Biology subjects

Moskwa, N.

Publications and source records attributed to Moskwa, N..

5 recordsLinked to original sources

bioRxiv2026

A Denisovan-derived Alu insertion in OCA2 contributes to pigmentation diversity in present-day Melanesians

Modern humans inherited DNA from Neanderthals and Denisovans, but the contribution of introgressed structural variants (SVs) to present-day human phenotypes and adaptation remains poorly understood. Here, we used a graph-genome approach to genotype 96,277 SVs in 3,332 present-day humans and three high-coverage archaic hominin genomes, identifying 153 candidate introgressed SVs. These SVs are enriched for signatures of local adaptation compared to non-introgressed SVs (p-value = 3.04 x 10-7). Among these, we focused on a Denisovan-derived Alu insertion located in intron 18 of OCA2, a gene central to pigmentation. This introgressed Alu insertion is most frequently observed (> 60%) in Indigenous people from Bougainville Island of Melanesia, and is significantly associated with increased skin pigmentation in this region. To assess its functional impact, the Alu insertion was introduced into human induced pluripotent stem cells (iPSCs), which were subsequently differentiated into melanocytes. Melanocytes harboring the Alu insertion demonstrated elevated OCA2 expression, increased pigmentation, and higher levels of enhancer activity compared to controls. Collectively, these findings highlight introgressed SVs as a significant source of adaptive and phenotypic diversity in modern humans and implicate the Denisovan-derived Alu insertion in OCA2 in pigmentation variation among present-day Melanesian populations.

genomics↗

bioRxiv2025

Structural Variants at Intronic CTCF Loop Anchors Drive Differential Exon Usage

CTCF-mediated chromatin loops are known to influence gene regulation, yet their role in pre-mRNA splicing remains incompletely understood. Here, we demonstrate that structural variants (SVs) at the anchors of intronic CTCF loops can modulate exon usage. By integrating high-resolution three-dimensional (3D) genome organization and gene expression datasets from C57BL/6J (B6) and 129S1/SvImJ (129S) mouse embryonic stem cells (ESCs), with structural variant (SV) maps from the 129S mouse, we identified thousands of intron-anchored CTCF loops. Our data indicate that SVs intersecting loop anchors are more frequently associated with differential exon inclusion events than with changes in overall gene expression. CRISPR/Cas9 deletion of two SV-harboring intronic CTCF sites in Numbl and Ireb2 validated the predicted splicing shifts observed between B6 and 129S ESC that correspond with diminished long-range chromatin looping. Our findings reveal a direct mechanistic link between 3D genome architecture and alternative splicing and highlight non-coding SVs as modulators of transcript diversity. Our study has thus identified a novel class of CTCF-bound regulatory elements regulating alternative splicing. Cataloging and validating these functional elements will elucidate molecular mechanisms underlying phenotypic variation within populations.

molecular biology↗

bioRxiv2021

PDFGRα+ Stromal Cells Promote Salivary Gland Proacinar Differentiation Through FGF2-dependent BMP7 Signaling.

3.0Stromal cells can direct epithelial differentiation during organ development; however, these pathways remain poorly defined. FGF signaling is essential for submandibular salivary gland development, and FGF2 can regulate proacinar cell differentiation in organoids through autocrine signaling in stromal cells. We performed scRNA Seq and identified stromal cell subsets expressing Fgf2 and Fgf10 that also express Pdgfr. When combined with epithelial cells in organoids, MACS-sorted PDGFR+ cells sufficiently promoted proacinar differentiation. Gene expression analysis revealed FGF2 activates the gene Bmp7 in the stroma. BMP7 could replace stromalsignaling and stimulate epithelial acinar differentiation but not branching. However, in the absence of FGF2, pathway analysis revealed that the stromal cells differentiated into myofibroblasts. Myofibroblast differentiation was induced when we treated organoids with TGF{beta}1, which also prevented proacinar differentiation. Conversely, FGF2 reversed TGF{beta}s effects. Dissecting pathways driving acinar differentiation will facilitate development of regenerative therapies. 2.0 Summary StatementEmbryonic salivary glands contain multiple stromal cell populations. FGF2 maintains the stromal Pdgfr+ population in-vitro. The PDGFR+ stromal cells drive early epithelial secretory cell differentiation using BMP7.

developmental biology↗

bioRxiv2021

Unlabeled salivary gland organoids have distinct Raman signatures following FGF2-induced proacinar cell differentiation

Organoids are self-organized three-dimensional (3D) tissue cultures that model the structure and function of organs to provide insights into signaling during organ formation and have translational applications in disease modeling and assessing drug responses. Due to their heterogeneity, there is a need for non-destructive methods to identify the differentiation state, or the phenotype, of organoids. As organoids often contain complex mixtures of basement membrane and/or extracellular matrix proteins, which are often highly auto-fluorescent, it typically makes low-resolution Raman measurements a challenge. We developed Raman confocal micro-spectroscopy methods to avoid and minimize the matrix signal and define specific Raman signatures for growth factor-differentiated and non-differentiated organoids. In complex, branched salivary gland organoids derived from mouse embryonic epithelial and stromal cells embedded within the laminin-rich basement membrane matrix, Matrigel, we identified specific Raman spectral signatures for organoids in different differentiation states. We report that either comparison of spectral signatures or multivariate SVD analysis can be used to distinguish between organoids treated with FGF2, organoids treated with EGF, and non-treated controls. Raman spectral signatures can be used to non-invasively distinguish between different phenotypes in the 3D context of unlabeled organoids. HighlightsO_LIFGF2-dependent proacinar cell differentiation in salivary organoids have unique Raman signatures detected with a novel confocal-based Raman imaging approach. C_LIO_LIThese signatures can be used in unlabeled salivary organoids to monitor proacinar cell differentiation. C_LIO_LIConfocal-based Raman imaging may be applicable to monitoring differentiation state of other types of organoids. C_LI

biophysics↗

bioRxiv2021

The Transcriptional Co-Activator Taz Contributes to the Differentiation of a Salivary Gland Epithelial Cell Line Towards a Myoepithelial Phenotype

The salivary gland can be permanently impaired by radiation treatment for head and neck cancers. Efforts at tissue regeneration have focused on saliva-producing acinar cells. However, myoepithelial cells are also critical to gland function, but mechanisms that regulate their differentiation are poorly defined. To study myoepithelial differentiation, we employed mSG-PAC1 murine salivary gland epithelial cells. We demonstrate that mSG-PAC1 spheroids exhibit phenotypic plasticity between pro-acinar and myoepithelial cell fates. Increased expression of pro-acinar/acinar or myoepithelial RNAs was identified from spheroids cultured under different media conditions by microarray followed by gene-set enrichment analysis. Spheroids cultured with different medium components expressed proteins typical of either acinar or myoepithelial cells, as detected by immunocytochemistry. We demonstrate that the pattern of TAZ expression in the epithelial compartment of the differentiating murine salivary gland correlates with the expression of the myoepithelial marker alpha-SMA, as is the case for TAZ expression in mSG-PAC1 spheroids. Our analysis also indicates that YAP/TAZ target genes are upregulated together with myoepithelial markers. Importantly, siRNA targeting of TAZ expression in mSG-PAC1 spheroids diminished the expression of myoepithelial markers. Our results in this in vitro cell model implicate TAZ signaling in myoepithelial differentiation.

cell biology↗