{"doi":"10.1101/2020.07.31.231308","title":"Transcriptional Atlas of Ileal-Anal Pouch Immune Cells from Ulcerative Colitis Patients","abstract":"ABSTRACT How the human intestinal immune system is distinctly organized to respond to inflammation is still poorly understood. Here, we used single-cell RNA-sequencing to examine lamina propria CD45+ hematopoietic cells from patients with inflammatory bowel disease that have undergone ileal pouch-anal anastomosis, or the colon mucosa of ulcerative colitis patients. We identified a population of IL1B + antimicrobial macrophages and FOXP3 /+ BATF + T cells that are associated and expanded in inflamed tissues, which we further validated in other scRNA-seq datasets from IBD patients. CD8+ T cells were unexpectedly more abundant in the pouch than colon. Cell type specific markers obtained from single-cell RNA-sequencing was used to infer representation from bulk RNA sequencing datasets, which further implicated antimicrobial macrophages expressing IL1B with S100A8/A9 calprotectin as being associated with inflammation, as well as Bacteroides and Escherichia bacterial species. Finally, we find that non-responsiveness to anti-integrin biologic therapies in UC patients is associated with the signature of this antimicrobial macrophage population in a subset of patients. This study identified conserved and distinct features of intestinal inflammation between parts of the small and large intestine undergoing similar inflammation conditions.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":130579,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9078,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":345072,"name":"Jordan E. Axelrad","orcid":"0000-0003-1951-7790","position":1,"is_corresponding":false},{"id":290357,"name":"Ashley M. Hine","orcid":null,"position":2,"is_corresponding":false},{"id":583842,"name":"Shannon Chang","orcid":null,"position":3,"is_corresponding":false},{"id":583290,"name":"Suparna A. Sarkar","orcid":"0000-0002-3114-3173","position":4,"is_corresponding":false},{"id":253549,"name":"Jian-Da Lin","orcid":"0000-0003-3697-4766","position":5,"is_corresponding":false},{"id":2201,"name":"Kelly V. Ruggles","orcid":"0000-0002-0152-0863","position":6,"is_corresponding":false},{"id":288836,"name":"David Hudesman","orcid":"0000-0001-8318-5271","position":7,"is_corresponding":false},{"id":241178,"name":"Ken Cadwell","orcid":"0000-0002-5860-0661","position":8,"is_corresponding":false},{"id":253555,"name":"P’ng Loke","orcid":"0000-0002-6211-3292","position":9,"is_corresponding":false},{"id":253551,"name":"Joseph C. Devlin","orcid":"0000-0002-0003-4812","position":0,"is_corresponding":true}],"reference_count":71,"raw_metadata":null,"created_at":"2026-07-18T23:15:56.698770Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}