Ariceta, B. | Search bioRxiv

bioRxiv2026

Mapping Disease Transitions from Premalignant, Asymptomatic to Advanced Myeloma through Integrative Epigenomic and Transcriptional Analyses

AbstractMultiple myeloma (MM) evolves from asymptomatic precursor conditions through progressive genetic and epigenetic remodeling, yet the regulatory mechanisms driving the development toward more active stages of the disease remain poorly understood. Here, we integrated bulk-based paired chromatin accessibility and activation, and transcriptomic profiling across disease stages to map regulatory remodeling during myeloma development. We identified a progressive increase in chromatin accessibility; furthermore, this epigenetic reconfiguration is accompanied by a stage-dependent shift from promoter-centered regulation in precursor states toward enhancer-dominated transcriptional control in active MM. Motif enrichment and regulatory network analyses identified both established and previously underappreciated transcription factors (TFs), including members of the IRF, MEF2, and FOX families, associated with disease-stage-specific transcriptional programs. Among these, MEF2D and FOXK2 emerged as candidate regulators of pathways involved in cell survival and chemotaxis. Functional perturbation demonstrated that MEF2D depletion markedly impaired MM cell viability, whereas inhibition of either MEF2D or FOXK2 reduced chemotactic migration. Together, these findings provide a stage-resolved framework of epigenetic and transcriptional remodeling across myeloma development, revealing regulatory programs established in precursor conditions and progressively reinforced during disease evolution, while identifying candidate transcriptional dependencies with potential biological and therapeutic relevance.

cancer biology↗

bioRxiv2026

Clonal Hematopoiesis Instructs Maladaptive Tissue Repair to Promote Fibrosis

Tissue repair is increasingly recognized as a systemic process influenced by age-associated changes beyond the injured organ itself. Clonal hematopoiesis of indeterminate potential (CHIP), a common consequence of somatic evolution in hematopoietic stem cells, has been linked to inflammatory disorders, yet whether it directly regulates tissue remodeling remains unclear. Here, we integrate population genomics, preclinical models, and human lung analyses to examine the role of CHIP in fibrotic lung disease. In large cohorts, idiopathic pulmonary fibrosis (IPF) was associated with a distinct CHIP mutational spectrum enriched for non-DNMT3A variants and for larger mutant clones. In mouse models, hematopoietic mutations exacerbated bleomycin-induced fibrosis and reprogrammed macrophages toward inflammatory, profibrotic states, including expansion of a distinct, injury-responsive SPP1+ population conserved in human disease. CHIP-associated macrophages were sufficient to directly promote fibroblast activation and alter epithelial differentiation, linking hematopoietic genotype to parenchymal remodeling. Consistently, a CHIP-derived macrophage transcriptional signature predicted adverse outcomes in independent IPF cohorts. Notably, immune and epithelial alterations were detectable even in the absence of overt injury, indicating that CHIP establishes a primed tissue environment permissive for maladaptive repair. Together, these findings identify clonal hematopoiesis as a systemic regulator of tissue repair and demonstrate that somatic evolution in blood can actively instruct organ remodeling through immune-parenchymal interactions. This framework supports the possibility that disease-associated selective pressures may shape clonal architecture with functional consequences for organ health.

immunology↗