Biology subjects

Koppelman, G. H.

Publications and source records attributed to Koppelman, G. H..

7 recordsLinked to original sources

bioRxiv2026

A repair-associated bronchial epithelial differentiation trajectory through KRT14+ basal and hillock-like cells drives airway inflammation and remodelling in childhood-onset asthma

The bronchial epithelium in asthma is vulnerable to damage and has impaired barrier function, but the mechanisms by which it contributes to airway inflammation and remodelling remain unclear. Here, we dissect these epithelial and immunological disease mechanisms by establishing a comprehensive single cell atlas of the bronchial wall from 21 patients with childhood-onset asthma and 25 matched healthy controls. We identify a novel asthma-associated non-canonical epithelial differentiation trajectory in which a repair-associated KLF4+ basal cell subset differentiates into KRT13+ hillock-like cells through a proliferative KRT14+ intermediate. In vitro cultured matched primary bronchial epithelial cells show that this trajectory is retained in absence of exogenous factors. We find that IL-13 induces hillock-like cell differentiation into CEACAM5hi goblet cells, driving goblet cell metaplasia. Repair-associated basal cells and transitioning CEACAM5hi hillock-like cells strongly contribute to airway inflammation and remodelling. In turn, dendritic cells and mast cells promote a state of highly active epithelial differentiation, which shows increased multiciliated cell fate decisions, in concordance with an increase in multiciliated cell death observed in asthma. Proportions of the epithelial cells of the non-canonical differentiation trajectory are associated with clinical outcomes such as disease severity, FeNO, and small airway function.

immunology↗

bioRxiv2026

UnBlender: validating individual analyses in respiratory bulk RNA-seq cell type deconvolution

Analysis of RNA-seq data of respiratory samples has contributed much to our understanding of lung disease. However, bulk RNA-seq data are dependent on both cell type composition and the transcriptional activity of these samples constituent cells, which complicates interpretation. Cell type deconvolution is frequently used to estimate cell type proportions of bulk transcriptomic gene expression data and improve interpretation of bulk transcriptomics data. However, accuracy of the estimated cell type proportions reported after deconvolution is unknown, which may have a negative impact on the validity of the conclusions drawn. Here, we present UnBlender, a pipeline that enables respiratory scientists to perform cell type deconvolution and routinely evaluate deconvolution accuracy of their approach. UnBlender allows for custom cell type deconvolution tailored to the research question at hand, using consensus cell type labels and validating the approach to promote accurate, reproducible results.

bioinformatics↗

bioRxiv2023

Childhood-onset asthma is characterized by airway epithelial hillock-to-squamous differentiation in early life

Childhood-onset asthma is characterized by Type 2-inflammation and airway wall remodeling, but mechanisms of asthma development in the first years of life remain unclear. Here, we investigate transcriptional changes in airway wall biopsies of 22 symptomatic one year old children and relate these to asthma at school age. We demonstrate that pre-asthmatic children (n = 10) overexpressed a gene signature characteristic for an airway epithelial differentiation trajectory via hillock cells towards squamous cells (adjusted p-value 8.06e-16), whilst there was no association with gene signatures of Type 2-inflammation or eosinophil activation. Genes expressed along this trajectory are linked to an altered epithelial barrier function, innate immune activation and extracellular matrix remodeling. Functional GWAS analysis supports a causal link between childhood-onset, but not adult-onset asthma, and the hillock-squamous cell differentiation trajectory. Next, we confirmed the presence of hillock-like cells at the RNA and protein level in pediatric upper and lower airway samples. These findings identify a novel mechanism by which an aberrant airway epithelial differentiation trajectory may contribute to a pre-asthmatic state, highlighting the difference between the early origins of childhood-onset asthma and adult asthma, and point to possible new targets for the early diagnosis and treatment of asthma in the first two years of life. One Sentence SummaryRNA sequencing in bronchial biopsies from wheezing infants and children < 2 years shows evidence for an airway epithelial hillock-to-squamous differentiation pathway that marks the development of asthma.

genomics↗

bioRxiv2023

Airway epithelial response to RSV is impaired in multiciliated and goblet cells in asthma

In patients with asthma, respiratory syncytial virus (RSV) infections can cause disease exacerbations by infecting the epithelial layer of the airways, inducing an innate and adaptive immune response. The type-I interferon antiviral response of epithelial cells upon RSV infection is found to be reduced in asthma in most -but not all-studies. Moreover, the molecular mechanisms that cause the differences in the asthmatic bronchial epithelium in response to viral infection are poorly understood. Here, we investigated the transcriptional response to RSV infection of primary bronchial epithelial cells (pBECs) from asthma patients(n=8) and healthy donors(n=8). The pBECs obtained from bronchial brushes were differentiated in air-liquid interface conditions and infected with RSV. After three days, cells were processed for single-cell RNA sequencing. A strong antiviral response to RSV was observed for all cell types present, from both asthma patients and healthy donors. Most differentially regulated genes following RSV infection were found in cells transitioning from basal to secretory. Goblet cells from asthma patients showed lower expression of genes involved in the interferon response. In multiciliated cells, an impairment of the signaling pathways involved in the response to RSV in asthma was observed, including no enrichment of the type-III interferon response. Our results highlight that the response to RSV infection of the bronchial epithelium in asthma and healthy airways was largely similar. However, in asthma, the response of goblet and the multiciliated cells was impaired, highlighting the need for studying airway epithelial cells at high resolution in the context of asthma exacerbations. What is already know on this topicThe airway epithelium response to RSV is altered in asthma. However, literature remains conflicted about the exact changes in the antiviral response, and the mechanisms causing these changes are yet to be found. What this study addsThis study describes extensively the response of the bronchial epithelial cells (BECs) to RSV for both healthy subjects and asthma patients, at a single-cell resolution. It highlights the major overlap between healthy and asthma in the antiviral response to RSV. It allows the identification of specific genes and cell types that show a different behavior in response to RSV in asthma compared to healthy. How this study might affect research, practice or policyOur study indicates that goblet and multiciliated cells are the most relevant BECs to further investigate in the context of drug development for RSV-induced asthma exacerbation. It also suggests that focusing research on the cross-talk between the epithelial and the immune cells, or into investigating a potential delayed response in asthma would be the best way forward into understanding the mechanisms involved in the asthma response to RSV.

molecular biology↗

bioRxiv2022

FDA-Approved Drug Screening in Patient-Derived Organoids Demonstrates Potential of Drug Repurposing for Rare Cystic Fibrosis Genotypes

BackgroundPreclinical cell-based assays that recapitulate human disease play an important role in drug repurposing. We previously developed a functional forskolin induced swelling (FIS) assay using patient-derived intestinal organoids (PDIOs), allowing functional characterization of CFTR, the gene mutated in people with cystic fibrosis (pwCF). CFTR function-increasing pharmacotherapies have revolutionized treatment for approximately 85% of people with CF, but a large unmet need remains to identify new treatments for all pwCF. MethodsWe used 76 non-homozygous F508del-CFTR PDIOs to test the efficacy of 1400 FDA-approved drugs on improving CFTR function, as measured in FIS assays. ResultsBased on the results of a secondary validation screen, we investigated CFTR elevating function of PDE4 inhibitors and currently existing CFTR modulators in further detail. We show that PDE4 inhibitors are potent CFTR function inducers in PDIOs and that CFTR modulator treatment rescues of CF genotypes that are currently not eligible for this therapy. ConclusionsThis study exemplifies the feasibility of high-throughput compound screening using PDIOs and we show the potential of repurposing drugs for pwCF that are currently not eligible for therapies. One-sentence SummaryWe screened 1400 FDA-approved drugs in CF patient-derived intestinal organoids using the previously established functional FIS assay, and show the potential of repurposing PDE4 inhibitors and CFTR modulators for rare CF genotypes.

molecular biology↗

bioRxiv2021

Integration of public DNA methylation and expression networks via eQTMs improves prediction of functional gene-gene associations

Gene co-expression networks can be used to infer functional relationships between genes, but they do not work well for all genes. We investigated whether DNA methylation can provide complementary information for such genes. We first carried out an eQTM meta-analysis of 3,574 gene expression and methylation samples from blood, brain and nasal epithelial brushed cells to identify links between methylated CpG sites and genes. This revealed 6,067 significant eQTM genes, and we observed that histone modification information is predictive of both eQTM direction and presence, enabling us to link many CpG sites to genes. We then generated a co-methylation network - MethylationNetwork - using 27,720 publicly available methylation profiles and integrated it with a public RNA-seq co-expression dataset of 31,499 samples. Here, we observed that MethylationNetwork can identify experimentally validated interacting pairs of genes that could not be identified in the RNA-seq datasets. We then developed a novel integration pipeline based on CCA and used the integrated methylation and gene networks to predict gene pairs reported in the STRING database. The integrated network showed significantly improved prediction performance compared to using a DNA co-methylation or a gene co-expression network alone. This is the first study to integrate data from two -omics layers from unmatched public samples across different tissues and diseases, and our results highlight the issues and potential of integrating public datasets from multiple molecular phenotypes. The eQTMs we identified can be used as an annotation resource for epigenome-wide association, and we believe that our integration pipeline can be used as a framework for future -omics integration analyses of public datasets. We provide supporting materials and results, including the harmonized DNA methylation data from multiple tissues and diseases in https://data.harmjanwestra.nl/comethylation/, the discovered and predicted eQTMs, the corresponding CCA components and the trained prediction models in a Zenodo repository (https://zenodo.org/record/4666994). We provide notebooks to facilitate use of the proposed pipeline in a GitHub repository (https://github.com/molgenis/methylationnetwork).

bioinformatics↗

bioRxiv2019

A cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease

Human lungs enable efficient gas exchange, and form an interface with the environment which depends on mucosal immunity for protection against infectious agents. Tightly controlled interactions between structural and immune cells are required to maintain lung homeostasis. Here, we use single cell transcriptomics to chart the cellular landscape of upper and lower airways and lung parenchyma in health. We report location-dependent airway epithelial cell states, and a novel subset of tissue-resident memory T cells. In lower airways of asthma patients, mucous cell hyperplasia is shown to stem from a novel mucous ciliated cell state, as well as goblet cell hyperplasia. We report presence of pathogenic effector Th2 cells in asthma, and find evidence for type-2 cytokines in maintaining the altered epithelial cell states. Unbiased analysis of cell-cell interactions identify a shift from airway structural cell communication in health to a Th2-dominated interactome in asthma.

immunology↗