  Donor T cell mediated graft vs. host effects may result from the aggregate
alloreactivity to minor histocompatibility antigens (mHA) presented by the HLA
in each donor-recipient pair (DRP) undergoing stem cell transplantation (SCT).
Whole exome sequencing has demonstrated extensive nucleotide sequence variation
in HLA-matched DRP. Non-synonymous single nucleotide polymorphisms (nsSNPs) in
the GVH direction (polymorphisms present in recipient and absent in donor) were
identified in 4 HLA-matched related and 5 unrelated DRP. The nucleotide
sequence flanking each SNP was obtained utilizing the ANNOVAR software package.
All possible nonameric-peptides encoded by the non-synonymous SNP were then
interrogated in-silico for their likelihood to be presented by the HLA class I
molecules in individual DRP, using the Immune-Epitope Database (IEDB) SMM
algorithm. The IEDB-SMM algorithm predicted a median 18,396 peptides/DRP which
bound HLA with an IC50 of <500nM, and 2254 peptides/DRP with an IC50 of <50nM.
Unrelated donors generally had higher numbers of peptides presented by the HLA.
A similarly large library of presented peptides was identified when the data
was interrogated using the Net MHCPan algorithm. These peptides were uniformly
distributed in the various organ systems. The bioinformatic algorithm presented
here demonstrates that there may be a high level of minor histocompatibility
antigen variation in HLA-matched individuals, constituting an HLA-specific
alloreactivity potential. These data provide a possible explanation for how
relatively minor adjustments in GVHD prophylaxis yield relatively similar
outcomes in HLA matched and mismatched SCT recipients.
