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Biology subjects

Sin, D. D.

Publications and source records attributed to Sin, D. D..

11 recordsLinked to original sources

Airway Epithelial SARS-CoV-2 Infectious and Repair Responses: Relationships to Age, Sex, and Post-COVID Pulmonary Syndromes

The long-term pulmonary sequelae of SARS-CoV-2 respiratory infections reflect infection severity, innate and adaptive immunity, and respiratory epithelial repair. This study investigated the acute and reparative responses as a function of age and sex in primary human bronchial epithelial (HBE) cultures utilizing a 14-day SARS-CoV-2 infection protocol. SARS-CoV-2 infection peaked at 3 days post-infection (dpi) with an [~] 2 log titer suppression at 14 dpi. SARS-CoV-2 infection induced interferon, interferon-induced gene, and cell damage responses. No age- or sex-dependent effects on SARS-CoV-2 infection were detected. Airway epithelia repaired to an abnormal mucus metaplastic/inflammatory state that reflected potentially beneficial and adverse consequences at 14 dpi. Repair processes were infection severity-dependent, not sex-dependent, and were more robust in young donor cultures. Analyses of long-COVID subjects with persistent pulmonary fibrosis or persistent bronchitic airway diseases exhibited expression of HBE 14 dpi failed repair gene signatures, including ISG gene signatures. Human airway epithelial repair post-SARS-CoV-2 is prolonged and incomplete in vitro over 14 days, and persistently abnormal repair may contribute to phenotypes of people with long-COVID pulmonary syndrome.

cell biology↗

SMART: reference-free deconvolution for spatial transcriptomics using marker-gene-assisted topic models

Spatial transcriptomics (ST) offers valuable insights into gene expression patterns within the spatial context of tissue. However, most technologies do not have a single-cell resolution, masking the signal of the individual cell types. Here, we present SMART, a reference-free deconvolution method that simultaneously infers the cell type-specific gene expression profile and the cellular composition at each spot. Unlike most existing methods that rely on having a single-cell RNA-sequencing dataset as the reference, SMART only uses marker gene symbols as the prior knowledge to guide the deconvolution process and outperforms the existing methods in realistic settings when an ideal reference dataset is unavailable. SMART also provides a two-stage approach to enhance its performance on cell subtypes. Allowing the inclusion of covariates, SMART provides condition-specific estimates and enables the identification of cell type-specific differentially expressed genes across conditions, which elucidates biological changes at a single-cell-type resolution.

bioinformatics↗

Single-cell RNA-sequencing of bronchoscopy specimens: development of a rapid, minimal-handling protocol

Single-cell RNA-sequencing (scRNA-seq) is an important tool for understanding disease pathophysiology, including airways diseases. Currently, the majority of scRNA-seq studies in airways diseases have used invasive methods (airway biopsy, surgical resection) which carry inherent risks and thus present a major limitation to scRNA-seq investigation of airway pathology. Bronchial brushing, where the airway mucosa is sampled using a cytological brush, is a viable, less invasive method of obtaining airway cells for scRNA-seq. Here we are describing the development of a rapid and minimal-handling protocol for preparing single cell suspensions from bronchial brush specimens for scRNA-seq. Our optimized protocol maximises cell recovery and cell quality, and may facilitate large-scale profiling of the airway transcriptome at single cell resolution. Lay abstractSingle-cell RNA-sequencing (scRNA-seq) measures the gene expression of individual cells, and may be useful for understanding disease processes. scRNA-seq may be used to investigate lung diseases, but using invasive methods such as biopsy or surgery limits our ability to conduct large research studies. Bronchial brushing, where a soft brush is used to collect cells from inside the lungs, is a safer method but we need a better way to isolate individual cells from the brush specimens. We developed a method that is faster and involves less handling of the specimens compared to other published methods. Our method may therefore be useful for conducting large scRNA-seq studies in lung diseases.

genomics↗

Age-associated Differences in the Human Lung Extracellular Matrix

IntroductionExtracellular matrix (ECM) remodelling has been associated with chronic lung diseases. However, information about specific age-associated differences in lung ECM is currently limited. In this study we aimed to identify and localize age-associated ECM differences in human lung using comprehensive transcriptomic, proteomic and immunohistochemical analyses. MethodsOur previously identified age-associated gene expression signature of the lung was re-analysed limiting it to an aging signature based on 270 control patients (37-80 years) and focused on the Matrisome core geneset using geneset enrichment analysis. To validate the age-associated transcriptomic differences on protein level, we compared the age-associated ECM genes (F <0.05) with a profile of age-associated proteins identified from a lung tissue proteomics dataset from 9 control patients (49-76 years) (FDR<0.05). Extensive immunohistochemical analysis was used to localize the age-associated ECM differences in lung tissues from control patients (9-82 years). ResultsComparative analysis of transcriptomic and proteomic data identified 7 ECM proteins with higher expression with age at both gene and protein level: COL1A1, COL6A1, COL6A2, COL14A1, FBLN2, LTBP4 and LUM. With immunohistochemistry we demonstrated higher protein expression with age for COL6A2 in whole tissue, parenchyma, airway wall and blood vessel, for COL14A1 in bronchial epithelium and blood vessel, and for FBLN2 and COL1A1 in lung parenchyma. ConclusionOur study revealed that higher age is associated with lung ECM remodelling, with specific differences occurring in defined regions within the lung. These differences may affect lung structure and physiology with aging and as such may increase susceptibility for developing chronic lung diseases. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSsummarise the state of scientific knowledge on this subject before you did your study and why this study needed to be done. In animal models, it has been demonstrated that aging alters the composition of the lung ECM, with more deposition of collagen and degradation of elastin. Similar ECM differences have been observed in age-associated chronic lung diseases, including COPD; moreover, we observed in lung tissue that several ECM genes associate differently with age in COPD patients compared to non-COPD controls(1). Detailed knowledge on age-associated changes in specific ECM proteins as well as regional differences within the lung is lacking. What this study addssummarise what we now know as a result of this study that we did not know before. We identified 7 age-associated ECM proteins i.e. COL1A1, COL6A1, COL6A2 COL14A1, FBLN2, LTBP4 and LUM with higher transcript and protein levels in human lung tissue with age. Extensive immunohistochemical analysis revealed significant age-associated differences for 3 of these ECM proteins in specific compartments of the lung, with the most notable differences in the blood vessels and parenchyma. How this study might affect research, practice, or policysummarise the implications of this study. The identification of age-associated differences in specific human lung ECM proteins lays a new foundation for the investigation of ECM differences in age-associated chronic lung diseases. Additionally, examining the function of these age-associated ECM proteins and their cellular interactions in lung injury and repair responses may provide novel insight in mechanisms underlying chronic lung diseases.

molecular biology↗

Gene Expression Network Analysis Provides Potential Targets Against SARS-CoV-2

ABSTRACTBACKGROUND Cell entry of SARS-CoV-2, the novel coronavirus causing COVID-19, is facilitated by host cell angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). We aimed to identify and characterize genes that are co-expressed with ACE2 and TMPRSS2, and to further explore their biological functions and potential as druggable targets.METHODS Using the gene expression profiles of 1,038 lung tissue samples, we performed a weighted gene correlation network analysis (WGCNA) to identify modules of co-expressed genes. We explored the biology of co-expressed genes using bioinformatics databases, and identified known drug-gene interactions.RESULTS ACE2 was in a module of 681 co-expressed genes; 12 genes with moderate-high correlation with ACE2 (r>0.3, FDR<0.05) had known interactions with existing drug compounds. TMPRSS2 was in a module of 1,086 co-expressed genes; 15 of these genes were enriched in the gene ontology biologic process ‘Entry into host cell’, and 53 TMPRSS2-correlated genes had known interactions with drug compounds.CONCLUSION Dozens of genes are co-expressed with ACE2 and TMPRSS2, many of which have plausible links to COVID-19 pathophysiology. Many of the co-expressed genes are potentially targetable with existing drugs, which may help to fast-track the development of COVID-19 therapeutics.Competing Interest StatementS.M. reports personal fees from Novartis and Boehringer-Ingelheim, outside the submitted work. W.T. reports fees to Institution from Roche-Ventana, AbbVie, Merck-Sharp-Dohme and Bristol-Myers-Squibb, outside the submitted work. M.B. reports research grants paid to University from Astra Zeneca, Novartis, outside the submitted work. D.D.S. reports research funding from AstraZeneca and received honoraria for speaking engagements from Boehringer Ingelheim and AstraZeneca over the past 36 months, outside of the submitted work.View Full Text

genomics↗

The protective effect of club cell secretory protein (CC-16) on COPD risk and progression: a Mendelian randomisation study

BackgroundThere are currently no robust biomarkers of chronic obstructive pulmonary disease (COPD) risk or progression. Club cell secretory protein-16 (CC-16) is associated with the clinical expression of COPD. We aimed to determine if there is a causal effect of serum CC-16 level on COPD risk and/or progression using Mendelian randomisation (MR) analysis. MethodsWe performed a genome-wide association meta-analysis for serum CC-16 in two COPD cohorts (Lung Health Study [LHS], n=3,850 and ECLIPSE, n=1,702). We then used the CC-16-associated single-nucleotide polymorphisms (SNPs) in MR analysis to estimate the causal effect of serum CC-16 on COPD risk (International COPD Genetics Consortium/UK-Biobank dataset; n=35,735 cases, n=222,076 controls) and progression (change in forced expiratory volume in 1 s [FEV1] in LHS and ECLIPSE). We also determined the associations between SNPs associated with CC-16 and gene expression using n=1,111 lung tissue samples from the Lung eQTL Study. ResultsWe identified 7 SNPs independently associated (p<5x10-8) with serum CC-16 levels; 6 of these were novel. MR analysis suggested a protective causal effect of increased serum CC-16 on COPD risk (p=0.008) and progression (LHS only, p=0.02). Five of the SNPs were also associated with gene expression in lung tissue, including that of the CC-16-encoding gene SCGB1A1 (false discovery rate<0.1). ConclusionWe have identified several novel genetic variants associated with serum CC-16 level in COPD cohorts. These genetic associations suggest a potential causal effect of serum CC-16 on COPD risk and progression. Further investigation of CC-16 as a biomarker or therapeutic target in COPD is warranted. KEY MESSAGESWhat is the key question? Can genetics help uncover a causal effect of serum CC-16 level on COPD risk and/or progression? What is the bottom line? There is a protective effect of genetically-increased serum CC-16 on both COPD risk and progression (as measured by change in FEV1 over time), which may be due to increased expression of the CC-16-encoding gene SCGB1A1 in the lung. Why read on? This is the first study to demonstrate a possible causal effect of serum CC-16 in people with COPD, and highlights the potential for CC-16 as a biomarker or therapeutic target.

genomics↗

Development and External Validation of the Acute COPD Exacerbation Prediction Tool (ACCEPT)

BackgroundAccurate prediction of exacerbation risk enables personalised chronic obstructive pulmonary disease (COPD) care. We developed and validated a generalisable model to predict the individualised rate and severity of COPD exacerbations. MethodsWe pooled data from three COPD trials on patients with a history of exacerbations. We developed a mixed-effect model to predict exacerbations over one-year. Severe exacerbations were those requiring inpatient care. Predictors were a history of exacerbations, age, sex, body mass index, smoking status, domiciliary oxygen therapy, lung function, symptom burden, and current medication use. ECLIPSE, a multicentre cohort study, was used for external validation. ResultsThe development dataset included 2,380 patients (mean 64{middle dot}7 years, 1373 [57{middle dot}7%] men, mean exacerbation rate 1{middle dot}42/year, 0{middle dot}29/year [20{middle dot}5%] severe). When validated against all COPD patients in ECLIPSE (n=1819, mean 63{middle dot}3 years, 1186 [65{middle dot}2%] men, mean exacerbation rate 1{middle dot}20/year, 0{middle dot}27/year [22{middle dot}2%] severe), the area-under-curve was 0{middle dot}81 (95%CI 0{middle dot}79-0{middle dot}83) for [&ge;]2 exacerbations and 0{middle dot}77 (95%CI 0{middle dot}74-0{middle dot}80) for [&ge;]1 severe exacerbation. Predicted rates were 0{middle dot}25/year for severe and 1{middle dot}31/year for all exacerbations, close to the observed rates (0{middle dot}27/year and 1{middle dot}20/year, respectively). In ECLIPSE patients with a prior exacerbation history (n=996, mean 63{middle dot}6 years, 611 (61{middle dot}3%) men, mean exacerbation rate 1{middle dot}82/year, 0{middle dot}40/year [22{middle dot}0%] severe), the area-under-curve was 0{middle dot}73 (95%CI 0{middle dot}70-0{middle dot}76) for [&ge;]2 exacerbations and 0{middle dot}74 (95%CI 0{middle dot}70-0{middle dot}78) for [&ge;]1 severe exacerbation. Calibration was accurate for severe exacerbations (predicted=0{middle dot}37/year, observed=0{middle dot}40/year) and all exacerbations (predicted=1{middle dot}80/year, observed=1{middle dot}82/year). The model is accessible at http://resp.core.ubc.ca/ipress/accept. InterpretationThis model can be used as a decision tool to personalise COPD treatment and prevent exacerbations. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSPreventing future exacerbations is a major goal in COPD care. Because of adverse effects, preventative treatments should be reserved for those at a higher risk of future exacerbations. Predicting exacerbation risk in individual patients can guide these clinical decisions. A 2017 systematic review reported that of the 27 identified COPD exacerbation prediction tools, only two had reported external validation and none was ready for clinical implementation. To find the studies that were published afterwards, we searched PubMed for articles on development and validation of COPD exacerbation prediction since 2015, using the search terms "COPD", "exacerbation", "model", and "validation". We included studies that reported prediction of either the risk or the rate of exacerbations and excluded studies that did not report external validation. Our literature search revealed two more prediction models neither of which was deemed generalisable due to lack of methodological rigour, or local and limited nature of the data available to investigators. Added value of this studyWe used data from three randomised trials to develop ACCEPT, a clinical prediction tool based on routinely available predictors for COPD exacerbations. We externally validated ACCEPT in a large, multinational prospective cohort. To our knowledge, ACCEPT is the first COPD exacerbation prediction tool that jointly estimates the individualised rate and severity of exacerbations. Successful external validation of ACCEPT showed that its generalisability can be expanded across geography and beyond the setting of therapeutic trials. ACCEPT is designed to be easily applicable in clinical practice and is readily accessible as a web application. Implications of all the available evidenceCurrent guidelines rely on a history of exacerbations as the sole predictor of future exacerbations. Simple clinical and demographic variables, in aggregate, can be used to predict COPD exacerbations with improved accuracy. ACCEPT enables a more personalised approach to treatment based on routinely collected clinical data by allowing clinicians to objectively differentiate risk profiles of patients with similar exacerbation history. Care providers and patients can use individualised exacerbation risk estimates to decide on preventive therapies based on objectively-established or patient-specific thresholds for treatment benefit and harm. COPD clinical researchers can use this tool to target enriched populations for enrolment in clinical trials.

epidemiology↗

Widespread Sexual Dimorphism in the Transcriptome of Human Airway Epithelium in Response to Smoking

Epidemiological studies have shown that female smokers are at higher risk of chronic obstructive pulmonary disease (COPD). Female patients have worse symptoms and health status and increased risk of exacerbations. We determined the differences in the transcriptome of the airway epithelium between males and females at baseline and in response to smoking. We processed public gene expression data of human airway epithelium into a discovery cohort of 211 subjects (never smokers n=68; current smokers n=143) and two replication cohorts of 104 subjects (21 never, 52 current, and 31 former smokers) and 238 subjects (99 current and 139 former smokers. We analyzed gene differential expression with smoking status, sex, and smoking-by-sex interaction and used network approaches for modules level analyses. We identified and replicated two differentially expressed modules between the sexes in response to smoking with genes located throughout the autosomes and not restricted to sex chromosomes. The two modules were enriched in autophagy (up-regulated in female smokers) and response to virus and type 1 interferon signaling pathways which were down-regulated in female smokers compared to males. The results offer insights into the molecular mechanisms of the sexually dimorphic COPD risk and presentation potentially enabling a precision medicine approach to COPD.

genomics↗

SNPs associated with HHIP expression have differential effects on lung function in males and females

Adult lung function is highly heritable and 279 genetic loci were recently reported as associated with spirometry-based measures of lung function. Though lung development and function differ between males and females throughout life, there has been no genome-wide study to identify genetic variants with differential effects on lung function in males and females. Here, we present the first genome-wide genotype-by-sex interaction study on four lung function traits in 303,612 participants from the UK Biobank. We detected five SNPs showing genome-wide significant (P<5 x 10-8) interactions with sex on lung function, as well as 21 suggestively significant interactions (P<1 x 10-6). The strongest sex interaction signal came from rs7697189 at 4:145436894 on forced expiratory volume in 1 second (FEV1) (P = 3.15 x 10-15), and was replicated (P = 0.016) in 75,696 individuals in the SpiroMeta consortium. Sex-stratified analyses demonstrated that the minor (C) allele of rs7697189 increased lung function to a greater extent in males than females (untransformed FEV1 {beta} = 0.028 [SE 0.0022] litres in males vs {beta} = 0.009 [SE 0.0014] litres in females), and this effect was not accounted for by differential effects on height, smoking or age at puberty. This SNP resides upstream of the gene encoding hedgehog-interacting protein (HHIP) and has previously been reported for association with lung function and HHIP expression in lung tissue. In our analyses, while HHIP expression in lung tissue was significantly different between the sexes with females having higher expression (most significant probeset P=6.90 x 10-6) after adjusting for age and smoking, rs7697189 did not demonstrate sex differential effects on expression. Establishing the mechanism by which HHIP SNPs have different effects on lung function in males and females will be important for our understanding of lung health and diseases, such as chronic obstructive pulmonary disease (COPD), in both sexes.

genetics↗

Leveraging lung tissue transcriptome to uncover candidate causal genes in COPD genetic associations

We collated 129 non-overlapping risk loci for chronic obstructive pulmonary disease (COPD) from the GWAS literature. Using recent and complementary integrative genomics approaches, combining GWAS and lung eQTL results, we identified 12 novel COPD loci and corresponding causal genes. In addition, we mapped candidate causal genes for 60 out of the 129 GWAS-nominated loci as well as for four sub-genome-wide significant COPD risk loci derived from the largest GWAS on COPD. Mapping causal genes in lung tissue represents an important contribution on the genetics of COPD, enriches our biological interpretation of GWAS findings, and brings us closer to clinical translation of genetic associations.

genomics↗

Characterising undiagnosed chronic obstructive pulmonary disease: a systematic review and meta-analysis

BackgroundA significant proportion of patients with chronic obstructive pulmonary disease (COPD) remain undiagnosed. Characterising these patients can increase our understanding of the hidden burden of COPD and the effectiveness of case detection interventions.\n\nMethodsWe conducted a systematic review and meta-analysis to compare patient and disease risk factors between patients with undiagnosed persistent airflow limitation and those with diagnosed COPD. We searched MEDLINE and EMBASE for observational studies of adult patients meeting accepted spirometric definitions of COPD. We extracted and pooled summary data on the proportion or mean of each risk factor among diagnosed and undiagnosed patients (unadjusted analysis), and coefficients for the adjusted association between risk factors and diagnosis status (adjusted analysis). This protocol is registered with PROSPERO (CRD42017058235).\n\nFindings2,083 records were identified through database searching and 16 articles were used in the meta-analyses. Diagnosed patients were less likely to have mild (v. moderate to very severe) COPD (odds ratio [OR] 0{middle dot}30, 95% CI 0{middle dot}24-0{middle dot}37, 6 studies) in unadjusted analysis. This association remained significant but its strength was attenuated in the adjusted analysis (OR 0{middle dot}72, 95% CI 0{middle dot}58-0{middle dot}89, 2 studies). Diagnosed patients were more likely to report respiratory symptoms such as wheezing (OR 3{middle dot}51, 95% CI 2{middle dot}19-5{middle dot}63, 3 studies) and phlegm (OR 2{middle dot}16, 95% CI 1{middle dot}38-3{middle dot}38, 3 studies), had more severe dyspnoea (modified Medical Research Council scale mean difference 0{middle dot}52, 95% CI 0{middle dot}40-0{middle dot}64, 3 studies) and slightly greater smoking history than undiagnosed patients. Patient age, sex, current smoking status, and the presence of coughing were not associated with a previous diagnosis.\n\nInterpretationPatients with undiagnosed persistent airflow limitation had less severe airflow obstruction and fewer respiratory symptoms than diagnosed patients. This indicates that there is lower disease burden among undiagnosed patients compared to those with diagnosed COPD, which may significantly delay the diagnosis of COPD.\n\nFundingCanadian Institutes of Health Research.\n\nDeclaration of interestsWe declare no competing interests.\n\nAuthor ContributionsMS, SB, and KJ formulated the study idea and designed the study. KJ and SG performed all data analyses and MS, SB and DS contributed to interpretation of findings. KJ wrote the first draft of the manuscript. All authors critically commented on the manuscript and approved the final version. MS is the guarantor of the manuscript.

epidemiology↗