Genetic testing in diffuse parenchymal lung disease

The increasing trend and the seasonal variation in attendance of diffuse parenchymal lung disease patients presenting to a pulmonary clinic in Eastern India

Background:

Diffuse parenchymal lung disease (DPLD) is not an uncommon problem in clinical practice. Although the exact prevalence of DPLD in India is not known, the relative etiological distribution in DPLD in India has been reported. There has been no information as regards the seasonality of the disease.

Patients and Methods:

The archive of the Institute of Pulmocare and Research, Kolkata, was searched for the number of new patients registered at the outpatient department to a single consultant (practicing in the same style on appointment only) over years from 2009 to 2019. The attendance (absolute and relative) was arranged year wise and then month wise to look for the annual and seasonal trends, if any.

Results:

A total of 2226 patients were registered from 2009 to 2019. There has been a steady increase in both the absolute number (104 in 2009 to 204 in 2019) and the relative percentage of attendance (4.36% in 2009 to 6.9% in 2019) of new registration of DPLD patients over the years. Regarding seasonal variation, two consistent peaks in attendance have been observed as December–January and April–May over the years with dips in February and September; the first being more consistent then the latter.

Conclusions:

The increase in relative attendance in the DPLD patients over the years needs further investigation to establish a rising trends in incidence and prevalence of DPLD. The unequivocal trend in seasonal variation needs attention and further research.

Novel idiopathic pulmonary fibrosis susceptibility variants revealed by deep sequencing

Background

Specific common and rare single nucleotide variants (SNVs) increase the likelihood of developing sporadic idiopathic pulmonary fibrosis (IPF). We performed target-enriched sequencing on three loci previously identified by a genome-wide association study to gain a deeper understanding of the full spectrum of IPF genetic risk and performed a two-stage case–control association study.

Methods

A total of 1.7 Mb of DNA from 181 IPF patients was deep sequenced (>100×) across 11p15.5, 14q21.3 and 17q21.31 loci. Comparisons were performed against 501 unrelated controls and replication studies were assessed in 3968 subjects.

Results

36 SNVs were associated with IPF susceptibility in the discovery stage (p<5.0×10⁻⁸). After meta-analysis, the strongest association corresponded to rs35705950 (p=9.27×10⁻⁵⁷) located upstream from the mucin 5B gene (MUC5B). Additionally, a novel association was found for two co-inherited low-frequency SNVs (<5%) in MUC5AC, predicting a missense amino acid change in mucin 5AC (lowest p=2.27×10⁻²²). Conditional and haplotype analyses in 11p15.5 supported the existence of an additional contribution of MUC5AC variants to IPF risk.

Conclusions

This study reinforces the significant IPF associations of these loci and implicates MUC5AC as another key player in IPF susceptibility.

Deep sequencing of genome-wide association study hits identified novel low-frequency variants associated with IPF susceptibility.http://bit.ly/2IF4AT8

A novel germline mutation of the SFTPA1 gene in familial interstitial pneumonia

Different genes related to alveolar stability have been associated with familial interstitial pneumonia (FIP). Here, we report a novel, rare SFTPA1 variant in a family with idiopathic interstitial pneumonia (IIP). We performed whole-exome sequencing on germline DNA samples from four members of one family; three of them showed signs of pulmonary fibrosis (idiopathic interstitial pneumonia) with autosomal-dominant inheritance. A heterozygous single nucleotide variant c.532 G > A in the SFTPA1 gene has been identified. This variant encodes the substitution p.(Val178Met), localized within the carbohydrate recognition domain of surfactant protein A and segregates with the genes causing idiopathic interstitial pneumonia. This rare variant has not been previously reported. We also analyzed the detected sequence variant in the protein structure in silico. The replacement of valine by the larger methionine inside the protein may cause a disruption in the protein structure. The c.532 G > A variant was further validated using Sanger sequencing of the amplicons, confirming the diagnosis in all symptomatic family members. Moreover, this variant was also found by Sanger sequencing in one other symptomatic family member and one young asymptomatic family member. The autosomal-dominant inheritance, the family history of IIP, and the evidence of a mutation occurring in part of the SFTPA1 gene all suggest a novel variant that causes FIP.

Researchers have identified a novel mutation that causes inheritable and ultimately deadly scarring of the tiny air sacs in the lungs, the alveoli. In familial interstitial pneumonia (FIP), alveoli are scarred and stiffened by inflammation, not by bacterial infection as the word ‘pneumonia’ usually indicates. Michael Doubek at University Hospital and Central European Institute of Technology, Brno, Czech Republic and co-workers investigated a suspected case of FIP following the early death of one family member. Sequencing the genomes of other family members revealed that they shared a mutation in a protein that keeps alveoli moist, aiding oxygen absorption. Computer analysis showed that the mutation probably changed the protein’s shape, preventing it from functioning. Identifying mutations that cause FIP will help provide proactive treatment for family members who are at risk but not yet showing symptoms.