American Association for Cancer Research
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FIGURE 2 from Multi-omics Analysis of a Fecal Microbiota Transplantation Trial Identifies Novel Aspects of Acute GVHD Pathogenesis

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posted on 2024-06-10, 14:20 authored by Armin Rashidi, Maryam Ebadi, Tauseef U. Rehman, Heba Elhusseini, David Kazadi, Hossam Halaweish, Mohammad H. Khan, Andrea Hoeschen, Qing Cao, Xianghua Luo, Amanda J. Kabage, Sharon Lopez, Sivapriya Ramamoorthy, Shernan G. Holtan, Daniel J. Weisdorf, Alexander Khoruts, Christopher Staley

Microbiota clusters and aGVHD risk. A, Principal coordinates analysis of early post-FMT/placebo gut microbiota using topic model-based cluster abundances, with groups defined according to treatment arm. B, Same analysis as in A, but with groups defined according to subsequent development of grade II–IV aGVHD or not. C, Comparison between early post-FMT versus early post-placebo samples in topic model-based cluster abundances. D, Same analysis as in C, but with groups defined based on the occurrence of subsequent grade II–IV aGVHD. Samples are early post-FMT/placebo. E, Principal coordinates analysis of pre-FMT/placebo gut microbiota using topic model-based cluster abundances, with groups defined according to GVHD prophylaxis. P values in A, B, and E are from an adonis test with 999 permutations, with percent variation explained by each axis is shown in parentheses. 95% ellipses are shown. P values in C are from a Wilcoxon test after Bonferroni correction. Comparisons in D were not statistically significant. In C and D, each box shows the median (horizontal middle line) and interquartile range. Whisker lines indicate nonoutlier maximum and minimum values. A small jitter is included for better visualization. aGVHD: acute graft-versus-host disease; FMT: fecal microbiota transplantation; PC: principal coordinate; PTCy: posttransplantation cyclophosphamide.


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UMN | Clinical and Translational Science Institute, University of Minnesota (CTSI)

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Acute GVHD (aGVHD) is a major complication of allogeneic hematopoietic cell transplantation (alloHCT) associated with gut microbiota disruptions. However, whether therapeutic microbiota modulation prevents aGVHD is unknown. We conducted a randomized, placebo-controlled trial of third-party fecal microbiota transplantation (FMT) administered at the peak of microbiota injury in 100 patients with acute myeloid leukemia receiving induction chemotherapy and alloHCT recipients. Despite improvements in microbiome diversity, expansion of commensals, and shrinkage of potential pathogens, aGVHD occurred more frequently after FMT than placebo. Although this unexpected finding could be explained by clinical differences between the two arms, we asked whether a microbiota explanation might be also present. To this end, we performed multi-omics analysis of preintervention and postintervention gut microbiome and serum metabolome. We found that postintervention expansion of Faecalibacterium, a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, predicted a higher risk for aGVHD. Faecalibacterium expansion occurred predominantly after FMT and was due to engraftment of unique donor taxa, suggesting that donor Faecalibacterium-derived antigens might have stimulated allogeneic immune cells. Faecalibacterium and ursodeoxycholic acid (an anti-inflammatory secondary bile acid) were negatively correlated, offering an alternative mechanistic explanation. In conclusion, we demonstrate context dependence of microbiota effects where a normally beneficial bacteria may become detrimental in disease. While FMT is a broad, community-level intervention, it may need precision engineering in ecologically complex settings where multiple perturbations (e.g., antibiotics, intestinal damage, alloimmunity) are concurrently in effect. Post-FMT expansion of Faecalibacterium, associated with donor microbiota engraftment, predicted a higher risk for aGVHD in alloHCT recipients. Although Faecalibacterium is a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, our findings suggest that it may become pathogenic in the setting of FMT after alloHCT. Our results support a future trial with precision engineering of the FMT product used as GVHD prophylaxis after alloHCT.