Donor T cell alloreactivity in hematopoietic stem cell transplantation (HSCT) can result in acute graft-versus-host disease (GVHD) which is a major cause of morbidity and mortality that limits the clinical use of HSCT. Despite the potential large diversity in possible T cells (1015) it is thought that within each individual patient undergoing HSCT, a tractable and defined number of T cell clones mediate GVHD. We hypothesized that the identification of the most frequent T cell clones in the gastrointestinal (GI) tract of human patients with GVHD and subsequent tracking of these clones in the peripheral blood may provide a way to bracket and study disease related clones.
To investigate T cell clonal dynamics in human GVHD, we collected endoscopic GI tract biopsy samples and matched blood specimens for twelve patients undergoing myeloblative HSCT with suspected GI GVHID prior to or within one day of corticosteroid therapy. We also collected peripheral blood thirty days after biopsy. Five of these patients were negative for GVHD or had mild grade I/II GI GVHD, whereas seven had severe and fatal grade III/IV GI GVHD. These patients had heterogenous indications, conditioning regimens and GVHD prophylaxis which included cyclosporine, tacrolimus and methotrexate. None of the patients had cytomegolovirus (CMV) colitis or other identifiable GI or significant systemic infectious complications, although four patients had low-level blood CMV positivity by PCR. As a control, we compared endoscopic GI biopsies from patients with inflammatory bowel disease as well as normal healthy screening subjects. We extracted genomic DNA and performed T cell receptor (TCR) β CDR3 repertoire sequencing at Stanford and with GigaGen GigaMune Rep-Seq™, both using the Illumina next generation sequencing MiSeq™ and HiSeq™ platforms.
For each tissue sample from each patient, between 1,000–4,000 unique T cell sequences were observed in endoscopic tissue samples (2–6 samples per patient). We sorted the most frequent clones in the GI tissue samples by rank order and fractionated the top 100 clones for analysis. Many of these top clones were found in the matched peripheral blood at the time of diagnosis with most of these occurring at frequencies well below those in the GI tissue. For the patients with negative or mild GVHD at the time of diagnosis, the GI-identified clones that were found in the peripheral blood had a mean frequency and standard deviation of 0.001369 +/− 0.0016. This is indistinguishable from peripheral blood samples from patients with severe GVHD which showed a mean frequency and standard deviation of 0.0013 +/− 0.0009 (P=0.36, 2 tailed t-test).
We next tracked the GI-identified clones in the peripheral blood to the obtain fold change of the clones at thirty days after diagnosis to the time of diagnosis. The patients with negative or mild GVHD had a mean, median, and standard deviation in fold change of 1.9, 1.7, and 0.9 respectively. The patient with severe GVHD patients had a mean, median and standard deviation in fold change of 32.2, 30.7, and 17.3. A two tailed t-test comparison of the two groups showed they were statistically distinguishable with p-values of 0.0003 for examination of the mean fold change and 0.0005 for the median fold change.
For patients with severe GVHD, the peripheral blood at 30 days after diagnosis showed a highly oligoclonal expansion of individually private GI-identified clones. Many of these clones were identified in their respective donor T cell pool. For those patients evaluated with upper and lower endoscopy, many clones were shared between the colon and duodenum or gastrum, however, the dominant clones between these sites appeared to be different.
We found that a comparison of the fold change in the peripheral blood frequencies of the top one hundred clones identified in the GI tract biopsies can statistically distinguish five negative or mild GVHD patients from seven severe and fatal cases. These results support the use of T cell repertoire sequencing and associated approaches in human patients to both clarify the pathophysiology of the disease and eventually perhaps to provide an independent immune biomarker that could guide therapy. A major challenge will be to further phenotype and examine the T cell clones identified in the GI tissue and to investigate ways to determine which clones are highly associated or even causal to GVHD.
Meyer:GigaGen Inc: Consultancy, Equity Ownership. Löhr:GigaGen Inc.: Employment, Equity Ownership. Hsu:GigaGen Inc.: Employment, Equity Ownership. Johnson:GigaGen Inc.: Employment, Equity Ownership.
Asterisk with author names denotes non-ASH members.