RT Journal Article
SR Electronic
T1 Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides Demonstrates Different Alloreactivity Potential In HLA-Matched and Mismatched Donor-Recipient Pairs
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 024828
DO 10.1101/024828
A1 B Abdul Razzaq
A1 A Scalora
A1 VN Koparde
A1 J Meier
A1 M Mahmood
A1 S Salman
A1 M Jameson-Lee
A1 M Serrano
A1 N Sheth
A1 M Voelkner
A1 DJ Kobulnicky
A1 CH Roberts
A1 A Ferreira-Gonzalez
A1 MH Manjili
A1 GA Buck
A1 MC Neale
A1 AA Toor
YR 2015
UL http://biorxiv.org/content/early/2015/08/17/024828.abstract
AB Immune reconstitution kinetics and subsequent clinical outcomes in HLA matched recipients of allogeneic stem cell transplantation (SCT) are variable and difficult to predict. Considering SCT as a dynamical system, may allow sequence differences across the exomes of the transplant donors and recipients to be used to simulate an alloreactive T cell response, which may allow better clinical outcome prediction. To accomplish this, whole exome sequencing was performed on 34 HLA matched SCT donor-recipient pairs (DRP), and the nucleotide sequence differences translated to peptides. The binding affinity of the peptides to the relevant HLA in each DRP was determined. The resulting array of peptide-HLA binding affinity values in each patient was considered as an operator modifying a hypothetical T cell repertoire vector, in which each T cell clone proliferates in accordance to the logistic equation of growth. Using an iterating system of matrices, each simulated T cell clone’s growth was calculated with the steady state population being proportional to the magnitude of the binding affinity of the driving HLA-peptide complex. Incorporating competition between T cell clones responding to different HLA-peptide complexes reproduces a number of features of clinically observed T cell clonal repertoire in the simulated repertoire. These include, sigmoidal growth kinetics of individual T cell clones and overall repertoire, Power Law clonal frequency distribution, increase in repertoire complexity over time with increasing clonal diversity and finally, alteration of clonal dominance when a different antigen array is encountered, such as in stem cell transplantation. The simulated, alloreactive T cell repertoire was markedly different in HLA matched DRP. The patterns were differentiated by rate of growth, and steady state magnitude of the simulated T cell repertoire and demonstrate a possible correlation with survival. In conclusion, exome wide sequence differences in DRP may allow simulation of donor alloreactive T cell response to recipient antigens and may provide a quantitative basis for refining donor selection and titration of immunosuppression following SCT.