Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation

Abstract

Environmental enteropathy (EE) is a subclinical condition of the small intestine that is highly prevalent in low- and middle-income countries. It is thought to be a key contributing factor to childhood malnutrition, growth stunting, and diminished oral vaccine responses. Although EE has been shown to be the by-product of a recurrent enteric infection, its full pathophysiology remains unclear. Here, we mapped the cellular and molecular correlates of EE by performing high-throughput, single-cell RNA-sequencing on 33 small intestinal biopsies from 11 adults with EE in Lusaka, Zambia (eight HIV-negative and three HIV-positive), six adults without EE in Boston, United States, and two adults in Durban, South Africa, which we complemented with published data from three additional individuals from the same clinical site. We analyzed previously defined bulk-transcriptomic signatures of reduced villus height and decreased microbial translocation in EE and showed that these signatures may be driven by an increased abundance of surface mucosal cells—a gastric-like subset previously implicated in epithelial repair in the gastrointestinal tract. In addition, we determined cell subsets whose fractional abundances associate with EE severity, small intestinal region, and HIV infection. Furthermore, by comparing duodenal EE samples with those from three control cohorts, we identified dysregulated WNT and MAPK signaling in the EE epithelium and increased proinflammatory cytokine gene expression in a T cell subset highly expressing a transcriptional signature of tissue-resident memory cells in the EE cohort. Together, our work elucidates epithelial and immune correlates of EE and nominates cellular and molecular targets for intervention.

Direct therapeutic effect of sulfadoxine-pyrimethamine on nutritional deficiency-induced enteric dysfunction in a human Intestine Chip

“… 5 , 20 For example, inflammatory diseases such as inflammatory bowel disease (IBD) are associated with certain antimicrobial genes like DUOX2 and DUOXA2, and elevated DUOX2 levels in the intestine often indicate increased inflammation and mucosal dysbiosis. 21 , 22 We observed that exposure to ND in healthy donors did not dramatically alter to the expression of these genes. This is interesting because it may indicate that short-term malnutrition might not be sufficient to induce significant changes in those genes compared to chronic conditions like those observed in EED and IBD patients.…”

An ecological study of the association between childhood stunting, water, sanitation, and protein access, 2001-20

“…Underlying this issue is our previously limited understanding of the pathophysiology of this condition, which has been expanding by leaps and bounds in the last decade. Recent work has highlighted in both pre-clinical studies and clinical trials the potential value of amino acid supplementation 18,19,21,27 , and the potentially core contribution of deficient animal protein intake, and our work demonstrates that this is highly likely to be a major contributing factor in EE and the stunting syndrome.…”

“…Mechanistic work attempting to recapitulate the EE phenotype has also noted a requirement for protein/amino acid deficiency: both murine and gut-on-a-chip culture work demonstrate that deficiency in amino acids, especially tryptophan, is necessary to generate the appropriate phenotype 17,18 . Translational work looking at adults with EE have similar findings: a recent study using single cell RNA sequencing of Zambian adults with EE noted deficiency of tryptophan, which as a precursor of serotonin and a modulator of indolamine 2-3 dioxygenase (IDO), a substantial immune activity and epithelial regulator, whose activity as documented by kynurenine/tryptophan ratio is directly associated with growth outcomes [19][20][21][22][23][24][25][26] . The aggregate evidence suggests a key mechanistic component of EE disease formation may be driven or reflected by absence of animal protein intake with resulting amino acid deficiency, particularly tryptophan deficiency.…”

Potential determinants of low circulating glucagon‐like peptide 2 concentrations in Zambian children with non‐responsive stunting

“…EECs are part of a population of rarer cell types that play crucial roles in tissue maintenance but cannot always be detected by bulk RNA sequencing as they only make up 1% of all epithelial cells. Single cell transcriptomics may be a better way of detecting the presence of such rarefied gene transcripts (Kummerlowe et al., 2022 ).…”