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. 2018 Oct 20;19(1):94.
doi: 10.1186/s12863-018-0679-7.

Exome sequencing identifies gene variants and networks associated with extreme respiratory outcomes following preterm birth

Aaron Hamvas  1   2 , Rui Feng  3 , Yingtao Bi  4 , Fan Wang  3 , Soumyaroop Bhattacharya  5 , Jared Mereness  5 , Madhurima Kaushal  6 , C Michael Cotten  7 , Philip L Ballard  8 , Thomas J Mariani  9   10 ; PROP Investigators
Collaborators, Affiliations

Exome sequencing identifies gene variants and networks associated with extreme respiratory outcomes following preterm birth

Aaron Hamvas et al. BMC Genet. .

Abstract

Background: Previous studies have identified genetic variants associated with bronchopulmonary dysplasia (BPD) in extremely preterm infants. However, findings with genome-wide significance have been rare, and not replicated. We hypothesized that whole exome sequencing (WES) of premature subjects with extremely divergent phenotypic outcomes could facilitate the identification of genetic variants or gene networks contributing disease risk.

Results: The Prematurity and Respiratory Outcomes Program (PROP) recruited a cohort of > 765 extremely preterm infants for the identification of markers of respiratory morbidity. We completed WES on 146 PROP subjects (85 affected, 61 unaffected) representing extreme phenotypes of early respiratory morbidity. We tested for association between disease status and individual common variants, screened for rare variants exclusive to either affected or unaffected subjects, and tested the combined association of variants across gene loci. Pathway analysis was performed and disease-related expression patterns were assessed. Marginal association with BPD was observed for numerous common and rare variants. We identified 345 genes with variants unique to BPD-affected preterm subjects, and 292 genes with variants unique to our unaffected preterm subjects. Of these unique variants, 28 (19 in the affected cohort and 9 in unaffected cohort) replicate a prior WES study of BPD-associated variants. Pathway analysis of sets of variants, informed by disease-related gene expression, implicated protein kinase A, MAPK and Neuregulin/epidermal growth factor receptor signaling.

Conclusions: We identified novel genes and associated pathways that may play an important role in susceptibility/resilience for the development of lung disease in preterm infants.

Keywords: Bronchopulmonary dysplasia (BPD); Prematurity and respiratory outcomes program (PROP).

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Conflict of interest statement

Authors’ information

PROP Investigators:

Cincinnati Children’s Hospital Medical Center:

Barbara Alexander, RN, Claire Chougnet, PhD, Tari Gratton, PA, James M. Greenberg, MD, Cathy Grisby, BSN, CCRC, William Hardie, MD, Alan H. Jobe MD, PhD, Beth Koch, BHS, RRT, RPFT, Karen McDowell, MD, Kelly Thornton BS.

Washington University:

Pamela Bates, CRT, RPFT, RPSGT, Claudia Cleveland, RRT, Thomas Ferkol, MD, Aaron Hamvas, MD, Julie Hoffmann, RN, Mark R. Holland, PhD, James Kemp, MD, Philip T. Levy, MD, Laura Linneman, RN, Jayne Sicard-Su, RN, Gina Simpson, RRT, CPFT, Gautam K. Singh, MD, Barbara Warner, MD.

University of California at San Francisco:

Investigators

Philip L. Ballard, MD, PhD1, Roberta A. Ballard, MD1, David J. Durand, MD2, Eric C. Eichenwald, MD4, Roberta L. Keller, MD1, Amir M. Khan, MD4, Leslie Lusk, MD1, Jeffrey D. Merrill, MD3, Dennis W. Nielson, MD, PhD1, Elizabeth E. Rogers, MD1.

Research Staff

Jeanette M. Asselin, MS, RRT-NPS2, Samantha Balan1, Katrina Burson, RN, BSN4, Cheryl Chapin1, Erna Josiah-Davis, RN, NP3, Carmen Garcia, RN, CCRP4, Hart Horneman1, Rick Hinojosa, BSRT, RRT, CPFT-NPS4, Christopher Johnson, MBA, RRT4, Susan Kelley, RRT1, Karin L. Knowles1, M. Layne Lillie, RN, BSN4, Karen Martin, RN4, Sarah Martin, RN, BSN1, Julie Arldt-McAlister, RN, BSN4, Georgia E. McDavid, RN4, Lori Pacello, RCP2, Shawna Rodgers, RN, BSN4, Daniel K. Sperry, RN4,1

1Department of Pediatrics, University of California San Francisco, San Francisco, CA; 2Children’s Hospital and Research Center Oakland, Oakland, CA.

3Alta Bates Summit Medical Center, Berkeley, CA.

4University of Texas Health Science Center- Houston, Houston, TX.

Vanderbilt University:

Judy Aschner, MD, Amy B Beller BSN, Candice Fike, MD, Scott Guthrie, MD, Tina Hartert, MD, Nathalie Maitre, MD, Paul Moore, MD, Mark O′ Hunt, Theresa J. Rogers, RN, Odessa L. Settles, RN, MSN, CM, Steven Steele, RN, Marshall Summar, MD, Sharon Wadley, BSN, RN, CLS.

University of Rochester-University at Buffalo:

Investigators

Carl D’Angio, MD, Vasanth Kumar, MD, Tom Mariani, PhD, Gloria Pryhuber, MD, Clement Ren, MD, Anne Marie Reynolds, MD, MPH, Rita M. Ryan, MD, Kristin Scheible, MD, Timothy Stevens, MD, MPH.

Technical Staff

Heidie Huyck, BS, Valerie Lunger, MS

Study Staff

Shannon Castiglione, RN, Aimee Horan, LPN, Deanna Maffet, RN, Jane O’Donnell, PNP, Michael Sacilowski, MAT, Tanya Scalise, RN, BSN, Elizabeth Werner, MPH, Jason Zayac, BS Respiratory Therapists and Nurses:

Kim Bordeaux, RRT, Pam Brown, RRT, Julia Epping, AAS, RT, Lisa Flattery-Walsh, RRT, Donna Germuga, RRT, CPFT, Nancy Jenks, RN, Mary Platt, RN, Eileen Popplewell, RRT, Sandra Prentice, CRT.

Duke University:

Kim Ciccio, RN, C. Michael Cotten, M.D., Kim Fisher, Ph.D., Jack Sharp, M.D., Judith A. Voynow, M.D.*.

*Present address, Virginia Commonwealth University.

Indiana University:

Charles Clem, RRT, Stephanie Davis, M.D., Susan Gunn, NNP, CCRC, Lauren Jewett, RN, CCRC Brenda Poindexter, M.D., M.S.#.

#Present address, University of Cincinnati.

Steering Committee Chair:

Lynn M. Taussig, MD, University of Denver.

NHLBI Program Officer:

Carol J. Blaisdell, MD.

University of Pennsylvania Data Coordinating Center:

Scarlett Bellamy, ScD, Maria Blanco, BS, Denise Cifelli, MS, Sara DeMauro, MD, Jonas Ellenberg, PhD, Rui Feng, PhD, Melissa Fernando, MPH, Howard Panitch, MD, Barbara Schmidt, MD, MSc, Pamela Shaw, PhD, Ann Tierney, BA, MS

Ethics approval and consent to participate

Studies at each of the participating PROP sites were IRB-approved and all parents consented to collection and sequencing of infant DNA and collection of clinical data.

Consent for publication

All parents consented to publication of data without identifiers.

Competing interests

All authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Analytical Design Schematic. Represented are the three separate approaches and the number of variants, genes and pathways identified at each step in the analysis of whole exome sequence data obtained from 146 subjects
Fig. 2
Fig. 2
Genome-wide Association Results. We performed genome-wide association analysis using either (a) all common variants (MAF > 0.05) or (b) combined rare and common variants at each individual gene locus (FFB-SKAT), comparing the affected group to the unaffected group. Manhattan plots show the strength of association for all variants, organized by chromosomal locus, with genes demonstrating greatest association indicated by name
Fig. 3
Fig. 3
Gene Expression-Informed Pathway Analysis. Shown is a summary of pathway analysis results for genes with variants demonstrating association with respiratory outcomes. Separate analyses were performed for gene sets identified from analysis of common variants (Common), unique variants only identified in affected subjects (Unique BPD), unique variants only identified in the unaffected subjects (Unique No BPD), and combined common and rare variants (Common + Rare). Standard pathway analyses were supplemented with gene expression data from lung tissue from subjects with BPD and appropriate controls. Top canonical pathways identified (rows) are listed for each analysis (columns), with significance (− logP) and directionality (activated/inhibited). Interestingly, some biological functions were commonly identified including PKA (activated in affected subjects, inhibited in unaffected subjects), corticotropin releasing hormone (inhibited in affected), UVA-induced MAPK (inhibited in affected) and sperm motility (inhibited in affected)
See this image and copyright information in PMC

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