Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants

Chronic obstructive pulmonary disease (COPD), diagnosed by reduced lung function, is a leading cause of morbidity and mortality. We performed whole genome sequence (WGS) analysis of lung function and COPD in a multi-ethnic sample of 11,497 participants from population- and family-based studies, and 8499 individuals from COPD-enriched studies in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program. We identify at genome-wide significance 10 known GWAS loci and 22 distinct, previously unreported loci, including two common variant signals from stratified analysis of African Americans. Four novel common variants within the regions of PIAS1, RGN (two variants) and FTO show evidence of replication in the UK Biobank (European ancestry n ~ 320,000), while colocalization analyses leveraging multi-omic data from GTEx and TOPMed identify potential molecular mechanisms underlying four of the 22 novel loci. Our study demonstrates the value of performing WGS analyses and multi-omic follow-up in cohorts of diverse ancestry.

Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma

BACKGROUND

Asthma is a common respiratory disorder with a highly heterogeneous nature that remains poorly understood. The objective was to use whole genome sequencing (WGS) data to identify regions of common genetic variation contributing to lung function in individuals with a diagnosis of asthma.

METHODS

WGS data were generated for 1,053 individuals from trios and extended pedigrees participating in the family-based Genetic Epidemiology of Asthma in Costa Rica study. Asthma affection status was defined through a physician's diagnosis of asthma, and most participants with asthma also had airway hyperresponsiveness (AHR) to methacholine. Family-based association tests for single variants were performed to assess the associations with lung function phenotypes.

RESULTS

A genome-wide significant association was identified between baseline FEV1/FVC ratio and a single-nucleotide polymorphism in the top hit cysteine-rich secretory protein LCCL domain-containing 2 (CRISPLD2) (rs12051168; P = 3.6 × 10-8 in the unadjusted model) that retained suggestive significance in the covariate-adjusted model (P = 5.6 × 10-6). Rs12051168 was also nominally associated with other related phenotypes: baseline FEV1 (P = 3.3 × 10-3), postbronchodilator (PB) FEV1 (7.3 × 10-3), and PB FEV1/FVC ratio (P = 2.7 × 10-3). The identified baseline FEV1/FVC ratio and rs12051168 association was meta-analyzed and replicated in three independent cohorts in which most participants with asthma also had confirmed AHR (combined weighted z-score P = .015) but not in cohorts without information about AHR.

CONCLUSIONS

These findings suggest that using specific asthma characteristics, such as AHR, can help identify more genetically homogeneous asthma subgroups with genotype-phenotype associations that may not be observed in all children with asthma. CRISPLD2 also may be important for baseline lung function in individuals with asthma who also may have AHR.

Omega-3 Fatty Acids and Genome-Wide Interaction Analyses Reveal DPP10-Pulmonary Function Association

RATIONALE

Omega-3 polyunsaturated fatty acids (n-3 PUFAs) have anti-inflammatory properties that could benefit adults with comprised pulmonary health.

OBJECTIVE

To investigate n-3 PUFA associations with spirometric measures of pulmonary function tests (PFTs) and determine underlying genetic susceptibility.

METHODS

Associations of n-3 PUFA biomarkers (α-linolenic acid, eicosapentaenoic acid, docosapentaenoic acid [DPA], and docosahexaenoic acid [DHA]) were evaluated with PFTs (FEV1, FVC, and FEV1/FVC) in meta-analyses across seven cohorts from the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (N = 16,134 of European or African ancestry). PFT-associated n-3 PUFAs were carried forward to genome-wide interaction analyses in the four largest cohorts (N = 11,962) and replicated in one cohort (N = 1,687). Cohort-specific results were combined using joint 2 degree-of-freedom (2df) meta-analyses of SNP associations and their interactions with n-3 PUFAs.

RESULTS

DPA and DHA were positively associated with FEV1 and FVC (P < 0.025), with evidence for effect modification by smoking and by sex. Genome-wide analyses identified a novel association of rs11693320-an intronic DPP10 SNP-with FVC when incorporating an interaction with DHA, and the finding was replicated (P2df = 9.4 × 10-9 across discovery and replication cohorts). The rs11693320-A allele (frequency, ∼80%) was associated with lower FVC (PSNP = 2.1 × 10-9; βSNP = -161.0 ml), and the association was attenuated by higher DHA levels (PSNP×DHA interaction = 2.1 × 10-7; βSNP×DHA interaction = 36.2 ml).

CONCLUSIONS

We corroborated beneficial effects of n-3 PUFAs on pulmonary function. By modeling genome-wide n-3 PUFA interactions, we identified a novel DPP10 SNP association with FVC that was not detectable in much larger studies ignoring this interaction.

TRP functions in the broncho-pulmonary system

The current understanding of the role of transient receptor potential (TRP) channels in the airways and lung was initially based on the localization of a series of such channels in a subset of sensory nerve fibers of the respiratory tract. Soon after, TRP channel expression and function have been identified in respiratory nonneuronal cells. In these two locations, TRPs regulate physiological processes aimed at integrating different stimuli to maintain homeostasis and to react to harmful agents and tissue injury by building up inflammatory responses and repair processes. There is no doubt that TRPs localized in the sensory network contribute to airway neurogenic inflammation, and emerging evidence underlines the role of nonneuronal TRPs in orchestrating inflammation and repair in the respiratory tract. However, recent basic and clinical studies have offered clues regarding the contribution of neuronal and nonneuronal TRPs in the mechanism of asthma, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, cough, and other respiratory diseases.

[Respiratory system response to cooling in subjects with single nucleotide polymorphism rs11562975 in gene of thermosensitive TRPM8 ion channel]

On the basis of genomic studies in subjects belonged to Russian ethnic group it was identified individuals with heterozygous genotype, containing the C-allele in single nucleotide polymorphism rs11562975, located in 6 exon of the gene encoding the temperature-sensitive ion channel TRPM8. Subjects with heterozygous genotype GC were characterized by not only increased sensation to cold but also hypometabolic response to local skin cooling and non-temperature activation of TRPM8 ion channel by menthol--decrease in total metabolism, pulmonary ventilation and coefficient of oxygen extraction. The subjects with homozygous genotype GG had a lower cold sensation and adequate response to local skin cooling in respect to thermoregulation--decrease in respiratory heat loss and increase in the lipid metabolism.

Lung morphology: a cadaver study in Indian population

Knowledge of anatomical variations of lung is required by clinicians for accurate interpretation on different imaging techniques. During routine dissection in the anatomy department, a single lung extending uniformly throughout the thoracic cavity was detected in a 35 year old male cadaver. Thereafter a cadaver study was undertaken to report the prevalence of variations involving number, lobes and fissures of lung in Indian population. The thoracic cavities of 29 properly embalmed cadavers containing lungs were dissected and morphological features like number, fissures and lobes were observed for the presence of anatomical variations. The aforementioned single lung cadaver had associated dextrocardia. One accessory lobe on the inferior aspect was observed in 27.2% of lungs studied, whereas supernumerary fissures which were most common in right lower lobe were detected in 35% of lung specimens. The transverse fissure on the right lung was absent in 7.1% and incomplete in 50% of lung specimens. In the right lung, the oblique fissure was absent in 7.1% and incomplete in 39.3% of specimens. The oblique fissure was absent in 10.7% and incomplete in 35.7% of left lungs. Comparative analysis of our work with previous data in the literature suggest that different studies performed on radiological images reported greater prevalence of incomplete or absent pulmonary fissures as compared to various cadaver studies. Our aforementioned findings regarding the variations seen in fissures and lobes of both lungs were different from previous studies. Variations of lung anatomy are important for both the diagnosis and treatment of various diseases involving all the domains of medicine.

Genetic identification of an embryonic parafacial oscillator coupling to the preBötzinger complex

The hindbrain transcription factors Phox2b and Egr2 (also known as Krox20) are linked to the development of the autonomic nervous system and rhombomere-related regulation of breathing, respectively. Mutations in these proteins can lead to abnormal breathing behavior as a result of an alteration in an unidentified neuronal system. We characterized a bilateral embryonic parafacial (e-pF) population of rhythmically bursting neurons at embryonic day (E) 14.5 in mice. These cells expressed Phox2b, were derived from Egr2-expressing precursors and their development was dependent on the integrity of the Egr2 gene. Silencing or eliminating the e-pF oscillator, but not the putative inspiratory oscillator (preBötzinger complex, preBötC), led to an abnormally slow rhythm, demonstrating that the e-pF controls the respiratory rhythm. The e-pF oscillator, the only one active at E14.5, entrained and then coupled with the preBötC, which emerged independently at E15.5. These data establish the dual organization of the respiratory rhythm generator at the time of its inception, when it begins to drive fetal breathing.