Список литературы

1. Ярилин А.А. Иммунология / А.А. Ярилин. – Москва: ГЭОТАР-Медиа, 2010.

2. Ганковская Л.В. Основы общей иммунологии. Учебно-методическое пособие для студентов медицинских вузов / Л.В. Ганковская, Л.С. Намазова-Баранова, Р.Я. Мешкова. – Москва: ПедиатрЪ, 2014.

3. Murugan A. Statistical inference of the generation probability of T-cell receptors from sequence repertoires / A. Murugan [et al.] // Proceedings of the National Academy of Sciences. – 2012. – Vol. 109. – № 40. – P. 16161-16166.

4. consortium M. sequencing. Complete sequence and gene map of a human major histocompatibility complex / M. sequencing consortium // Nature. – 1999. – Vol. 401. – № 6756. – P. 921-923.

5. IPD-IMGT/HLA database statistics.

6. Robinson J. IPD-IMGT/HLA Database / J. Robinson [et al.] // Nucleic Acids Research. – 2019.

7. Cao K. Analysis of the frequencies of HLA-A, B, and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations / K. Cao [et al.] // Human Immunology. – 2001. – Vol. 62. – № 9. – P. 1009-1030.

8. Autoimmunity: From Bench to Bedside. Autoimmunity / eds. J.-M. Anaya [et al.] PMID: 29087650. – Bogota (Colombia): El Rosario University Press, 2013.

9. White K.D. HLA and the Pharmacogenomics of Drug Hypersensitivity / K.D. White, S. Gaudieri, E.J. Phillips // DOI: 10.1016/B978-0-12-386882-4.00021-9. – Elsevier, 2014. – P. 437-465.

10. Мерфи К. Иммунобиология по Джанвею / К. Мерфи, К. Уивер. – 9. – Москва: Логосфера, 2020.

11. Lanier L.L. NK CELL RECOGNITION / L.L. Lanier // Annual Review of Immunology. – 2005. – Vol. 23. – № 1. – P. 225-274.

12. Alfonso C. Nonclassical MHC Class II Molecules / C. Alfonso, L. Karlsson // Annual Review of Immunology. – 2000. – Vol. 18. – № 1. – P. 113-142.

13. Dash R. In silico-based vaccine design against Ebola virus glycoprotein / R. Dash [et al.] // Advances and Applications in Bioinformatics and Chemistry. – 2017. – Vols. Volume 10. – P. 11-28.

14. Viana Invenção M. da C. Development of synthetic antigen vaccines for COVID-19 / M. da C. Viana Invenção [et al.] // Human Vaccines & Immunotherapeutics. – 2021. – Vol. 17. – № 11. – P. 3855-3870.

15. Bjorkman P.J. The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens / P.J. Bjorkman [et al.] // Nature. – 1987. – Vol. 329. – № 6139. – P. 512-518.

16. Тибирькова Е.В. РОЛЬ ИММУНОЛОГИЧЕСКОЙ ТОЛЕРАНТНОСТИ В ПОДДЕРЖАНИИ ГОМЕОСТАЗА / Е.В. Тибирькова [et al.].

17. Trolle T. The Length Distribution of Class IRestricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC AlleleSpecific Binding Preference / T. Trolle [et al.] // The Journal of Immunology. – 2016. – Vol. 196. – № 4. – P. 1480-1487.

18. Bjorkman P.J. Structures of two classes of MHC molecules elucidated: crucial differences and similarities / P.J. Bjorkman, W.P. Burmeister // Current Opinion in Structural Biology. – 1994. – Vol. 4. – Structures of two classes of MHC molecules elucidated. – № 6. – P. 852-856.

19. Deakin J.E. Evolution and comparative analysis of the MHC Class III inflammatory region / J.E. Deakin [et al.] // BMC Genomics. – 2006. – Vol. 7. – № 1. – P. 281.

20. Schmidt J. Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and provides insight into immunoediting / J. Schmidt [et al.] // Cell Reports Medicine. – 2021. – Vol. 2. – № 2. – P. 100194.

21. Matsumura M. Emerging Principles for the Recognition of Peptide Antigens by MHC Class I Molecules / M. Matsumura [et al.] // Science. – 1992. – Vol. 257. – № 5072. – P. 927-934.

22. Bjorkman P.J. The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens / P.J. Bjorkman [et al.] // Nature. – 1987. – Vol. 329. – № 6139. – P. 512-518.

23. Ting J.P.-Y. Genetic Control of MHC Class II Expression / J.P.-Y. Ting, J. Trowsdale // Cell. – 2002. – Vol. 109. – № 2. – P. S21-S33.

24. Hewitt E.W. The MHC class I antigen presentation pathway: strategies for viral immune evasion / E.W. Hewitt // Immunology. – 2003. – Vol. 110. – The MHC class I antigen presentation pathway. – № 2. – P. 163-169.

25. Rutigliano H.M. Trophoblast Major Histocompatibility Complex Class I Expression Is Associated with Immune-Mediated Rejection of Bovine Fetuses Produced by Cloning / H.M. Rutigliano [et al.] // Biology of Reproduction. – 2016. – Vol. 95. – № 2. – P. 39-39.

26. Bevan M.J. Cross-priming / M.J. Bevan // Nature Immunology. – 2006. – Vol. 7. – № 4. – P. 363-365.

27. Rock K.L. Present Yourself! By MHC Class I and MHC Class II Molecules / K.L. Rock, E. Reits, J. Neefjes // Trends in Immunology. – 2016. – Vol. 37. – № 11. – P. 724-737.

28. Gong B. The ubiquitin-proteasome system: Potential therapeutic targets for alzheimer’s disease and spinal cord injury / B. Gong [et al.] // Frontiers in Molecular Neuroscience. – 2016. – Vol. 9. – The ubiquitin-proteasome system.

29. Tanaka K. The proteasome: Overview of structure and functions / K. Tanaka // Proceedings of the Japan Academy, Series B. – 2009. – Vol. 85. – The proteasome. – № 1. – P. 12-36.

30. Kloetzel P.-M. Antigen processing by the proteasome / P.-M. Kloetzel // Nature Reviews Molecular Cell Biology. – 2001. – Vol. 2. – № 3. – P. 179-188.

31. Harris J.L. Substrate speci¢city of the human proteasome / J.L. Harris [et al.]. – P. 11.

32. Murata S. The immunoproteasome and thymoproteasome: functions, evolution and human disease / S. Murata [et al.] // Nature Immunology. – 2018. – Vol. 19. – The immunoproteasome and thymoproteasome. – № 9. – P. 923-931.

33. Murata S. The immunoproteasome and thymoproteasome: functions, evolution and human disease / S. Murata [et al.] // Nature Immunology. – 2018. – Vol. 19. – The immunoproteasome and thymoproteasome. – № 9. – P. 923-931.

34. Murata S. Regulation of CD8 ⁺ T Cell Development by Thymus-Specific Proteasomes / S. Murata [et al.] // Science. – 2007. – Vol. 316. – № 5829. – P. 1349-1353.

35. Takahama Y. β5t-containing thymoproteasome: specific expression in thymic cortical epithelial cells and role in positive selection of CD8+ T cells / Y. Takahama [et al.] // Current Opinion in Immunology. – 2012. – Vol. 24. – β5t-containing thymoproteasome. – № 1. – P. 92-98.

36. Kniepert A. The unique functions of tissue-specific proteasomes / A. Kniepert, M. Groettrup // Trends in Biochemical Sciences. – 2014. – Vol. 39. – № 1. – P. 17-24.

37. Mediani L. Defective ribosomal products challenge nuclear function by impairing nuclear condensate dynamics and immobilizing ubiquitin / L. Mediani [et al.] // The EMBO Journal. – 2019. – Vol. 38. – № 15.

38. Dolan B.P. Defective Ribosomal Products Are the Major Source of Antigenic Peptides Endogenously Generated from Influenza A Virus Neuraminidase / B.P. Dolan [et al.] // The Journal of Immunology. – 2010. – Vol. 184. – № 3. – P. 1419-1424.

39. Pishesha N. A guide to antigen processing and presentation / N. Pishesha, T.J. Harmand, H.L. Ploegh // Nature Reviews Immunology. – 2022. – Vol. 22. – № 12. – P. 751-764.

40. Suzuki T. The cytoplasmic peptide:N-glycanase (NGLY1) Structure, expression and cellular functions / T. Suzuki, C. Huang, H. Fujihira // Gene. – 2016. – Vol. 577. – The cytoplasmic peptide. – № 1. – P. 1-7.

41. Kasteren S.I. van. Chemical biology of antigen presentation by MHC molecules / S.I. van Kasteren [et al.] // Current Opinion in Immunology. – 2014. – Vol. 26. – P. 21-31.

42. Hanada K. Immune recognition of a human renal cancer antigen through post-translational protein splicing / K. Hanada, J.W. Yewdell, J.C. Yang // Nature. – 2004. – Vol. 427. – № 6971. – P. 252-256.

43. Admon A. Are There Indeed Spliced Peptides in the Immunopeptidome? / A. Admon // Molecular & Cellular Proteomics. – 2021. – Vol. 20. – P. 100099.

44. Liepe J. A large fraction of HLA class I ligands are proteasome-generated spliced peptides / J. Liepe [et al.] // Science. – 2016. – Vol. 354. – № 6310. – P. 354-358.

45. Vigneron N. Production of spliced peptides by the proteasome / N. Vigneron [et al.] // Molecular Immunology. – 2019. – Vol. 113. – P. 93-102.

46. Vigneron N. Peptide splicing by the proteasome / N. Vigneron [et al.] // Journal of Biological Chemistry. – 2017. – Vol. 292. – № 51. – P. 21170-21179.

47. Mansurkhodzhaev A. Proteasome-Generated cis-Spliced Peptides and Their Potential Role in CD8+ T Cell Tolerance / A. Mansurkhodzhaev [et al.] // Frontiers in Immunology. – 2021. – Vol. 12. – P. 614276.

48. Mishto M. An in silicoin vitro Pipeline Identifying an HLA-A*02:01+ KRAS G12V+ Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients / M. Mishto [et al.] // Frontiers in Immunology. – 2019. – Vol. 10. – An in silicoin vitro Pipeline Identifying an HLA-A*02. – P. 2572.

49. Kato K. Characterization of Proteasome-Generated Spliced Peptides Detected by Mass Spectrometry / K. Kato [et al.] // The Journal of Immunology. – 2022. – Vol. 208. – № 12. – P. 2856-2865.

50. Lichti C.F. Navigating Critical Challenges Associated with Immunopeptidomics-Based Detection of Proteasomal Spliced Peptide Candidates / C.F. Lichti [et al.] // Cancer Immunology Research. – 2022. – Vol. 10. – № 3. – P. 275-284.

51. Rock K.L. Protein degradation and the generation of MHC class I-presented peptides / K.L. Rock [et al.] // DOI: 10.1016/S0065-2776(02)80012-8. – Elsevier, 2002. – Vol. 80. – P. 1-70.

52. Craiu A. Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide / A. Craiu [et al.] // Proceedings of the National Academy of Sciences. – 1997. – Vol. 94. – № 20. – P. 10850-10855.

53. Stoltze L. Two new proteases in the MHC class I processing pathway / L. Stoltze [et al.] // Nature Immunology. – 2000. – Vol. 1. – № 5. – P. 413-418.

54. Rock K.L. Proteases in MHC Class I Presentation and Cross-Presentation / K.L. Rock, D.J. Farfán-Arribas, L. Shen // The Journal of Immunology. – 2010. – Vol. 184. – № 1. – P. 9-15.

55. Kunisawa J. The Group II Chaperonin TRiC Protects Proteolytic Intermediates from Degradation in the MHC Class I Antigen Processing Pathway / J. Kunisawa, N. Shastri // Molecular Cell. – 2003. – Vol. 12. – № 3. – P. 565-576.

56. Daumke O. Functional asymmetry of the ATP-binding-cassettes of the ABC transporter TAP is determined by intrinsic properties of the nucleotide binding domains: Modular function of TAP domains / O. Daumke, M.R. Knittler // European Journal of Biochemistry. – 2001. – Vol. 268. – Functional asymmetry of the ATP-binding-cassettes of the ABC transporter TAP is determined by intrinsic properties of the nucleotide binding domains. – № 17. – P. 4776-4786.

57. Urlinger S. Intracellular Location, Complex Formation, and Function of the Transporter Associated with Antigen Processing in Yeast / S. Urlinger [et al.] // European Journal of Biochemistry. – 1997. – Vol. 245. – № 2. – P. 266-272.

58. Blees A. Assembly of the MHC I peptide-loading complex determined by a conserved ionic lock-switch / A. Blees [et al.] // Scientific Reports. – 2015. – Vol. 5. – № 1. – P. 17341.

59. Lehnert E. Structure and Dynamics of Antigenic Peptides in Complex with TAP / E. Lehnert, R. Tampé // Frontiers in Immunology. – 2017. – Vol. 8.

60. Grossmann N. Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter / N. Grossmann [et al.] // Nature Communications. – 2014. – Vol. 5. – № 1. – P. 5419.

61. Abele R. The ABCs of Immunology: Structure and Function of TAP, the Transporter Associated with Antigen Processing / R. Abele, R. Tampé // Physiology. – 2004. – Vol. 19. – The ABCs of Immunology. – № 4. – P. 216-224.

62. Herget M. Purification and Reconstitution of the Antigen Transport Complex TAP / M. Herget [et al.] // Journal of Biological Chemistry. – 2009. – Vol. 284. – № 49. – P. 33740-33749.

63. Endert P.M. van. A sequential model for peptide binding and transport by the transporters associated with antigen processing / P.M. van Endert [et al.] // Immunity. – 1994. – Vol. 1. – № 6. – P. 491-500.

64. Gorbulev S. Allosteric crosstalk between peptide-binding, transport, and ATP hydrolysis of the ABC transporter TAP / S. Gorbulev, R. Abele, R. Tampé // Proceedings of the National Academy of Sciences. – 2001. – Vol. 98. – № 7. – P. 3732-3737.

65. Herget M. Conformation of peptides bound to the transporter associated with antigen processing (TAP) / M. Herget [et al.] // Proceedings of the National Academy of Sciences. – 2011. – Vol. 108. – № 4. – P. 1349-1354.

66. Androlewicz M.J. Human transporters associated with antigen processing possess a promiscuous peptide-binding site / M.J. Androlewicz, P. Cresswell // Immunity. – 1994. – Vol. 1. – № 1. – P. 7-14.

67. Uebel S. Recognition principle of the TAP transporter disclosed by combinatorial peptide libraries / S. Uebel [et al.] // Proceedings of the National Academy of Sciences. – 1997. – Vol. 94. – № 17. – P. 8976-8981.

68. Blees A. Structure of the human MHC-I peptide-loading complex / A. Blees [et al.] // Nature. – 2017. – Vol. 551. – № 7681. – P. 525-528.

69. Serwold T. ERAAP customizes peptides for MHC class I molecules in the endoplasmic reticulum / T. Serwold [et al.] // Nature. – 2002. – Vol. 419. – № 6906. – P. 480-483.

70. Yewdell J.W. Don’t mess with ERAAP! / J.W. Yewdell, X. Lu // Nature Immunology. – 2012. – Vol. 13. – № 6. – P. 526-528.

71. Osborne A.R. PROTEIN TRANSLOCATION BY THE SEC61/SECY CHANNEL / A.R. Osborne, T.A. Rapoport, B. van den Berg // Annual Review of Cell and Developmental Biology. – 2005. – Vol. 21. – № 1. – P. 529-550.

72. Meusser B. ERAD: the long road to destruction / B. Meusser [et al.] // Nature Cell Biology. – 2005. – Vol. 7. – ERAD. – № 8. – P. 766-772.

73. Nussbaum A.K. PAProC: a prediction algorithm for proteasomal cleavages available on the WWW / A.K. Nussbaum [et al.] // Immunogenetics. – 2001. – Vol. 53. – PAProC. – № 2. – P. 87-94.

74. Hattotuwagama C.K. Quantitative online prediction of peptide binding to the major histocompatibility complex / C.K. Hattotuwagama [et al.] // Journal of Molecular Graphics and Modelling. – 2004. – Vol. 22. – № 3. – P. 195-207.

75. Doytchinova I.A. EpiJen: a server for multistep T cell epitope prediction / I.A. Doytchinova, P. Guan, D.R. Flower // BMC Bioinformatics. – 2006. – Vol. 7. – EpiJen. – № 1. – P. 131.

76. Dhanda S.K. IEDB-AR: immune epitope databaseanalysis resource in 2019 / S.K. Dhanda [et al.] // Nucleic Acids Research. – 2019. – Vol. 47. – IEDB-AR. – № W1. – P. W502-W506.

77. Vita R. The Immune Epitope Database (IEDB): 2018 update / R. Vita [et al.] // Nucleic Acids Research. – 2019. – Vol. 47. – The Immune Epitope Database (IEDB). – № D1. – P. D339-D343.

78. Roetschke H.P. InvitroSPI and a large database of proteasome-generated spliced and non-spliced peptides / H.P. Roetschke [et al.] // Scientific Data. – 2023. – Vol. 10. – № 1. – P. 18.

79. Willimsky G. In vitro proteasome processing of neo-splicetopes does not predict their presentation in vivo / G. Willimsky [et al.] // eLife. – 2021. – Vol. 10. – P. e62019.

80. Toes R.E.M. Discrete Cleavage Motifs of Constitutive and Immunoproteasomes Revealed by Quantitative Analysis of Cleavage Products / R.E.M. Toes [et al.] // Journal of Experimental Medicine. – 2001. – Vol. 194. – № 1. – P. 1-12.

81. Emmerich N.P.N. The Human 26 S and 20 S Proteasomes Generate Overlapping but Different Sets of Peptide Fragments from a Model Protein Substrate / N.P.N. Emmerich [et al.] // Journal of Biological Chemistry. – 2000. – Vol. 275. – № 28. – P. 21140-21148.

82. Toseland C.P. AntiJen: A quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data / C.P. Toseland [et al.] // Immunome Research. – 2005. – Vol. 1. – AntiJen. – № 1. – P. 4.

83. Lata S. MHCBN 4.0: A database of MHC/TAP binding peptides and T-cell epitopes / S. Lata, M. Bhasin, G.P. Raghava // BMC Research Notes. – 2009. – Vol. 2. – MHCBN 4.0. – № 1. – P. 61.

84. Diez-Rivero C.M. Quantitative modeling of peptide binding to TAP using support vector machine / C.M. Diez-Rivero [et al.] // Proteins: Structure, Function, and Bioinformatics. – 2010. – Vol. 78. – № 1. – P. 63-72.

85. Bagaev D.V. VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium / D.V. Bagaev [et al.] // Nucleic Acids Research. – 2020. – Vol. 48. – VDJdb in 2019. – № D1. – P. D1057-D1062.

86. Tickotsky N. McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences / N. Tickotsky [et al.] // Bioinformatics. – 2017. – Vol. 33. – McPAS-TCR. – № 18. – P. 2924-2929.

87. Rammensee H.-G. SYFPEITHI: Database for MHC ligands and peptide motifs / H.-G. Rammensee [et al.] // Immunogenetics. – 1999. – Vol. 50. – SYFPEITHI. – № 3-4. – P. 213-219.

88. Reche P.A. EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology / P.A. Reche [et al.] // Bioinformatics. – 2005. – Vol. 21. – EPIMHC. – № 9. – P. 2140-2141.

89. Bhasin M. Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences / M. Bhasin, G.P.S. Raghava // Nucleic Acids Research. – 2005. – Vol. 33. – Pcleavage. – № Web Server. – P. W202-W207.

90. Nielsen M. The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage / M. Nielsen [et al.] // Immunogenetics. – 2005. – Vol. 57. – The role of the proteasome in generating cytotoxic T-cell epitopes. – № 1-2. – P. 33-41.

91. Gomez-Perosanz M. Identification of CD8+ T cell epitopes through proteasome cleavage site predictions / M. Gomez-Perosanz [et al.] // BMC Bioinformatics. – 2020. – Vol. 21. – № S17. – P. 484.

92. Zhang G. PREDTAP: a system for prediction of peptide binding to the human transporter associated with antigen processing / G. Zhang [et al.] // Immunome Research. – 2006. – Vol. 2. – PREDTAP. – № 1. – P. 3.

93. Nielsen M. NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence / M. Nielsen [et al.] // PLoS ONE. – 2007. – Vol. 2. – № 8. – P. e796.

94. Phloyphisut P. MHCSeqNet: a deep neural network model for universal MHC binding prediction / P. Phloyphisut [et al.] // BMC Bioinformatics. – 2019. – Vol. 20. – MHCSeqNet. – № 1. – P. 270.

95. O’Donnell T.J. MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing / T.J. O’Donnell, A. Rubinsteyn, U. Laserson // Cell Systems. – 2020. – Vol. 11. – MHCflurry 2.0. – № 1. – P. 42-48.e7.

96. Stranzl T. NetCTLpan: pan-specific MHC class I pathway epitope predictions / T. Stranzl [et al.] // Immunogenetics. – 2010. – Vol. 62. – NetCTLpan. – № 6. – P. 357-368.

97. Wu J. DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity / J. Wu [et al.] // Frontiers in Immunology. – 2019. – Vol. 10. – DeepHLApan. – P. 2559.

98. Alvarez B. NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions / B. Alvarez [et al.] // Molecular & Cellular Proteomics. – 2019. – Vol. 18. – № 12. – P. 2459-2477.

99. Paul S. Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system / S. Paul [et al.] // PLOS Computational Biology. – 2020. – Vol. 16. – № 5. – P. e1007757.

100. Mei S. A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction / S. Mei [et al.] // Briefings in Bioinformatics. – 2020. – Vol. 21. – № 4. – P. 1119-1135.