Dynamical system modeling to simulate donor T cell response to whole exome sequencing-derived recipient peptides: Understanding randomness in alloreactivity incidence following stem cell transplantation

• Published in: PloS one Vol. 12; no. 12; p. e0187771
• Main Authors: Koparde, Vishal, Abdul Razzaq, Badar, Suntum, Tara, Sabo, Roy, Scalora, Allison, Serrano, Myrna, Jameson-Lee, Max, Hall, Charles, Kobulnicky, David, Sheth, Nihar, Feltz, Juliana, Contaifer, Daniel, Wijesinghe, Dayanjan, Reed, Jason, Roberts, Catherine, Qayyum, Rehan, Buck, Gregory, Neale, Michael, Toor, Amir
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.12.2017; Public Library of Science (PLoS)
• Subjects: Analysis; Antigens; Binding; Biology and Life Sciences; Bone marrow; Cancer; Cell Transplantation; Clinical outcomes; Computer and Information Sciences; Computer simulation; Cytotoxicity; Dynamical systems; Exome sequencing; Genetic aspects; Graft-versus-host reaction; Histocompatibility antigen HLA; Humans; Incidence; Internal medicine; Leukemia; Lymphocytes; Lymphocytes T; Mathematical analysis; Matrix algebra; Matrix methods; Medicine; Medicine and Health Sciences; Minor histocompatibility antigens; Models, Theoretical; Peptides; Peptides - immunology; Pharmacy; Physical Sciences; Physiological aspects; Proteins; Randomness; Research and Analysis Methods; Sequences; Single-nucleotide polymorphism; Stem Cell Transplantation; Stem cells; T cells; T-Lymphocytes - immunology; Transplantation; Transplants & implants; Whole Exome Sequencing; United States; United States > US; Virginia
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0187771

Quantitative relationship between the magnitude of variation in minor histocompatibility antigens (mHA) and graft versus host disease (GVHD) pathophysiology in stem cell transplant (SCT) donor-recipient pairs (DRP) is not established. In order to elucidate this relationship, whole exome sequencing (WES) was performed on 27 HLA matched related (MRD), & 50 unrelated donors (URD), to identify nonsynonymous single nucleotide polymorphisms (SNPs). An average 2,463 SNPs were identified in MRD, and 4,287 in URD DRP (p<0.01); resulting peptide antigens that may be presented on HLA class I molecules in each DRP were derived in silico (NetMHCpan ver2.0) and the tissue expression of proteins these were derived from determined (GTex). MRD DRP had an average 3,670 HLA-binding-alloreactive peptides, putative mHA (pmHA) with an IC50 of <500 nM, and URD, had 5,386 (p<0.01). To simulate an alloreactive donor cytotoxic T cell response, the array of pmHA in each patient was considered as an operator matrix modifying a hypothetical cytotoxic T cell clonal vector matrix; each responding T cell clone's proliferation was determined by the logistic equation of growth, accounting for HLA binding affinity and tissue expression of each alloreactive peptide. The resulting simulated organ-specific alloreactive T cell clonal growth revealed marked variability, with the T cell count differences spanning orders of magnitude between different DRP. Despite an estimated, uniform set of constants used in the model for all DRP, and a heterogeneously treated group of patients, higher total and organ-specific T cell counts were associated with cumulative incidence of moderate to severe GVHD in recipients. In conclusion, exome wide sequence differences and the variable alloreactive peptide binding to HLA in each DRP yields a large range of possible alloreactive donor T cell responses. Our findings also help understand the apparent randomness observed in the development of alloimmune responses.