Spatial Transcriptomics of Tissue-Based Immune Response to Acute Graft-Versus-Host Disease of the Lower Gastrointestinal Tract

Background: Corticosteroid resistant acute graft-versus-host disease (GVHD) of the lower gastrointestinal (GI) tract is a leading cause of morbidity and mortality after allogeneic hematopoietic cell transplantation. We hypothesized that distinct gene expression profiles exist within affected GI tissue at GVHD diagnosis and may be associated with treatment outcomes.

Methods: Unstained tissue sections from 33 patients with biopsy-confirmed acute lower GI GVHD were used for spatial transcriptomics using the NanoString GeoMx^TM Digital Spatial Profiler (DSP) platform. Fluorescent morphology markers (PanCK, CD45 and CD31) were used to visualize the epithelial, immune and endothelial compartments and guide capture of RNA expression profiles using the GeoMx^TM Human Whole Transcriptome Atlas (18,676 genes). A total of 739 areas of interest (AOIs) were sampled across the 33 patients with a total of 57,960 immune, 37,610 epithelial, and 2298 vascular endothelial cells analyzed (average of 1756.4 immune, 1139.7 epithelial and 69.6 endothelial cells per case). The gene specific oligos were quantified using Illumina's i5 x i7 dual-indexing system and sequenced on the Illumina NextSeq 500 using a 2 x 75 MidOutput v2.5 flow cell. The FASTQ files were processed to generate target probe-specific count files and saved in DCC format. Gene expression files were normalized per NanoString protocol. All unsupervised clustering and differential expression were done in Bioconductor in the R statistical computing space.

Results: The gene expression data for each AOI of immune, epithelial, and endothelial cells were normalized and the top 500 most variable genes were used for unsupervised hierarchical clustering to obtain an unbiased classification of different subtypes. There were two clear major AOI clusters for each of the cellular compartments with immune clustering shown in Figure 1A. The left immune cluster (IC1) and the right immune cluster (IC2) were then evaluated for association with clinical GVHD outcomes. IC1 had an over-representation of patients with steroid sensitive GVHD (Fisher exact p value = <0.0001) and AOIs with low grade pathology (Fisher exact p value = 0.031). To obtain gene level differences between IC1 and IC2, differential expression was performed using a Wilcoxon Rank Sum test and volcano plots were generated to illustrate the most differentially expressed genes across the visual AOI-based clusters (Figure 1B). Genes with an adjusted p-value of 0.05 for association with the particular arm of the volcano plot and at least a 2-fold change over the other cluster were considered significant. Gene set enrichment analysis (GSEA) using curated datasets from MSigDB was performed and identified that IC1 genes were enriched for IFNγ response (q value = 2.99e^-5), TNFα signaling (q value = 2.99e^-5) and inflammatory response (q value = 0.0063). These IC1 differentially expressed genes included CD74 (835 vs. 361.6 mean normalized gene transcripts), LYZ, β2-microglobulin, C1QB and CD68. IC2, on the other hand, had a prominent exhausted/immunosuppressive signature significantly enriched for Th17 cell genes (q value = 0.027) by GSEA. Notable genes that were statistically significant were FCF1 (152.3 vs. 74 mean normalized transcripts) and USP17L11 (78.3 vs. 36.4 mean normalized transcripts). Extension of this analysis to the epithelial (EC) and vascular endothelial (VC) cell compartments also identified distinct clustering with both having an inflamed (EC1 and VC1) and a basal-like state (EC2 and VC2). Interestingly, the inflamed epithelial cells (EC2) associated with immunosuppressive IC2 immune cells (Fisher exact p-value = 0.006), but inflamed vascular endothelium (VC1) associated with the pro-inflammatory IC1 immune cells (Fisher exact p-value = 0.0005).

Conclusion: Spatial transcriptomics provides high resolution gene expression profiles in distinct cellular compartments in human acute GI GVHD samples and provides a better understanding of the relationship of the immune response with epithelial and vascular endothelial cell phenotypes. Initial analysis demonstrates that an inflammatory immune signature is associated with steroid responsive acute GI GVHD and an exhausted phenotype with steroid resistance. Future studies are needed to confirm the predictive value of specific gene expression profiles as biomarkers of corticosteroid response at diagnostic biopsy.

Ting:ROME Therapeutics: Consultancy, Divested equity in a private or publicly-traded company in the past 24 months; Tekla Capital: Consultancy; Ikena Oncology: Consultancy; Foundation Medicine, Inc.: Consultancy; NanoString Technologies: Consultancy; Pfizer: Consultancy; PanTher Therapeutics: Divested equity in a private or publicly-traded company in the past 24 months; TellBio Inc: Divested equity in a private or publicly-traded company in the past 24 months; ACD-Biotechne: Other: Research Support; PureTech Health LLC: Other: Research support; Ribon Therapeutics: Other: Research support; Massachusetts General Hospital: Other: interests were reviewed and are managed by MGH; Mass General Brigham: Other: interests were reviewed and are managed by mgb. Chen:Gamida Cell: Consultancy; Equillium: Consultancy; Celularity: Consultancy; Actimium: Consultancy; Incyte: Consultancy; Jasper: Consultancy; Novartis: Consultancy. Defilipp:Omeros: Consultancy; Kadmon: Consultancy; Syndax Pharmaceuticals: Consultancy; Taiho Oncology: Research Funding; Regimmune: Research Funding; Incyte: Consultancy, Research Funding.