Biology subjects

Waseem, M.

Publications and source records attributed to Waseem, M..

3 recordsLinked to original sources

bioRxiv2026

Human skin fibrosis with iPSC-derived organoids reveals RUNX2-mediated fibroblast reprogramming

Fibrotic skin diseases are characterized by persistent fibroblast activation and extracellular matrix remodeling, yet the mechanisms governing fibroblast state transitions remain incompletely understood. Here, we established a human iPSC-derived skin organoid model of fibrosis through chronic TGF-{beta} stimulation. Single-cell RNA sequencing combined with immunofluorescence-based spatial analysis revealed dynamic fibroblast state transitions, spatial reorganization, and expansion of activated fibroblast populations during fibrotic remodeling. Integration with human scleroderma single-cell datasets demonstrated conserved fibroblast states and transcriptional programs between organoids and patient tissues. We further identified broad induction of RUNX2 in the dermal compartment during fibrosis, and RUNX2 depletion attenuated fibrotic marker expression. CUT&RUN profiling revealed RUNX2 occupancy at fibrosis-associated loci, including RUNX1 and LOXL2. Using a machine learning-guided screening approach, we identified F0565-0303, a small molecule that suppressed RUNX2-dependent fibrotic programs in vitro and reduced fibrosis in a bleomycin-induced mouse model. Together, these findings establish human skin organoids as a platform for modeling fibrosis and nominate RUNX2 as a potential therapeutic target.

bioengineering↗

bioRxiv2026

Centromeric α-satellite DNA is a hotspot of genotoxic damage, incomplete repair, and cytoplasmic mislocalization

Centromeric -satellite DNA constitutes a highly repetitive and structurally specialized component of the human genome, yet the mechanisms underlying its damage susceptibility and repair fidelity under genotoxic stress remain undefined. Here, we demonstrate that genotoxic stress preferentially targets active centromeres, generating DNA double-strand breaks (DSBs) within -satellite arrays. Using bleomycin as a defined genotoxic perturbation, we identify dynamic alterations in centromeric repeat content, manifesting as net copy number losses and gains across multiple chromosome-specific -satellite arrays following damage. Similar centromere-associated damage signatures are observed in fibroblasts from patients with limited cutaneous systemic sclerosis, indicating that these features extend beyond experimental systems. Centromeric DSBs engage ATM-dependent DNA damage signaling and are repaired predominantly through RAD51-associated homologous recombination; however, repair fails to fully restore centromeric integrity. This incomplete repair is associated with defects in kinetochore organization, chromosome missegregation, and the formation of micronuclei containing centromeric DNA. Notably, [~]30% of these structures retain CENP-B but lacks detectable CENP-A, indicating disruption of centromere chromatin organization. Centromeric chromatin is frequently mislocalized to the cytoplasm following nuclear envelope perturbation, where immunofluorescence analysis reveals proximity to MHC class II (HLA-DRB1). Together, these findings establish centromeric -satellite DNA as a vulnerability hotspot under genotoxic stress, with implications for chromosome instability and chromatin antigen exposure in fibrosis-associated autoimmunity.

genetics↗

bioRxiv2025

Centromere instability links genome damage to immune activation in systemic sclerosis

Systemic sclerosis (SSc) is a fibrotic autoimmune disease in which genomic sources of instability and their immunological consequences remain poorly defined. We show that bleomycin, a widely used SSc fibrosis model, induces DNA double-strand breaks (DSBs) at active centromeres. Similar centromeric damage signatures were observed in fibroblasts from patients with limited cutaneous SSc, consistent with prior observations. Quantification of -satellite repeat content revealed dynamic changes in repeat abundance, consistent with deletions and insertions and incomplete restoration following damage. These breaks are repaired primarily ATM-dependent, RAD51-associated homologous recombination, but repair remains incomplete. Incomplete repair is associated with altered kinetochore assembly, chromosome missegregation, and increased formation of micronuclei and cytoplasmic chromatin enriched in centromere proteins. These fragments escape via nuclear envelope rupture and show spatial colocalization with MHC class II molecules. Together, these findings establish bleomycin-induced centromere damage as a tractable model to study active-centromere instability, its incomplete repair, and the resulting chromatin mislocalization in fibroblasts, with features relevant to systemic sclerosis.

genetics↗