Study of Environmental Enteropathy and Malnutrition (SEEM) in Pakistan: protocols for biopsy based biomarker discovery and validation

Najeeha T Iqbal, Sana Syed, Kamran Sadiq, Marium N Khan, Junaid Iqbal, Jennie Z Ma, Fayaz Umrani, Sheraz Ahmed, Elizabeth A Maier, Lee A Denson, Yael Haberman, Monica M McNeal, Kenneth D R Setchell, Xueheng Zhao, Shahida Qureshi, Lanlan Shen, Christopher A Moskaluk, Ta-Chiang Liu, Omer Yilmaz, Donald E Brown, Michael J Barratt, Vanderlene L Kung, Jeffrey I Gordon, Sean R Moore, S Asad Ali, Najeeha T Iqbal, Sana Syed, Kamran Sadiq, Marium N Khan, Junaid Iqbal, Jennie Z Ma, Fayaz Umrani, Sheraz Ahmed, Elizabeth A Maier, Lee A Denson, Yael Haberman, Monica M McNeal, Kenneth D R Setchell, Xueheng Zhao, Shahida Qureshi, Lanlan Shen, Christopher A Moskaluk, Ta-Chiang Liu, Omer Yilmaz, Donald E Brown, Michael J Barratt, Vanderlene L Kung, Jeffrey I Gordon, Sean R Moore, S Asad Ali

Abstract

Background: Environmental Enteropathy (EE), characterized by alterations in intestinal structure, function, and immune activation, is believed to be an important contributor to childhood undernutrition and its associated morbidities, including stunting. Half of all global deaths in children < 5 years are attributable to under-nutrition, making the study of EE an area of critical priority.

Methods: Community based intervention study, divided into two sub-studies, 1) Longitudinal analyses and 2) Biopsy studies for identification of EE features via omics analyses. Birth cohorts in Matiari, Pakistan established: moderately or severely malnourished (weight for height Z score (WHZ) < - 2) children, and well-nourished (WHZ > 0) children. Blood, urine, and fecal samples, for evaluation of potential biomarkers, will be collected at various time points from all participants (longitudinal analyses). Participants will receive appropriate educational and nutritional interventions; non-responders will undergo further evaluation to determine eligibility for further workup, including upper gastrointestinal endoscopy. Histopathological changes in duodenal biopsies will be compared with duodenal biopsies obtained from USA controls who have celiac disease, Crohn's disease, or who were found to have normal histopathology. RNA-Seq will be employed to characterize mucosal gene expression across groups. Duodenal biopsies, luminal aspirates from the duodenum, and fecal samples will be analyzed to define microbial community composition (omic analyses). The relationship between histopathology, mucosal gene expression, and community configuration will be assessed using a variety of bioinformatic tools to gain better understanding of disease pathogenesis and to identify mechanism-based biomarkers. Ethical review committees at all collaborating institutions have approved this study. All results will be made available to the scientific community.

Discussion: Operational and ethical constraints for safely obtaining intestinal biopsies from children in resource-poor settings have led to a paucity of human tissue-based investigations to understand and reverse EE in vulnerable populations. Furthermore, EE biomarkers have rarely been correlated with gold standard histopathological confirmation. The Study of Environmental Enteropathy and Malnutrition (SEEM) is designed to better understand the pathophysiology, predictors, biomarkers, and potential management strategies of EE to inform strategies to eradicate this debilitating pathology and accelerate progress towards the 2030 Sustainable Development Goals.

Trial registration: Retrospectively registered; clinicaltrials.gov ID NCT03588013 .

Keywords: Childhood undernutrition; Duodenal biopsies; Endoscopy; Environmental enteropathy; Gut barrier function; Low- middle income countries; Mucosal gene expression; Small intestinal microbiota.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Conceptual framework for hypothesis testing in SEEM. The severity of clinical phenotypes in Matiari children with wasting and suboptimal response to nutritional rehabilitation will highly correlate with the histopathological appearance of duodenal biopsies; duodenal and fecal dysbiosis; perturbation of duodenal gene expression profiles; systemic biochemical profiles; and children’s genotypes. The image in the top right panel demonstrates the histological changes observed in the small intestine as environmental enteropathy progresses. Note: L:R lactulose:rhamnose ratio, EE environmental enteropathy, GI gastrointestinal, HLA Human Leukocyte Antigen
Fig. 2
Fig. 2
SEEM Data Collection Process. Note: CHW community health workers, UGI upper GI, WHZ weight for height Z score
Fig. 3
Fig. 3
SEEM transcriptome/genetics/biomarkers/microbiome framework at the time of endoscopy. a Is a detailed description of how samples will be collected throughout the study process from the birth cohorts; b Shows the groups, samples, and planned analyses at the time of endoscopy. Note for a: WHZ Weight-for-Height Z score, RF  Random Forest, EGD Esophagogastroduodenoscopy, infants* = 0 — 3 months old. Note for b: SEEM Study of Environmental Enteropathy and Malnutrition, CCHMC Cincinnati Children’s Hospital Medical Center, IBD Inflammatory Bowel Disease, CBC complete blood count, CRP C-Reactive Protein, EE Environmental Enteropathy, * = with a preference to enroll children under 5 years of age
Fig. 4
Fig. 4
Framework of data flow in SEEM. Description of how data will be transferred between institutions and a summary of the samples/analyses conducted at each institute. Note: AKU Aga Khan University, L:R Lactulose:Rhamnose ratio, Bx biopsy, EE Environmental enteropathy, CCHMC Cincinnati Children’s Hospital Medical Center, HLA Human Leukocyte Antigen, UVA University of Virginia, ‘omics multiomics, H&E  Haemotoxylin and Eosin, IHC Immunohistochemistry, EEDBI Environmental Enteric Dysfunction Biopsy Initiative, WUPAX Washington University Digital Pathology Exchange, GF Germ Free

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