Biology subjects

Fine, M.

Publications and source records attributed to Fine, M..

6 recordsLinked to original sources

bioRxiv2025

Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics

Subcellular RNA localization, including nuclear retention and apical-basal compartmentalization in polarized epithelia plays a central role in post-transcriptional regulation. However, methods for high-throughput mapping of mRNA localization within intact tissue sections remain limited. Here, we apply high-resolution spatial transcriptomics (VisiumHD) to systematically resolve intracellular mRNA localization across diverse mammalian tissues. We introduce a computational approach that extracts subcellular features from spatial data and quantifies transcript localization patterns. Using this framework, we map apical-basal mRNA localization and nuclear retention in gastrointestinal epithelia and in liver hepatocytes. Our analyses reveal conserved and tissue-specific localization signatures that can be readily obtained from standard high-definition spatial transcriptomics experiments. This approach broadens the scope of spatial transcriptomics by enabling routine investigation of intracellular RNA distributions in both healthy and diseased tissues.

systems biology↗

bioRxiv2024

Heat stress drives rapid viral and antiviral innate immunity activation in Hexacorallia

The cnidarian class Hexacorallia, encompassing stony corals and sea anemones, plays a critical role in marine ecosystems. Coral bleaching, the disruption of the symbiosis between stony corals and zooxanthellate algae, is driven by climate change-induced seawater warming and further exacerbated by pathogenic microbes. However, how pathogens, especially viruses, contribute to accelerated bleaching remains poorly understood. The present study utilizes the model sea anemone Nematostella vectensis to explore these dynamics by creating a transgenic line with a reporter gene regulated by sequences from two RIG-I-like receptor (RLR) genes involved in antiviral responses. Under heat stress, the reporter gene showed significant upregulation, indicating that these regulatory sequences are indeed responsive to thermal stress. Analyses of transcriptome data of N. vectensis, Exaiptasia diaphana (another sea anemone), and the stony coral Stylophora pistillata revealed stress-induced activation of a set of bona fide immune-related genes conserved between the three species. Population-specific differences in stress-induced transcriptional responses of immune-related genes were evident in both Nematostella and Stylophora, depending on geographic origin. In Exaiptasia, the presence or absence of zooxanthellae also influenced stress-induced immune gene expression. To test whether the viruses themselves may contribute to this immune response under stress, we subjected Nematostella polyps to variable periods of heat stress and measured the transcript levels of resident viruses as well as selected antiviral genes. While the antiviral genes responded within 1-3 hours of heat stress, viral gene expression was already upregulated within 30 minutes, suggesting that their increase might be contributing to the elevated immune response under stress, and consequentially, the further demise of organismal homeostasis. These findings highlight the complex interplay between environmental stress, viruses, immune responses, and symbiotic states in Hexacorallia. Better understanding of these mechanisms could provide insights into the role of immune pathways in coral resilience and bleaching in a changing climate.

evolutionary biology↗

bioRxiv2018

PIP4Ks Suppress Insulin Signaling Through a Catalytic-Independent Mechanism

Insulin stimulates conversion of phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) to phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P3), which mediates downstream cellular responses. PI(4,5)P2 is produced by phosphatidylinositol-4-phosphate 5-kinases (PIP5Ks) and byphosphatidylinositol-5-phosphate 4-kinases (PIP4Ks). Here we show that deletion of the three genes that encode PIP4Ks (PIP4K2A, PIP4K2B and PIP4K2C) in vitro results in a paradoxical increase in PI(4,5)P2 and a subsequent increase in insulin-stimulated production of PI(3,4,5)P3. Surprisingly, reintroduction of either wild-type or kinase-dead forms of the PIP4Ks restored cellular PI(4,5)P2 levels and insulin stimulation of the PI3K pathway. These effects are explained by an increase in PIP5K activity upon deletion of PIP4Ks, which we demonstrate can suppress PIP5K activity in vitro through a direct binding interaction. Collectively, our work reveals an important non-catalytic function of PIP4Ks in suppressing PIP5K-mediated PI(4,5)P2 synthesis and insulin-dependent conversion to PI(3,4,5)P3 by PI3K enzymes and suggests that pharmacological depletion of PIP4K enzymes using emerging degrader technologies could represent a novel strategy for stimulating insulin signaling.

cell biology↗

bioRxiv2018

Tissue- and cellular-level allocation of autotrophic and heterotrophic nutrients in the coral symbiosis -- A NanoSIMS study

Corals access inorganic seawater nutrients through their autotrophic endosymbiotic dinoflagellates, but also capture planktonic prey through heterotrophic feeding. Correlating NanoSIMS and TEM imaging, we visualize and quantify the subcellular fate of autotrophic and heterotrophic C and N in the coral Stylophora pistillata using stable isotopes. Six scenarios were compared after 6h: autotrophic pulse (13C-bicarbonate, 15N-nitrate) in either unfed or regularly fed corals, and heterotrophic pulse (13C-, 15N-labelled brine shrimps) in regularly fed corals; each at ambient and elevated temperature. Host assimilation of photosynthates was similar under fed and unfed conditions, but symbionts assimilated 10% more C in fed corals. Photoautotrophic C was primarily channelled into host lipid bodies, whereas heterotrophic C and N were generally co-allocated to the tissue. Food-derived label was detected in some subcellular structures associated with the remobilisation of host lipid stores. While heterotrophic input generally exceeded autotrophic input, it was more negatively affected by elevated temperature. The reduced input from both feeding modes at elevated temperature was accompanied by a shift in the partitioning of C and N, benefiting epidermis and symbiont. This study provides a unique view on the nutrient partitioning in corals and highlights the tight connection of nutrient fluxes in symbiotic partners.

physiology↗

bioRxiv2018

Massive surface membrane expansion without involvement of classical exocytic mechanisms.

Activation of TMEM16F, a Ca2+ -dependent ion channel and lipid scramblase, causes massive surface membrane expansion in multiple cell types by unresolved mechanisms. We describe here that membrane expansion reflects opening of deeply invaginating surface membrane compartments when anionic phospholipids are lost from the cytoplasmic membrane leaflet. Compartments that open contain vesicle-associated membrane proteins (VAMPs) and can open with as little as one micromolar free Cai2+. Cationic peptides that sequester anionic phospholipids open the compartments from the cytoplasmic side without Ca2+. Monovalent cations facilitate membrane expansion via coupled permeation with anionic phospholipids through TMEM16F. When monovalent cation concentrations are reduced, membrane expansion can be reversed by changing ion gradients and membrane voltage. Depolarization closes the compartments by generating inward cation gradients through TMEM16F that promote influx of anionic phospholipids. In summary, TMEM16F-mediated membrane expansion likely does not reflect exocytosis but rather the relaxation of constrictions that close surface membrane invaginations.\n\nSummaryThe surface membrane of diverse cell types can be remodeled by opening and closing surface invaginations that are held shut by proteins that bind negatively charged lipids and constrict the orifices of these compartments.

cell biology↗

bioRxiv2018

TMEM16F activation by Ca2+ triggers plasmalemma expansion and directs PD-1 trafficking

TMEM16F, an ion channel gated by high cytoplasmic Ca2+, is required for cell surface phosphatidylserine exposure during platelet aggregation and T cell activation. Here we demonstrate in Jurkat T cells and HEK293 cells that TMEM16F activation triggers large-scale surface membrane expansion in parallel with lipid scrambling. Following TMEM16F mediated scrambling and surface expansion, cells undergo extensive membrane shedding. The membrane compartment that expands the cell surface does not involve endoplasmic reticulum or acidified lysosomes. Surprisingly, T cells lacking TMEM16F expression not only fail to expand surface membrane, but instead rapidly internalize membrane via massive endocytosis (MEND). The T cell co-receptor PD-1 is selectively shed when TMEM16F triggers membrane expansion, while it is selectively internalized in the absence of TMEM16F. Its participation in this trafficking is determined by its single transmembrane domain. Thus, we establish a fundamental role for TMEM16F as a regulator of Ca2+-activated membrane trafficking.

cell biology↗