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Jehan F, Sazawal S, Baqui AH, Nisar MI, Dhingra U, Khanam R, Ilyas M, Dutta A, Mitra DK, Mehmood U, Deb S, Mahmud A, Hotwani A, Ali SM, Rahman S, Nizar A, Ame SM, Moin MI, Muhammad S, Chauhan A, Begum N, Khan W, Das S, Ahmed S, Hasan T, Khalid J, Rizvi SJR, Juma MH, Chowdhury NH, Kabir F, Aftab F, Quaiyum A, Manu A, Yoshida S, Bahl R, Rahman A, Pervin J, Winston J, Musonda P, Stringer JSA, Litch JA, Ghaemi MS, Moufarrej MN, Contrepois K, Chen S, Stelzer IA, Stanley N, Chang AL, Hammad GB, Wong RJ, Liu C, Quaintance CC, Culos A, Espinosa C, Xenochristou M, Becker M, Fallahzadeh R, Ganio E, Tsai AS, Gaudilliere D, Tsai ES, Han X, Ando K, Tingle M, Marić I, Wise PH, Winn VD, Druzin ML, Gibbs RS, Darmstadt GL, Murray JC, Shaw GM, Stevenson DK, Snyder MP, Quake SR, Angst MS, Gaudilliere B, Aghaeepour N. Multiomics Characterization of Preterm Birth in Low- and Middle-Income Countries. JAMA Netw Open 2020; 3:e2029655. [PMID: 33337494 PMCID: PMC7749442 DOI: 10.1001/jamanetworkopen.2020.29655] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
IMPORTANCE Worldwide, preterm birth (PTB) is the single largest cause of deaths in the perinatal and neonatal period and is associated with increased morbidity in young children. The cause of PTB is multifactorial, and the development of generalizable biological models may enable early detection and guide therapeutic studies. OBJECTIVE To investigate the ability of transcriptomics and proteomics profiling of plasma and metabolomics analysis of urine to identify early biological measurements associated with PTB. DESIGN, SETTING, AND PARTICIPANTS This diagnostic/prognostic study analyzed plasma and urine samples collected from May 2014 to June 2017 from pregnant women in 5 biorepository cohorts in low- and middle-income countries (LMICs; ie, Matlab, Bangladesh; Lusaka, Zambia; Sylhet, Bangladesh; Karachi, Pakistan; and Pemba, Tanzania). These cohorts were established to study maternal and fetal outcomes and were supported by the Alliance for Maternal and Newborn Health Improvement and the Global Alliance to Prevent Prematurity and Stillbirth biorepositories. Data were analyzed from December 2018 to July 2019. EXPOSURES Blood and urine specimens that were collected early during pregnancy (median sampling time of 13.6 weeks of gestation, according to ultrasonography) were processed, stored, and shipped to the laboratories under uniform protocols. Plasma samples were assayed for targeted measurement of proteins and untargeted cell-free ribonucleic acid profiling; urine samples were assayed for metabolites. MAIN OUTCOMES AND MEASURES The PTB phenotype was defined as the delivery of a live infant before completing 37 weeks of gestation. RESULTS Of the 81 pregnant women included in this study, 39 had PTBs (48.1%) and 42 had term pregnancies (51.9%) (mean [SD] age of 24.8 [5.3] years). Univariate analysis demonstrated functional biological differences across the 5 cohorts. A cohort-adjusted machine learning algorithm was applied to each biological data set, and then a higher-level machine learning modeling combined the results into a final integrative model. The integrated model was more accurate, with an area under the receiver operating characteristic curve (AUROC) of 0.83 (95% CI, 0.72-0.91) compared with the models derived for each independent biological modality (transcriptomics AUROC, 0.73 [95% CI, 0.61-0.83]; metabolomics AUROC, 0.59 [95% CI, 0.47-0.72]; and proteomics AUROC, 0.75 [95% CI, 0.64-0.85]). Primary features associated with PTB included an inflammatory module as well as a metabolomic module measured in urine associated with the glutamine and glutamate metabolism and valine, leucine, and isoleucine biosynthesis pathways. CONCLUSIONS AND RELEVANCE This study found that, in LMICs and high PTB settings, major biological adaptations during term pregnancy follow a generalizable model and the predictive accuracy for PTB was augmented by combining various omics data sets, suggesting that PTB is a condition that manifests within multiple biological systems. These data sets, with machine learning partnerships, may be a key step in developing valuable predictive tests and intervention candidates for preventing PTB.
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Affiliation(s)
- Fyezah Jehan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sunil Sazawal
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Abdullah H. Baqui
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Usha Dhingra
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Rasheda Khanam
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Muhammad Ilyas
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Arup Dutta
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Dipak K. Mitra
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Usma Mehmood
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Saikat Deb
- Centre for Public Health Kinetics, New Delhi, Delhi, India
- Public Health Laboratory-Ivo de Carneri, Pemba Island, Zanzibar
| | - Arif Mahmud
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Sayedur Rahman
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ambreen Nizar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Mamun Ibne Moin
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Sajid Muhammad
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Nazma Begum
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Waqasuddin Khan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sayan Das
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Salahuddin Ahmed
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Tarik Hasan
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Javairia Khalid
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Syed Jafar Raza Rizvi
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Nabidul Haque Chowdhury
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fahad Aftab
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Abdul Quaiyum
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Alexander Manu
- Maternal, Newborn, Child and Adolescent Health Research, World Health Organization, Geneva, Switzerland
| | - Sachiyo Yoshida
- Maternal, Newborn, Child and Adolescent Health Research, World Health Organization, Geneva, Switzerland
| | - Rajiv Bahl
- Maternal, Newborn, Child and Adolescent Health Research, World Health Organization, Geneva, Switzerland
| | - Anisur Rahman
- Matlab Health Research Centre, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jesmin Pervin
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jennifer Winston
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill
| | - Patrick Musonda
- School of Public Health, University of Zambia, Lusaka, Zambia
| | - Jeffrey S. A. Stringer
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill
| | - James A. Litch
- Global Alliance to Prevent Prematurity and Stillbirth, Seattle, Washington
| | - Mohammad Sajjad Ghaemi
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
- Digital Technologies Research Centre, National Research Council Canada, Toronto, Ontario, Canada
| | - Mira N. Moufarrej
- Department of Bioengineering, Stanford University, Stanford, California
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Songjie Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Ina A. Stelzer
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Natalie Stanley
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Alan L. Chang
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Ghaith Bany Hammad
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Ronald J. Wong
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Candace Liu
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | | | - Anthony Culos
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Maria Xenochristou
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Martin Becker
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Ramin Fallahzadeh
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Edward Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Amy S. Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Dyani Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Eileen S. Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Xiaoyuan Han
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Kazuo Ando
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Martha Tingle
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Ivana Marić
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Paul H. Wise
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Virginia D. Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California
| | - Maurice L. Druzin
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California
| | - Ronald S. Gibbs
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California
| | - Gary L. Darmstadt
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | | | - Gary M. Shaw
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - David K. Stevenson
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, California
| | - Martin S. Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
- Department of Biomedical Informatics, Stanford University School of Medicine, Stanford, California
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