Biology subjects

Koksal, B.

Publications and source records attributed to Koksal, B..

4 recordsLinked to original sources

bioRxiv2026

Gene function and expression profiling in yeast spores, killifish diapause embryos, and their post-dormant offspring cells

Dormancy is a reversible cellular state characterised by suspended proliferation and increased stress resilience, enabling long-term viability under adverse conditions. Although dormant cells are critical for the life cycle of diverse organisms, from microbes to humans, they are understudied compared to proliferating cells. We present a comparative investigation of dormant cells in two divergent species: spores of fission yeast and diapause embryos of turquoise killifish. A genome-wide screen for genes affecting the lifespan and heat-shock resilience of spores uncovered a trade-off between longevity and heat resistance, and considerable differences in the genetic basis for lifespan between spores and chronologically aging yeast cells. RNA-seq and mass-spectrometry analyses revealed substantial transcriptomic and proteomic changes in spores and diapause embryos, with ribosomal proteins induced as transcripts but repressed as proteins. Transcriptomic regulation of biological processes, but less so of specific genes, is broadly conserved across yeast spores, killifish diapause, and human dormant cancer cells, including the induction of autophagy- and translation-related processes and the repression of cell cycle-related processes. Spores and diapause embryos modulate their transcriptomes and proteomes in response to heat stress and prolonged time. These RNA and protein expression changes are uncoupled and differ from aging-related expression signatures in yeast cells and adult fish. Cells derived from older or stressed spores retain phenotypic differences for several cell divisions, reflected in altered expression signatures, lifespan and stress resilience. Similarly, diapause duration and heat exposure are associated with long-term expression signatures in post-diapause embryos before hatching. This study highlights core biological processes and principles that are remarkably conserved in distinct types of dormant cells.

genetics↗

bioRxiv2025

Obesogenic diet alters decidual differentiation and cell-cell communication in the mouse uterus

Maternal obesity is associated with increased risk of infertility, implantation failure, miscarriage, and other pregnancy complications. While prior studies have linked obesity to uterine dysfunction and impaired endometrial biology, how obesity alters the cellular and molecular landscape of the early pregnant endometrium remains poorly understood. Here, we perform single-cell RNA sequencing of embryonic day 5.5 uterus from control and obesogenic mice to generate a cellular atlas of the early decidualizing endometrium. We identify obesity-associated transcriptional changes across multiple Endometrial Stromal Cell (ESC) states and innate immune populations, including uterine natural killer cells and macrophages. Computational modeling reveals that maternal obesity disrupts distinct routes of ESC differentiation during decidualization and leads to shifts in ESC-derived cues known to impact innate immune responses. These findings provide a comprehensive single-cell resource of the post-implantation mouse endometrium while simultaneously generating critical insight into how maternal obesity reprograms the maternal-fetal interface in early pregnancy.

developmental biology↗

bioRxiv2022

Single-cell assessment of trophoblast stem cell-based organoids as human placenta-modeling platforms

The recent discovery of human trophoblast stem cells (hTSC) and techniques allowing for trophoblast organoid (TOrg) culture have established promising approaches for studying human trophoblast development. To validate the accuracy of these models at single-cell resolution, we directly compared in vitro TOrg cultures derived from primary progenitor cytotrophoblasts (CTB) or commercially available hTSC lines to in vivo human trophoblasts using a scRNA-seq approach. While patient-derived (PD)- and hTSC-derived TOrgs overall reflect cell differentiation trajectories with accuracy, specific features related to trophoblast state make-up, distinct sub-paths of differentiation, and predicted transcriptional drivers regulating stem cell maintenance were shown to be misaligned in the in vitro platforms. This is best exemplified by the identification of a distinct progenitor state in hTSC-derived TOrgs that showed characteristics of CTB- and extravillous-like cell states. Together, this work provides a comprehensive resource that identifies underlying strengths and limitations of current TOrg platforms. Summary StatementSingle-cell transcriptomics provides comprehensive comparison between trophoblast organoids derived from commercially available trophoblast stem cells and first-trimester primary human cytotrophoblasts. HIGHLIGHTSO_LIAn integrated single cell transcriptomic atlas of placental and organoid trophoblasts establishes a comprehensive and public web-based resource C_LIO_LIDirect comparison of trophoblasts from placental/decidual tissue to trophoblasts extracted from two distinct organoid platforms highlights both conserved and divergent features C_LIO_LIComputational modeling describes novel trophoblast states and routes of cell differentiation in human trophoblast organoids C_LI IN BRIEFWhile the merits and utility of current trophoblast organoid cultures have been established, high-resolution assessment and comparison of conserved and divergent features of these systems to cell states and differentiation trajectories of trophoblasts in situ or in vitro has not been performed. Here, Shannon et al. generate a single-cell transcriptomic atlas of two trophoblast organoids that comprehensively define the similarities and discrepancies in relation to trophoblasts from the placental-maternal interface.

developmental biology↗

bioRxiv2021

Hypoxia induces a transcriptional early primitive streak signature in pluripotent cells enhancing spontaneous elongation and lineage representation in gastruloids

The cellular microenvironment together with intrinsic regulators shapes stem cell identity and differentiation capacity. Mammalian early embryos are exposed to hypoxia in vivo and appear to benefit from hypoxic culture in vitro. Yet, components of the hypoxia response and how their interplay impacts stem cell transcriptional networks and lineage choices remain poorly understood. Here we investigated the molecular effects of acute and prolonged hypoxia on distinct embryonic and extraembryonic stem cell types as well as the functional impact on differentiation potential. We find a temporal and cell type-specific transcriptional response including an early primitive streak signature in hypoxic embryonic stem (ES) cells. Using a 3D gastruloid differentiation model, we show that hypoxia-induced T expression enables symmetry breaking and axial elongation in the absence of exogenous WNT activation. Importantly, hypoxia also modulates T levels in conventional gastruloids and enhances representation of endodermal and neural markers. Mechanistically, we identify Hif1 as a central factor that mediates the transcriptional response to hypoxia in balance with epigenetic and metabolic rewiring. Our findings directly link the microenvironment to stem cell function and provide a rationale supportive of applying physiological conditions in models of embryo development

developmental biology↗