Effects of Acute and Chronic Type I Interferon Stimulation on Human Cardiomyocytes

Persistent type I interferon activity is a hallmark of systemic lupus erythematosus (SLE) and contributes to extra-renal organ injury, yet the temporal transcriptomic response of human cardiomyocytes has not been mapped. To address this gap, AC16 ventricular cardiomyocytes were stimulated with recombinant IFN-α (1 000 U mL⁻¹) under three time courses: a single 24 h pulse (acute), a 24 h pulse followed by a 5-day recovery (chronic-hold), and two 24 h pulses separated by a 4-day recovery (repeat). Triplicate RNA-seq profiles captured robust induction of canonical interferon-stimulated genes immediately after exposure, whereas expression largely returned to baseline after the recovery periods, indicating that the cardiomyocyte interferon response is transient rather than self-sustaining. The dataset comprises raw FASTQ files, md5 checksums, gene-level count tables, and TPM matrices, providing a reference for benchmarking innate immune–cardiac interactions, validating bioinformatic pipelines, and integrating multi-omics studies. Proteomic and metabolomic measurements from the same biological replicates are being deposited separately in public repositories and can be cross-referenced to extend analyses of interferon kinetics. AC16 cells (ATCC CRL-4021) were cultured in DMEM/F-12 plus 10 percent FBS at 37 °C with 5 percent CO₂ and treated with IFN-α or vehicle under the three regimens described above, with three independent biological replicates per condition. Total RNA (325 ng) was poly-A–enriched using the NEBNext Poly(A) Magnetic Isolation Module, and strand-specific libraries were prepared with the IDT xGen Broad-Range RNA Library Prep Kit (12 PCR cycles). Library size and concentration were verified on an Agilent 4200 TapeStation and Qubit fluorometer, pooled, and sequenced on an Illumina NovaSeq X (single-end 1 × 75 bp, target 30 million reads per sample). Reads were quality-trimmed with Trim Galore, aligned to GRCh38 using STAR 2.7.11a, and quantified at the gene level with featureCounts against Gencode v41; TPM normalization, differential expression with DESeq2, and PCA were performed in R. Library preparation and lane assignment were randomized to minimize batch effects, and standard QC metrics confirmed library complexity and alignment quality. Matching cell pellets were retained for proteomic and metabolomic analysis, which will be released through PRIDE and MetaboLights to facilitate multi-layer interrogation of interferon-driven pathways in SLE-relevant cardiac models.