Journal: bioRxiv

Article Title: Dissecting Regulatory Non-Coding Heart Disease GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Pathophysiological Relevance to Heart Failure

doi: 10.1101/2024.10.08.617295

Figure Lengend Snippet: Bulk RNA-seq of HCM, NHCFV, and iHCF cells. A) Pearson correlation coefficients of transcriptome-wide expression levels in HCM, NHCFV, and iHCF. B) Heatmap of expression levels (log 2 (FPKQ+1) of cardiomyocyte marker genes and cardiac fibroblast marker genes in cell types used in this study.

Article Snippet: Specifically, we cultured 50 million primary Human Cardiac Myocytes (HCM) cells as well as Normal Human Cardiac Fibroblasts – Ventricular (NHCFV) primary cells, which are commercially available from PromoCell and Lonza respectively.

Techniques: RNA Sequencing Assay, Expressing, Marker

Journal: bioRxiv

Article Title: Dissecting Regulatory Non-Coding Heart Disease GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Pathophysiological Relevance to Heart Failure

doi: 10.1101/2024.10.08.617295

Figure Lengend Snippet: Tracing regulatory circuits from GWAS signals to target genes using functional genomics. (A) Graphical summary of analyses annotating GWAS loci with 3D chromatin interaction and open chromatin data to prioritize functional variants and identify target genes that may underlie disease associations. Significant eQTLs further corroborated these SNP-gene relationships. (B) Analysis workflow for integration of genetic, expression, and functional genomic data. We layered significant pairwise interactions (chromatin loops) with SNPs and TSSs filtered for accessible regions and highlighted those in expressed TFs’ footprints and expressed target genes, as well as GTEx eQTLs, to identify putative active and functional SNP-gene pairs. (C) Genome-wide contact maps of high-resolution Hi-C interactions from primary human cardiac myocytes (HCM) and normal human cardiac fibroblasts –ventricular (NHCFV) (D) Number of GWAS SNPs associated with heart disease-related traits, including heart failure.

Article Snippet: Specifically, we cultured 50 million primary Human Cardiac Myocytes (HCM) cells as well as Normal Human Cardiac Fibroblasts – Ventricular (NHCFV) primary cells, which are commercially available from PromoCell and Lonza respectively.

Techniques: Functional Assay, Expressing, Genome Wide, Hi-C

Journal: bioRxiv

Article Title: Dissecting Regulatory Non-Coding Heart Disease GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Pathophysiological Relevance to Heart Failure

doi: 10.1101/2024.10.08.617295

Figure Lengend Snippet: Prioritization of active and functional heart disease-associated SNP-gene pairs in human cardiac myocytes (HCM) and normal human cardiac fibroblasts – ventricular (NHCFV) combining genetics, epigenetics, and transcriptomics. A) Sankey diagram of the cell type-specific variation observed in heart disease-associated SNPs and gene accessibility after filtering for open chromatin, chromatin interaction, and expression features, as outlined in . B) Quantification of accessible SNPs identified in HCM and NHCFV that are within known transcription factor (TF) footprints of TFs that also have detectable mRNA expression. C) Number and overlap of active and functional SNP-gene pairs and corresponding unique target genes identified by GOTHiC and HICCUPS across HCM and NHCFV cells.

Article Snippet: Specifically, we cultured 50 million primary Human Cardiac Myocytes (HCM) cells as well as Normal Human Cardiac Fibroblasts – Ventricular (NHCFV) primary cells, which are commercially available from PromoCell and Lonza respectively.

Techniques: Functional Assay, Expressing

Journal: Basic Research in Cardiology

Article Title: Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in heart failure with preserved ejection fraction

doi: 10.1007/s00395-024-01074-w

Figure Lengend Snippet: Comparison and interpretation of fibroblast disease signatures from different heart failure models. A Comparing intersections of upregulated genes in different heart failure (HF) models. B Intersection quantification via Jaccard index. C Comparison of direction of regulation between studies. Pearson correlation was calculated between log fold change vectors of signature genes in pairwise comparisons. Each study comparison was based on the upregulated genes from the study on the x-axis. ** p < 0.01. D Heatmaps of gene set overrepresentation in study specific fibroblast disease signatures. Hypergeometric test with Benjamini–Hochberg correction, * q < 0.01, ** q < 0.001, *** q < 0.0001. E Estimated pathway activities with PROGENy based on effect size (log fold change) of footprint genes compared between HF models. F Expression values of selected fibrosis and inflammatory genes in individual fibroblasts in HFpEF (purple) and control (orange) mice. All genes were significantly upregulated (Wilcoxon test, adj. p value < 0.05). G Immunofluorescence images of collagen IV (red) and DAPI (blue) staining of left ventricular heart sections. Lower panels show magnifications of the areas marked by white boxes. White arrows indicate capillaries or larger blood vessels. Scale bars in the right bottom corner indicate 50 μm length. H Immunohistological staining of Angptl4 protein in left ventricular heart sections

Article Snippet: Human primary cardiac ventricular fibroblasts (Lonza, #CC-2904) at passage 6 were cultured according to the manufacturers recommendations and respective basal and growth media.

Techniques: Comparison, Expressing, Control, Immunofluorescence, Staining

Journal: Basic Research in Cardiology

Article Title: Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in heart failure with preserved ejection fraction

doi: 10.1007/s00395-024-01074-w

Figure Lengend Snippet: Angptl4 improves diastolic dysfunction by reducing collagen IV deposition in vivo and in vitro. A In vivo study design comparing recombinant murine Angptl4 peptide (rANGPTL4, 200 ng in 50 µl NaCl) vs. NaCl control (0.9%, 50 µl) administration every second day i.p. for 5 weeks starting after 5 weeks of dietary induction. Murine HFpEF induction by 0.5 g/L L-NAME and 60% high-fat diet for 10 weeks in total. Echocardiography (echo) captured cardiac systolic and diastolic function at baseline, after 5 (prior to i.p. injection start) and 10 weeks. Created with BioRender. B Time course of diastolic function determined by E/E’ (PW Doppler velocity across the mitral valve (E) and peak tissue Doppler at the mitral valve annulus (E’) during early diastole). n = 10/10/9/9. C Comparison of the experimental groups after 10 weeks. n = 10/10/9/9. One-way ANOVA with Tukey correction for multiple comparison or Kruskal–Wallis test according to normality determined by Shapiro–Wilk test. p values < 0.09 shown above bars, p < 0.05 defined as statistically significant. HW/TL heart weight/ tibia length, LA left atrium, LVEF left ventricular ejection fraction, LWDd left ventricular lateral wall diameter in end-diastole from short axis views D Comparison of E/E’ after 10 weeks in HFpEF mice either treated with control or rANGPTL4. n = 9/9, unpaired t test, p value shown above bar. E Experimental design (left panel) of stimulating human ventricular cardiac fibroblasts (cFBs) in vitro with 2 µg/ml human recombinant ANGPTL4 or PBS for 24 h. Resulting mRNA levels (right panel) were determined by qPCR and values indicate fold change relative to control mean. n = 12/12, unpaired t test or Mann–Whitney test according to normality determined by Shapiro–Wilk test, p values shown above bars. Created with BioRender. F Representative immunofluorescence stainings of collagen IV 1:200 (pink) and DAPI (blue). Whole heart long-axis cryo-sections depicted in the top row with white boxes indicating magnifications shown in bottom row and respective scale bars. G Quantification of F by scanning whole heart sections using a slide scanner and semi-automated analysis of the whole left ventricular (LV) tissue by normalizing the collagen IV positive LV area to total LV area using QuPath. One-way ANOVA, p values < 0.05 shown above bars

Article Snippet: Human primary cardiac ventricular fibroblasts (Lonza, #CC-2904) at passage 6 were cultured according to the manufacturers recommendations and respective basal and growth media.

Techniques: In Vivo, In Vitro, Recombinant, Control, Injection, Comparison, MANN-WHITNEY, Immunofluorescence