Study of environmental enteropathy and malnutrition (SEEM) in Pakistan: Protocols for biopsy based biomarker discovery and validation

Authors: IQBAL, NAJEEHA - Aga Khan University; SYED, SANA - Aga Khan University; SADIQ, KAMRAN - Aga Khan University; KHAN, MARIUM - University Of Virginia; IQBAL, JUNAID - Aga Khan University; MA, JENNIE - University Of Virginia; UMRANI, FAYAZ - Aga Khan University; AHMED, SHERAZ - Aga Khan University; MAIER, ELIZABETH - Children'S Hospital - Cincinnati, Ohio; DENSON, LEE - Children'S Hospital - Cincinnati, Ohio; HABERMAN, YAEL - Children'S Hospital - Cincinnati, Ohio; MCNEAL, MONICA - Children'S Hospital - Cincinnati, Ohio; SETCHELL, KENNETH - Children'S Hospital - Cincinnati, Ohio; ZHAO, XUEHENG - Children'S Hospital - Cincinnati, Ohio; QURESHI, SHAHIDA - Aga Khan University; SHEN, LANLAN - Children'S Nutrition Research Center (CNRC); MOSKALUK, CHRISTOPHER - University Of Virginia; LIU, TA-CHIANG - Washington University School Of Medicine; YILMAZ, OMER - Massachusetts General Hospital; BROWN, DONALD - Massachusetts Institute Of Technology; BARRATT, MICHAEL - Washington University School Of Medicine; KUNG, VANDERIENE - Washington University School Of Medicine; GORDON, JEFFREY - Washington University School Of Medicine; MOORE, SEAN - University Of Virginia; ALI, S - Aga Khan University

Submitted to: BMC Pediatrics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/31/2019
Publication Date: 7/22/2019
Citation: Iqbal, N.T., Syed, S., Sadiq, K., Khan, M.N., Iqbal, J., Ma, J.Z., Umrani, F., Ahmed, S., Maier, E.A., Denson, L.A., Haberman, Y., McNeal, M.M., Setchell, K.D., Zhao, X., Qureshi, S., Shen, L., Moskaluk, C.A., Liu, T., Yilmaz, O., Brown, D.E., Barratt, M.J., Kung, V.L., Gordon, J.I., Moore, S.R., Ali, S.A. 2019. Study of environmental enteropathy and malnutrition (SEEM) in Pakistan: Protocols for biopsy based biomarker discovery and validation. BMC Pediatrics. 19:247. https://doi.org/10.1186/s12887-019-1564-x
DOI: https://doi.org/10.1186/s12887-019-1564-x

Interpretive Summary: 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. Our study of Environmental Enteropathy and Malnutrition (SEEM) in Pakistan is designed to better understand the pathophysiology, predictors, biomarkers, and potential management strategies of EE. The Environmental Enteric Dysfunction Biopsy Initiative Consortium has been assembled from the Bill and Melinda Gates Foundation and this paper describes our SEEM Pakistan study protocols including the materials that are being collected along with proposed analysis including the use of fecal intestinal epithelial cells as a "liquid biopsy" for epigenetic biomarker discovery and validation. Our publication will improve the operational and ethical limitations for safely obtaining intestinal biopsies from children in resource-poor setting, thereby yielding reproducible results.

Technical Abstract: 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. 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. 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.