Copelan, E. A. Hematopoietic stem-cell transplantation. N. Engl. J. Med. 354, 1813–1826 (2006).
Griffioen, M., van Bergen, C. A. & Falkenburg, J. H. Autosomal minor histocompatibility antigens: how genetic variants create diversity in immune targets. Front. Immunol. 7, 100 (2016).
Mutis, T., Xagara, A. & Spaapen, R. M. The connection between minor h antigens and neoantigens and the missing link in their prediction. Front. Immunol. 11, 1162 (2020).
Zeiser, R. & Blazar, B. R. Acute graft-versus-host disease—biologic process, prevention, and therapy. N. Engl. J. Med. 377, 2167–2179 (2017).
Zeiser, R. & Blazar, B. R. Pathophysiology of chronic graft-versus-host disease and therapeutic targets. N. Engl. J. Med. 377, 2565–2579 (2017).
Aljurf, M. et al. Worldwide network for blood & marrow transplantation (WBMT) special article, challenges facing emerging alternate donor registries. Bone Marrow Transplant. 54, 1179–1188 (2019).
Cieri, N., Maurer, K. & Wu, C. J. 60 years young: the evolving role of allogeneic hematopoietic stem cell transplantation in cancer immunotherapy. Cancer Res. 81, 4373–4384 (2021).
Bolon, Y., Atshan, R., Allbee-Johnson, M., Estrada-Merly, N. & Lee, S. Current use and outcome of hematopoietic stem cell transplantation: CIBMTR summary slides. CIBMTR https://cibmtr.org/CIBMTR/Resources/Summary-Slides-Reports (2022).
Spellman, S. R. Hematology 2022—what is complete HLA match in 2022? Hematology Am. Soc. Hematol. Educ. Program 2022, 83–89 (2022).
Goulmy, E., Gratama, J. W., Blokland, E., Zwaan, F. E. & van Rood, J. J. A minor transplantation antigen detected by MHC-restricted cytotoxic T lymphocytes during graft-versus-host disease. Nature 302, 159–161 (1983).
Wang, W. et al. Human H–Y: a male-specific histocompatibility antigen derived from the SMCY protein. Science 269, 1588–1590 (1995).
Den Haan, J. M. et al. Identification of a graft versus host disease-associated human minor histocompatibility antigen. Science 268, 1476–1480 (1995).
Goulmy, E., Termijtelen, A., Bradley, B. A. & van Rood, J. J. Y-antigen killing by T cells of women is restricted by HLA. Nature 266, 544–545 (1977).
Goulmy, E. et al. Mismatches of minor histocompatibility antigens between HLA-identical donors and recipients and the development of graft-versus-host disease after bone marrow transplantation. N. Engl. J. Med. 334, 281–285 (1996).
Spierings, E. et al. Multicenter analyses demonstrate significant clinical effects of minor histocompatibility antigens on GvHD and GvL after HLA-matched related and unrelated hematopoietic stem cell transplantation. Biol. Blood Marrow Transplant. 19, 1244–1253 (2013).
Grumet, F. C. et al. CD31 mismatching affects marrow transplantation outcome. Biol. Blood Marrow Transplant. 7, 503–512 (2001).
McCarroll, S. A. et al. Donor–recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease. Nat. Genet. 41, 1341–1344 (2009).
Spellman, S. et al. Effects of mismatching for minor histocompatibility antigens on clinical outcomes in HLA-matched, unrelated hematopoietic stem cell transplants. Biol. Blood Marrow Transplant. 15, 856–863 (2009).
Kogler, G. et al. Recipient cytokine genotypes for TNF-α and IL-10 and the minor histocompatibility antigens HY and CD31 codon 125 are not associated with occurrence or severity of acute GVHD in unrelated cord blood transplantation: a retrospective analysis. Transplantation 74, 1167–1175 (2002).
Martin, P. J. et al. A model of minor histocompatibility antigens in allogeneic hematopoietic cell transplantation. Front. Immunol. 12, 782152 (2021).
Story, C. M. et al. Genetics of HLA peptide presentation and impact on outcomes in HLA-matched allogeneic hematopoietic cell transplantation. Transplant. Cell Ther. 27, 591–599 (2021).
Warren, E. H. et al. Effect of MHC and non-MHC donor/recipient genetic disparity on the outcome of allogeneic HCT. Blood 120, 2796–2806 (2012).
Bykova, N. A., Malko, D. B. & Efimov, G. A. In silico analysis of the minor histocompatibility antigen landscape based on the 1000 Genomes project. Front. Immunol. 9, 1819 (2018).
Jadi, O. et al. Associations of minor histocompatibility antigens with outcomes following allogeneic hematopoietic cell transplantation. Am. J. Hematol. 98, 940–950 (2023).
Lang, F., Schrors, B., Lower, M., Tureci, O. & Sahin, U. Identification of neoantigens for individualized therapeutic cancer vaccines. Nat. Rev. Drug Discov. 21, 261–282 (2022).
Fotakis, G., Trajanoski, Z. & Rieder, D. Computational cancer neoantigen prediction: current status and recent advances. Immunooncol. Technol. 12, 100052 (2021).
Peters, B., Nielsen, M. & Sette, A. T cell epitope predictions. Annu. Rev. Immunol. 38, 123–145 (2020).
Sarkizova, S. et al. A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nat. Biotechnol. 38, 199–209 (2020).
Reynolds, G. et al. Developmental cell programs are co-opted in inflammatory skin disease. Science 371, eaba6500 (2021).
Aizarani, N. et al. A human liver cell atlas reveals heterogeneity and epithelial progenitors. Nature 572, 199–204 (2019).
MacParland, S. A. et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat. Commun. 9, 4383 (2018).
Vieira Braga, F. A. et al. A cellular census of human lungs identifies novel cell states in health and in asthma. Nat. Med. 25, 1153–1163 (2019).
Laughney, A. M. et al. Regenerative lineages and immune-mediated pruning in lung cancer metastasis. Nat. Med. 26, 259–269 (2020).
Parikh, K. et al. Colonic epithelial cell diversity in health and inflammatory bowel disease. Nature 567, 49–55 (2019).
Wang, Y. et al. Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. J. Exp. Med. 217, e20191130 (2020).
Williams, D. W. et al. Human oral mucosa cell atlas reveals a stromal-neutrophil axis regulating tissue immunity. Cell 184, 4090–4104 (2021).
Bannier-Hélaouët, M. et al. Exploring the human lacrimal gland using organoids and single-cell sequencing. Cell Stem Cell 28, 1221–1232 (2021).
Kanate, A. S. et al. Indications for hematopoietic cell transplantation and immune effector cell therapy: guidelines from the American Society for Transplantation and Cellular Therapy. Biol. Blood Marrow Transplant. 26, 1247–1256 (2020).
Van Galen, P. et al. Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity. Cell 176, 1265–1281 (2019).
Tyner, J. W. et al. Functional genomic landscape of acute myeloid leukaemia. Nature 562, 526–531 (2018).
Lonsdale, J. et al. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580–585 (2013).
Jiang, L. et al. A quantitative proteome map of the human body. Cell 183, 269–283 (2020).
Uhlen, M. et al. A genome-wide transcriptomic analysis of protein-coding genes in human blood cells. Science 366, eaax9198 (2019).
Cesana, M. et al. A CLK3-HMGA2 alternative splicing axis impacts human hematopoietic stem cell molecular identity throughout development. Cell Stem Cell 22, 575–588 (2018).
Drissen, R., Thongjuea, S., Theilgaard-Monch, K. & Nerlov, C. Identification of two distinct pathways of human myelopoiesis. Sci. Immunol. 4, eaau7148 (2019).
Kim, H. T. et al. Donor and recipient sex in allogeneic stem cell transplantation: what really matters. Haematologica 101, 1260–1266 (2016).
Ofran, Y. et al. Diverse patterns of T-cell response against multiple newly identified human Y chromosome-encoded minor histocompatibility epitopes. Clin. Cancer Res. 16, 1642–1651 (2010).
Miklos, D. B. et al. Antibody response to DBY minor histocompatibility antigen is induced after allogeneic stem cell transplantation and in healthy female donors. Blood 103, 353–359 (2004).
Feng, X., Hui, K. M., Younes, H. M. & Brickner, A. G. Targeting minor histocompatibility antigens in graft versus tumor or graft versus leukemia responses. Trends Immunol. 29, 624–632 (2008).
Bachireddy, P. et al. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Cell Rep. 37, 109992 (2021).
Bachireddy, P. et al. Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect. Sci. Transl. Med. 12, eabb7661 (2020).
Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).
Torikai, H. et al. A novel HLA-A*3303-restricted minor histocompatibility antigen encoded by an unconventional open reading frame of human TMSB4Y gene. J. Immunol. 173, 7046–7054 (2004).
Ouspenskaia, T. et al. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat. Biotechnol. 40, 209–217 (2022).
Andreatta, M. et al. MS-Rescue: a computational pipeline to increase the quality and yield of immunopeptidomics experiments. Proteomics 19, e1800357 (2019).
Lee, P. C. et al. Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma. J. Clin. Invest. 132, e151666 (2022).
Oliveira, G. et al. Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma. Nature 596, 119–125 (2021).
Vita, R. et al. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 47, D339–D343 (2019).
Chowell, D. et al. TCR contact residue hydrophobicity is a hallmark of immunogenic CD8+ T cell epitopes. Proc. Natl Acad. Sci. USA 112, E1754–E1762 (2015).
Schaefer, M. R. et al. A novel trafficking signal within the HLA-C cytoplasmic tail allows regulated expression upon differentiation of macrophages. J. Immunol. 180, 7804–7817 (2008).
Gabrielsen, I. S. M. et al. Transcriptomes of antigen presenting cells in human thymus. PLoS ONE 14, e0218858 (2019).
Park, J. E. et al. A cell atlas of human thymic development defines T cell repertoire formation. Science 367, eaay3224 (2020).
Holtan, S. G. et al. Composite end point of graft-versus-host disease-free, relapse-free survival after allogeneic hematopoietic cell transplantation. Blood 125, 1333–1338 (2015).
1000 Genomes Project Consortium et al. A global reference for human genetic variation. Nature 526, 68–74 (2015).
Lin, M. J. et al. Cancer vaccines: the next immunotherapy frontier. Nat. Cancer 3, 911–926 (2022).
Rojas, L. A. et al. Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer. Nature 618, 144–150 (2023).
Lansford, J. L. et al. Computational modeling and confirmation of leukemia-associated minor histocompatibility antigens. Blood Adv. 2, 2052–2062 (2018).
Olsen, K. S. et al. Shared graft-versus-leukemia minor histocompatibility antigens in DISCOVeRY-BMT. Blood Adv. 7, 1635–1649 (2023).
Parkhurst, M. R. et al. Unique neoantigens arise from somatic mutations in patients with gastrointestinal cancers. Cancer Discov. 9, 1022–1035 (2019).
Wolff, D. et al. National Institutes of Health Consensus Development Project on criteria for clinical trials in chronic graft-versus-host disease: IV. The 2020 highly morbid forms report. Transplant. Cell Ther. 27, 817–835 (2021).
Lybaert, L. et al. Neoantigen-directed therapeutics in the clinic: where are we? Trends Cancer 9, 503–519 (2023).
Bacigalupo, A. & Jones, R. PTCy: the ‘new’ standard for GVHD prophylaxis. Blood Rev. 62, 101096 (2023).
Murata, M., Warren, E. H. & Riddell, S. R. A human minor histocompatibility antigen resulting from differential expression due to a gene deletion. J. Exp. Med. 197, 1279–1289 (2003).
Broen, K. et al. A polymorphism in the splice donor site of ZNF419 results in the novel renal cell carcinoma-associated minor histocompatibility antigen ZAPHIR. PLoS ONE 6, e21699 (2011).
Griffioen, M. et al. Identification of 4 novel HLA-B*40:01 restricted minor histocompatibility antigens and their potential as targets for graft-versus-leukemia reactivity. Haematologica 97, 1196–1204 (2012).
Spierings, E. et al. Identification of HLA class II-restricted H–Y-specific T-helper epitope evoking CD4+ T-helper cells in H–Y-mismatched transplantation. Lancet 362, 610–615 (2003).
Coghill, J. M. et al. Effector CD4+ T cells, the cytokines they generate, and GVHD: something old and something new. Blood 117, 3268–3276 (2011).
Jones, S. C., Murphy, G. F., Friedman, T. M. & Korngold, R. Importance of minor histocompatibility antigen expression by nonhematopoietic tissues in a CD4+ T cell-mediated graft-versus-host disease model. J. Clin. Invest. 112, 1880–1886 (2003).
Chaves, F. A., Lee, A. H., Nayak, J. L., Richards, K. A. & Sant, A. J. The utility and limitations of current web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection. J. Immunol. 188, 4235–4248 (2012).
Dohner, H. et al. Diagnosis and management of AML in adults: 2017 ELN recommendations from an international expert panel. Blood 129, 424–447 (2017).
Greenberg, P. L. et al. Revised international prognostic scoring system for myelodysplastic syndromes. Blood 120, 2454–2465 (2012).
Przepiorka, D. et al. 1994 consensus conference on acute GVHD grading. Bone Marrow Transplant. 15, 825–828 (1995).
Glucksberg, H. et al. Clinical manifestations of graft-versus-host disease in human recipients of marrow from HLA-matched sibling donors. Transplantation 18, 295–304 (1974).
Pavletic, S. Z. et al. NCI first international workshop on the biology, prevention, and treatment of relapse after allogeneic hematopoietic stem cell transplantation: report from the committee on the epidemiology and natural history of relapse following allogeneic cell transplantation. Biol. Blood Marrow Transplant. 16, 871–890 (2010).
Parry, E. M. et al. Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome. Nat. Med. 29, 158–169 (2023).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).
Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).
Kim, H. et al. Development of a validated interferon score using NanoString technology. J. Interferon Cytokine Res. 38, 171–185 (2018).
Liberzon, A. et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 1, 417–425 (2015).
Poplin, R. et al. A universal SNP and small-indel variant caller using deep neural networks. Nat. Biotechnol. 36, 983–987 (2018).
Quentmeier, H. et al. The LL-100 panel: 100 cell lines for blood cancer studies. Sci Rep. 9, 8218 (2019).
Szolek, A. et al. OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics 30, 3310–3316 (2014).
Klaeger, S. et al. Optimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples. Mol. Cell. Proteomics 20, 100133 (2021).
Cui, K. H., Warnes, G. M., Jeffrey, R. & Matthews, C. D. Sex determination of preimplantation embryos by human testis-determining-gene amplification. Lancet 343, 79–82 (1994).
Bui, H. H. et al. Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics 7, 153 (2006).
Samarajiwa, S. A., Forster, S., Auchettl, K. & Hertzog, P. J. INTERFEROME: the database of interferon regulated genes. Nucleic Acids Res. 37, D852–D857 (2009).
Hookeri, N. nidhih2/mhags: v1.0.0 (v1.0.0). Zenodo https://doi.org/10.5281/zenodo.11658572 (2024).
Hookeri, N. nidhih2/mhags-fm: v1.0.0 (v1.0.0). Zenodo https://doi.org/10.5281/zenodo.11658599 (2024).
