Abstract: We previously described clinically relevant reductions in fecal microbiota diversity in patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT). Recipients of high-dose chemotherapy and autologous HCT (auto-HCT) incur similar antibiotic exposures and nutritional alterations. To characterize the fecal microbiota in the auto-HCT population, we analyzed 1161 fecal samples collected from 534 adult recipients of auto-HCT for lymphoma, myeloma, and amyloidosis in an observational study conducted at 2 transplantation centers in the United States. By using 16S ribosomal gene sequencing, we assessed fecal microbiota composition and diversity, as measured by the inverse Simpson index. At both centers, the diversity of early pretransplant fecal microbiota was lower in patients than in healthy controls and decreased further during the course of transplantation. Loss of diversity and domination by specific bacterial taxa occurred during auto-HCT in patterns similar to those with allo-HCT. Above-median fecal intestinal diversity in the periengraftment period was associated with decreased risk of death or progression (progression-free survival hazard ratio, 0.46; 95% confidence interval, 0.26-0.82; P = .008), adjusting for disease and disease status. This suggests that further investigation into the health of the intestinal microbiota in auto-HCT patients and posttransplant outcomes should be undertaken.

Abstract: Studies of the relationship between the gastrointestinal microbiota and outcomes in allogeneic hematopoietic stem cell transplantation (allo-HCT) have thus far largely focused on early complications, predominantly infection and acute graft-versus-host disease (GVHD). We examined the potential relationship of the microbiome with chronic GVHD (cGVHD) by analyzing stool and plasma samples collected late after allo-HCT using a case-control study design. We found lower circulating concentrations of the microbe-derived short-chain fatty acids (SCFAs) propionate and butyrate in day 100 plasma samples from patients who developed cGVHD, compared with those who remained free of this complication, in the initial case-control cohort of transplant patients and in a further cross-sectional cohort from an independent transplant center. An additional cross-sectional patient cohort from a third transplant center was analyzed; however, serum (rather than plasma) was available, and the differences in SCFAs observed in the plasma samples were not recapitulated. In sum, our findings from the primary case-control cohort and 1 of 2 cross-sectional cohorts explored suggest that the gastrointestinal microbiome may exert immunomodulatory effects in allo-HCT patients at least in part due to control of systemic concentrations of microbe-derived SCFAs.

Abstract: Introduction: Graft-versus-host-disease (GVHD) arises from the inflammatory cascade triggered by alloreactive T cell following allogeneic hematopoietic cell transplantation (allo-HCT). The tissues most frequently involved by GVHD include the small and large intestines, skin, and liver. Prior studies of T cell receptor (TCR) sequencing in diagnostic biopsies and blood have identified dominant T cell clones in GVHD-affected tissues that were not abundant in circulation or shared across multiple patients, but this has not been studied in sites poorly accessible to biopsy nor in lymphoid tissues in humans. We hypothesized that the GVHD-affected tissues have distinct TCR repertoires reflecting the differential expression of allo-antigens at different anatomic sites. Methods: We performed rapid autopsies on patients whose post allo-HCT course was complicated by GVHD to profile the TCR repertoire in tissues inaccessible to biopsy. Tissues were obtained from seven patients (HLA-identical allografts with a variety of graft sources and GVHD-prophylaxis regimens), all with active GVHD and/or on immunosuppression for GVHD control. Spleen, liver, skin, and multiple sites along the gastrointestinal (GI) tract were sampled, when possible, from the esophagus to the rectum. When available, blood and bone marrow mononuclear cells were also viably preserved. T cell receptors were sequenced from 38 different snap-frozen tissues from five patients via genomic DNA based next-generation sequencing of the TCR-beta CDR3 (ImmunoSeq, Adaptive Biotechnologies). Four out of five subjects sequenced had skin and GI GVHD, one only GI. In parallel, TCRs were sequenced from GVHD-affected tissues from a major and minor mouse model of GVHD: BALB/c 7-14 days after HCT with C57BL/6 T cells and C57BL/6 mice & gt; 30 days after HCT with LP/J T cells. Results: Sequences representing 264,678 productive TCRs were recovered from the human autopsy samples with over 100 unique clones for nearly all tissues (mean 1539; standard deviation 1626). We found virtually no TCR clones defined by nucleotide sequence shared across patients, even in the context of shared HLA haplotypes (4/5 patients shared HLA-A*02-01). This is consistent with prior studies of diagnostic biopsies describing a paucity of clones shared across patients. We observed greater repertoire overlap between sites within the GI tract compared to other tissues in a given patient, as measured by the Jensen Shannon Diversity (JSD) index, especially compared to the skin, another GVHD-affected tissue. Despite differences in global repertoires across tissues, some clones were shared across all samples for a given patient, with at least one clone present among the top twenty clones by frequency for each tissue with sufficient sampling. A strikingly similar pattern of repertoire sharing across tissues was observed in the TCR repertoires of a major and minor mouse model of GVHD. While tissues within the GI tract and mesenteric lymph nodes shared the most clones in the mice, there were also dominant clones shared across tissues outside the GI tract. Individual mice with GVHD had highly divergent repertoires from each other in spite of the markedly controlled setting including inbred mice with the same donor T cell pool for each transplant, consistent with the notion that T cells that mediate GVHD may be present at very low frequency in the pool of naïve T cells in the allograft. Conclusion: This work characterizes T cell repertoire in GVHD in human tissues that have not been previously available, including lymphoid tissues and small intestine samples. Combined with the mouse data, this study reveals the relationships between TCR repertoires across different tissues, highlighting the striking diversity of clones driving the GVHD process across tissues and individuals. Although some even dominant clones are shared across all tissues within an individual, each sampled site had a tissue-specific clonal composition. While GVHD-directed therapy focuses primarily on the inhibition of the T cells themselves, additional attention must be devoted to understanding the pattern of target tissue-specific antigen expression in order to identify the key drivers of GVHD. Disclosures Giardina: Seres Therapeutics: Other: salary support. Slingerland:Seres Therapeutics: Other: salary support. Jenq:Kaleido Biosciences: Membership on an entity's Board of Directors or advisory committees; Karius Dx: Speakers Bureau; Merck: Consultancy; MicrobiomeDx: Consultancy; Prolacta: Consultancy; Seres Therapeutics: Membership on an entity's Board of Directors or advisory committees, Patents & Royalties: January 1, 2040. Giralt:Sanofi: Membership on an entity's Board of Directors or advisory committees, Research Funding; PFIZER: Membership on an entity's Board of Directors or advisory committees, Research Funding; GSK: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Johnson & Johnson: Membership on an entity's Board of Directors or advisory committees, Research Funding; Actinuum: Other: Advisory board, Research Funding; BMS: Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Other: Advisory Board, Research Funding; KITE: Membership on an entity's Board of Directors or advisory committees; SPECTRUM Pharma: Membership on an entity's Board of Directors or advisory committees; Jensenn: Membership on an entity's Board of Directors or advisory committees, Research Funding; JAZZ Pharmaceutical: Membership on an entity's Board of Directors or advisory committees; MILTENYI: Research Funding; TAKEDA: Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Membership on an entity's Board of Directors or advisory committees; OMEROS: Research Funding. Perales:Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Omeros: Honoraria, Membership on an entity's Board of Directors or advisory committees; Medigene: Membership on an entity's Board of Directors or advisory committees, Other; Celgene: Honoraria; Bellicum: Honoraria, Membership on an entity's Board of Directors or advisory committees; Abbvie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Miltenyi Biotec: Research Funding; Kite/Gilead: Honoraria, Research Funding; Incyte Corporation: Honoraria, Research Funding; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees; MolMed: Membership on an entity's Board of Directors or advisory committees; NexImmune: Membership on an entity's Board of Directors or advisory committees; Cidara Therapeutics: Other; Nektar Therapeutics: Honoraria, Membership on an entity's Board of Directors or advisory committees; Merck: Consultancy, Honoraria; Servier: Membership on an entity's Board of Directors or advisory committees, Other; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees. Iacobuzio-Donahue:BMS: Research Funding. van den Brink:Seres Therapeutics: Consultancy, Patents & Royalties, Research Funding; DKMS Medical Council: Membership on an entity's Board of Directors or advisory committees; Forty-Seven, Inc: Consultancy; Juno Therapeutics: Patents & Royalties; WindMIL Therapeutics: Honoraria; Rheos: Honoraria; Pharmacyclics: Consultancy, Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy; Magenta: Honoraria; Kite Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees. Peled:Seres Therapeutics: Patents & Royalties, Research Funding; Davolterra: Consultancy.