Extended Data Fig. 6: Characterization of gene expression profiles in rectal biopsies in an Israeli cohort of PLWH and microbial profiles from stool samples of FMT- and PBS-treated mice.
(a) Study design. PLWH with low ( < 200 µl−1) and high ( ≥ 500 µl−1) peripheral blood CD4+ T cells and HC underwent endoscopy. A rectal biopsy for bulk RNA sequencing was collected. (b) Principal component analysis (PC) of transcriptomic profiles between the three groups. (c) Differentially expressed genes between the low and high group. Wald test with FDR correction (DESeq2). Dashed lines: p adjusted of 0.05. Differentially abundant genes are shown in color; black, non-differentially abundant genes. (d) PC analysis of microbial profiles from stool samples of FMT-treated mice and PBS-treated controls from two independent experiments. HC, healthy controls; high, PLWH with high peripheral blood CD4+ T cells ( ≥ 500 µl−1); low, PLWH with low peripheral blood CD4+ T cells ( < 200 µl−1); ns, not significant; PC, principal component; FC, fold change; PLWH, people living with human immunodeficiency virus; FMT, fecal microbiome transplantation; PBS, phosphate-buffered saline; Padj, adjusted P value.
