Single-cell Atlas of the Human Neonatal Small Intestine Affected by Necrotizing Enterocolitis

Overview

Journal PLoS Biol

Specialty Biology

Date 2023 May 19

PMID 37205711

Authors

Adi Egozi

Oluwabunmi Olaloye

Lael Werner

Tatiana Silva

Blake McCourt

Richard W Pierce

Xiaojing An

Fujing Wang

Kong Chen

Jordan S Pober

Dror Shouval

Shalev Itzkovitz

Liza Konnikova

Affiliations

Soon will be listed here.

Abstract

Necrotizing enterocolitis (NEC) is a gastrointestinal complication of premature infants with high rates of morbidity and mortality. A comprehensive view of the cellular changes and aberrant interactions that underlie NEC is lacking. This study aimed at filling in this gap. We combine single-cell RNA sequencing (scRNAseq), T-cell receptor beta (TCRβ) analysis, bulk transcriptomics, and imaging to characterize cell identities, interactions, and zonal changes in NEC. We find an abundance of proinflammatory macrophages, fibroblasts, endothelial cells as well as T cells that exhibit increased TCRβ clonal expansion. Villus tip epithelial cells are reduced in NEC and the remaining epithelial cells up-regulate proinflammatory genes. We establish a detailed map of aberrant epithelial-mesenchymal-immune interactions that are associated with inflammation in NEC mucosa. Our analyses highlight the cellular dysregulations of NEC-associated intestinal tissue and identify potential targets for biomarker discovery and therapeutics.

Citing Articles

Piezo1 promotes the progression of necrotizing enterocolitis by activating the Ca2(+)/CaMKII-dependent pathway.

Li Z, Jiang Q, Wei J, Dang D, Meng Z, Wu H Commun Biol. 2025; 8(1):417.

PMID: 40074811 PMC: 11904196. DOI: 10.1038/s42003-025-07821-6.

REGγ-mediated Barrier Disruption and NF-κB Activation Aggravates Intestinal Inflammation in Necrotizing Enterocolitis.

Li Y, Pan D, Liu H, Xie W, Li X, Mu X Inflammation. 2024; .

PMID: 39653983 DOI: 10.1007/s10753-024-02203-2.

Human Milk Supports Robust Intestinal Organoid Growth, Differentiation, and Homeostatic Cytokine Production.

Smith L, Santiago E, Eke C, Gu W, Wang W, Llivichuzhca-Loja D Gastro Hep Adv. 2024; 3(8):1030-1042.

PMID: 39529649 PMC: 11550179. DOI: 10.1016/j.gastha.2024.07.007.

The Human Milk-derived Peptide Drives Rapid Regulation of Macrophage Inflammation Responses in the Neonatal Intestine.

Yuan F, Han X, Huang M, Su Y, Zhang Y, Hu M Cell Mol Gastroenterol Hepatol. 2024; 19(2):101420.

PMID: 39414025 PMC: 11652890. DOI: 10.1016/j.jcmgh.2024.101420.

A spatial expression atlas of the adult human proximal small intestine.

Harnik Y, Yakubovsky O, Hoefflin R, Novoselsky R, Bahar Halpern K, Barkai T Nature. 2024; 632(8027):1101-1109.

PMID: 39112711 DOI: 10.1038/s41586-024-07793-3.

References

Dingle B, Liu Y, Fatheree N, Min J, Rhoads J, Tran D . FoxP3⁺ regulatory T cells attenuate experimental necrotizing enterocolitis. PLoS One. 2013; 8(12):e82963. PMC: 3867412. DOI: 10.1371/journal.pone.0082963. View

Anttila A, Kauppinen H, Koivusalo A, Heikkila P, Savilahti E, Rintala R . T-cell-mediated mucosal immunity is attenuated in experimental necrotizing enterocolitis. Pediatr Surg Int. 2003; 19(5):326-30. DOI: 10.1007/s00383-003-1004-7. View

Kaemmerer E, Schneider U, Klaus C, Plum P, Reinartz A, Adolf M . Increased levels of deleted in malignant brain tumours 1 (DMBT1) in active bacteria-related appendicitis. Histopathology. 2012; 60(4):561-9. DOI: 10.1111/j.1365-2559.2011.04159.x. View

Ivashkiv L, Donlin L . Regulation of type I interferon responses. Nat Rev Immunol. 2013; 14(1):36-49. PMC: 4084561. DOI: 10.1038/nri3581. View

Dantoft W, Martinez-Vicente P, Jafali J, Perez-Martinez L, Martin K, Kotzamanis K . Genomic Programming of Human Neonatal Dendritic Cells in Congenital Systemic and Cytomegalovirus Infection Reveal Plastic and Robust Immune Pathway Biology Responses. Front Immunol. 2017; 8:1146. PMC: 5622154. DOI: 10.3389/fimmu.2017.01146. View

Wittkopf N, Pickert G, Billmeier U, Mahapatro M, Wirtz S, Martini E . Activation of intestinal epithelial Stat3 orchestrates tissue defense during gastrointestinal infection. PLoS One. 2015; 10(3):e0118401. PMC: 4370566. DOI: 10.1371/journal.pone.0118401. View

Takahashi R, Nishimoto S, Muto G, Sekiya T, Tamiya T, Kimura A . SOCS1 is essential for regulatory T cell functions by preventing loss of Foxp3 expression as well as IFN-{gamma} and IL-17A production. J Exp Med. 2011; 208(10):2055-67. PMC: 3182063. DOI: 10.1084/jem.20110428. View

Ramilowski J, Goldberg T, Harshbarger J, Kloppmann E, Kloppman E, Lizio M . A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun. 2015; 6:7866. PMC: 4525178. DOI: 10.1038/ncomms8866. View

Crane M, Daley J, Van Houtte O, Brancato S, Henry Jr W, Albina J . The monocyte to macrophage transition in the murine sterile wound. PLoS One. 2014; 9(1):e86660. PMC: 3899284. DOI: 10.1371/journal.pone.0086660. View

10.

Holman R, Stoll B, Clarke M, Glass R . The epidemiology of necrotizing enterocolitis infant mortality in the United States. Am J Public Health. 1998; 87(12):2026-31. PMC: 1381250. DOI: 10.2105/ajph.87.12.2026. View

11.

Raffin C, Pignon P, Celse C, Debien E, Valmori D, Ayyoub M . Human memory Helios- FOXP3+ regulatory T cells (Tregs) encompass induced Tregs that express Aiolos and respond to IL-1β by downregulating their suppressor functions. J Immunol. 2013; 191(9):4619-27. DOI: 10.4049/jimmunol.1301378. View

12.

Xia X, Wang D, Yu L, Wang B, Wang W, Jiao C . Activated M1 macrophages suppress c-kit expression via TNF-α-mediated upregulation of miR-222 in Neonatal Necrotizing Enterocolitis. Inflamm Res. 2021; 70(3):343-358. DOI: 10.1007/s00011-021-01441-6. View

13.

Konnikova L, Boschetti G, Rahman A, Mitsialis V, Lord J, Richmond C . High-dimensional immune phenotyping and transcriptional analyses reveal robust recovery of viable human immune and epithelial cells from frozen gastrointestinal tissue. Mucosal Immunol. 2018; 11(6):1684-1693. PMC: 6512331. DOI: 10.1038/s41385-018-0047-y. View

14.

Xin H, Lian Q, Jiang Y, Luo J, Wang X, Erb C . GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing. Genome Biol. 2020; 21(1):188. PMC: 7393741. DOI: 10.1186/s13059-020-02084-2. View

15.

Yin Y, Liu F, Li Y, Tang R, Wang J . mRNA expression of TLR4, TLR9 and NF-κB in a neonatal murine model of necrotizing enterocolitis. Mol Med Rep. 2016; 14(3):1953-6. PMC: 4991741. DOI: 10.3892/mmr.2016.5455. View

16.

Marischen L, Englert A, Schmitt A, Einsele H, Loeffler J . Human NK cells adapt their immune response towards increasing multiplicities of infection of Aspergillus fumigatus. BMC Immunol. 2018; 19(1):39. PMC: 6299526. DOI: 10.1186/s12865-018-0276-6. View

17.

Gaffen S, Jain R, Garg A, Cua D . The IL-23-IL-17 immune axis: from mechanisms to therapeutic testing. Nat Rev Immunol. 2014; 14(9):585-600. PMC: 4281037. DOI: 10.1038/nri3707. View

18.

Neu J, Walker W . Necrotizing enterocolitis. N Engl J Med. 2011; 364(3):255-64. PMC: 3628622. DOI: 10.1056/NEJMra1005408. View

19.

Tubau-Juni N, Bassaganya-Riera J, Leber A, Zoccoli-Rodriguez V, Kronsteiner B, Viladomiu M . Identification of new regulatory genes through expression pattern analysis of a global RNA-seq dataset from a Helicobacter pylori co-culture system. Sci Rep. 2020; 10(1):11506. PMC: 7359330. DOI: 10.1038/s41598-020-68439-8. View

20.

Jia H, Sodhi C, Yamaguchi Y, Lu P, Ladd M, Werts A . Toll Like Receptor 4 Mediated Lymphocyte Imbalance Induces Nec-Induced Lung Injury. Shock. 2018; 52(2):215-223. PMC: 6387863. DOI: 10.1097/SHK.0000000000001255. View