Biology subjects

Sun, S.

Publications and source records attributed to Sun, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

The Pathological Role and Therapeutic potential of ALDH2 in acrolein detoxification Following Spinal Cord Injury in Mice

Oxidative stress and lipid peroxidation-derived aldehydes, such as acrolein, play a central role in the pathology of spinal cord injury (SCI) and have emerged as promising therapeutic targets. Mitochondrial aldehyde dehydrogenase-2 (ALDH2) is a key oxidoreductase responsible for detoxifying reactive aldehydes. Pharmacological activation of ALDH2 using Alda-1, a selective agonist, has been shown to reduce aldehyde accumulation, alleviate inflammation, and enhance functional recovery in experimental SCI models. However, approximately 8% of the global population carries the ALDH2*2 mutation, which severely impairs this detoxification pathway. In this study, we used a transgenic ALDH2*2 mouse model to investigate the role of ALDH2 in SCI pathology. This model mimics the human ALDH2*2 condition, allowing us to examine the impact of impaired aldehyde clearance on acrolein accumulation and its pathological consequences. We modulated endogenous aldehyde detoxification through both genetic deficiency and pharmacological activation with Alda-1. Our results showed that ALDH2 deficiency led to significantly elevated acrolein levels, which were associated with increased microglial activation, cytokine storm, neuronal loss, demyelination, and tissue damage compared to wild-type (WT) mice. Treatment with Alda-1 enhanced ALDH2 activity and significantly reduced acrolein levels in both ALDH2*2 and WT mice from 2 to 28 days post-SCI. This was accompanied by reduced inflammation, improved preservation of myelin, and marked improvements in locomotor and sensory function, especially in ALDH2*2 mice. Notably, even beyond the traditionally ideal treatment window, Alda-1 treatment remained effective in promoting recovery, particularly in motor function and to a greater extent in ALDH2*2 mice. Our study comprehensively evaluated ALDH2s role in SCI by both genetically impairing and pharmacologically enhancing its activity, highlighting ALDH2 as a critical modulator of acrolein-mediated damage and suggesting its potential as a therapeutic target, especially for individuals with the ALDH2*2 mutation.

neuroscience↗

bioRxiv2025

Quantitative Assessment of Protein-DNA Interactions via SYBR Green Fluorescence

Protein-DNA interactions are crucial for cellular processes, but current quantification methods lack sensitivity. We developed the Real-time PCR-based DNA Binding Assay (RP-DBA) to detect and quantify these interactions. The target protein, expressed as a Strep-tag II fusion, is purified and incubated with double-stranded DNA probes containing 4 bp 3 overhangs. Protein-DNA complexes are immobilized on Strep-Tactin beads, washed, and eluted. A complementary single-stranded DNA amplification arm is added, extended by Taq polymerase, and quantified via qPCR with SYBR Green. RP-DBA enables real-time kinetic analysis and is 4- to 10-fold more sensitive than EMSA, depending on amplification arm length (30-90 bp). Its simplicity, speed, accuracy, and high-throughput potential make it a valuable tool for advancing molecular biology research.

molecular biology↗

bioRxiv2025

OriGene: A Self-Evolving Virtual Disease Biologist Automating Therapeutic Target Discovery

Here, we present OriGene, a self-evolving multi-agent system that functions as a virtual disease biologist, systematically identifying original and mechanistically grounded therapeutic targets at scale. OriGenes architecture integrates over 600 specialized tools through a Model Context Protocol (MCP), enabling it to reason across diverse data modalities including genomics, protein networks, pharmacology, clinical records and literature evidence, to generate and prioritize target discovery hypotheses. We implemented a strategy combining a knowledge graph-based Tool RAG with an advanced agent selection mechanism to enable dynamic, context-aware tool deployment. Through a self-evolving framework, OriGene continuously integrates human and experimental feedback to iteratively refine its core thinking templates, tool composition, and analytical protocols, thereby enhancing both accuracy and adaptability over time. To comprehensively evaluate its performance, we established TRQA, an original benchmark comprising over 1,900 expert-level question-answer pairs spanning a wide range of diseases and target classes. OriGene consistently outperforms human experts, leading research agents, and state-of-the-art large language models in accuracy, recall, and robustness, particularly under conditions of data sparsity or noise. Critically, OriGene nominated previously underexplored therapeutic targets for liver (GPR160) and colorectal cancer (ARG2), which demonstrated significant anti-tumor activity in patient-derived organoid and tumor fragment models mirroring human clinical exposures. These findings demonstrate OriGenes potential as a scalable and adaptive platform for AI-driven discovery of mechanistically grounded therapeutic targets, offering a new paradigm to accelerate drug development.

bioinformatics↗

bioRxiv2025

A continuum reaction-diffusion model for spread of gene silencing in chromosomal inactivation

Regulation of gene silencing in large regions of chromosomes is crucial for development and disease progression, and there has been an increasing interest in using it for new therapeutics. One example of massive gene silencing is X chromosome inactivation (XCI), a process essential for dosage compensation of X-linked genes. During XCI, most genes in the X chromosome are inactivated following the transcription of XIST, an X-linked long noncoding RNA. Recent experiments with transgenes showed that the spread of gene silencing can be induced by XIST transcription in cis, but the spread is restricted in space. The mechanism of controlling the spread remains unclear. In this work, we develop a continuum reaction-diffusion model that elucidates chromosomal inactivation through a bistable system governed by a regulatory network for XIST-mediated gene silencing. We find that the spread of XIST can be tuned by known negative feedback loops regulating its synthesis and degradation, and that the spread of gene silencing is controlled by a wave-pinning mechanism in which both global regulation of silencing complex and local variations of histone modifications can play crucial roles. In addition, we integrate the discrete three-dimensional arrangement of the X chromosome and autosomes into this continuous model. We use a 3D chromosome structure inferred from experimental data and our modeling framework to show the spatiotemporal regulation for spread of gene silencing. Our method enables the investigation for the inactivation dynamics of large regions of chromosomes with varying degrees of the spread of gene silencing. Our model provides mechanistic insights that quantitatively relate gene regulatory networks to tunability and stability of chromosomal inactivation. Author SummaryPrecise control of gene expression is a fundamental process in biology and turning off large parts of chromosomes is both common in many species and important for development and diseases. A well-known example of chromosomal scale gene silencing is X chromosome inactivation (XCI), which helps balancing gene activity between sexes. XCI is governed by the production of an RNA called XIST, leading to most genes on one X chromosome being turned off. Experiments have shown that XIST can trigger nearby genes to turn off in natural and engineered contexts, but this effect only spreads to specific regions. The exact mechanism for this limit is not very well understood. In this study, the authors created a mathematical model to explain how XIST spreads and controls gene activity. They found that feedback systems involving XIST regulations and chromatin modifications synergize and determine how far the inactivation spreads, through a process similar to a wave that gets "pinned" in place. They also included the 3D shape of chromosomes in their model to better understand how gene silencing happens over time and space. This model helps to quantitatively describe chromosome inactivation with gene regulatory networks.

systems biology↗

bioRxiv2025

Unisexual reproduction in the global human fungal pathogen Cryptococcus neoformans

The human fungal pathogen Cryptococcus species complex (encompassing C. neoformans, C. deneoformans, and the C. gattii species complexes) exhibit diversity in sexual reproduction, including -a mating, pseudosexual reproduction, as well as unisexual reproduction initiated from a single isolate or between isolates of the same mating type. A central conundrum is that while most Cryptococcus natural populations exhibit significant mating-type bias, genetic and genomic analyses show recombination occurs in nature. The discovery of unisexual reproduction in C. deneoformans provided insight; however, thus far unisexual reproduction has never been directly observed in the predominant global pathogenic species C. neoformans. Here, we provide evidence that mutating the RIC8 gene, which encodes a conserved guanine nucleotide exchange factor (GEF) involved in both chaperoning and activating G proteins, enables unisexual reproduction in C. neoformans. Additionally, we show that genetic variation in the natural population promotes unisexual reproduction, and unisexual reproduction in C. neoformans involves canonical meiotic recombination. Finally, we found that deletion of both GPA2 and GPA3 in the MAT background leads to self-filamentation without sporulation, suggesting that differential modulation of the G proteins, likely involving Ric8, could underlie the switch between different modes of sexual reproduction in Cryptococcus. Our study further highlights that the highly conserved Ric8 GEF can act as an important regulator of cellular development in response to environmental stimuli and could modulate sexual reproduction in nature. We hypothesize that unisexual reproduction occurs much more frequently in nature than currently appreciated, and possibly in other fungi and microbial eukaryotes as well. Significance statementSexual reproduction is a central tenet of the eukaryotic life cycle, essential for the long-term survival of a species by promoting genetic diversity and facilitating natural selection. In eukaryotes such as unicellular basidiomycetous fungi, sexual reproduction leads to hyphal growth and spore production, enabling escape from harsh environments and long-distance dispersal. Here, we report that mutating the RIC8 gene, encoding a conserved guanine nucleotide exchange factor (GEF) involved in activation of G proteins, enables unisexual reproduction in the predominant human fungal pathogen Cryptococcus neoformans that involves canonical meiosis. Our findings suggest that conditions might exist in nature that could induce, and even promote, unisexual reproduction in Cryptococcus, highlighting the complexity and importance of sexual reproduction in this prominent fungal pathogen.

genetics↗

bioRxiv2025

FoldBench: An All-atom Benchmark for Biomolecular Structure Prediction

Accurate prediction of biomolecular complex structures is fundamental for understanding biological processes and rational therapeutic design. Recent advances in deep learning methods, particularly all-atom structure prediction models, have significantly expanded their capabilities to include diverse biomolecular entities, such as proteins, nucleic acids, ligands, and ions. However, comprehensive benchmarks covering multiple interaction types and molecular diversity remain scarce, limiting fair and rigorous assessment of model performance and generalizability. To address this gap, we introduce FoldBench, an extensive benchmark dataset consisting of 1,522 biological assemblies categorized into nine distinct prediction tasks. Our evaluations reveal critical performance dependencies, showing that ligand docking accuracy notably diminishes as ligand similarity to the training set decreases, a pattern similarly observed in protein-protein interaction modeling. Furthermore, antibody-antigen predictions remain particularly challenging, with current methods exhibiting failure rates exceeding 50%. Among evaluated models, AlphaFold 3 consistently demonstrates superior accuracy across the majority of tasks. In summary, our results highlight significant advancements yet reveal persistent limitations within the field, providing crucial insights and benchmarks to inform future model development and refinement.

bioinformatics↗

bioRxiv2025

Redirecting cytomegalovirus immunity against pancreas cancer for immunotherapy

Immunotherapy shows limited success in pancreatic cancer, largely due to a low mutational burden and immunosuppressive microenvironment. Here we hypothesized that pre-existing antiviral immunity can be redirected to control pancreatic tumors. Cytomegalovirus (CMV, a {beta}-herpesvirus) was chosen, as the majority of the population is infected and it induces an extremely large/broad memory T cell response. Mice latently infected with murine CMV (MCMV) were orthotopically implanted with pancreatic cancer cells and treated with systemic injections of MCMV T-cell epitopes. The therapy promoted preferential accumulation of MCMV-specific T cells within pancreatic tumors, delaying tumor growth and increasing survival. Immunophenotyping and scRNAseq analyses showed these T cells were highly activated and cytotoxic, leading to increased tumor necrosis and caspase-3 activation. Finally, therapy was enhanced when combined with subtherapeutic doses of gemcitabine chemotherapy. Together, these results show that CMV-specific T cells can be repurposed to combat pancreatic cancer. SignificanceOur studies reveal that CMV-specific viral memory T cells can be re-directed to control a solid tumor normally refractory to immunotherapy via a simple, intravenous injection of T cell peptide epitopes. This mutation agnostic approach has significant potential for the development of "off-the-shelf" therapeutics by stimulating pre-existing antiviral memory and it is widely applicable due to the high prevalence of CMV.

cancer biology↗

bioRxiv2025

Divergent conformational mechanisms of JAK2V617F and TYK2V678F mutations in Thrombocythemia and related disorders: Molecular Dynamics insights into pathway activation and therapeutic targeting

Thrombocythemia and related disorders are primarily driven by persistent activation of the JAK-STAT signaling pathway, which is frequently associated with valine-to-phenylalanine (VF) point mutations in the JAK2 and TYK2 proteins. However, the precise mechanisms underlying the sustained downstream pathway activation induced by these mutations remain unclear. To investigate this, we employed molecular dynamics simulations and computational biophysical approaches to examine how VF mutations sustain JAK-STAT pathway activation. Our analyses, encompassing energetics, interaction forces, and surface electrostatic charge distributions, revealed that these mutations predominantly alter the spatial conformations and stability of the proteins by modulating inter-dimeric interaction forces and binding free energies. Specifically, the V617F mutation in JAK2 enhanced the stability of the JAK2 dimer and suppressed the activity of the JH2 pseudokinase domain. Similarly, the V678F mutation in TYK2 reducing the binding strength of the JH1 kinase domain and the binding free energy, increasing the binding affinity at the dimer interface. Both mutations ultimately resulted in heightened JH1 kinase domain activity and aberrant activation of downstream signaling pathways. Electrostatic analyses further demonstrated that JAK2V617F strengthened attractive forces within the dimer and TYK2V678F mutation mitigated repulsive forces. Decreased binding free energy confirmed enhanced dimer stability in JAK2V617F and TYK2V678F mutants, driven by distinct mechanisms: reinforced JH2 domain interactions in JAK2V617F and domain compaction with reoriented interfaces in TYK2V678F. These insights delineate the mutation-specific allosteric networks that underpin the pathogenesis of thrombocythemia. Furthermore, they establish a molecular foundation for designing isoform-selective inhibitors that target conformational vulnerabilities, thereby presenting novel therapeutic opportunities. Author SummaryO_LIThe VF mutations located in JAK2 and TYK2 stabilizes the JH2 pseudokinase domain and enhances dimer interfaces to disrupt autoinhibition in JAK2, while it induces structural reorganization of the dimer FERM/SH2 domains and JH1 kinase conformation to promote substrate accessibility in TYK2. C_LIO_LIWe developed a novel multiscale analyses framework, integrating conformational analysis, electrostatic analysis, hydrogen bond and salt bridges, and free energy decomposition, to collaboratively elucidate the effects of VF mutations on the protein multimers. C_LIO_LIThese findings highlights divergent allosteric networks underlying pathogenic signaling, offering a molecular mechanisms for designing isoform-selective inhibitors targeting conformational vulnerabilities in myeloproliferative disorders. C_LI

biophysics↗

bioRxiv2025

Light-induced structural adaptation of the bundle-shaped phycobilisome from thylakoid-lacking cyanobacterium Gloeobacter violaceus

Gloeobacter diverged from other lineages early in cyanobacterial evolution, preferentially growing under low light intensity conditions. Among cyanobacteria, G. violaceus exhibits unique features, including lack of a thylakoid membrane and bundle-shaped antenna phycobilisomes (PBSs), densely packed and well-organized on the plasma membrane. However, without high-resolution structures, it has remained unclear how G. violaceus PBSs assemble into a bundle-shaped configuration. Here we solved the cryo-EM structures of PBSs from G. violaceus cells cultured under low (Sr-PBS) or moderate (Lr-PBS) light intensity. These structures revealed two unique linker proteins, LRC91kDa and LRC81kDa, that play a key role in the PBS architecture. Analysis of the bilin arrangement indicated that the bundle-shaped structure allows efficient energy transfer among rods. Moreover, comparison between Lr-PBS and Sr-PBS uncovered a distinct mode of adaption to increased light intensity wherein the ApcA2-ApcB3-ApcD layer can be blocked from binding to the core by altering structural elements exclusively found in the G. violaceus LCM. This study illustrates previously unrecognized mechanisms of assembly and adaptation to varying light intensity in the bundle-shaped PBS of G. violaceus.

biophysics↗

bioRxiv2025

Tet1 safeguards lineage allocation in intestinal stem cells

Intestinal stem cells (ISCs) balance self-renewal and differentiation to maintain the intestinal epithelial barrier, which is replaced weekly throughout adult life. Genetic control of ISC differentiation is well-defined relative to transcription factor (TF) activity, but less is known regarding the role of chromatin regulation in ISC biology. Prior work from our lab and others has shown that Tet1, a chromatin modifying enzyme involved in DNA demethylation, is specifically enriched in ISCs and early secretory progenitors. While constitutive loss of Tet1 is associated with defects in early postnatal ISC development, its role in adult ISC biology remains unknown. Here, we show that Tet1 safeguards ISC fate decisions by reducing sensitivity to extrinsic signaling. Inducible, intestine-specific Tet1 knockout mice (Tet1iKO) exhibit environmentally sensitive phenotypes, including absorptive differentiation bias and premature expression of mature absorptive transcripts in ISCs. These phenotypes are largely "silenced" in animals housed in a high-level barrier facility, where Tet1iKO epithelium closely resembles controls. Despite the lack of baseline phenotype in these conditions, Tet1iKO mice retain increased sensitivity to pro-differentiation signaling. In vivo, succinate administration induces increased tuft and goblet cell hyperplasia in the absence of Tet1, while Tet1iKO organoids cultured with IL-4 or DAPT exhibit increased tuft and enteroendocrine cell specification, respectively. While ATAC-seq of Tet1iKO ISCs reveals minimal changes in chromatin accessibility, footprinting analysis suggests increased binding of lineage-specific TFs and CTCF even in the absence of cellular phenotypes. Together, our data demonstrate that Tet1 serves as a "buffer" against ISC differentiation and suggest that it does so in a lineage agnostic manner that is not dependent on changes in chromatin accessibility.

cell biology↗

bioRxiv2025

CASTOR1: A Novel Tumor Suppressor Linking mTORC1 and KRAS Pathways in Tumorigenesis and Resistance to KRAS-Targeted Therapies in Non-Small Cell Lung Cancer

Cytosolic arginine sensor for mTORC1 Subunit 1 (CASTOR1) functions as a key regulator of mechanistic target of rapamycin complex 1 (mTORC1) signaling. Despite its frequent dysregulation in cancers via mechanisms such as KSHV microRNA-mediated inhibition or AKT-driven phosphorylation and degradation, the impact of CASTOR1 loss on tumor initiation and progression remains poorly understood. Here, we identify CASTOR1 as a critical tumor suppressor in non-small cell lung cancer (NSCLC) by demonstrating that its genetic ablation amplifies tumorigenesis in a KRAS-driven genetically engineered mouse model (GEMM;LSL-KRASG12D). CASTOR1 deficiency markedly enhances lung tumor incidence, accelerates tumor progression, and increases proliferative indices in KRASG12D-driven tumors (KRASG12D;C1KO) compared to CASTOR1 wild type (WT) tumors (KRASG12D;C1WT). Advanced-stage tumors exhibit elevated phosphorylated CASTOR1 (pCASTOR1) and reduced total CASTOR1 levels, suggesting active degradation during tumorigenesis. Mechanistically, CASTOR1 loss amplifies mTORC1 signaling, as evidenced by heightened phosphorylation of downstream effectors 4EBP1 and S6, while also augmenting AKT and ERK activation, uncovering a crosstalk between the PI3K/AKT/mTORC1 and KRAS/ERK pathways. Furthermore, CASTOR1 ablation induces genome instability, which may contribute to enhanced tumor incidence and progression. Importantly, CASTOR1 deficiency confers resistance to KRASG12D-specific inhibitors, while over half of KRASG12D;C1WT tumors also display resistance. Organoids derived from KRASG12D;C1KO and KRASG12D;C1WT tumors reveal a correlation between KRAS inhibitor resistance and hyperactivation of mTORC1, with mTORC1 and PI3K inhibitors sensitizing resistant tumors to KRASG12D-targeted therapies. These findings position CASTOR1 as a novel tumor suppressor that modulates mTORC1 and KRAS signaling to constrain NSCLC progression. Our study further highlights the therapeutic potential of combining mTORC1 or ERK inhibitors with KRAS-targeted therapies for NSCLC characterized by hyperactive KRAS signaling and impaired CASTOR1 activity. HighlightsO_LICASTOR1 functions as a tumor suppressor in NSCLC by limiting KRAS-driven tumor initiation and progression. C_LIO_LICASTOR1 is frequently lost or inactivated in wild-type tumors during tumor progression, contributing to advanced-stage malignancies. C_LIO_LICASTOR1 deficiency amplifies mTORC1 signaling and enhances PI3K/AKT and KRAS/ERK crosstalk, driving tumorigenesis and resistance to KRAS-specific inhibitors. C_LIO_LICombining mTORC1 or PI3K inhibitors with KRAS-targeted therapies effectively overcomes resistance in KRAS-driven NSCLC. C_LI

cancer biology↗

bioRxiv2025

Nanotechnology-Driven Synergy: Research Effects of Curcumin Nanosuspension and Fluconazole Combination in Overcoming Azole Resistance in Candida Albicans

The increasing prevalence of invasive fungal infections, particularly life-threatening disseminated candidiasis caused by C. albicans, highlights the critical demand for novel therapeutic strategies. This study explores the antifungal potential of curcumin nanosuspension (CNS) alone and in combination with azoles, emphasizing synergistic mechanisms to counter drug resistance. CNS substantially improved curcumins aqueous solubility and enabled sustained in vitro release, overcoming its inherent bioavailability limitations. Checkerboard assays demonstrated synergistic interactions between CNS and fluconazole (FLC) against planktonic cells (FICI: 0.38-0.5) and early-stage C.albicans biofilms (FICI <0.5). Morphological analyses revealed that the combination suppressed hyphal formation and disrupted biofilm architecture--key virulence traits of C.albicans. Mechanistically, qPCR data indicated downregulation of adhesion-related genes (ALS1, ALS3, HWP1, EFG1), impairing fungal colonization. The synergy likely stems from dual mechanisms: facilitated FLC cellular uptake and inhibition of efflux pumps.These findings point out a nanotechnology-driven strategy to revitalize existing azoles through rational combination therapies. The improved bioavailability of CNS and their biofilm-penetrating capacity position this approach as a promising solution for managing refractory candidiasis, offering a pathway to circumvent antifungal resistance.

pharmacology and toxicology↗

bioRxiv2025

Chromosomal Aneuploidy in Normal, Non-Neuronal Brain Nuclei of Glioblastoma Patients is Not a Cancer Driver

Aneuploidy is a hallmark of cancers, including high-grade glioma (GBM), one of the most aggressive brain tumors. To assess whether increased aneuploidy already occurs in normal brain tissue of GBM patients, we performed single-nucleus whole-genome sequencing on 225 non-neuronal cortical nuclei from 12 disease-free individuals and 6 GBM patients, in the latter analyzing both tumor and non-tumor distal regions. Somatic aneuploidy was found in approximately 15% of non-neuronal nuclei in the adult human cortex, with recurrent chromosome 16p aneuploidy in up to 4% of nuclei. In contrast, about 51% of GBM tumor nuclei showed frequent aneuploidy of chromosomes 7 and 10, consistent with known GBM profiles. Notably, non-tumor brain regions from GBM patients exhibited aneuploidy frequencies and patterns similar to controls, including recurrent 16p involvement. These findings indicate that somatic aneuploidy in non-neuronal cells is a normal feature of the adult human brain and not linked to increased GBM risk.

cancer biology↗

bioRxiv2025

From Decay to Rhythm: Sustained Biological Oscillators Require More Than Chemistry Alone

Many biological systems exhibit sustained, coherent oscillations despite substantial noise. In contrast, chemical reaction systems governed by Markovian dynamics cannot sustain coherent ensemble oscillations, as the stochastic nature of state transitions inevitably causes the oscillation period to drift. To overcome this limitation, we propose a general mechanism that couples a Markovian system to at least one other degree of freedom, such as a mechanical system, to achieve noiseresistant coherent oscillations with a desired frequency. We introduce two approaches, targeting different dynamical modes in the Markovian system, and derive a governing principle for the non-Markovian system by analyzing the eigenvalues of the coupled dynamics. This principle is validated using a trimolecular reaction system, successfully producing sustained and coherent oscillations. Our study provides theoretical insights into how any chemical system can be coupled to another non-Markovian system to produce sustained and coherent oscillations with a precise period. We also make a fundamental observation that stability and control of stable limit cycles must arise from the non-Markovian part of the coupled system.

biophysics↗

bioRxiv2025

STRIPAK complex defects result in pseudosexual reproduction in Cryptococcus neoformans

STRIPAK is an evolutionarily conserved signaling complex that coordinates diverse cellular processes across fungi and animals. In the human fungal pathogen Cryptococcus neoformans, STRIPAK was recently shown to play critical roles in maintaining genome stability and controlling both sexual and asexual development. In Cryptococcus, sexual reproduction is closely linked to virulence, and our findings demonstrate that the STRIPAK complex plays key roles in both processes. Here, we further investigate the specific roles of the STRIPAK catalytic subunit Pph22 and its regulatory partner Far8 during sexual development. We show that while pph22{Delta} mutants are defective in -a sexual reproduction, exhibiting impaired meiotic progression and a failure to produce viable spores, the deletion of PPH22 resulted in exclusive pseudosexual reproduction, with progeny inheriting nuclear genomes solely from the wild-type parent. Overexpression of PPG1, a related phosphatase, rescued growth and developmental defects in pph22{Delta} mutants, and restored the preference for -a sexual reproduction over pseudosexual reproduction during mating, suggesting functional redundancy within the STRIPAK signaling network. Furthermore, deletion of FAR8, another component of the STRIPAK complex, also led to a high rate of pseudosexual reproduction during -a sexual mating, reinforcing the role of STRIPAK in modulating reproductive modes in C. neoformans, possibly through regulating nuclear inheritance and meiotic progression. Together, these findings highlight the distinct contributions of STRIPAK to sexual reproduction in C. neoformans and suggest that disruptions of this complex affect genome integrity and inheritance mechanisms, with broader implications for fungal adaptation and pathogenesis.

genetics↗

bioRxiv2025

Chemical Compensation to Mechanical Loss in CellMechanosensation

Mammalian cells sense and respond to environmental changes using a complex and intelligent system that integrates chemical and mechanical signals. The transduction of mechanical cues into chemical changes modulates cell physiology, allowing a cell to adapt to its microenvironment. Understanding how the chemical and mechanical regulatory modules interact is crucial for elucidating mechanisms of mechanosensation and cellular homeostasis. In this study, we find that cells exhibit non-monotonic changes in cell volume and intracellular pH when subjected to physical stimuli and varying degrees of actomyosin cytoskeleton disruption. We discover that these non-monotonic responses are mediated by a chemical compensation mechanism, where the attenuation of actomyosin activity stimulates the activity of PI3K/Akt pathway. This, in turn, activates sodium-hydrogen exchanger 1 (NHE1), resulting in elevated intracellular pH and increased cell volume. Furthermore, we identify a competitive interaction between the PI3K/Akt and MAPK/ERK pathways - two major regulators of cell proliferation and motility. This competition modulates the chemical compensation based on the relative activities of these pathways. Our mathematical modeling reveals the network structure that is essential for establishing the non-monotonic response. Interestingly, this regulatory system is altered in HT1080 fibrosarcoma, highlighting a potential mechanistic divergence in cancer cells in contrast to their normal-like counterpart, such as NIH 3T3 and HFF-1 fibroblasts. Overall, our work reveals a compensatory mechanism between chemical and mechanical signals, providing a novel infrastructure to elucidate the integrated mechanochemical response to environmental stimuli.

biophysics↗

bioRxiv2025

5-ethynyluridine perturbs nuclear RNA metabolism to promote the nuclear accumulation of TDP-43 and other RNA binding proteins

TDP-43, an essential nucleic acid binding protein and splicing regulator, is broadly disrupted in neurodegeneration. TDP-43 nuclear localization and function depend on the abundance of its nuclear RNA targets and its recruitment into large ribonucleoprotein complexes, which restricts TDP-43 nuclear efflux. To further investigate the interplay between TDP-43 and nascent RNAs, we aimed to employ 5-ethynyluridine (5EU), a widely used uridine analog for click chemistry labeling of newly transcribed RNAs. Surprisingly, 5EU induced the nuclear accumulation of TDP-43 and other RNA-binding proteins and attenuated TDP-43 mislocalization caused by disruption of the nuclear transport apparatus. RNA FISH demonstrated 5EU-induced nuclear accumulation of polyadenylated and GU-repeat-rich RNAs, suggesting increased retention of both processed and intronic RNAs. TDP-43 eCLIP confirmed that 5EU preserved TDP-43 binding at predominantly GU-rich intronic sites. RNAseq revealed significant 5EU-induced changes in alternative splicing, accompanied by an overall reduction in splicing diversity, without any major changes in RNA stability or TDP-43 splicing regulatory function. These data suggest that 5EU may impede RNA splicing efficiency and subsequent nuclear RNA processing and export. Our findings have important implications for studies utilizing 5EU and offer unexpected confirmation that the accumulation of endogenous nuclear RNAs promotes TDP-43 nuclear localization.

cell biology↗

bioRxiv2025

RNA sequence analysis of somatic mutations in aging and Parkinson's Disease

Parkinsons Disease (PD) is an age-related neurodegenerative disorder that has been associated with increased DNA damage. To test if PD is associated with increased somatic mutations, we analyzed RNA-seq data in whole blood from 5 visits of the Parkinsons Progression Markers Initiative for clonally amplified somatic variants. Comprehensive analysis of RNA-sequencing data revealed a total of 5,927 somatic variants (2.4 variants per sample on average). Mutation frequencies were significantly elevated in PD subjects as compared to age-matched controls at the time of the last visit. This was confirmed by RNA analysis of substantia nigra. By contrast, the fraction of carriers with clonal hematopoiesis, was significantly reduced in old PD patients as compared to old healthy controls. These results indicate that while the overall mutation rate is higher in PD, specific clonally amplified mutations are protective against PD, as has been found for Alzheimers Disease.

genetics↗