Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease

Genome-wide association study identifies novel susceptible loci and evaluation of polygenic risk score for chronic obstructive pulmonary disease in a Taiwanese population

BACKGROUND

Chronic Obstructive Pulmonary Disease (COPD) describes a group of progressive lung diseases causing breathing difficulties. While COPD development typically involves a complex interplay between genetic and environmental factors, genetics play a role in disease susceptibility. This study used genome-wide association studies (GWAS) and polygenic risk score (PRS) to elucidate the genetic basis for COPD in Taiwanese patients.

RESULTS

GWAS was performed on a Taiwanese COPD case-control cohort with a sample size of 5,442 cases and 17,681 controls. Additionally, the PRS was calculated and assessed in our target groups. GWAS results indicate that although there were no single nucleotide polymorphisms (SNPs) of genome-wide significance, prominent COPD susceptibility loci on or nearby genes such as WWTR1, EXT1, INTU, MAP3K7CL, MAMDC2, BZW1/CLK1, LINC01197, LINC01894, and CFAP95 (C9orf135) were identified, which had not been reported in previous studies. Thirteen susceptibility loci, such as CHRNA4, AFAP1, and DTWD1, previously reported in other populations were replicated and confirmed to be associated with COPD in Taiwanese populations. The PRS was determined in the target groups using the summary statistics from our base group, yielding an effective association with COPD (odds ratio [OR] 1.09, 95% confidence interval [CI] 1.02-1.17, p = 0.011). Furthermore, replication a previous lung function trait PRS model in our target group, showed a significant association of COPD susceptibility with PRS of Forced Expiratory Volume in one second (FEV1)/Forced Vital Capacity (FCV) (OR 0.89, 95% CI 0.83-0.95, p = 0.001).

CONCLUSIONS

Novel COPD-related genes were identified in the studied Taiwanese population. The PRS model, based on COPD or lung function traits, enables disease risk estimation and enhances prediction before suffering. These results offer new perspectives on the genetics of COPD and serve as a basis for future research.

Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop

Studies of asthma and allergy are generating increasing volumes of omics data for analysis and interpretation. The National Institute of Allergy and Infectious Diseases (NIAID) assembled a workshop comprising investigators studying asthma and allergic diseases using omics approaches, omics investigators from outside the field, and NIAID medical and scientific officers to discuss the following areas in asthma and allergy research: genomics, epigenomics, transcriptomics, microbiomics, metabolomics, proteomics, lipidomics, integrative omics, systems biology, and causal inference. Current states of the art, present challenges, novel and emerging strategies, and priorities for progress were presented and discussed for each area. This workshop report summarizes the major points and conclusions from this NIAID workshop. As a group, the investigators underscored the imperatives for rigorous analytic frameworks, integration of different omics data types, cross-disciplinary interaction, strategies for overcoming current limitations, and the overarching goal to improve scientific understanding and care of asthma and allergic diseases.

Transgenerational Epigenetic Inheritance of Cardiovascular Diseases: A Network Medicine Perspective

INTRODUCTION

The ability to identify early epigenetic signatures underlying the inheritance of cardiovascular risk, including trans- and intergenerational effects, may help to stratify people before cardiac symptoms occur.

METHODS

Prospective and retrospective cohorts and case-control studies focusing on DNA methylation and maternal/paternal effects were searched in Pubmed from 1997 to 2023 by using the following keywords: DNA methylation, genomic imprinting, and network analysis in combination with transgenerational/intergenerational effects.

RESULTS

Maternal and paternal exposures to traditional cardiovascular risk factors during critical temporal windows, including the preconceptional period or early pregnancy, may perturb the plasticity of the epigenome (mainly DNA methylation) of the developing fetus especially at imprinted loci, such as the insulin-like growth factor type 2 (IGF2) gene. Thus, the epigenome is akin to a "molecular archive" able to memorize parental environmental insults and predispose an individual to cardiovascular diseases onset in later life. Direct evidence for human transgenerational epigenetic inheritance (at least three generations) of cardiovascular risk is lacking but it is supported by epidemiological studies. Several blood-based association studies showed potential intergenerational epigenetic effects (single-generation studies) which may mediate the transmittance of cardiovascular risk from parents to offspring.

DISCUSSION

In this narrative review, we discuss some relevant examples of trans- and intergenerational epigenetic associations with cardiovascular risk. In our perspective, we propose three network-oriented approaches which may help to clarify the unsolved issues regarding transgenerational epigenetic inheritance of cardiovascular risk and provide potential early biomarkers for primary prevention.

The AGE-RAGE Axis and the Pathophysiology of Multimorbidity in COPD

Chronic obstructive pulmonary disease (COPD) is a disease of the airways and lungs due to an enhanced inflammatory response, commonly caused by cigarette smoking. Patients with COPD are often multimorbid, as they commonly suffer from multiple chronic (inflammatory) conditions. This intensifies the burden of individual diseases, negatively affects quality of life, and complicates disease management. COPD and comorbidities share genetic and lifestyle-related risk factors and pathobiological mechanisms, including chronic inflammation and oxidative stress. The receptor for advanced glycation end products (RAGE) is an important driver of chronic inflammation. Advanced glycation end products (AGEs) are RAGE ligands that accumulate due to aging, inflammation, oxidative stress, and carbohydrate metabolism. AGEs cause further inflammation and oxidative stress through RAGE, but also through RAGE-independent mechanisms. This review describes the complexity of RAGE signaling and the causes of AGE accumulation, followed by a comprehensive overview of alterations reported on AGEs and RAGE in COPD and in important co-morbidities. Furthermore, it describes the mechanisms by which AGEs and RAGE contribute to the pathophysiology of individual disease conditions and how they execute crosstalk between organ systems. A section on therapeutic strategies that target AGEs and RAGE and could alleviate patients from multimorbid conditions using single therapeutics concludes this review.

Genetic analysis and prenatal diagnosis of short-rib thoracic dysplasia 3 with or without polydactyly caused by compound heterozygous variants of DYNC2H1 gene in four Chinese families

Background: To describe the genetic variation of dynein cytoplasmic 2 heavy chain 1 (DYNC2H1) gene in four Chinese families affected with short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3), and to provide evidence for accurate prenatal diagnosis and genetic counseling.

Methods: The detailed clinical prenatal sonographic features of four fetuses with SRTD3 were carried out. Trio-whole exome sequencing (WES) and proband-WES sequencing was applied to filtrated causative variants in four families. The causative variants of each family were validated in by Sanger sequencing. Bioinformation analysis was applied to predict the harmfulness of these mutations and perform the protein-protein interaction network and Gene Ontology (GO) analysis. A vitro minigene splicing assay was conducted to assess the influence of the splice site variant.

Results: Typical characterization of the four fetuses included short long bones, short ribs, narrow chest, hand and foot posture abnormalities, femur short in diameter and slightly bowing, cardiac abnormalities, and so on. Moreover, eight compound heterozygous variants of DYNC2H1 (NM_001080463.2): c.3842A>C (p.Tyr1281Ser) and c.8833-1G>A, c.8617A>G (p.Met2873Val) and c.7053_7054del (p.Cys2351Ter), c.5984C>T (p.Ala1995Val) and c.10219C>T (p.Arg3407Ter), c.5256del (p.Ala1753GlnfsTer13) and c.9737C>T (p.Thr3246Ile), were identified. Among which, c.10219C>T (p.Arg3407Terp), c.5984C>T (p.Ala1995Val) and c.9737C>T (p.Thr3246Ile) were reported in ClinVar databases, and c.8617A>G (p.Met2873Val), c.10219C>T (p.Arg3407Ter), c.5984C>T (p.Ala1995Val) were found in HGMD databases. Four variants (c.3842A>C (p.Tyr1281Ser), c.8833-1G>A, c.7053_7054del (p.Cys2351Ter) and c.5256del (p.Ala1753GlnfsTer13) were first reported as novel mutations. According to the ACMG guidelines, c.8617A>G (p.Met2873Val), c.7053_7054del (p.Cys2351Ter), c.5984C>T (p.Ala1995Val), c.10219C>T (p.Arg3407Ter) and c.5256del (p.Ala1753GlnfsTer13) were rated as pathogenic or likely pathogenic variants, others variants were predicted to be variants of uncertain significance mutations. The minigene assay results indicated that c.8833-1G>A caused the skipping over exon 56, resulting in exon 56 loss.

Conclusion: In our study, we analyzed the genetic mutations in four fetuses with SRTD3 by whole exome sequencing and identified pathogenic variants causing SRTD3. Our results expand the mutation spectrum of DYNC2H1 in SRTD3, which is helpful for the accurate prenatal diagnosis of SRTD3 fetuses and provide useful strategies for genetic counseling.

The Efficacy and Safety of Budesonide/Glycopyrronium/Formoterol in the Treatment of COPD in the Elderly

Objective

Chronic obstructive pulmonary disease (COPD) is a major and difficult disease of the chronic respiratory system that is common and frequent, with a huge disease burden. The aim of this study was to investigate the efficacy and safety of budesonide/glyburide/formoterol fumarate (BGF) in the treatment of COPD.

Methods

A comprehensive literature search was conducted in PubMed, Embase, Cochrane Library, and Web of Science. The basic features of the seven pieces of literature were identified using the search strategy. The sample size range was 130∼1264.

Results

The effects of BGF increased FEV1 in patients with COPD (mean difference = 2.86, 95%CI: 2.71–3.01, p < 0.00001). The effects of BGF improved in patients with ≥1 TEAE in patients with COPD, and was not statistically significant after treatment (Odds rate = 1.00, 95%CI: 0.85–1.17, p=0.97). The effects of BGF increased in patients with TEAEs related a to study treatment in patients with COPD (odds rate = 1.27, 95% CI: 1.03–1.57, p=0.02). The effects of BGF in decreased patients with serious TEAEs in patients with COPD (odds rate = −0.02, 95% CI: −0.03–−0.00, p=0.04). The effects of BGF decreased the death rate in patients with COPD, and were not statistically significant after treatment (odds rate = 0.77, 95% CI: 0.31–1.97, p=0.59). The effects of BGF decreased the hypertension rate in patients with COPD (odds rate = 0.92, 95% CI: 0.44–1.89, p=0.81), and was not statistically significant after treatment. The effects of BGF increased pneumonia in patients with COPD (odds rate = 1.55, 95% CI: 0.81–2.97, p=0.19), and were not statistically significant after treatment. The effects of BGF increased FEV1, increased patients with TEAEs related a to study treatment, and decreased patients with serious TEAEs in patients with COPD.

Conclusion

This study elucidates the efficacy and safety of BGF in the treatment of COPD with a view to providing a clinical reference.

RAGE against the Machine: Can Increasing Our Understanding of RAGE Help Us to Battle SARS-CoV-2 Infection in Pregnancy?

The receptor of advanced glycation end products (RAGE) is a receptor that is thought to be a key driver of inflammation in pregnancy, SARS-CoV-2, and also in the comorbidities that are known to aggravate these afflictions. In addition to this, vulnerable populations are particularly susceptible to the negative health outcomes when these afflictions are experienced in concert. RAGE binds a number of ligands produced by tissue damage and cellular stress, and its activation triggers the proinflammatory transcription factor Nuclear Factor Kappa B (NF-κB), with the subsequent generation of key proinflammatory cytokines. While this is important for fetal membrane weakening, RAGE is also activated at the end of pregnancy in the uterus, placenta, and cervix. The comorbidities of hypertension, cardiovascular disease, diabetes, and obesity are known to lead to poor pregnancy outcomes, and particularly in populations such as Native Hawaiians and Pacific Islanders. They have also been linked to RAGE activation when individuals are infected with SARS-CoV-2. Therefore, we propose that increasing our understanding of this receptor system will help us to understand how these various afflictions converge, how forms of RAGE could be used as a biomarker, and if its manipulation could be used to develop future therapeutic targets to help those at risk.