Biology subjects

Arava, M.

Publications and source records attributed to Arava, M..

3 recordsLinked to original sources

bioRxiv2025

Resolving the molecular niche of pulmonary fibrosis using cryopreserved human precision cut lung slices

Background and methodsPulmonary fibrosis (PF) manifests locally and heterogeneously in the diseased lung. To uncover mechanistic underpinnings, we have utilized cryopreserved fibrotic human precision-cut lung slices (PCLS), and using single-cell spatial transcriptomics, mapped and interpreted the transcriptomic regulation of effector cell types/states. ResultsCryopreserved-thawed fibrotic human PCLS retained canonical molecular and cellular PF hallmarks including fibroblast and myofibroblast accumulation, epithelial depletion, and vascular remodeling. Notably, these cellular changes were spatially co-incident with 1) collagen-rich regions enriched for extracellular matrix (ECM)-related genes (e.g., COL1A1, SPARC), 2) expanded fibroblast-endothelial crosstalk with enhanced chemokine signaling (CXCL12- CXCR4), 3) integrin-driven mesenchymal signaling targets (ANGPTL-integrin), 4) stress-adapted and immune-interacting Alveolar Type 2 cells with impaired surfactant gene expression, and 5) endothelial reprogramming toward a contractile and profibrotic phenotype. At the transcriptomic level, the spatially-defined fibrotic niche was characterized by increased gene expression related to immune responses (IGKC and IGHG1), fibrosis (collagen, fibronectin, and DCN), mechanotransduction (MYH11, TPM2, ACTG2, ACTA2), immune cell recruitment (CCL2, IL6, ICAM1), ECM remodeling (e.g. thrombospondin 1, THBS1), and decreased gene expression related to surfactant production (SFTPB, SFTPC). At the functional level, the fibrotic niches were defined by the activation of three fibroblast mediating signaling pathways: (1) the matricellular glycoprotein, SPARC, (2) Relaxin signaling, and (3) multiple immunoglobulin transcripts, including IGHA1, IGHG1, IGHG3, and IGKC. ConclusionsWe verify model fidelity, identify both known and unanticipated pro-fibrotic genes, and advocate for the expanded use of spatial transcriptomic measurements using cryopreserved human PCLS for disease modeling and drug discovery.

genomics↗

bioRxiv2023

Gene-specific reactivation of X-linked genes upon Xist loss is linked to the chromatin states in extraembryonic endoderm and epiblast stem cells

In eutherian mammals, X-chromosome dosage between sexes is balanced through the inactivation of one of the two X-chromosomes in female cells. In mouse, X-inactivation initiates at [~]4-8 cell stages of embryogenesis, where paternal-X undergoes imprinted X-inactivation. Subsequently, it switches to random X-inactivation in post-iplantation epiblast. The initiation of XCI is orchestrated by Xist. However, the role of Xist in the maintenance of X-chromosome inactivation remains underexplored. Here, we have explored the role of Xist in the maintenance of X-inactivation in extraembryonic endoderm stem cells (XEN) and epiblast stem cells (EpiSC), which undergo imprinted and random form of X-inactivation respectively. We show that removal of Xist leads to the partial reactivation of inactive-X chromosome. Intriguingly, many reactivated genes were found to be common between XEN and EpiSC, indicating these genes require Xist to maintain their silent state irrespective of the lineages or forms of X-inactivation. Notably, despite Xist ablation and the subsequent removal of DNA methylation, several X-linked genes remained resistant to reactivation, indicating the involvement of other factors in maintaining the silencing of these genes. On the other hand, we show that genes on the inactive-X with low levels of H3K9me3 and high levels of H3K27me3 are more susceptible to reactivation upon the loss of Xist. Interestingly, active-X homolog of the reactivated genes was found to be enriched with H3K4me3 and H3K27ac. Taken together, our study sheds light on the role of chromatin states in the reactivation of X-linked genes following the loss of Xist in XEN and EpiSC.

genetics↗

bioRxiv2019

Single Cell Analysis Reveals Partial Reactivation of X-chromosome Instead of chromosome wide dampening in Naive Human Pluripotent Stem Cells

Recently, a unique form of X-chromosome dosage compensation has been demonstrated in human preimplantation embryos, which happens through the dampening of X-linked gene expression from both X-chromosomes. Subsequently, X-chromosome dampening has also been demonstrated in female human pluripotent stem cells (hPSCs) during the transition from primed to naive state. However, the existence of dampened X-chromosomes remains controversial in both embryos and hPSCs. Specifically, in preimplantation embryos it has been shown that there is inactivation of X-chromosome instead of dampening. Here, we have performed allelic analysis of X-linked genes at the single cell level in hPSCs and found that there is partial reactivation of the inactive X-chromosome instead of chromosome-wide dampening upon conversion from primed to naive state. In addition, our analysis suggests that the reduced X-linked gene expression in naive hPSCs might be the consequence of erasure of active X-chromosome upregulation.

genetics↗