biostudies-arrayexpressDavid JohnMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17560Clonal haematopoiesis (CH), the expansion of blood-cell clones carrying acquired mutations, is an independent risk factor for cardiovascular disease. Although mutations in DNMT3A and TET2 are well studied, the cardiovascular consequences of KDM6A mutations remain unclear. KDM6A is an X-linked histone demethylase that is commonly mutated in patients with heart failure. Here, we perform multi-omics profiling and functional characterisation of mouse models and patient-derived data to show that haematopoietic KDM6A loss impairs cardiac recovery after myocardial infarction. KDM6A deficiency increases myeloid-cell recruitment to the injured heart and reprogrammes monocytes, macrophages and neutrophils towards inflammatory, migratory and glycolytic states. Patients with heart failure and KDM6A-driven CH show similar pro-inflammatory monocyte signatures. KDM6A-silenced macrophages promote cardiomyocyte hypertrophy and cardiac fibroblast activation. Importantly, IL-1β blockade post-MI rescued the adverse cardiac phenotype of haematopoietic KDM6A loss. These findings identify KDM6A-driven CH as a driver of immune dysregulation and IL-1β signalling as a potential therapeutic target in in CH-associated heart failure.biostudies-arrayexpressNucleic Acid Extraction - Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s guidelines. RNA content and purity were assessed by spectrophotometry (NanoDrop Technologies). mRNA expression was quantified by RT-qPCR using total RNA, which was reversed transcribed by MuLV reverse transcriptase (Thermo Fisher Scientific) and random hexamer primers (Thermo Fisher Scientific)Sample Collection - VaviCre (B6.Cg-Commd10Tg(Vav1-icre)A2Kio/J, Jackson laboratory) heterozygous male mice were bred with female Kdm6afl/fl (B6;129S-Kdm6atm1.1Kaig/J, Jackson laboratory) homozygous mice to establish VaviCreKdm6afl/f offspring with a haematopoietic specific KDM6A knockout (referred to in this manuscript as Kdm6aΔ-Haem mice). Control mice (referred to in this manuscript as Kdm6aWT mice) were littermates lacking the VaviCre transgene. Phenotyping experiments included both male and female mice.Library Construction - cDNA synthesis was performed according to the protocol: (Primer annealing) 65°C x 5 min, (Primer elongation) 25°C x 10 min, (Reverse transcription) 37°C x 50 min, (Enzyme denaturation) 70°C x 15 min. Expression levels of mRNA were detected by using Fast SYBR Green Applied Biosystems and an Applied Biosystems Viia7 machine. Cycling conditions on the machine were as follows: (Hold) 95°C x 30 sec, (PCR) 95°C x 1 sec, 60°C x 20 sec repeated for 40 cycles, (Melt curve) 95°C x 15 sec, 60°C x 60 sec, 95°C x 15 sec. Expression levels were additionally detected using the Taqman based system using the TaqMan™ Fast Advanced Master Mix. Cycling conditions on the machine were as follows: (Hold) 95°C x 20 sec, (PCR) 95°C x 1 sec, 60°C x 20 sec repeated for 40 cycles. Relative gene expression was calculated with the QuantStudio Real-Time PCR software (version 1.3) using 2-ΔCt or 2-ΔΔCt. Rplp0 was used as housekeeping gene. SYBR green sequences and Taqman probe IDs can be found in the Supplementary Table.Sample Treatment - urine IL-1β was inhibited post-MI via intraperitoneal injection of InVivoMAb anti-mouse/rat IL-1β antibody (Armenian hamster IgG isotype, clone B122, BE0246, BioXcell) at a dosage of 10mg/kg. Control animals were given InVivoMAb polyclonal Armenian hamster IgG (BE0091, BioXcell) at the same dosage. Injection volume was 100μl and the dilutant was InVivoPure pH 7.0 Dilution Buffer (BioXcell). Mice were given a total of 4 injections post-MI; the first one 2 hours post-MI and then three more at a weekly basis before termination of the experiment at 4 weeks post-MI.Growth Protocol - The animals were sedated using isoflurane, and pain relief was provided through an intraperitoneal injection of Buprenorphine (0.1 mg/kg body weight) along with an intercostal nerve block using Bupivacaine (1 mg/kg body weight, 0.25% concentration). For postoperative pain management, Buprenorphine and Carprofen (5 mg/kg body weight) were administered every 12 or 24 hours for three days. To prevent infection after surgery, Ampicillin (100 mg/kg body weight) was added to the drinking water. The myocardial infarction (MI) was induced by permanently ligating the left anterior descending coronary artery while the animals were under mechanical ventilation.Sequencing - For genome-wide analysis of gene expression, RNA sequencing libraries from isolated mRNA were generated and sequenced by the Institute for Lung Health (ILH) – Genomics and Bioinformatics – at the Justus-Liebig-University (JLU) Giessen (Germany). Total RNA (200 ng) was used to enrich for polyadenylated mRNA followed by cDNA sequencing library preparation utilizing the Illumina® Stranded mRNA Prep Kit (Illumina) according to the manufacturer’s instructions. After library quality control by capillary electrophoresis (4200 TapeStation, Agilent), cDNA libraries were sequenced on the Illumina NextSeq 2000 platform generating 50 bp paired-end reads.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Reads were mapped via STAR (v2.7.11b) against the mouse reference genome (GRCM38.97) with the additional parameters --quantMode GeneCounts and --outSAMtype BAM SortedByCoordinate. Gene count matrices were analyzed with DESeq2 (version 1.52.0)64 in R. Differential gene expression was performed comparing anti-IL-1β-treated samples with IgG controls using a design of ~ treatment. Lowly expressed genes were filtered by retaining genes with counts ≥10 in at least two samples. Gene set enrichment analysis was performed with fgsea with mouse MSigDB Hallmark gene sets. Genes were ranked by the DESeq2 Wald statistic and enrichment significance was assessed using FDR-adjusted p-values.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 2000RNA-seq of coding RNAMus musculusDavid JohnfalseHaematopoietic loss of KDM6A impairs cardiac recovery in heart failure via epigenetic reprogramming of myeloid cells (Bulk RNA-SEQ Mouse)Clonal haematopoiesis (CH), the expansion of blood-cell clones carrying acquired mutations, is an independent risk factor for cardiovascular disease. Although mutations in DNMT3A and TET2 are well studied, the cardiovascular consequences of KDM6A mutations remain unclear. KDM6A is an X-linked histone demethylase that is commonly mutated in patients with heart failure. Here, we perform multi-omics profiling and functional characterisation of mouse models and patient-derived data to show that haematopoietic KDM6A loss impairs cardiac recovery after myocardial infarction. KDM6A deficiency increases myeloid-cell recruitment to the injured heart and reprogrammes monocytes, macrophages and neutrophils towards inflammatory, migratory and glycolytic states. Patients with heart failure and KDM6A-driven CH show similar pro-inflammatory monocyte signatures. KDM6A-silenced macrophages promote cardiomyocyte hypertrophy and cardiac fibroblast activation. Importantly, IL-1β blockade post-MI rescued the adverse cardiac phenotype of haematopoietic KDM6A loss. These findings identify KDM6A-driven CH as a driver of immune dysregulation and IL-1β signalling as a potential therapeutic target in in CH-associated heart failure.2026-08-24T00:00:00Z2026-08-24T01:00:51.164Z2026-08-21T14:25:05.098ZE-MTAB-17560ERP204077EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969