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Hum Genomics. 2016 Jan 7;10:1. doi: 10.1186/s40246-015-0058-7.

Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility.

Author information

1
Lovelace Respiratory Research Institute, 2425 Ridgecrest Drive SE, Albuquerque, NM, 87108, USA.
2
Department of Genetics, Rutgers, The State University of New Jersey, 145 Bevier Road, Piscataway, NJ, 08854, USA.
3
Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
4
Department of Internal Medicine, University of New Mexico and New Mexico VA Health Care System, Albuquerque, NM, USA.
5
Biomedical Research Institute of New Mexico, Albuquerque, NM, USA.
6
Department of Medicine, University of Iowa, Iowa City, IA, USA.
7
Department of Genetics, Rutgers, The State University of New Jersey, 145 Bevier Road, Piscataway, NJ, 08854, USA. xing@biology.rutgers.edu.
8
Lovelace Respiratory Research Institute, 2425 Ridgecrest Drive SE, Albuquerque, NM, 87108, USA. nyunoya.toru@gmail.com.
9
Department of Internal Medicine, University of New Mexico and New Mexico VA Health Care System, Albuquerque, NM, USA. nyunoya.toru@gmail.com.

Abstract

BACKGROUND:

Chronic obstructive pulmonary disease (COPD) is characterized by an irreversible airflow limitation in response to inhalation of noxious stimuli, such as cigarette smoke. However, only 15-20 % smokers manifest COPD, suggesting a role for genetic predisposition. Although genome-wide association studies have identified common genetic variants that are associated with susceptibility to COPD, effect sizes of the identified variants are modest, as is the total heritability accounted for by these variants. In this study, an extreme phenotype exome sequencing study was combined with in vitro modeling to identify COPD candidate genes.

RESULTS:

We performed whole exome sequencing of 62 highly susceptible smokers and 30 exceptionally resistant smokers to identify rare variants that may contribute to disease risk or resistance to COPD. This was a cross-sectional case-control study without therapeutic intervention or longitudinal follow-up information. We identified candidate genes based on rare variant analyses and evaluated exonic variants to pinpoint individual genes whose function was computationally established to be significantly different between susceptible and resistant smokers. Top scoring candidate genes from these analyses were further filtered by requiring that each gene be expressed in human bronchial epithelial cells (HBECs). A total of 81 candidate genes were thus selected for in vitro functional testing in cigarette smoke extract (CSE)-exposed HBECs. Using small interfering RNA (siRNA)-mediated gene silencing experiments, we showed that silencing of several candidate genes augmented CSE-induced cytotoxicity in vitro.

CONCLUSIONS:

Our integrative analysis through both genetic and functional approaches identified two candidate genes (TACC2 and MYO1E) that augment cigarette smoke (CS)-induced cytotoxicity and, potentially, COPD susceptibility.

PMID:
26744305
PMCID:
PMC4705629
DOI:
10.1186/s40246-015-0058-7
[Indexed for MEDLINE]
Free PMC Article

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