Functional screen of inflammatory bowel disease genes reveals key epithelial functions

Genome Med. 2021 Nov 11;13(1):181. doi: 10.1186/s13073-021-00996-7.

Abstract

Background: Genetic studies have been tremendously successful in identifying genomic regions associated with a wide variety of phenotypes, although the success of these studies in identifying causal genes, their variants, and their functional impacts has been more limited.

Methods: We identified 145 genes from IBD-associated genomic loci having endogenous expression within the intestinal epithelial cell compartment. We evaluated the impact of lentiviral transfer of the open reading frame (ORF) of these IBD genes into the HT-29 intestinal epithelial cell line via transcriptomic analyses. By comparing the genes in which expression was modulated by each ORF, as well as the functions enriched within these gene lists, we identified ORFs with shared impacts and their putative disease-relevant biological functions.

Results: Analysis of the transcriptomic data for cell lines expressing the ORFs for known causal genes such as HNF4a, IFIH1, and SMAD3 identified functions consistent with what is already known for these genes. These analyses also identified two major clusters of genes: Cluster 1 contained the known IBD causal genes IFIH1, SBNO2, NFKB1, and NOD2, as well as genes from other IBD loci (ZFP36L1, IRF1, GIGYF1, OTUD3, AIRE and PITX1), whereas Cluster 2 contained the known causal gene KSR1 and implicated DUSP16 from another IBD locus. Our analyses highlight how multiple IBD gene candidates can impact on epithelial structure and function, including the protection of the mucosa from intestinal microbiota, and demonstrate that DUSP16 acts a regulator of MAPK activity and contributes to mucosal defense, in part via its regulation of the polymeric immunoglobulin receptor, involved in the protection of the intestinal mucosa from enteric microbiota.

Conclusions: This functional screen, based on expressing IBD genes within an appropriate cellular context, in this instance intestinal epithelial cells, resulted in changes to the cell's transcriptome that are relevant to their endogenous biological function(s). This not only helped in identifying likely causal genes within genetic loci but also provided insight into their biological functions. Furthermore, this work has highlighted the central role of intestinal epithelial cells in IBD pathophysiology, providing a scientific rationale for a drug development strategy that targets epithelial functions in addition to the current therapies targeting immune functions.

Keywords: Inflammatory bowel diseases; Mucosal immunity; Secretory immunoglobulins; Type I interferon response.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • AIRE Protein
  • Butyrate Response Factor 1 / genetics
  • Carrier Proteins / genetics
  • Dual-Specificity Phosphatases / genetics
  • Epithelial Cells / metabolism
  • Gastrointestinal Microbiome
  • HEK293 Cells
  • Humans
  • Immunoglobulins
  • Inflammatory Bowel Diseases / genetics*
  • Inflammatory Bowel Diseases / metabolism*
  • Interferon Regulatory Factor-1 / genetics
  • Intestinal Mucosa / metabolism
  • Intestines
  • Mitogen-Activated Protein Kinase Phosphatases / genetics
  • Paired Box Transcription Factors / genetics
  • Protein Kinases / genetics
  • Transcription Factors / genetics
  • Transcriptome
  • Ubiquitin-Specific Proteases / genetics

Substances

  • Butyrate Response Factor 1
  • Carrier Proteins
  • GIGYF1 protein, human
  • IRF1 protein, human
  • Immunoglobulins
  • Interferon Regulatory Factor-1
  • Paired Box Transcription Factors
  • Transcription Factors
  • ZFP36L1 protein, human
  • homeobox protein PITX1
  • Protein Kinases
  • KSR-1 protein kinase
  • Mitogen-Activated Protein Kinase Phosphatases
  • DUSP16 protein, human
  • Dual-Specificity Phosphatases
  • OTUD3 protein, human
  • Ubiquitin-Specific Proteases