Title:
METHOD FOR IDENTIFYING T-CELL EPITOPE SEQUENCE, AND APPLICATION OF SAME
Document Type and Number:
WIPO Patent Application WO/2022/270631
Kind Code:
A1
Abstract:
The present disclosure provides a method for identifying an epitope sequence. The method according to the present disclosure is for identifying an epitope sequence related a specific physiological state of a test subject, and comprises: A) a step for acquiring BCR repertoire and/or TCR repertoire data related the specific physiological state of the test subject; B) a step for specifying a TREM sequence (repertoire specific TREM sequence) from the BCR repertoire and/or TCR repertoire data; C) a step for acquiring a reference TREM sequence related to the test subject; D) a step for specifying a repertoire- reference common specific TREM sequence from the reference TREM sequence and the repertoire specific TREM sequence; and E) a step for determining, on the basis the repertoire- reference common specific TREM sequence, whether the a peptide sequence including the repertoire- reference common specific TREM sequence is an epitope sequence related to the specific physiological state of the test subject.
Inventors:
SUZUKI RYUJI (JP)
SHIN-I TADASU (JP)
NAKAMURA YUKIO (JP)
SASAMURA TAKESHI (JP)
SHIN-I TADASU (JP)
NAKAMURA YUKIO (JP)
SASAMURA TAKESHI (JP)
Application Number:
PCT/JP2022/025376
Publication Date:
December 29, 2022
Filing Date:
June 24, 2022
Export Citation:
Assignee:
REPERTOIRE GENESIS INC (JP)
International Classes:
C12N15/11; C07K14/705; C07K14/725; C12Q1/68; C40B40/10; G01N33/53
Domestic Patent References:
| WO2019217655A1 | 2019-11-14 | |||
| WO2015075939A1 | 2015-05-28 | |||
| WO2017159686A1 | 2017-09-21 | |||
| WO2015075939A1 | 2015-05-28 | |||
| WO1995018145A1 | 1995-07-06 |
Foreign References:
| JP2021105709A | 2021-07-26 |
Other References:
HØGLUND RUNE A., LOSSIUS ANDREAS, JOHANSEN JORUNN N., HOMAN JANE, BENTH JŪRATĖ ŠALTYTĖ, ROBINS HARLAN, BOGEN BJARNE, BREMEL ROBERT: "In Silico Prediction Analysis of Idiotope-Driven T–B Cell Collaboration in Multiple Sclerosis", FRONTIERS IN IMMUNOLOGY, vol. 8, 1 October 2017 (2017-10-01), pages 1255, XP093016870, DOI: 10.3389/fimmu.2017.01255
HØGLUND RUNE A., BREMEL ROBERT D., HOMAN E. JANE, TORSETNES SILJE BØEN, LOSSIUS ANDREAS, HOLMØY TRYGVE: "CD4+ T Cells in the Blood of MS Patients Respond to Predicted Epitopes From B cell Receptors Found in Spinal Fluid", FRONTIERS IN IMMUNOLOGY, vol. 11, 9 April 2020 (2020-04-09), XP093016868, DOI: 10.3389/fimmu.2020.00598
NAKAMURA YUKIO, LING MOI MENG, SHIINA TAKASHI, SHIN-I TADASU, SUZUKI RYUJI: "Idiotope-driven T-B collaboration-based T-cell epitope prediction using B-cell receptor repertoire sequences in infectious diseases ", SSRN, 26 March 2022 (2022-03-26), XP093016866
WEISSBOGEN, CELL, vol. 64, no. 4, 1991, pages 767 - 776
JOAO, IMMUNOL, vol. 172, no. 8, 2004, pages 4709 - 4716
BEEMD R ET AL., CYTOMETRY, vol. 40, 2000, pages 336 - 345
MACISAAC C ET AL., J IMMUNOL METHODS, vol. 283, 2003, pages 9 - 15
TEMBHARE P ET AL., AM J CLIN PATHOL, vol. 135, 2011, pages 890 - 900
LANGERAK AW ET AL., BLOOD, vol. 98, 2001, pages 165 - 173
REBAI N ET AL., PROCNATL ACAD SCI USA, vol. 91, 1994, pages 1529 - 1533
MATSUTANI T ET AL., HUM IMMUNOL, vol. 56, 1997, pages 57 - 69
MATSUTANI T ET AL., BR J HAEMATOL, vol. 109, 2000, pages 759 - 769
MATSUTANI T ET AL., MOL IMMUNOL, vol. 44, 2007, pages 2378 - 2387
MATSUTANI T ET AL., MOL IMMUNOL, vol. 48, 2011, pages 623 - 629
RUDOLPH MG ET AL., ANNU REV IMMUNOL., vol. 24, 2006, pages 419 - 66
MOISE L ET AL., HUM VACCIN IMMUNOTHER., vol. 9, no. 7, July 2013 (2013-07-01), pages 1577 - 86
CALLS JJ ET AL., OS COMPUT BIOL., vol. 8, no. 3, 2012, pages e1002412
SCHWARTZ RH. ET AL., ANNU REV IMMUNOL., vol. 3, 1985, pages 237 - 61
RUDOLPH ET AL., ANNU. REV. IMMUNOL., vol. 24, 2006, pages 419 - 466
BATZER ET AL., NUCLEIC ACID RES., vol. 19, 1991, pages 5081
OHTSUKA ET AL., J.BIOL. CHEM., vol. 260, 1985, pages 2605 - 2608
ROSSOLINI ET AL., MOL. CELL. PROBES, vol. 8, 1994, pages 91 - 98
MARKET, PROCNATL ACAD SCI USA, vol. 81, no. 18, September 1984 (1984-09-01), pages 5662 - 5666
ZOLLER ET AL., NUCLEIC ACIDS RES., vol. 10, no. 20, 25 October 1982 (1982-10-25), pages 6487 - 6500
WANG ET AL., SCIENCE, vol. 224, no. 4656, 29 June 1984 (1984-06-29), pages 1431 - 1433
AUSUBEL, F. M.: "Current Protocols in Molecular Biology", 1987, GREENE PUB. ASSOCIATES AND WILEY-INTERSCIENCE, article "DNA Cloning 1: Core Techniques, A Practical Approach"
SHIMIZU ET AL., NATURE BIOTECHNOLOGY, vol. 19, 2001, pages 751 - 755
ALTSCHUL ET AL., J. MOL. BIOL., vol. 215, 1990, pages 403 - 410
PEARSONLIPMAN, PROC. NATL. ACAD. SCI., USA, vol. 85, 1988, pages 2444 - 2448
SMITHWATERMAN, J. MOL. BIOL., vol. 147, 1981, pages 195 - 197
NEEDLEMANWUNSCH, J. MOL. BIOL., vol. 48, 1970, pages 443 - 453
N. K. JERNE: "Ann. Immunol.", vol. 125C, 1974, INST. PASTEUR, pages: 373 - 389
CALLS JJ ET AL., PLOS COMPUT BIOL, vol. 8, no. 3, 2012, pages e1002412
MADIN ET AL., PROC. NATL. ACAD. SCI. USA, vol. 97, no. 2, 2000, pages 559 - 564
R. LUNDBLAD: "Chemical Reagents for Protein Modification", 2005, CRC PRESS
ZHOU ET AL., BLOOD, vol. 86, 1995, pages 3295 - 3301
LU ET AL., J. ORG. CHEM., vol. 46, 1981, pages 3433
SNINSKY, J. J. ET AL.: "Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology", 1999, GREENE PUB. ASSOCIATES AND WILEY-INTERSCIENCE
BRUNSVIG P FAAMDAL SGJERTSEN M KKVALHEIM GMARKOWSKI-GRIMSRUD C JSVE IDYRHAUG MTRACHSEL SMULLER MERIKSEN J A: "Telomerase peptide vaccination: a phase I/II study in patients with non-small cell lung cancer", CANCER IMMUNOL IMMUNOTHER., vol. 55, no. 12, 2006, pages 1553 - 1564, XP019422504, DOI: 10.1007/s00262-006-0145-7
M. STAEHLERA. STENZLP. Y. DIETRICHT. EISENA. HAFERKAMPJ. BECKA. MAYERS. WALTERH. SINGHJ. FRISCH: "An open label study to evaluate the safety and immunogenicity of the peptide based cancer vaccine IMA901", ASCO MEETING, 2007
LONGENECKER ET AL., ANN. NY ACAD. SCI., vol. 690, 1993, pages 276 - 291
A. KIBBE: "Handbook of Pharmaceutical Excipients", 2000, AMERICAN PHARMACEUTICAL ASSOCIATION AND PHARMACEUTICAL PRESS
THOMAS A MSANTARSIERO L MLUTZ E RARMSTRONG T DCHEN Y CHUANG L QLAHERU D AGOGGINS MHRUBAN R HJAFFEE E M: "Mesothelin-specific CD8(+) T cell responses provide evidence of in vivo cross-priming by antigen-presenting cells in vaccinated pancreatic cancer patients", J EXP MED., vol. 200, no. 3, 2 August 2004 (2004-08-02), pages 297 - 306
CONRY ET AL., SEMINARS IN ONCOLOGY, vol. 23, 1996, pages 135 - 147
CONDON ET AL., NATURE MEDICINE, vol. 2, 1996, pages 1122 - 1127
GONG ET AL., NATURE MEDICINE, vol. 3, 1997, pages 558 - 561
ZHAI ET AL., J. IMMUNOL., vol. 156, 1996, pages 700 - 710
GRAHAM ET AL., INT J. CANCER, vol. 65, 1996, pages 664 - 670
ROTH ET AL., SCAND. J. IMMUNOLOGY, vol. 43, 1996, pages 646 - 651
INNIS, M. A.: "PCR Protocols: A Guideto Methods and Applications", 1990, ACADEMIC PRESS
GAIT, M. J.: "Oligonucleotide Synthesis: A Practical Approach", 1985, IRL PRESS
ECKSTEIN, F.: "Oligonucleotides and Analogues: A Practical Approach", 1991, IRL PRESS
ADAMS, R. L. ET AL.: "The Biochemistry of the Nucleic Acids", 1992, CHAPMAN HALL
SHABAROVA, Z. ET AL., ADVANCED ORGANIC CHEMISTRY OF NUCLEIC ACIDS, 1994
BLACKBURN, G. M. ET AL.: "Nucleic Acids in Chemistry and Biology", 1996, OXFORD UNIVERSITY PRESS
IDENSHI DONYUHATSUGEN KAISEKI: "Bessatsu Jikken Igaku [Experimental Medicine, Supplemental Volume", 1997, YODOSHA, article "Jikken Ho [Experimental Methods for Transgenesis & Expression Analysis"
GIBAS C. ET AL.: "Developing Bioinformatics ComputerSkills", 2001, O'REILLY
MOUNT D. W.: "Bioinformatics: Sequence and Genome Analysis", 2004, CSHL PRESS
PEVZNER P. ET AL.: "Bioinformatics for Biologist", 2011, CAMBRIDGE UNIVERSITY PRESS
SUMIO KANNO ET AL.: "Advanced Methods for Next-generation Sequencers by Purpose", CELL ENGINEERING ANNEX, 2012
HØGLUND RUNE A., BREMEL ROBERT D., HOMAN E. JANE, TORSETNES SILJE BØEN, LOSSIUS ANDREAS, HOLMØY TRYGVE: "CD4+ T Cells in the Blood of MS Patients Respond to Predicted Epitopes From B cell Receptors Found in Spinal Fluid", FRONTIERS IN IMMUNOLOGY, vol. 11, 9 April 2020 (2020-04-09), XP093016868, DOI: 10.3389/fimmu.2020.00598
NAKAMURA YUKIO, LING MOI MENG, SHIINA TAKASHI, SHIN-I TADASU, SUZUKI RYUJI: "Idiotope-driven T-B collaboration-based T-cell epitope prediction using B-cell receptor repertoire sequences in infectious diseases ", SSRN, 26 March 2022 (2022-03-26), XP093016866
WEISSBOGEN, CELL, vol. 64, no. 4, 1991, pages 767 - 776
JOAO, IMMUNOL, vol. 172, no. 8, 2004, pages 4709 - 4716
BEEMD R ET AL., CYTOMETRY, vol. 40, 2000, pages 336 - 345
MACISAAC C ET AL., J IMMUNOL METHODS, vol. 283, 2003, pages 9 - 15
TEMBHARE P ET AL., AM J CLIN PATHOL, vol. 135, 2011, pages 890 - 900
LANGERAK AW ET AL., BLOOD, vol. 98, 2001, pages 165 - 173
REBAI N ET AL., PROCNATL ACAD SCI USA, vol. 91, 1994, pages 1529 - 1533
MATSUTANI T ET AL., HUM IMMUNOL, vol. 56, 1997, pages 57 - 69
MATSUTANI T ET AL., BR J HAEMATOL, vol. 109, 2000, pages 759 - 769
MATSUTANI T ET AL., MOL IMMUNOL, vol. 44, 2007, pages 2378 - 2387
MATSUTANI T ET AL., MOL IMMUNOL, vol. 48, 2011, pages 623 - 629
RUDOLPH MG ET AL., ANNU REV IMMUNOL., vol. 24, 2006, pages 419 - 66
MOISE L ET AL., HUM VACCIN IMMUNOTHER., vol. 9, no. 7, July 2013 (2013-07-01), pages 1577 - 86
CALLS JJ ET AL., OS COMPUT BIOL., vol. 8, no. 3, 2012, pages e1002412
SCHWARTZ RH. ET AL., ANNU REV IMMUNOL., vol. 3, 1985, pages 237 - 61
RUDOLPH ET AL., ANNU. REV. IMMUNOL., vol. 24, 2006, pages 419 - 466
BATZER ET AL., NUCLEIC ACID RES., vol. 19, 1991, pages 5081
OHTSUKA ET AL., J.BIOL. CHEM., vol. 260, 1985, pages 2605 - 2608
ROSSOLINI ET AL., MOL. CELL. PROBES, vol. 8, 1994, pages 91 - 98
MARKET, PROCNATL ACAD SCI USA, vol. 81, no. 18, September 1984 (1984-09-01), pages 5662 - 5666
ZOLLER ET AL., NUCLEIC ACIDS RES., vol. 10, no. 20, 25 October 1982 (1982-10-25), pages 6487 - 6500
WANG ET AL., SCIENCE, vol. 224, no. 4656, 29 June 1984 (1984-06-29), pages 1431 - 1433
AUSUBEL, F. M.: "Current Protocols in Molecular Biology", 1987, GREENE PUB. ASSOCIATES AND WILEY-INTERSCIENCE, article "DNA Cloning 1: Core Techniques, A Practical Approach"
SHIMIZU ET AL., NATURE BIOTECHNOLOGY, vol. 19, 2001, pages 751 - 755
ALTSCHUL ET AL., J. MOL. BIOL., vol. 215, 1990, pages 403 - 410
PEARSONLIPMAN, PROC. NATL. ACAD. SCI., USA, vol. 85, 1988, pages 2444 - 2448
SMITHWATERMAN, J. MOL. BIOL., vol. 147, 1981, pages 195 - 197
NEEDLEMANWUNSCH, J. MOL. BIOL., vol. 48, 1970, pages 443 - 453
N. K. JERNE: "Ann. Immunol.", vol. 125C, 1974, INST. PASTEUR, pages: 373 - 389
CALLS JJ ET AL., PLOS COMPUT BIOL, vol. 8, no. 3, 2012, pages e1002412
MADIN ET AL., PROC. NATL. ACAD. SCI. USA, vol. 97, no. 2, 2000, pages 559 - 564
R. LUNDBLAD: "Chemical Reagents for Protein Modification", 2005, CRC PRESS
ZHOU ET AL., BLOOD, vol. 86, 1995, pages 3295 - 3301
LU ET AL., J. ORG. CHEM., vol. 46, 1981, pages 3433
SNINSKY, J. J. ET AL.: "Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology", 1999, GREENE PUB. ASSOCIATES AND WILEY-INTERSCIENCE
BRUNSVIG P FAAMDAL SGJERTSEN M KKVALHEIM GMARKOWSKI-GRIMSRUD C JSVE IDYRHAUG MTRACHSEL SMULLER MERIKSEN J A: "Telomerase peptide vaccination: a phase I/II study in patients with non-small cell lung cancer", CANCER IMMUNOL IMMUNOTHER., vol. 55, no. 12, 2006, pages 1553 - 1564, XP019422504, DOI: 10.1007/s00262-006-0145-7
M. STAEHLERA. STENZLP. Y. DIETRICHT. EISENA. HAFERKAMPJ. BECKA. MAYERS. WALTERH. SINGHJ. FRISCH: "An open label study to evaluate the safety and immunogenicity of the peptide based cancer vaccine IMA901", ASCO MEETING, 2007
LONGENECKER ET AL., ANN. NY ACAD. SCI., vol. 690, 1993, pages 276 - 291
A. KIBBE: "Handbook of Pharmaceutical Excipients", 2000, AMERICAN PHARMACEUTICAL ASSOCIATION AND PHARMACEUTICAL PRESS
THOMAS A MSANTARSIERO L MLUTZ E RARMSTRONG T DCHEN Y CHUANG L QLAHERU D AGOGGINS MHRUBAN R HJAFFEE E M: "Mesothelin-specific CD8(+) T cell responses provide evidence of in vivo cross-priming by antigen-presenting cells in vaccinated pancreatic cancer patients", J EXP MED., vol. 200, no. 3, 2 August 2004 (2004-08-02), pages 297 - 306
CONRY ET AL., SEMINARS IN ONCOLOGY, vol. 23, 1996, pages 135 - 147
CONDON ET AL., NATURE MEDICINE, vol. 2, 1996, pages 1122 - 1127
GONG ET AL., NATURE MEDICINE, vol. 3, 1997, pages 558 - 561
ZHAI ET AL., J. IMMUNOL., vol. 156, 1996, pages 700 - 710
GRAHAM ET AL., INT J. CANCER, vol. 65, 1996, pages 664 - 670
ROTH ET AL., SCAND. J. IMMUNOLOGY, vol. 43, 1996, pages 646 - 651
INNIS, M. A.: "PCR Protocols: A Guideto Methods and Applications", 1990, ACADEMIC PRESS
GAIT, M. J.: "Oligonucleotide Synthesis: A Practical Approach", 1985, IRL PRESS
ECKSTEIN, F.: "Oligonucleotides and Analogues: A Practical Approach", 1991, IRL PRESS
ADAMS, R. L. ET AL.: "The Biochemistry of the Nucleic Acids", 1992, CHAPMAN HALL
SHABAROVA, Z. ET AL., ADVANCED ORGANIC CHEMISTRY OF NUCLEIC ACIDS, 1994
BLACKBURN, G. M. ET AL.: "Nucleic Acids in Chemistry and Biology", 1996, OXFORD UNIVERSITY PRESS
IDENSHI DONYUHATSUGEN KAISEKI: "Bessatsu Jikken Igaku [Experimental Medicine, Supplemental Volume", 1997, YODOSHA, article "Jikken Ho [Experimental Methods for Transgenesis & Expression Analysis"
GIBAS C. ET AL.: "Developing Bioinformatics ComputerSkills", 2001, O'REILLY
MOUNT D. W.: "Bioinformatics: Sequence and Genome Analysis", 2004, CSHL PRESS
PEVZNER P. ET AL.: "Bioinformatics for Biologist", 2011, CAMBRIDGE UNIVERSITY PRESS
SUMIO KANNO ET AL.: "Advanced Methods for Next-generation Sequencers by Purpose", CELL ENGINEERING ANNEX, 2012
Attorney, Agent or Firm:
YAMAMOTO, Shusaku et al. (JP)
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