Biology subjects

Chen, S.

Publications and source records attributed to Chen, S..

At least 163 records · Page 9Linked to original sources

bioRxiv2026

Scalable Generation of Universal hiPSC-Derived Vascular Progenitor Cells for Safe and Sustained Revascularization in Chronic Limb-Threatening Ischemia

BackgroundChronic limb-threatening ischemia (CLTI) is the most severe form of peripheral artery disease and can result in debilitating tissue damage, limb loss, and mortality if left untreated. Despite surgical bypass and endovascular interventions, there is high unmet need to develop novel therapies that can restore durable blood flow and rescue limb function in patients whose disease is not amenable to surgical bypass and endovascular procedures. Human induced pluripotent stem cell (hiPSC)-derived vascular progenitor cells (VPC) hold promise for addressing this unmet need, yet their clinical adoption will require a scalable and consistently high-quality cell product that can be used safely in a large number of CLTI patients. MethodsHere, we report a robust, scalable GMP-adaptable platform for generating universally immuno-compatible VPC from human leukocyte antigen (HLA) class I/II-edited hiPSCs with extensive characterization of phenotypic and functional attributes critical to address key translational gaps in developing cell-based therapies for CLTI. We have interrogated their therapeutic efficacy in multiple murine CLTI models using a combination of clinically relevant endpoints, histology, and tissue-based RNAseq analysis. ResultsWe found that VPC-treated mice exhibited significantly improved perfusion ratios and preserved limb function, reduced inflammation, and increased physiological neovascularization without pathological malformations. ConclusionsGenetic modification conferring hypoimmune status coupled with a robust differentiation process enables large scale production of an "off-the shelf" high-quality VPC product with the potential to address unmet need in CLTI patients regardless of HLA status.

cell biology↗

bioRxiv2026

Integration of early-stage cryopreservation and cell cycle modulation into a flexible kidney organoid differentiation system

Kidney organoids derived from human pluripotent stem cells (hPSCs) represent a promising platform for modeling nephrogenesis and renal diseases. However, conventional differentiation protocols are continuous and time-sensitive, limiting their scalability and reproducibility. Here, we developed a method to pause and resume organoid formation through cryopreservation at an early differentiation stage using a chemically defined formulation that maintains high post-thaw viability and differentiation potential. We further found that synchronizing hPSCs in the G1 phase with PD-0332991 enhanced post-thaw organoid formation and transcriptional fidelity, while G2 phase enrichment with Ro-3306 promoted the development of SLC12A3-positive distal convoluted tubules. The post-thaw organoids exhibited well-organized nephron architecture and function comparable to uninterrupted cultured controls. This platform proved effective for modeling BK polyomavirus (BKV) infection, drug-induced nephrotoxicity, and renal fibrosis. Together, our cryopreservation and cell cycle synchronization strategy provides a flexible, practical framework to advance organoid-based research and translation.

developmental biology↗

bioRxiv2026

PathDiffusion: modeling protein folding pathway using evolution-guided diffusion

Despite remarkable advances in protein structure prediction, a fundamental question remains unresolved: how do proteins fold from unfolded conformations into their native states? Here, we introduce PathDiffusion, a novel generative framework that simulates protein folding pathways using evolution-guided diffusion models. PathDiffusion first extracts structure-aware evolutionary information from 52 million predicted structures the AlphaFold database. Then an evolution-guided diffusion model with a dual-score fusion strategy is trained to generate high-fidelity folding pathways. Unlike existing deep learning methods, which primarily sample equilibrium ensembles, PathDiffusion explicitly models the temporal evolution of folding. On a benchmark of 52 proteins with experimentally validated folding pathways, PathDiffusion accurately reconstructs the order of folding events. We further demonstrate its versatility across four challenging applications: (1) recapitulating Antons molecular dynamics trajectory for 12 fast-folding proteins, (2) reproducing functionally important local folding-unfolding transitions in 20 proteins, (3) characterizing conformational ensembles of 50 intrinsically disordered proteins, and (4) resolving distinct folding mechanisms among 3 TIM-barrel proteins. We anticipate that PathDiffusion will be a valuable tool for probing protein folding mechanisms and dynamics at scale.

bioinformatics↗

bioRxiv2026

Hidden stop codons orchestrate mRNA fate by ambushing ribosomal frameshifting associated with codon usage

In eukaryotes, the mRNA stability is generally shaped by codon usage bias, the uneven preferences for synonymous codons, in a translation-dependent manner. However, the conserved mechanism linking codon to mRNA decay remains elusive. Hidden stop codons (HSCs), defined as stop codons located in the +1 or -1 frame relative to canonical ORF, are widespread across all genomes but largely uncharacterized. Here, we demonstrate that in both fungi and human cells, HSCs play an conserved and mechanistic role in promoting mRNA decay by rapidly terminating out-of-frame translation promoted by nonoptimal codons, primarily through +1 ribosomal frameshifting. In the filamentous fungus Neurospora crassa, partially deleting HSCs via synonymous substitutions in the clock gene frequency increases mRNA stability and disrupts circadian rhythmicity. In human cells, acute depletion of translation termination factor eRF1 impairs recognition of HSCs, leading to global stabilization of mRNAs enriched in nonoptimal codons and HSCs. In both Neurospora and humans, these mRNAs are in part degraded through the NMD pathway via UPF1. Collectively, these findings suggest that in eukaryotes, HSCs serve as surveillance elements to monitor ribosomal frameshifting and out-of-translation promoted by nonoptimal codons, thereby initiating mRNA decay through NMD.

molecular biology↗

bioRxiv2026

Isolation and Characterisation of Hair Follicle-Derived Melanocytes

Melanocytes are unique population of cells which produce melanin pigment. However, the property of melanocytes from hair follicle and epidermis, particularly, their molecular signatures remained largely unknown. In this study, we investigated the properties of epidermis and hair follicle melanocytes by biochemical and molecular biological assays. We found that epidermal melanocytes are differentiated and mature form of hair follicle melanocytes, and they are potentially related. Irradiation with NB-UVB did not induce cell death of hair follicle melanocytes as observed in epidermal melanocytes, but activate hair follicle melanocytes, promote proliferation and migration. In situ study suggested that after UVB irradiation, root sheath of hair follicles, particularly proximity of interfollicular epidermis and hair bulb become darker, suggesting migration and maturation of hair follicle melanocytes after UVB irradiation, rather than cell death. This observation provides hints and evidence to the relationship between hair follicle and epidermal melanocytes, helps to explain the contradiction of melanocytes cell death after UVB irradiation and the use of UVB in treatment of vitiligo lesion, as well as the perifollicular repigmentation phenomenon observed in vitiligo lesion after NB-UVB phototherapy.

cell biology↗

bioRxiv2026

Architecting cis-regulation to quantitatively tune gene expression in cereals

Precise modulation of gene expression via cis-regulatory editing holds promise for non-transgenic crop improvement, but the sequence-to-function relationships that govern plant promoter activity remain poorly understood. Here, we develop a massively parallel reporter assay (MPRA) in Sorghum bicolor to systematically measure the effects of >30,000 CRISPR-like mutations-deletions, substitutions, and motif insertions-across entire native promoters and 5' untranslated regions (UTRs) of three photosynthesis genes: PsbS, Raf1, and SBPase. We find that gene expression is most tunable within a [~]500 base pair core promoter region, where mutational effects are reproducible across biological replicates and predictive of protein output. Within these regions, we identify compact deletions and motif insertions that strongly increase protein production (>30-fold relative to wild type), exceeding the performance of transgenic enhancer elements. Mutation-effect relationships are gene-specific, highlighting the need for tailored regulatory maps. Our results establish a high-throughput strategy for cis-regulatory fine-mapping that enables crop improvements via minimal, precise, and non-transgenic gene edits.

synthetic biology↗

bioRxiv2026

Induction of ferroptotic and amyloidogenic signatures linked to Alzheimers disease by chemically distinct air pollutants

Air pollution (AirP) exposure is associated with increased Alzheimers disease (AD) risk, yet AirP is chemically heterogeneous, complicating identification of shared pathogenic drivers. We examined acute cortical responses to two metal-rich AirP sources, diesel exhaust particles (DEP) and World Trade Center (WTC) dust, and compared them to woodsmoke (WS), a particulate exposure with low metal content. DEP and WTC elicited highly convergent transcriptional responses, sharing over 1200 differentially expressed genes linked to inflammation, ferroptosis, neuronal remodeling, and amyloid processing. These changes were accompanied by impaired antioxidant activity and increased lipid peroxidation within lipid rafts, a membrane microdomain critical for amyloid processing, resulting in increased A{beta} generation. In contrast, WS produced a distinct transcriptional signature and failed to induce ferroptotic priming or lipid peroxidation, consistent with its low metal composition. Together, these findings implicate metals as a shared driver linking diverse AirP exposures to amyloidogenic vulnerability and elevated AD risk. Graphical AbstractAcute AirP exposure converges on ferroptotic priming, amyloidogenic processing, and white-matter vulnerability. Acute exposure to metal-rich AirP, such as DEP or WTC introduces redox-active metals and particulate matter that promote lipid peroxidation, amyloidogenesis, and altered transcriptional regulation in the brain. AirP exposure engages xenobiotic metabolism pathways (AhR/ARNT), activates iron and heme handling through ferritinophagy (NCOA4) and heme oxygenase activity (HMOX1), and blunts lipid peroxide detoxification systems, including glutathione peroxidase 4 (GPx4), ferroptosis suppressor protein 1 (FSP1), and glutathione (GSH) synthesis. These changes promote ferroptotic priming and lipid raft oxidation, facilitating amyloid precursor protein (APP) processing by secretases (ADAM10, BACE1, {gamma}-secretase) and increasing amyloid-{beta} (A{beta}) generation. In parallel, transcriptional and cell-state remodeling involving neuronal and oligodendrocyte responses contribute to selective white-matter vulnerability, particularly within the corpus callosum. Together, these pathways provide a mechanistic framework linking acute AirP exposure to convergent oxidative, amyloidogenic, and microstructural changes relevant to Alzheimers disease pathology. O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/696601v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@3a22dcorg.highwire.dtl.DTLVardef@c6ae26org.highwire.dtl.DTLVardef@1d3412forg.highwire.dtl.DTLVardef@5cb011_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

All-in-one Single-Cell Proteomic Analysis of Protein Alterations in Human Oocytes Undergoing in Vitro Aging

Study questionWhat specific proteomic changes and molecular markers associated with in vitro aging occur in human oocytes? Summary answerSingle-cell proteomic analysis revealed the protein dynamics during the in vitro aging of oocytes. Subsequent functional analysis highlighted key biological processes affected in aged oocytes and identified several genes as candidate key factors for oocyte and early embryo quality. What is known alreadyOvulated oocytes undergo a time-dependent degradation process if fertilization does not occur within a specific window. This aging process leads to morphological, molecular, and epigenetic changes that can compromise oocyte quality and subsequent embryo development. In previous studies, transcriptome sequencing in humans and mice has revealed serial changes in aging oocytes including oxidative stress, mitochondrial dysfunction, DNA damage, and alterations in cell cycle regulation. These changes can lead to apoptosis, chromosomal abnormalities, and epigenetic modifications, all of which negatively affect oocyte quality. However, research regarding protein level changes and regulatory mechanisms in human oocytes during in vitro aging remains unclear. Study design, size, durationUtilizing "All-in-one" single-cell proteomics, we investigated the protein expression levels in human oocytes at the germinal vesicle (GV) stage and metaphase II (M II) stage following 24 hours of in-vitro aging. We analyzed four groups of oocytes: fresh GV (n=8), in vitro-aged GV (n=9), fresh M II (n=11), and in vitro-aged M II (n=11). This approach allowed for a detailed comparison of proteomic changes associated with in vitro aging in oocytes at different developmental stages. Participants/materials, setting, methodsOocytes at GV and MII stage were collected for "All-in-one" single-cell quantitative proteomic respectively. Differentially expressed genes were analyzed using the R package DESeq2 or DEP (filtered with q-value[≤]0.05 and Foldchange[≥]1.5). EGSEA package was used to perform pathway analysis. Main results and the role of chanceThe proteomic analysis of fresh and in vitro-aged human GV and MII oocytes identified 3,268 proteins. In GV oocytes, compared to fresh samples, 73 proteins were upregulated and 90 were downregulated. Gene Ontology (GO) enrichment analyses revealed these DEPs were involved in key biological processes such as lysosome organization, spindle assembly and oxidative stress response. Gene Set Enrichment Analysis (GSEA) revealed a significant down regulation of genes associated with protein translation initiation and methylation pathways, while those in the apoptosis mitochondrial changes were upregulated. In MII oocytes, 63 proteins were upregulated and 69 were downregulated. GO analysis highlighted their involvement in cytoplasmic translation, ribosome biogenesis and oocyte development. GSEA showed that aged MII oocytes exhibited a downregulation of gene sets in protein translation but an upregulation in membrane fusion pathways compared to fresh oocytes. Furthermore, we identified proteins with consistent expression trends across both GV and MII stages, including MRFAP1 and MT2A, as candidate biomarkers for human oocyte aging in vitro. Limitations, reasons for cautionSingle cell proteomic techniques may not fully capture the dynamic range of proteins present within oocytes, leading to potential underrepresentation of low-abundance proteins that could play crucial roles. Furthermore, the heterogeneity within oocytes introduces variability that can obscure the identification of consistent proteomic signatures associated with oocyte quality or aging. Wider implications of the findingsThese findings not only provide an understanding of the protein changes underlying the in vitro aging of human oocytes but also offer potential biomarkers and intervention targets for future research and clinical applications in assisted reproductive technologies. Study funding/Competing interest(s)This project received funding from the National Natural Science Foundation of China (NO.82471693, 22574175); the Natural Science Foundation of Hunan Province (NO. 2024JJ4100), the Hunan Provincial Grant for Innovative Province Construction (2019SK4012), the Hundred Youth Talents Program of Hunan Province (to S.Z.), the Major Scientific Program of CITIC Group (No. 2023ZXKYB34100) and Scientific Research Foundation of Reproductive and Genetic Hospital of CITIC-XIANGYA (YNXM-202313, YNXM-202319, YNXM-202211). The authors have no conflicts of interest to declare.

developmental biology↗

bioRxiv2026

Ultra-fast genetic recovery of dead fish through cross-family germline stem cell transplantation

AbstactThe conservation of genetic resources from aquaculture species and endangered fish is increasingly challenged by large body size, long reproductive cycles, and limited opportunities for timely intervention after death. Here, we establish and validate an ultra-fast genetic platform based on germline stem cell transplantation to enable postmortem genetic recovery in fish. Using grass carp (Ctenopharyngodon idella) as a representative warm-water species, we systematically quantified the relationships among postmortem tissue freshness, germline stem cell viability, and transplantation efficiency, and demonstrated that low-temperature preservation plays a decisive role in maintaining germline activity after death. Germline stem cells isolated from deceased grass carp were transplanted into germ-cell-depleted zebrafish recipients, where they rapidly colonized recipient gonads, underwent proliferation and differentiation, and generated functional donor-derived gametes within three months. These gametes supported successful fertilization and normal embryonic development, ultimately yielding viable grass carp offspring. Our results reveal an intrinsic postmortem resilience of germline stem cells and demonstrate that cross-species transplantation into small, fast-maturing hosts can dramatically accelerate genetic recovery. This strategy overcomes key biological and logistical constraints associated with conventional breeding-based rescue approaches and provides a rapid, scalable, and broadly applicable framework for postmortem genetic resource conservation in aquaculture and endangered fish species.

zoology↗

bioRxiv2026

NORAD orchestrates KLC1-mediated SFPQ transport via liquid-liquid phase separation

Neuronal function requires precise long-distance axonal transport mediated by molecular motors and RNA-binding proteins like SFPQ, though regulatory mechanisms remain poorly defined. We identify long non-coding RNA NORAD as a master regulator of this process through liquid-liquid phase separation (LLPS). While SFPQ and kinesin-1 mediate cargo delivery, the specific RNA coordinating their interaction was unknown. We demonstrate NORAD directly binds kinesin light chain 1 (KLC1) and promotes SFPQ condensation into dynamic LLPS droplets, enabling efficient transport. CRISPR-assisted mapping and functional assays show NORAD depletion disrupts granule dynamics, impairs neuroprotective mRNA localization, and induces axonal degeneration. In vitro reconstitution confirms NORAD-KLC1 synergy enhances SFPQ phase separation, and neuron-specific knockout mice exhibit motor deficits with reduced neuronal density. These findings establish the first evidence of lncRNA NORAD-mediated LLPS in axonal transport, revealing a new paradigm for RNA-guided neuronal maintenance.

molecular biology↗

bioRxiv2026

A comprehensive analysis of flagellar mutations in Vibrio cholerae: Trade-off mechanisms between motility loss and host adaptability

IntroductionCholera, caused by Vibrio cholerae, is a severe diarrheal disease threatening global health. The flagellum of V. cholerae functions not only for motility but also as an environmental sensor regulating virulence. The trade-off mechanism between motility loss and enhanced host adaptation remains unclear. ObjectiveThis study aimed to elucidate how flagellar mutations, which lead to a loss of motility, affect host adaptability in V. cholerae and to uncover the underlying molecular basis. MethodsWe analyzed 3,135 cholera-related samples to identify mutation hotspots in flagellar genes. A relevant flagellar mutant library was constructed and assessed for host adaptability. Multiple approaches, including molecular, genetic, transcriptomic, and proteomic analyses, were applied to dissect the FlgM-mediated pathway, with key findings revalidated in an adult mouse model using a specifically constructed 6N-labeled mutant pool. ResultsBig data analysis reveals those flagellar mutations in V. cholerae cluster in key structural and regulatory genes, including flhB, fliA, fliF, fliD, and fliM. Flagellar mutations led to a scenario where the secretion level of the regulator FlgM was negatively correlated with host adaptability. Intracellular FlgM inactivates either the {sigma}28 factor FliA directly or acts through the VarS/VarA-CsrA/BCD system, ultimately leading to the derepression of the quorum-sensing master regulator named hapR. HapR can directly bind to the promoters of genes involving in methionine transportation to regulate adaptability of V. cholerae. The 6N-labeled mutants pool experiment reconfirmed that motility loss promotes host adaptability via the FlgM-FliA-HapR-methionine axis. ConclusionOur findings demonstrate that secretion levels of the flagellar regulator FlgM drive an adaptive shift in V. cholerae from motility to host adaptability, mediated through quorum sensing and methionine metabolic reprogramming. This reveals a novel mechanism underlying bacterial evolution and pathogenicity.

microbiology↗

bioRxiv2026

Genomic and pan-genomic insight into longan domestication and improvement

Longan (Dimocarpus longan) is a tropical tree in Sapindaceae family with economic importance known for its nutritous fruits. Genetic improvement of longan requires knowledge of reliable molecular markers and functional genes associated with key traits. However, it is largely impeded by lacking a complete genome and pangenome reference encompassing the broad genetic diversity in diverse longan germplasms. Here, we present a telomere-to-telomere (T2T) gap-free genome of longan cultivar Shixia and a graph-based pangenome constructed using newly assembled chromosome-level genomes of 101 accessions. We completely assemble the longan centromere regions primarily composed of Gypsy-CRM retrotransposons. The pan-genome analysis reveals 58,978 non-redundant structural variants (SVs) that exhibit signs of genomic selective sweep during longan domestication and breeding. Additionally, haplotype-resolved genome analysis suggests allele-specific gene expression associated with SV-driven changes in 3D genome architecture. Importantly, the graph-based pan-genome empowers population-scale SV genotyping and genomewide association with various longan traits. SV-GWAS revealed 12 QTLs significantly linked with longan maturity period. Among them, a 758bp insertion is located downstream of the DlDAZ gene encoding a C2H2 zinc-finger transcription factor, and DIDAZ-transgenic tomatoes showed delayed maturity. Together, our T2T genome and pan-genome provide valuable resources to facilitate longan genetic research and precise improvement.

genomics↗

bioRxiv2026

Progenitor Diversity and Architecture of the Human Ganglionic Eminences Shaping the Basal Ganglia

The embryonic medial and lateral ganglionic eminences (MGE, LGE) are the principal sources of most neurons and glia for the basal ganglia. In primates, the MGE has a distinctive cytoarchitecture characterized by doublecortin enriched cellular nests (DENs), yet the architectonic organization underlying DEN formation, the molecular heterogeneity of ganglionic eminence progenitors and their lineage relationships, remain poorly understood. Here, using paired single-nucleus transcriptomics and chromatin accessibility profiling of the three GEs, we identify distinct progenitor populations, delineate their gene regulatory networks, and reconstruct their lineage trajectories. Live imaging reveals a unipolar outer radial glia-like population (GE-oRG) that undergoes mitotic somal translocation. Spatial transcriptomics identifies a distinct CRABP1+/ANGPT2+ domain within the MGE. Integrated spatial and electron microscopy demonstrates a periphery-to-center gradient of differentiation in the MGE. Leveraging DEN-forming MGE organoids derived from PCDH19 knockout human pluripotent stem cell lines, we identify the protocadherin, PCDH19, as a key regulator of DEN formation.

neuroscience↗

bioRxiv2026

CAR-T-drug conjugate against solid tumor

Chimeric antigen receptor (CAR)-T cell therapy has been clinically successful in hematologic cancers but faces challenges in solid tumors, primarily due to limited tumor infiltration, immunosuppressive tumor microenvironments (TME), and antigen heterogeneity. While combining CAR-T cell therapy with chemotherapy can enhance antitumor activity, this often leads to substantial systemic toxicity. In this study, we introduce CAR-T-drug conjugate (CAR-T-D-C), a new class of dual-functional therapeutics that effectively addresses these obstacles by integrating click chemistry for precise conjugation of cytotoxic agents onto antigen-specific CAR-T cells. By transforming the hostile TME into an ally, this approach facilitates localized delivery of cytotoxic payload directly to the tumor site, enhancing the overall effectiveness of CAR-T therapy in solid tumors. CAR-T-D-Cs with different CAR-T cell binders exhibit robust antitumor activity across diverse solid tumor models, including both human tumor xenografts and syngeneic models. Spatial transcriptomic studies reveals that CAR-T-D-C achieves improved CAR-T tumor infiltration and functional activation within the TME. Compared to conventional CAR-T therapy, CAR-T-D-C markedly enhances immune cell infiltration, augments effector functions, promotes antigen spreading, amplifies systemic immune responses, and improves overall anti-tumor immunity. CAR-T-D-C represents a versatile therapeutic concept that combines the potency of small molecule drugs and the specificity of CAR-T cells as a 2-in-1 immunochemotherapy for treatment of solid tumors.

immunology↗

bioRxiv2026

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4

The Not proteins of the Ccr4-Not complex regulate translation elongation dynamics, essential for proper folding and assembly of new proteins. In yeast, ribosomes with non-optimal codons in the A-site are enriched within the pool of ribosomes bound by Not4 and Not5. Such ribosomes accumulate in cells lacking Not4 or Not5 that show defects in co-translational assembly and aggregation of new proteins. Recently we observed that depletion of Not1 and Not4 inversely regulate changes in mRNA solubility, correlating with inverse codon-specific changes in A-site ribosome dwelling occupancies (RDOs). Here we describe that mRNAs less soluble upon Not4 depletion are enriched for targets of the RNA-binding protein Puf3. We determine that Puf3 contributes to inverse changes of A-site RDOs upon Not1 and Not4 depletion, in particular at rare arginine codons, and it contributes to changes in mRNA solubility in not4{Delta}. Moreover, deletion of Puf3 suppresses temperature sensitivity and protein aggregation in the not4{Delta} strain, while overexpression of Puf3 is toxic. Puf3 post-translational modifications and the Puf3 interactome are altered in not4{Delta}. Taken together, our results associate alterations in Puf3 post-translational status and function, including contribution to translation elongation dynamics, with not4{Delta} mutant phenotypes. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/695943v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@855afdorg.highwire.dtl.DTLVardef@118addaorg.highwire.dtl.DTLVardef@13dd015org.highwire.dtl.DTLVardef@12824c6_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

A Generative Foundation Model for Cryo-EM Densities

Single-particle cryo-electron microscopy (cryo-EM) enables structure determination of macromolecular complexes, yet reconstructions are often degraded by noise, anisotropic sampling and reconstruction artifacts. Correcting these effects is an ill-posed inverse problem that requires strong prior knowledge in addition to experimental data. Here we introduce cryoFM, a generative foundation model for cryo-EM densities that unifies data-driven structural priors with dataset-specific constraints within a Bayesian inference framework. CryoFM is trained in an unsupervised manner on thousands of high-quality cryo-EM maps using flow matching, learning a generalizable prior over macromolecular density distributions. Combined with explicit likelihood models describing experimental degradations, cryoFM enables flow posterior sampling, an inference-only procedure that performs denoising and restoration and refinement while remaining explicitly constrained by dataset-derived statistics. We show that this framework improves density reconstruction and refinement across diverse experimental settings, including preferred-orientation datasets and cases with strong spatial heterogeneity in signal-to-noise ratio, without introducing hallucinated features. In addition, cryoFM can be fine-tuned into conditional generative models for density post-processing, yielding maps with improved interpretability and fewer artifacts compared to existing supervised approaches. Together, cryoFM establishes generative foundation models as a principled and controllable framework for cryo-EM density reconstruction and modification.

biophysics↗

bioRxiv2025

A novel dephosphorylation peptide inhibits 17β-HSD1 enzyme activity in ovarian granulosa cells and breast cancer cells

Estradiol (E2), a pivotal mammalian reproductive hormone, is closely associated with estrogen-dependent diseases. 17{beta}-hydroxysteroid dehydrogenase type 1 (17{beta}-HSD1), a critical E2 synthesis enzyme, has been understudied for its post-translational regulation-despite its potential as a therapeutic target, no clinically approved inhibitors are currently available. In our investigation of porcine follicular atresia mechanisms, we identified five differentially phosphorylated residues in 17{beta}-HSD1. Using in vitro site-directed mutagenesis and transgenic mouse models carrying point mutations, we established that Ser30 and Ser274 are critical phosphorylation sites that robustly modulate 17{beta}-HSD1 enzymatic activity. We further demonstrated that activin A and insulin-like growth factor 1 (IGF-1) enhance 17{beta}-HSD1 activity by promoting its phosphorylation at these two sites. To target these regulatory residues, we designed and synthesized cell-penetrating peptides (CPPs) that specifically suppress 17{beta}-HSD1 phosphorylation. Functional assays conclusively demonstrated that these CPPs significantly suppressed 17{beta}-HSD1 activity in vitro. Notably, they also inhibited the proliferation, migration and invasion of MCF-7 cells, as well as tumor growth in a mouse model of breast cancer. Our study provides novel mechanistic insights into the regulation of 17{beta}-HSD1 and E2 synthesis, addressing a critical gap in steroid hormone biology. The identification of Ser30/Ser274 as functional phosphorylation sites and the development of CPP-based inhibitors offer both theoretical advances and translational potential, opening new avenues for the treatment of estrogen-dependent breast cancer.

cell biology↗

bioRxiv2025

A gastric microbial chromatin remodeler drives gastric cancer progression and immune evasion by reprogramming the host epigenome

Emerging evidence highlights the crucial role of microbial communities in modulating cancer development and progression. In gastric cancer (GC), we identify Streptococcus anginosus (SA) as a tumor-resident oncobacterium that drives both tumor progression and immune evasion. We define a novel mechanism in which SA secretes extracellular vesicles (saEVs) that translocate the bacterial chromatin remodeler saSNF2 into host cell. There, saSNF2 partners with host transcription factor TEAD1--through its ATPase activity and participation in BAF complex assembly--to coordinately activate oncogenic transcription. This transkingdom interaction upregulates the palmitoyltransferase ZDHHC11, which in turn stabilizes PD-L1 via palmitoylation to establish an immunosuppressive niche, while also amplifying other TEAD1 target genes to fuel tumor progression. Functionally, saEVs promote tumor growth and limit CD8+ T-cell infiltration in vivo. Strikingly, pharmacological inhibition of ZDHHC11 reverses immune evasion and synergizes with anti-PD-1 checkpoint blockade. Our results establish SA as a multifaceted driver of GC and reveal the saSNF2-ZDHHC11 axis as a promising target to potentiate immunotherapy.

cancer biology↗