Researchers Use Single-Cell RNA-Sequencing to Better Understand Gut Inflammation Associated With Malnutrition

Sep 1, 2022

Brooklyn, NY— Environmental enteropathy (EE), or gut inflammation due to environmental factors, is thought to be a major contributor to growth stunting, malnutrition, and reduced oral vaccine responses in millions of children and adults in low-resource settings.  The condition is often regarded as secondary to other issues such as frequent intestinal infections and poor access to sanitation infrastructure and clean water. While it is appreciated that gut inflammation can occur due to exposure to contaminated food or water, causing changes that make it difficult for children to absorb nutrients from food properly, exactly what those changes are at a cellular and molecular level remains poorly understood. In a recent paper in Science Translational Medicine, researchers at the Ragon Institute of MGH, MIT and Harvard; University Teaching Hospital Lusaka, Zambia; Queen Mary University of London; the University of California, San Francisco; and SUNY Downstate Health Sciences University used single-cell profiling to define the impact on the intestine of exposure to adverse environmental conditions in a disadvantaged community in Lusaka, Zambia. Their work provides a roadmap for future EE intervention studies.

The researchers examined 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, USA, and two adults in Durban, South Africa. They also incorporated published data on three additional individuals from the Durban site. They used single-cell RNA-sequencing, a technique that profiles the RNA levels of individual cells to better understand their characteristics and functions, to help uncover differences seen in the gut of individuals with EE. 

“Environmental enteropathy is in many ways a perfect application for single-cell RNA-sequencing,” says Conner Kummerlowe, PhD, a postdoctoral researcher at the Ragon Institute and lead author of the paper, adding that the condition has been systematically understudied. “To be able to just really unbiasedly go in and see what’s happening in this condition that’s poorly understood is really powerful.”

Previous research that analyzed EE biopsies histologically showed that in the small intestines of those with EE, the villi — structures that absorb nutrients from food — are shorter. It was also found that the gut’s barrier functions are responding in a pattern that resembles an attempt to keep harmful bacteria out, but which has the side effect of preventing nutrient absorption. In the new study, the researchers found evidence that this may be due to gut intestinal epithelial cells differentiating into surface mucosal cells – mucus-secreting cells normally found in the stomach help to protect against acid-associated damage. Furthermore, the team observed that these cells express antimicrobial genes including DUOX2, which had previously been described as a key marker of EE.

Surface mucosal cells are normally not found in the small intestine. One theory the researchers have is that mucosal cells may build up on the tips of the villi during wound-healing responses to infections from commonly occurring bacteria such as Helicobacter pylori. 

“The real power of methods like single-cell RNA-sequencing is that they take a global view of disease processes at the level at which biology operates – the level of the cell. Here, this let us identify unexpected cellular behaviors that we may be able to target to improve nutrient absorption,” says Alex K. Shalek, PhD, co-senior author of the paper and a Member of the Ragon Institute. Shalek is also a Core Member of the Institute for Medical Engineering and Science (IMES), an Associate Professor of Chemistry, and an Extramural Member of the Koch Institute at MIT, as well as an Institute Member of and member of the Broad Institute of Harvard and MIT.

By comparing EE samples with control cohorts, they also identified dysregulated WNT and MAPK cell signaling pathways and increased expression of proinflammatory genes in a subset of memory T cells. “Comparing these cell profiles allowed us to identify perturbations in absorptive cell replication and differentiation alongside specific changes in tissue resident memory T cells. These changes align with known defects in the function of the intestine in individuals with EE,” says Paul Kelly, MD, Professor of Tropical Gastroenterology at Queen Mary University of London and co-senior author of the study. 

The researchers also studied the potential impact of HIV infection and antiretroviral treatment on the pathology of EE. They found that samples from HIV+ individuals had higher EE severity and that there were telltale signs of HIV infection expressed in the duodenal bulb, the part of the small intestine located closest to the stomach.

The work identifies correlates of EE that may be cellular and molecular targets for intervention in the future. “Our findings have identified multiple possible therapeutic and prophylactic approaches, as well as suggested possible mechanisms to explain the efficacy of prior interventions that showed benefit,” says Thomas Wallach, MD, physician-scientist and pediatric gastroenterologist at SUNY Downstate Health Sciences University and co-senior author, who completed the research as a pediatric gastroenterology fellow at the University of California, San Francisco Medical Center. He further noted “our observation of signals linked with immune tolerance may also shed light onto mechanisms underlying the hygiene hypothesis,” a possible explanation of the relative rarity of autoimmune and allergic diseases in low-middle income countries.

This research was supported in part by grants from Barts and the London Charity, the Bill & Melinda Gates Foundation (OPP1066118), the NIH (5U24AI118672, DK007762, F30-AI143160-01A1, F32DK128872, R01DK126545, and R01GM135462), the HHMI Damon Runyon Cancer Research Foundation Fellowship (DRG-2274-16), the AGA Research Foundation’s AGA-Takeda Pharmaceuticals Research Scholar Award in IBD (AGA2020-13-01), the HDDC Pilot and Feasibility (P30 DK034854), the Wellcome Trust (202485/Z/16/Z and 201433/A/16/A), the Searle Scholars Program, the Beckman Young Investigator Program, Sloan Research Fellowship in Chemistry, the Ragon Institute, the Richard and Susan Smith Family Foundation, the Food Allergy Science Initiative, the Leona M. and Harry B. Helmsley Charitable Trust, the Pew Charitable Trusts Biomedical Scholars, and the New York Stem Cell Foundation.

About the Ragon Institute of MGH, MIT and Harvard

The Ragon Institute of MGH, MIT and Harvard was established in 2009 with a gift from the Phillip T. and Susan M. Ragon Foundation, with a collaborative scientific mission among these institutions to harness the immune system to combat and cure human diseases. Focusing on global infectious diseases, the Ragon Institute draws scientists, clinicians and engineers from diverse backgrounds and areas of expertise to study and understand the immune system with the goal of benefiting patients. For more information, visit

About University Teaching Hospital Lusaka
The vision of UTH is to be the center of excellence for health care in the country and the region by providing innovative treatment interventions through ongoing research, while the mission statement is to provide affordable quality health care; function as a referral center; train health care providers; conduct research to find solutions to existing health problems and for the development of science. In conformity with its mission statement, the hospital directs its efforts toward research, improving general medical services and to function as a tertiary health care institution. While recognizing that tertiary care services are highly specialized and expensive to provide, the challenge for the institution has been to reduce the expense of treatment abroad by offering such services locally. Over a period of time, the institution has built capacity in various areas of specialization such as cardiology; cardiac surgery, ART, PMTCT, ophthalmology, ENT, urology, orthopedics and pulmonary medicine.
About Queen Mary University of London

At Queen Mary University of London, we believe that a diversity of ideas helps us achieve the previously unthinkable. Throughout our history, we’ve fostered social justice and improved lives through academic excellence. And we continue to live and breathe this spirit today, not because it’s simply “the right thing to do” but for what it helps us achieve and the intellectual brilliance it delivers. Our reformer heritage informs our conviction that great ideas can and should come from anywhere. It’s an approach that has brought results across the globe, from the communities of east London to the favelas of Rio de Janeiro. We continue to embrace diversity of thought and opinion in everything we do, in the belief that when views collide, disciplines interact, and perspectives intersect, truly original thought takes form. 

About the University of California, San Francisco

The University of California, San Francisco (UCSF), one of the ten campuses of the University of California, is devoted solely to graduate education and research in the health sciences. In both size and number of students, UCSF is the smallest of the UC campuses. Nevertheless, its relative size belies its distinction as one of the leading biomedical research and health science education centers in the world. In addition, UCSF is a major health care delivery center in northern California with a high volume of regional, national, and international patient referrals. In keeping with our overarching mission of advancing health worldwide, UCSF is devoted at every level to serving the public. Over the last century, the original nucleus of affiliated academic schools and divisions (now the Schools of Medicine, Pharmacy, and Dentistry) has grown to include a School of Nursing and a Graduate Division. UCSF is one of the leading biomedical research and graduate education centers in the world, and it ranks in the top group of institutions of higher learning in total federal funding for research and training. UCSF has an annual budget of over $7 billion to support its various research, teaching, and patient care activities. We are committed to serving as an anchor institution, leveraging this budget as well as substantial human and intellectual resources to improve the long-term health and social welfare of San Francisco.


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About SUNY Downstate Health Sciences University

SUNY Downstate Health Sciences University is the borough's only academic medical center for health education, research, and patient care. It is a 342-bed facility serving the healthcare needs of New York City and Brooklyn's 2.6 million residents. University Hospital of Brooklyn (UHB) is Downstate's teaching hospital, backed by an outstanding medical school's expertise and world-class academic center research facilities. More than 800 physicians, representing 53 specialties and subspecialties—many of them ranked as tops in their fields—comprise Downstate's staff.

In addition to high-risk neonatal and infant services, pediatric nephrology, and dialysis (kidney diseases)—and offering the only kidney transplantation program in Brooklyn, among many other distinctive programs—Downstate also sponsors a major learning center for young children with developmental disorders and disabilities. In addition to UHB, Downstate comprises a College of Medicine, College of Nursing, School of Health Professions, a School of Graduate Studies, a School of Public Health, and a multifaceted biotechnology initiative, including the Downstate Biotechnology Incubator and BioBAT for early-stage and more mature companies, respectively. For more information, visit or follow us on Twitter at @sunydownstate.