAQKITQTQPGMFVQEKEAVTLDCTYDTSD PSYGLFWYKQPSSGEMIFLIYQGSYDQQNATEGRYSLNFQKARKSANLV ISASQLGDSAMYFCAMRPHFGNEKLITGTGIRLTIIPNIQNPDPAVYQL RDSKSSDKSVCLFTDFDSQINVSQSKDSDVYITDKTVLDMRSMDFKSNS AVAWSNKSDFACANAFNNSIIPEDIFFPSPESSCDVKLVEKSFETDTNL NFQNLSVIGFRILLLKVAGFNLLMTLRLWSS
(29) SEQ ID NO: 8 shows the TCR beta chain sequence of clone CTL 1A3/46
(30) TABLE-US-00009 MGTRLFFYVALCLLWTGHMDAGITQSPRHKVTETGTPVTLRCHQTENHR YMYWYRQDPGHGLRLIHYSYGVKDTDKGEVSDGYSVSRSKTEDFLLTLE SATSSQTSVYFCAISEKLAGAYEQYFGPGTRLTVTEDLKNVFPPEVAVF EPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPL KEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQD RAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYAV LVSALVLMAMVKRKDSRG*
(31) SEQ ID NOs: 9 to 26 show the CDR sequences of the TCR of the invention.
EXAMPLES
Example 1: Generation of Melanoma-Reactive CD8 Positive T Cells
(32) Out of the melanoma patient MA-MEL-86 four different permanent tumor cell lines (MA-MEL-86A, -86B, -86C, -86F) were established from separate lymph node metastases. Both MA-MEL-86B and MA-MEL-86F did not express HLA I on their cellular surface due to a biallelic mutation in the β2-microglobulin gene. The tumor cell line MA-MEL-86C lost one MLA haplotype. In contrast thereto, the MA-MEL-86A line expressed all HLA I alleles, but showed as the only one out of the four tumor cell lines no expression of melanosomal differentiation antigens (
(33) Tumor-reactive CD8 positive T cells were generated in so called mixed lymphocyte-tumor cell culture (MLTC) by weekly stimulation of lymphocytes taken from peripheral blood mononuclear cells, PBMCs, with autologous tumor cell lines MA-MEL-86A or MA-MEL-86C. Surprisingly, the inventors recognized that MLTC-responder lymphocytes in varying recognition patterns still recognized the HLA I negative variants MA-MEL-86B (
Example 2: Identification of CSF2RA
(34) A cDNA library of the melanoma cell line MEL-86A constructed in the eukaryotic expression vector pcDNA3.1 was screened with responder lymphocytes of MLTC 1A.1. In a first step, cDNA pools consisting of 100 cDNA clones were co-transfected with HLA I alleles of the patient into 293T-cells. The transfectants were tested for recognition by the T cells. One of the pools was found to be responsive. Subsequently, a step-by-step cDNA cloning was performed. In this way CSF2RA was identified as a target of the MLTC 1A.1 (
(35) TABLE-US-00010 TABLE 2 Allogeneic tumor lines recognized by the CSF2RA-reactive CTL 1A.1/506. Analyzed tumor lines recognition/n tested Melanomas 12/20 Pankreas carcinomas (PC) 2/2 Kidney carcinomas (RCC) 0/5 Acute myeloid Leukemias (AML) 5/13 Chronic myelogenous Leukemias (CML) 0/11 Colorectal carcinomas (CRC) 1/6 Lung carcinomas 1/4 Breast carcinoma 0/1 Ovarian carcinoma 1/1 Gallbladder carcinoma 1/1 Glioblastoma 0/11
(36) On the other hand, all tested normal cell lines, amongst others melanocytes, granulocytes and monocytes, derived from peripheral blood, were not recognized by the CSF2RA-reactive T cells (see
(37) Using flow cytometry the inventors furthermore showed that all CSF2RA-reactive T-cells were TCRαβ positive, CD3 positive and CD8 positive, and expressed the T cell receptor beta chain Vβ12 (TRBV10-3). The reactivity of these T cells could only be inhibited by antibodies against CD3 or CSF2RA, but not with antibodies against HLA I or II (see
(38) cDNAs of the alpha and the beta chain of the TCR of the HLA-independent CSF2RA-reactive T-cell clone 1A.1/506 were cloned and sequenced (see
Example 3: Identification of TRP-2
(39) In panel test 40 cDNA clones which encode known melanoma-associated antigens, were transfected into 293T cells. The transfectants were subsequently tested for recognition by responder lymphocytes of MLTCs 1C and 2C. It was found that both MLTCs and CTL clones derived thereof could recognize the HLA I negative tumor cell lines MA-MEL-86B and -86F and targeted the melanosomal differentiation antigen TRP-2. They cross-reacted with any of the TRP-2-expressing melanoma cell lines available in the laboratory as well as with normal melanocytes, and—after transfection with TRP-2—also with non-melanocytic cells of mouse, hamster and monkey origin (see
(40) Using flow cytometry the inventors furthermore showed that all TRP-2-reactive T cells were TCRαβ positive, CD3 positive and CD8 positive, and expressed the T-cell receptor beta chain (TRBV28). The reactivity of these T cells could only be inhibited by antibodies against CD3, but not by antibodies against HLA I or II.
(41) The direct recognition of TRP-2 by CD8 positive T cells would require the cell surface expression of the antigen. Indeed the inventors could show cell surface expression with a TRP-2 reactive antibody (see
(42) This result was further supported by the finding that a deletion of the transmembrane domain (TMD) of TRP-2 resulted in a loss of the recognition by the T cells, which could be reversed by the substitution with an unrelated TMD of HLA-A*24:01 (see
(43) cDNAs of the alpha and the beta chain of the TCR of the HLA-independent TRP-2-reactive T-cell clone 2C/417 were cloned and their function was tested via transfer into CD8 positive T cells of PBMCs of a healthy donor (SEQ ID NO: 5 and 6;
Example 4: Cloning, Ectopic Expression and Functional Analysis of a Second CSF2RA-Specific a/b T Cell Receptor
(44) The a- and b T cell receptor chain-(TCR-) cDNAs were isolated from the CSF2RA-specific CTL 1A.3/46 and cloned as a bicistronic construct into a retroviral vector (
(45) Cell surface expression of the CSF2RA-specific TCR in human T cells transduced with the native (left) and the chimerized (right) constructs is shown in
(46) In a response analysis of the CSF2RA-reactive CTL 1A.3/44 in comparison to CSF2RA-TCR-transduced allogeneic T cells CSF2RA-negative target cells (MA-MEL-86F and 293T) were not recognized while MA-MEL-86B cells expressing CSF2RA endogenously and 293T cells transfected with the antigen were recognized (