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Liu, W.

Publications and source records attributed to Liu, W..

At least 163 records · Page 9Linked to original sources

Nuclear 2'-O-methylation regulates RNA splicing through its binding protein FUBP1

2'-O-methylation (Nm) is an abundant RNA modification exists on different mammalian RNA species. However, potential Nm recognition by proteins has not been extensively explored. Here, we employed RNA affinity purification followed by mass spectrometry to identify Nm-binding proteins. The candidates exhibit enriched binding at known Nm sites. Interestingly, some candidates display nuclear localization and functions. We focused on the splicing factor FUBP1. Electrophoretic mobility shift assay (EMSA) validated preference of FUBP1 to Nm-modified RNA. As FUBP1 predominantly binds intronic regions, we profiled Nm sites in chromatin-associated RNA (caRNA) and found Nm enrichment within introns. Depletion of Nm led to increased exon skipping, suggesting Nm-dependent splicing regulation. The caRNA Nm sites overlap with FUBP1 binding sites, and Nm depletion reduced FUBP1 occupancy on modified regions. Furthermore, FUBP1 depletion induced exon skipping in Nm-modified genes, supporting its role in mediating Nm-dependent splicing regulation. Overall, our findings identify FUBP1 as an Nm-binding protein and uncover previously unrecognized nuclear functions for RNA Nm modification.

molecular biology↗

A biGWAS strategy reveals the genetic architecture of the interaction between wheat and Blumeria graminis f. sp. tritici

BackgroundWheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt) is one of the most significant diseases affecting global wheat production. Breeding for disease resistance (R) genes against Bgt often follows a boom-bust cycles, where cultivars with effective resistance are widely deployed on an expanding area until virulence emerges in the avirulence (Avr) pathogen population. While extensive effort has been devoted to identifying and cloning R genes, Avr genes remain relatively understudied, limiting our understanding of R-Avr interactions. That said, understanding R-Avr interactions is crucial for developing durable resistance strategies. ResultsWe conducted whole genome sequencing on 245 Bgt isolates collected from major wheat-growing regions in China, identifying 120 genetically unique isolates. Each of these unique isolates was inoculated and phenotyped on a diverse panel of wheat germplasm. Through Genome-Wide Association Analysis (GWAS) in both Bgt and wheat, we identified 65 Avr loci and 251 R loci overlapping with nine and eight cloned Avr or R genes, respectively. On average, each isolate carries eight Avr alleles, ranging from one to 17. Little geographical preference for Avr alleles or their combinations was observed, suggesting that disease resistance breeding against this pathogen should be coordinated at the national level. The level of resistance level is positively correlated with the number of R alleles carried by a wheat line, and the average frequency of an R allele is 2% among the wheat panel, indicating the potential for accumulating R alleles in breeding programs. We mapped 212 R-Avr interactions based on joint GWAS using both plant and pathogen genomes and cross-species epistasis, where a network of interactions was formed between wheat and Bgt. These interactions indicate that pyramiding five major R loci has the potential to confer resistance to half of the Avr loci. As a proof of concept, we successfully verified two previously described R-Avr pairs using tobacco experiments. Furthermore, we provided molecular validation evidence for three new Avr genes, including Bgt-50651, BgtE-5826 and BgtE-20009, and two new R-Avr interactions. Among them, Bgt-50651 interacts with Pm1a, Pm2a, and another unidentified R gene located near the Pm6/Pm52 interval. ConclusionOur study provides a framework for understanding the genetic interaction between plants and pathogens. The discovery of novel R/Avr loci and their complex interaction network underscores the need to integrate crop and pathogen genetic background, particularly the R/Avr allele composition, into breeding program design. These findings have significant implications for developing durable resistance strategies in wheat alongside offering valuable insights into the broader dynamics of plant-pathogen interactions.

genomics↗

Reshaping epistatic network modules enhances wheat yield potential

Increasing wheat yield is a key approach to ensuring global food security and an enduring focus in crop breeding. Here, we assembled a panel of 3,030 wheat lines to dissect the genetic mechanisms of yield improvement. We conducted large-scale field trials across five ecological environments over two consecutive years to evaluate yield performance and constructed a haplotype atlas using the Wheat 660K genotype array. 234 quantitative trait loci (QTLs) and 522 haplotype blocks (HBs) were identified for 14 traits through genome-wide association studies (GWAS), including 10 QTLs and 35 HBs associated with grain yield. Genomic analysis revealed that wheat yield improvement is primarily driven by changes in the epistatic network rather than the introduction of new haplotype segments. SNPs or HBs explain 53.3%-62.9% of the phenotypic variation in yield, whereas epistasis explains 70.4%, highlighting the role of epistasis in yield improvement. Moreover, yield improvement is significantly correlated with the accumulation of favorable epistatic modules. Pedigree-based analysis revealed that the modules remained relatively stable under the pressure of breeding selection, while new favorable modules were also created during hybrid breeding, highlighting that crop design breeding should be based on genetic modules. This study provides insights into genetic mechanism of wheat yield improvement and guidance for designing future wheat in the era of artificial intelligence.

genetics↗

Distinct yet Overlapping Functions of VMP1 and TMEM41B in Modulating Hepatic Lipoprotein Secretion and Autophagy in MASH

BackgroundTransmembrane protein 41B (TMEM41B) and vacuolar membrane protein 1 (VMP1) are endoplasmic reticulum (ER) scramblases that shuttle phospholipids between the inner and outer leaflets of the ER membrane. Both TMEM41B and VMP1 also play critical roles in regulating hepatic lipoprotein secretion and autophagy. Despite these similarities, whether TMEM41B and VMP1 exhibit different roles in very low-density lipoprotein (VLDL) secretion and autophagy in the pathogenesis of metabolic-associated steatotic liver disease (MASLD) remains unclear. MethodsWe created liver- and hepatocyte-specific single knockout (KO) and double knockout (DKO) mice for Tmem41b and Vmp1, as well as overexpression knock-in (KI) mice with hepatic overexpression of TMEM41B, Tmem41b KO/Vmp1 KI, and Vmp1 KO/Tmem41b KI. We conducted lipidomic, metabolomic, biochemical, and functional studies in these mice, fed either a chow diet or a MASLD diet. ResultsTMEM41B protein levels were decreased in the livers of human subjects with MASLD. The loss of hepatic Tmem41b impaired VLDL secretion, resulting in steatosis, inflammation, and fibrosis. Vmp1 KO mice exhibited similar phenotypes to DKO mice, displaying a more severe defect in VLDL secretion and greater liver injury than Tmem41b KO mice. Lipidomic analysis revealed decreased levels of phosphatidylcholine and phosphatidylethanolamine, along with increased neutral lipids in both Tmem41b KO and Vmp1 KO mice; however, these changes were generally more pronounced in Vmp1 KO mice. VMP1 and TMEM41B localized at the mitochondrial-associated membrane (MAM), and a reduction in mitochondria-ER contact was observed in hepatocytes deficient in either VMP1 or TMEM41B. Ultrastructural electron microscopy analysis showed increased accumulation of "lipid droplet" in the ER membrane bilayer and ER lumen in both Vmp1 KO and Tmem41b KO hepatocytes, with greater ER luminal "lipid droplet" accumulation in Tmem41b KO hepatocytes. The loss of hepatic Vmp1 or Tmem41b led to elevated levels of LC3-II and p62, with significantly higher levels of both markers in Vmp1 KO and DKO mouse livers compared to Tmem41b KO mouse livers. Restoring Vmp1 in Tmem41b KO mice partially improved defective VLDL secretion; however, high expression levels of VMP1 did not correct the hepatic autophagy defect. In contrast, restoring Tmem41b in Vmp1 KO mice dose-dependently enhanced both defective VLDL secretion and autophagy. Importantly, overexpression of hepatic TMEM41B mitigated diet-induced MASLD in mice. ConclusionThe loss of hepatic Vmp1 or Tmem41b decreases hepatic MAM and phospholipid content, leading to decreased VLDL secretion and promoting MASLD. While VMP1 and TMEM41B have overlapping functions, VMP1 appears to play a more critical role in regulating VLDL secretion and autophagy in mouse livers than TMEM41B.

cell biology↗

Synthesizing human-specific spike-in standards for RNA-seq experiments and assessing their technical performance

Using spike-in standards for RNA-seq experiments is critical to evaluate technical bias introduced during sample preparation, sequencing and analysis. Although some external RNA spike-in standards have been developed, species-specific spike-in standard was not reported yet. Here we developed the human-specific spike-in standards with 65 controls. We first extracted human endogenous RNAs with various lengths and GC contents, introduced random mutations approximately every 75 bp in each RNA, and then synthesized these RNAs as spike-in RNAs. After that, four mixtures of these spike-in RNAs covering a 220 dynamic range were obtained. To ensure the accuracy of RNA concentration, two rounds of ddPCR were conducted for each spike-in RNA and the intraclass correlation coefficient between two ddPCRs ranged from 0.9954 to 0.9971 after removing the two spike-in RNAs with the largest concentration difference. Furthermore, we showed that the sequencing error profiles were distinct between platforms and the library preparation procedures were related with the discrepancies in spike-in RNA read percent, transcript abundance, sequence coverage distribution, and differential gene expression. In addition, two regression models of sequence coverage were built based on RNA second structure and GC content, and 86.62%-91.78% of the variation can be explained. Our study demonstrates the technical performance of the human-specific spike-in standards for RNA-seq experiments and illustrates the biases across different libraries, platforms, and laboratories.

bioinformatics↗

AT1R and Integrin β3 Synergize to Drive Aortic Dissection via Non-Canonical Wnt/β-Catenin Signaling

Aortic dissection (AD), a life-threatening cardiovascular emergency, continues to impose high mortality due to insufficient therapeutic options, as monotherapy targeting angiotensin II type 1 receptor (AT1R) demonstrates limited clinical efficacy. Utilizing single-cell RNA sequencing, we identified integrin {beta}3 as a critical driver of AD progression, with expression levels positively correlated with disease severity. Histopathological validation in human AD specimens and a murine angiotensin II (AngII)-infusion model confirmed marked upregulation of integrin {beta}3 activation. Pharmacological blockade of integrin {beta}3 with Cyclo(-RGDfK) significantly attenuated aortic pathogenesis in vivo, reducing dissection incidence and aortic degeneration. Mechanistically, AngII-mediated AT1R activation induced formation of a receptor complex with integrin {beta}3, triggering its conformational activation. Transcriptomic profiling revealed that activated integrin {beta}3 potentiates vascular endothelial dysfunction by binding glycogen synthase kinase 3{beta} (GSK3{beta}), which stabilizes {beta}-catenin via a non-canonical Wnt signaling axis. This pathway drives endothelial barrier disruption, hallmarks of aortic wall destabilization in AD. Our findings unveil a previously unrecognized synergy between AT1R and integrin {beta}3, implicating aberrant Wnt/{beta}-catenin signaling as a nexus of endothelial injury in AD pathogenesis. These results advocate for a paradigm-shifting dual-therapeutic strategy concurrently targeting AT1R and integrin {beta}3 to restore vascular homeostasis, offering a mechanistically grounded approach to mitigate this lethal disease. This work bridges critical gaps in understanding AD pathophysiology and provides a transformative framework for precision therapeutics.

pharmacology and toxicology↗

STmiR: A Novel XGBoost-Based Framework for Spatially Resolved miRNA Activity Prediction

MicroRNAs (miRNAs) are critical regulators of gene expression in cancer biology; however, their spatial dynamics within tumor microenvironments (TME) remain underexplored owing to technical limitations in current spatial transcriptomics (ST) technologies. To address this gap, we present STmiR, a novel XGBoost-based framework for spatially resolved miRNA activity predictions. STmiR integrates bulk RNA-seq data (TCGA and CCLE) with spatial transcriptomics profiles to model nonlinear miRNA-mRNA interactions, achieving a high predictive accuracy (Spearmans {rho} > 0.8) across four major cancer types (breast, lung, ovarian, and prostate). Applied to 10X Visium ST datasets from nine cancers, STmiR identified six pan-cancer conserved miRNAs (e.g., hsa-miR-21, hsa-let-7a) consistently ranked in the top 40 across malignancies, and uncovered cell-type-specific regulatory networks in fibroblasts, B cells, and malignant cells. A breast cancer case study validated the utility of STmiR by linking miR-205 to androgen receptor (AR) signaling and miR-200b to epithelial-mesenchymal transition (EMT). By enabling the spatial mapping of miRNA activity, STmiR provides a transformative tool to dissect miRNA-mediated regulatory mechanisms in cancer progression and TME remodeling, with implications for biomarker discovery and precision oncology. HighlightsO_LIFirst integration of XGBoost and spatial transcriptomics: STmiR pioneers a machine learning framework to predict miRNA activity in spatially heterogeneous tissues, overcoming limitations of linear correlation-based methods. C_LIO_LIHigh accuracy and generalizability: Demonstrates robust performance (Spearmans {rho} > 0.8) across four cancer types validated by independent datasets. C_LIO_LIPan-cancer conserved miRNAs: Six miRNAs (e.g., hsa-miR-21 and hsa-let-7a) were shared across nine cancers, implicating their roles in core oncogenic pathways. C_LI Key ContributionsO_LIMethodological innovation: Combines XGBoosts nonlinear modeling with spatial transcriptomics to resolve miRNA activity in multicellular contexts. C_LIO_LIBiological discovery: Uncovers the conserved and context-dependent roles of miRNAs in tumor progression and microenvironment crosstalk. C_LIO_LITranslational impact: Provides a computational platform for identifying spatially regulated therapeutic targets in cancer. C_LI

bioinformatics↗

Retrieval practice prevents stress-induced inference impairment by restoring rapid memory reactivation

A hallmark of human memory is its ability to form novel inferences by linking discrete but related events. We examined whether acute stress impairs memory inference and if retrieval practice can buffer this effect. Participants were trained on image pairs, AB and BC, to establish interconnected triads (ABC) with a shared bridge element B. Twenty-four hours later, we induced acute stress in half of the participants and then tested their capacity to infer the indirect AC associations. Behavioral results indicated that acute stress-induced memory inference accuracy and speed, and retrieval practice was associated with attenuation of stress-induced impairment in A-C inference accuracy and speed. Using multivariate decoding analysis of human electroencephalogram (EEG) recordings, we found neural evidence that bridge element B is rapidly reactivated during the inferential process, a neural signature predictive of subsequent successful inference. Importantly, stress disrupts this rapid neural reactivation of the bridge element, but retrieval practice buffers the stress effect and enhances the strength of reactivation signals beyond the non-stress condition. Time-frequency analyses of theta oscillations mirrored these effects of stress and retrieval practice on inference performance and neural reactivation. Collectively, our findings pinpoint rapid reactivation of the bridge element as an essential neural mechanism for memory-based inference. Although susceptible to stress, this mechanism can be enhanced through retrieval practice, suggesting that building robust memory traces renders subsequent inferences resilient to stress.

neuroscience↗

TSHR-targeting nucleic acid aptamer treats Graves' ophthalmopathy via novel allosteric inhibition

Abnormal thyrotropin receptor (TSHR) signaling drives a spectrum of diseases affecting hundreds of millions globally, including Graves disease (GD), Graves ophthalmopathy (GO), hyperthyroidism, and thyroid cancers. Therefore, TSHR is considered an attractive therapeutic target with immense drug discovery potential. Currently, there are no clinically available TSHR inhibitors. To address this unmet medical need, we developed YC3, a functional nucleic acid aptamer targeting TSHR, via an innovative approach combining protein-targeting cell-SELEX and functional selection. YC3 exhibited nanomolar affinity with potent TSHR inhibition. Its therapeutic potential was comprehensively evaluated both in vitro and in vivo for GO. In GO patient-derived orbital fibroblasts (OFs), YC3 reversed thyroid-stimulating antibodies (TSAbs)-induced cell activation, suppressing inflammatory cytokines and extracellular matrix (ECM) secretion. In a GO mouse model, YC3 treatment markedly attenuated orbital inflammation, ECM deposition, and fibrosis, ameliorating the pathological remodeling of orbital tissue. Mechanistically, YC3 bound to a previously unidentified allosteric site within the leucine-rich repeat domain of TSHR, thereby inhibiting receptor activation. This study identifies YC3 as a promising TSHR-targeted therapy and unveils a new druggable site for inhibitor design. It also provides the first preclinical evidence supporting pharmacological TSHR inhibition for GO treatment, advancing therapeutic development for TSHR-related diseases.

biochemistry↗

The TONSL-MMS22L complex and FANCM form an interdependent complex on chromatin to counter replication stress

FANCM is branchpoint DNA translocase essential for cellular response to replication stress. Here, we show that replication stress stimulates FANCM and the TONSL-MMS22L heterodimer bound to histones H3-H4 to form an interdependent complex on chromatin. TONSL-MMS22L recruits FANCM and Fanconi anemia (FA) core complex to stalled and collapsed forks, maintains FANCM on replication-stressed chromatin, promotes FANCD2 monoubiquitination, facilitates both repair and replication traverse of DNA interstrand crosslinks (ICLs), and suppresses sister chromatid exchanges, through its interactions with FANCM and H3-H4. Reciprocally, both DNA translocase activity and phosphorylation of FANCM facilitate recruitment of TONSL-MMS22L and RAD51 to perturbed forks. Moreover, TONSL-MMS22L and FANCM function together to promote activation of the FA pathway, ICL repair, homologous recombination and replication traverse. Cancer patients with tumors with wildtype FANCM and low expression of TONSL-MMS22L have a more favorable prognosis than those with high expression. Thus, FANCM-TONSL-MMS22L acts coordinately as a complex on chromatin that resolves replication stress, and this complex may present a therapeutic target for wildtype FANCM-linked cancer.

cell biology↗

Murine Leukemia Virus GlycoGag Antagonizes SERINC5 via ER-phagy Receptor RETREG1

Serine incorporator 5 (SERINC5) is a host restriction factor that targets certain enveloped viruses, including human immunodeficiency virus type 1 (HIV-1) and murine leukemia virus (MLV). It integrates into the viral envelope from the cell surface, inhibiting viral entry. SERINC5 is transported to the cell surface via polyubiquitination, while a single K130R mutation retains it in the cytoplasm. Both HIV-1 Nef and MLV glycoGag proteins antagonize SERINC5 by reducing its expression in producer cells. Here, we report that MLV glycoGag employs selective autophagy to downregulate SERINC5, demonstrating a more potent mechanism for decreasing its cell surface expression. Although glycoGag is a type II integral membrane protein, it primarily localizes to the cytoplasm and undergoes rapid proteasomal degradation. Employing the K130R mutant, we show that Nef, primarily associated with the plasma membrane, downregulates SERINC5 only after it has trafficked to the cell surface, whereas glycoGag can reduce its expression before reaching the plasma membrane while still in the cytoplasm. Nonetheless, an interaction with SERINC5 stabilizes and recruits glycoGag to the plasma membrane, enabling it to downregulate SERINC5 from the cell surface. Through affinity-purified mass spectrometry analysis combined with CRISPR/Cas9 knockouts, we find that glycoGags activity depends on reticulophagy regulator 1 (RETREG1), an ER-phagy receptor. Further knockout experiments of critical autophagy genes demonstrate that glycoGag downregulates cytoplasmic SERINC5 via micro-ER-phagy. These findings provide crucial new insights into the ongoing arms race between retroviruses and SERINC5 during infection. AUTHOR SUMMARYHIV-1 Nef and MLV glycoGag are unrelated viral proteins, yet both counteract the same host restriction factor, SERINC5, to facilitate productive infection. In this study, we report a novel pathway through which glycoGag downregulates SERINC5. We demonstrate that while Nef downregulates SERINC5 only after it has trafficked to the cell surface, glycoGag can directly downregulate SERINC5 in the cytoplasm before it reaches the plasma membrane. Furthermore, we show that this pathway is mediated by the ER-phagy receptor RETREG1, which targets SERINC5 for degradation via micro-ER-phagy. This mechanism provides a more effective means of blocking SERINC5 antiviral activity. These findings reveal that retroviruses have evolved different strategies to antagonize SERINC5, highlighting the critical role of SERINC5 in restricting retroviral infections.

microbiology↗

Extrinsic Apoptosis and Necroptosis in Telencephalic Development: A Single-Cell Mass Cytometry Study

Regulated cell death is integral to sculpting the developing brain, yet the relative contributions of extrinsic apoptosis and necroptosis remain unclear. Here, we leverage single-cell mass cytometry (CyTOF) to characterize the cellular landscape of the mouse telencephalon in wild-type (WT), RIPK3 knockout (RIPK3 KO), and RIPK3/Caspase-8 double knockout (DKO) mice. Strikingly, combined deletion of RIPK3 and Caspase-8 leads to a 12.6% increase in total cell count, challenging the prevailing notion that intrinsic apoptosis exclusively governs developmental cell elimination. Detailed subpopulation analysis reveals that DKO mice display selective enrichment of Tbr2 intermediate progenitors and endothelial cells, underscoring distinct, cell type-specific roles for extrinsic apoptotic and necroptotic pathways. These findings provide a revised framework for understanding the coordinated regulation of cell number during telencephalic development and suggest potential mechanistic links to neurodevelopmental disorders characterized by aberrant cell death.

developmental biology↗

An integrated system for comprehensive mouse peripheral vestibular function evaluation based on Vestibulo-ocular Reflex

In the realms of both vestibular and auditory research, conducting vestibular function tests is essential. However, unlike the auditory function tests which utilize standard equipment such as the Auditory Brainstem Response (ABR) device, there is no equivalent widely adopted apparatus for vestibular tests. This is largely due to the intricate nature of the vestibular system and the challenges associated with assessing its functions. Vestibulo-ocular reflexes (VORs) are the compensatory ocular reflexes that ensure stable vision during head motion. VORs are widely used in clinics for diagnosing the vestibular deficit. In the research field, VORs, including angular VOR (aVOR) or off-vertical axis rotation (OVAR) tests, have been used by various groups to evaluate the mouse vestibular function. However, the effectiveness of VOR tests has not been systematically evaluated with proper animal models, and the lack of commercial equipment hampers its accessibility, confining vestibular testing to a select few labs. In this study, we developed an integrated instrument system with both aVOR and OVAR modes for evaluating mouse vestibular function. To demonstrate its efficacy, peripheral vestibular animal models, 1) Vestibulotoxicity drugs 3,3-iminodiproprionitrile (IDPN, 2 mg/g and 4 mg/g) induced; 2) Critical MET-related mutant (Cdh23v2J/v2J and TMC1-/-); 3) Vestibulo-specific mutant (Zpld1-/- for semicircular canal dysfunction and Otop1tlt/tlt for otoconia deficient; 4) Unilateral vestibular lesion (UVL) model by injecting gentamicin into horizontal semicircular canal, were constructed and evaluated with the system. The results showed 1) Quantification of the vestibular deficit is achieved in a daily manner; 2) Both the otolith organ and semicircular canals can be assessed respectively; and 3) The lesion side of UVL can be identified. During an 8-week study of IDPN vestibulotoxicity, the vestibular function of 3 groups of 20 animals was evaluated at 15 test days. These test results reveal the potential of our system as a standard system for evaluating common vestibular deficits in mice.

neuroscience↗

Mitochondrial accumulation and lysosomal dysfunction result in mitochondrial plaques in Alzheimer's disease

Dysfunctional mitophagy is a key component of Alzheimers disease (AD) pathology, yet direct in vivo evidence and mechanistic insights remain limited. Using a mitophagy reporter in an AD mouse model (APP/PSEN1/mt-Keima), we identified mitochondrial plaques (MPs) composed of accumulated mitochondria within or outside lysosomes in AD, but not normal mouse brains. Similar structures were also found in AD human brains, but not in healthy controls. Abnormal mitochondrial accumulation in dystrophic neurites, defective mitophagy, and impaired lysosomal function disrupted proper mitochondrial degradation, resulting in excessive mitochondria accumulation both within and outside autophagic vesicles. The resulting intensive mitochondria-containing neurites coalesce into MPs, which co-develop with amyloid plaques to form mixed plaques. These findings establish MPs as novel pathological entity and a promising therapeutic target in AD.

cell biology↗

Disruption of Mitochondrial Dynamics and Stasis Leads to Liver Injury and Tumorigenesis

Background & AimsMitochondrial dysfunction has been implicated in aging and various cancer development. As highly dynamic organelles, mitochondria constantly undergo fission, mediated by dynamin-related protein 1 (DRP1, gene name Dnm1l), and fusion, regulated by mitofusin 1 (MFN1), MFN2, and optic atrophy 1 (OPA1). However, whether and how dysregulation of mitochondria dynamics would be involved in liver pathogenesis and tumorigenesis is unknown. MethodsDnm1l Flox/Flox (Dnm1lF/F), Mfn1F/F and Mfn2F/F mice were crossed with albumin-Cre mice to generate liver-specific Dnm1l knockout (L-Dnm1l KO), L-Mfn1 KO, L-Mfn2 KO, L-Mfn1, Mfn2 double KO (DKO), and L-Mfn1, Mfn2, Dnm1l triple KO (TKO) mice. These mice were housed for various periods up to 18 months. Some mice also received hydrodynamic tail vein injections of a Sleeping Beauty transposon-transposase plasmid system with c-MYC and YAP. Blood and liver tissues were harvested for biochemical and histological analysis. ResultsL-Dnm1l KO mice had elevated serum alanine aminotransferase levels and increased hepatic fibrosis as early as two months of age. By 12 to 18 months, male L-Dnm1l KO mice developed spontaneous liver tumors, primarily hepatocellular adenomas. While female L-Dnm1l KO mice also developed liver tumors, their incidence was much lower. In contrast, neither L-Mfn1 KO nor L-Mfn2 KO mice had notable liver injury or tumorigenesis. However, a small portion of DKO mice developed tumors at 15-18 month-old. Increased DNA damage, senescence and compensatory proliferation were observed in L-Dnm1l KO mice but were less evident in L-Mfn1 KO, L-Mfn2 KO or DKO mice, indicating that mitochondrial fission is more important to maintain hepatocyte homeostasis and prevent liver tumorigenesis. Interestingly, further deletion of Mfn1 and Mfn2 in L-Dnm1l KO mice markedly abolished liver injury, fibrosis, and both spontaneous and oncogene-induced tumorigenesis. RNA sequencing and metabolomics analysis revealed significant activation of the cGAS-STING-interferon pathway and alterations in the tumor microenvironment pathways, alongside increased pyrimidine synthesis and metabolism in the livers of L-Dnm1l KO mice. Notably, the changes in gene expression and pyrimidine metabolism were considerably corrected in the TKO mice. ConclusionsMitochondrial dynamics and stability are essential for maintaining hepatic mitochondrial homeostasis and hepatocyte functions. Loss of hepatic DRP1 promotes liver tumorigenesis by increasing pyrimidine metabolism and activating the cGAS-STING-mediated innate immune response.

cell biology↗

ViFIT-assisted Histopathology: From H&E Style Standardization to Virtual Fiber Image Transformation

Deep learning-based virtual fiber staining provides a promising complement to routine H&E pathology. However, the reliance on predefined staining style inputs and manual intervention limits the clinical applicability of existing methods. To address these challenges, we introduce ViFIT-assisted histopathology, a two-stage diagnostic approach that integrates our proposed unsupervised deep learning-based virtual fiber transformation model (ViFIT). This approach enables the conversion of H&E-stained images with diverse styles into pathologist-preferred H&E images, while simultaneously generating content-consistent virtual fiber images containing label-free collagen fibers and stained reticular and elastic fibers. ViFIT-assisted histopathology reveals tumor-associated fibers and provides quantitative metrics across multiple intraoperative and postoperative cases. Experimental results demonstrate that ViFIT significantly outperforms state-of-the-art unsupervised methods in both style standardization and virtual staining, across various downstream tasks and cancer types. By eliminating the need for staining variation and manual annotation, ViFIT-assisted histopathology streamlines histopathology workflows, making it well-suited for multi-center consultations and differential diagnosis.

pathology↗

fCUT&Tag-seq: An Optimized CUT&Tag-based Method for High-Resolution Histone Modification and Chromatin-Binding Protein Profiling in both Model and Plant Pathogenic Fungi

Histone modifications and chromatin-binding proteins play crucial roles in regulating gene expression in eukaryotes, with significant implications for fungal pathogenicity and development. However, profiling these modifications or proteins across the genome in fungi remains challenging due to the technical limitations of the traditional, widely used ChIP-Seq method. Here, we present an optimized CUT&Tag-Seq protocol (fCUT&Tag-Seq) specifically designed for filamentous fungi and dimorphic fungi. Our approach involves the preparation of protoplasts and nuclear extraction to enhance antibody accessibility, along with formaldehyde crosslinking to improve protein-DNA binding efficiency. We then successfully applied fCUT&Tag-Seq to accurately profile multiple histone modifications like H3K9me3, H3K27me3, H3K4me3, and H3K18ac, across different plant pathogenic or model fungal species, including Verticillium dahliae, Neurospora crassa, Fusarium graminearum, and Sporisorium scitamineum, showing good signal-to-noise ratios, reproducibility, and detection sensitivity. Furthermore, we extended this method to profile chromatin-binding proteins, such as the histone acetyltransferase Gcn5. This study establishes fCUT&Tag-Seq as a robust and useful tool for fungal epigenetic research, enabling detailed exploration of chromatin dynamics and advancing our understanding of fungal gene regulation, development, and pathogenicity. Impact StatementWe developed a faster, lowLJinput method to study how genes are turned on and off in fungi, even in tough species that are difficult to analyze with standard methods. Our new approach, named fCUT&Tag-Seq, requires only 10,000 cells and can be completed in just two days. It delivers clearer, more reliable results and has already been successfully applied to multiple fungi, including crop pathogens. By revealing the molecular "control switches" that govern fungal development and virulence, we expect it will accelerate basic research and help identify new targets for controlling destructive plant diseases.

microbiology↗

Regulation of fatty acid oxidation involved in high altitude hypoxia induced cardiomyocyte ferroptosis via the SIRT1-PPARα-GPX4 signaling pathway

The heart experiences damage and undergoes changes in energy metabolism under condition of hypoxia. Ferroptosis is a novel form of cell death characterized by the accumulation of reactive oxygen species (ROS) and excessive lipid oxidation. However, the relationship between cardiac energy metabolism and ferroptosis at high altitudes remains unexplored. This study investigates the effects of high-altitude hypoxia on cardiac function and explores underlying mechanisms. The results demonstrate that exposure to high-altitude hypoxia induces structural and functional damage to the heart, leading to myocardial cell injury and oxidative stress, which are accompanied by ferroptosis. Inhibition of ferroptosis with Fer-1 significantly enhances hypoxia-induced expression of GPX4 and SLC7A11, reduces ROS levels, restores the GSH/GSSG ratio, and improves viability of hypoxia-damaged myocardial cells. Further investigation revealed that hypoxia induces mitochondrial damage and disrupts fatty acid {beta}-oxidation (FAO), accompanied by downregulation of PPAR. Activation of PPAR with WY14643 enhances FAO, suppresses ferroptosis, and boosts cell viability and ATP levels under hypoxic conditions. Overexpression of SIRT1 upregulates PPAR, enhances FAO, and mitigates ferroptosis, these effects are reversed by the PPAR inhibitor GW6471. Resveratrol, a natural SIRT1 activator, improves cardiac function and mitochondrial structure, enhances FAO, and reduces ferroptosis in high-altitude hypoxia-induced cardiac injury through the SIRT1-PPAR-GPX4 pathway. These findings identify the SIRT1-PPAR-GPX4 pathway as a potential therapeutic target for high-altitude-induced cardiac injury.

cell biology↗