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Biology subjects

Wei, X.

Publications and source records attributed to Wei, X..

At least 19 recordsLinked to original sources

Ancient genomes chronicle the history of adaptive evolution in East Asia

The transition from hunting and gathering to farming brought about novel selection pressures related to metabolism and immunity, but for East Asian populations the evolutionary genetic dynamics of these adaptations and their relationships to agriculture remain unclear. Using one of the largest datasets of ancient East Asian genomes (N=2236), we performed a genome-wide scan to identify selected variants and reconstructed their allele frequency changes over time and space. We tested for genetic association with farming using an environmental variable to represent historical farming intensity based on a large database of archaeobotanical sites (N=1220). Our analyses indicate selection began prior to the Neolithic for several well-established adaptive loci such as FADS1, FUT2, and OCA2. For rs1229984 at ADH1B, the strongest selection signal in our genome-wide scan, we observed variation in timing and strength of selection in East Eurasia and found evidence for a southern origin. Furthermore, ADH1B*48His was positively associated with wheat farming. Given these results, we propose a novel hypothesis about the fitness advantage of this variant. Our work underscores the heterogeneity in the strength and timing of selection across East Eurasia and provides a quantitative framework for testing agriculture's role as a selection pressure.

evolutionary biology↗

Single-nucleus chromatin accessibility time course of excisional wound repair in rat skin

We present a time-series single-nucleus ATAC-seq dataset from full-thickness excisional wounds in Sprague-Dawley rats. Samples were taken from unwounded skin (normal control) and at 1, 2, 5, 10, and 19 days post-wounding, spanning the inflammatory, proliferative, and remodeling phases of skin repair. We extracted nuclei with a two-step tissue dissociation protocol and prepared libraries using the DNBelab C Series Single-Nucleus ATAC Kit, then sequenced on the MGI DNBSEQ-T1 platform. After stringent quality filtering, 37,555 nuclei passed quality control; the resulting chromatin accessibility profiles cover 23 cell types: fibroblast subpopulations, keratinocytes, vascular endothelial cells, immune cells, and skin appendage cell types. This genome-wide chromatin accessibility dataset is a resource for studying regulatory dynamics during excisional wound repair and for comparing results with other wound healing systems.

bioinformatics↗

mtDNA Activates AIM2-Mediated PANoptosis in Interstitial Macrophages to Promote Immune Checkpoint Inhibitor Pneumonitis

Immune checkpoint inhibitor pneumonitis (CIP) is a serious immune-related adverse event, yet its mechanisms remain unclear. Using a mouse model of anti-PD-1-induced CIP, we show that PD-1 blockade induces pulmonary inflammation and dysfunction, accompanied by accumulation of lung interstitial macrophages (IMs) and PANoptosis, preferentially in IMs rather than alveolar macrophages. Anti-PD-1 also causes mitochondrial stress and cytosolic mtDNA accumulation. AIM2 deficiency attenuates pulmonary inflammation, IM accumulation, and PANoptosis-associated signaling; NLRP3 or GSDMD deficiency similarly reduces inflammation and PANoptotic responses. In macrophages, TNF- plus IFN-{gamma} induces mitochondrial dysfunction and cytosolic mtDNA accumulation, and mtDNA amplifies cytokine-induced cell death and caspase-1/GSDMD activation, which is abolished by AIM2 deficiency. Thus, AIM2-mediated PANoptosis in lung IMs drives CIP, and mtDNA-associated innate immune signaling amplifies inflammatory macrophage death during CIP.

immunology↗

Prognostic value, signal interaction network, and immune infiltration characteristics of MET gene expression in gastric cancer analyzed by multi-database bioinformatics

Objective Based on the bioinformatics method of multi-database integration, this study systematically analyzes the expression characteristics, clinical pathological correlation, prognostic value, potential molecular mechanisms, and immune infiltration patterns of hepatocyte growth factor receptor (MET) in gastric cancer. Methods The UALCAN and GEPIA databases were employed to examine the differential expression of MET between gastric cancer and normal gastric mucosal tissues, as well as its associations with clinicopathological features. Kaplan-Meier Plotter was utilized to evaluate the impact of MET expression on overall survival (OS) and progression-free survival (PFS). Protein-protein interaction (PPI) network was constructed via LinkedOmics, followed by Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of co-expressed genes. Four algorithms, TIMER, CIBERSORT, EPIC, and MCPcounter, were used to cross evaluate the correlation between MET expression and immune cell infiltration; Further validate the cell type specific expression of MET using the gastric cancer single-cell sequencing queues (GSE134520, GSE167297) built into the TISCH database. Results MET expression was significantly elevated in gastric cancer tissues compared with normal gastric mucosa (P < .05), and its expression level was significantly correlated with tumor grade and TNM stage. Patients with high MET expression exhibited significantly poorer OS and PFS than those with low MET expression (P < .05). The PPI network revealed that MET could interact with 20 key proteins, including EGFR, ERBB2, HGF, STAT3, and GRB2 etc. GO enrichment analysis suggests that differentially expressed genes are significantly enriched in functions such as the ERBB signaling pathway, cadherin binding, and DNA repair complexes; KEGG enrichment analysis showed that MET related genes were significantly enriched in pathways such as homologous recombination, nuclear cytoplasmic transport, mismatch repair, and oxidative phosphorylation. Immune infiltration analysis showed that the negative association between MET and B cells infiltration has cross algorithm robustness, while the association with neutrophils, CD8+ T cells, CD4+ T cells, and macrophages exhibits algorithmic heterogeneity or insignificance; There is no significant correlation between MET and common immune checkpoint molecules such as PD-1, PD-L1, CTLA4, etc. Single cell validation further confirmed that MET is mainly enriched in malignant epithelial cells and endothelial cells, and is almost not expressed in immune cells. Conclusions Multidimensional bioinformatic analyses demonstrate that elevated MET expression serves as an independent risk factor for unfavorable prognosis in gastric cancer. MET may mediate dual drug resistance in gastric cancer via crosstalk with multiple signaling molecules (including EGFR, ERBB2, HGF, STAT3 and GRB2) and dysregulation of the homologous recombination repair pathway. Results from multiple-algorithm immune infiltration analysis, single-cell dataset analysis and immune checkpoint correlation analysis indicate that MET exerts only modest direct regulatory effects on the gastric cancer immune microenvironment. This exploratory study offers systematic bioinformatic evidence supporting MET as a candidate prognostic biomarker and potential therapeutic target for gastric cancer. Further functional experiments and prospective cohort studies are required to validate its molecular mechanisms and clinical utility.

cancer biology↗

Spatiotemporal atlas resolves the mesenchymal-epithelial stem cell axis governing human hair follicle aging and pathology

How adult stem cell populations coordinate tissue regeneration across physiological and pathological states remains unclear. Hair follicles contain epithelial and mesenchymal stem cells that codetermine hair regeneration. Here, we integrate a multimodal spatiotemporal atlas with functional validation to define the mesenchymal-epithelial stem cell dynamics governing human hair follicle homeostasis, aging, and androgenetic alopecia. Aging is characterized by passive depletion of hDSC-derived regenerative cues, whereas AGA involves a shift of hDSC toward an inhibitory signaling hub that promotes HFSC dysfunction. We further pinpoint hDSC-secreted PTN as a key regenerative factor that promotes hair growth and counteracts androgen-induced growth suppression. This study provides a holistic framework of adult stem cell crosstalk across physiological and pathological states, offering a mechanistic roadmap to reinstate tissue regeneration.

cell biology↗

Sparse Linear Algebra Accelerates Genotype Representation Graph Computation at Biobank Scale

Biobank-scale genomic analyses are increasingly constrained by computational costs, as hundreds of thousands to millions of samples and variants must be analyzed together. The genotype representation graph (GRG) compactly encodes population genetic variation to accelerate computation, but the current approach does not exploit modern accelerator architectures. This work introduces Mikado, a new methodology for expressing GRG-based computation using sparse linear algebra primitives. Under a reverse topological ordering of the graph nodes, the GRG adjacency matrix is strictly block-lower-triangular, and the genotype matrix-vector product becomes a sparse triangular solve that can be further decomposed into a pipelined sequence of blocked sparse matrix-vector multiplies. By decoupling computation from graph representation, our approach exposes fine-grained parallelism and enables hardware-optimized sparse primitives on GPUs. Mikado achieves an order-of-magnitude speedup and cost savings for PCA and BOLT-LMM compared with the original GRG traversal approach, including on All of Us cohorts. It provides a scalable, hardware-portable, researcher-friendly tool for population genetics at biobank scale.

genomics↗

Large-Scale Network Embedding Predicts Opposing Functions of Adjacent Regions Within Human Prefrontal Cortex

Prefrontal regions are hypothesized to be organized hierarchically in support of cognitive control. Using precision functional MRI in three independent cohorts of intensively scanned participants (N=37), we consistently identified a lateral prefrontal cortex (LPFC) region linked to a canonical control network separate from a nearby rostral LPFC region linked to the action-mode network. Despite their spatial juxtaposition, the two regions were differentially coupled to the caudate and ventral putamen, suggesting they are components of segregated networks. Working memory demands activated the canonical LPFC control region but not the adjacent region. Contrasting go and no-go trials during target detection revealed a robust functional double dissociation during goal-directed behavior. The canonical LPFC control region activated when responses were withheld, while the putamen-coupled LPFC region increased activity during executed responses. These findings demonstrate that adjacent LPFC regions participate in opposing functions predicted by their embedding within distinct parallel large-scale networks.

neuroscience↗

Dissecting the TMEM132A-EGFR Dependency to Unlock Translational Therapeutic Opportunities for Pan-Solid Tumor

Solid tumors remain refractory to conventional treatments, yet cell surface proteins, by virtue of their extracellular accessibility and critical roles in tumor signaling, represent an attractive class of targets for precision-targeted therapy. Here, we report that TMEM132A is an essential and previously unrecognized pan-cancer target. TMEM132A interacts directly with EGFR and stabilizes its expression, thereby tethering EGFR at the plasma membrane and sustaining constitutive activation of lipid synthesis. Mechanistically, the TMEM132A-EGFR axis promotes lipogenesis by facilitating SREBP nuclear translocation, which in turn upregulates ACLY and ACSS2 expression to drive acetyl-CoA production and downstream lipid biosynthesis, ultimately disrupting lipid droplet homeostasis. To therapeutically target this axis, we developed a nanobody, LFNanoT132A#3, which effectively blocks the TMEM132A-EGFR interaction, abrogates downstream signaling activation, and potently inhibits proliferation across multiple solid tumor types. Notably, LFNanoT132A also exerts robust antitumor activity against H1975 xenografts, a model resistant to first- and second- generation EGFR inhibitors, underscoring its potential to overcome conventional drug resistance. Our findings establish TMEM132A#3 as a critical node in membrane-tethered oncogenic signaling and metabolic rewiring, and position LFNanoT132A#3 as a promising therapeutic candidate for precision cancer therapy.

cancer biology↗

A virus co-opts vector's m⁶A machinery for adaptive compensation

Insect vectors harbor diverse viruses that threaten human health and agricultural production, yet the genetic basis of mutualistic virus-vector interactions remain elusive. This underscores a long-standing paradox in pest management: viruses that cause destructive diseases also facilitate vector adaptation in ways that benefit both parties. Here we show that the globally devastating tomato yellow leaf curl virus (TYLCV) acts as a Cooperative Partner, co-opting its vector's m6A epitranscriptomic machinery to offset the reproductive fitness costs of neonicotinoid resistance in the whitefly. In resistant vectors, TYLCV infection alleviates reproductive deficits via the m6A-dependent pathway, where the methyltransferase METTL14 and demethylase ALKBH4 coordinately stabilize vitellogenin (Vg) transcripts to boost female fecundity. Mechanistically, the viral C2 and CP proteins directly interact with METTL14 and ALKBH4, respectively, remodeling their RNA binding affinity to facilitate mA modification on Vg. Disrupting either of these viral-vector protein interactions restores a reproductive cost phenotype in viruliferous resistant vectors, offering novel targets for sustainable pest control. Our findings uncover a fundamental role of epigenetic marks in adaptive trait, reshaping beneficial virus-vector relationships and providing new insights for innovative public health and crop protection strategies to address global challenges.

microbiology↗

TRAPPC8 Is an Endogenous Brake on UFMylation That Suppresses Tauopathy

UFMylation, a ubiquitin-like protein modification, drives tau spread through the brain, but what keeps this process in check has remained unclear. We show that TRAPPC8 acts as a natural brake on UFMylation, binding directly to the E1 enzyme UBA5 to dampen pathway activity. In Alzheimer's disease brain tissue, TRAPPC8 is reduced while UFMylation is elevated, suggesting this brake fails as disease progresses. Sustaining UFMylation in human iPSC-derived neurons increased tau aggregation and spread while disrupting lysosomal function and lipid balance. Restoring TRAPPC8-UBA5 binding reversed these defects through the lysosomal protein CLN8, which restored lysosomal function and reduced tau pathology. Notably, expressing just the UBA5-binding region of TRAPPC8 was enough to suppress tau pathology in vivo, marking it as a promising therapeutic target.

neuroscience↗

Integrative enhancer discovery identifies functional enhancer dependencies in pediatric acute myeloid leukemia

Pediatric acute myeloid leukemia (AML) is driven by aberrant transcriptional programs sustained by poorly defined cis-regulatory mechanisms. To systematically identify functional enhancer dependencies, we developed an integrative enhancer discovery strategy that combines H3K27ac CUT&Tag profiling, enhancer-associated transcription, and CRISPR interference (CRISPRi) screening. By leveraging enhancer-associated transcription to prioritize candidate regulatory elements, we identified 321 leukemia-associated enhancers for functional interrogation. This approach uncovered the hematopoietic MYB enhancer (H-ME) within the HBS1L-MYB-AHI1 locus as a critical regulator of leukemic growth. H-ME repression reduced chromatin accessibility and active histone marks at the MYB promoter, suppressed MYB expression, and induced differentiation-associated transcriptional programs. In contrast, selective depletion of the enhancer-associated transcript had no effect on MYB expression or leukemic proliferation, demonstrating that enhancer activity resides within the underlying regulatory DNA element rather than its mature RNA product. H-ME exhibited preferential activity in megakaryocytic leukemia, and its perturbation impaired leukemic growth in primary patient-derived models in vitro and in vivo. Together, our findings establish an integrative framework for the systematic discovery of functional enhancer dependencies and identified H-ME as an RNA-independent regulator of MYB in pediatric AML.

cancer biology↗

SPARKLE: evidence-constrained correction of local RNA leakage in high-resolution spatial transcriptomics

High-resolution sequencing-based spatial transcriptomics, including Stereo-seq and Visium HD, aggregates dense capture units into cell-resolved expression matrices. During tissue processing and permeabilization, RNA released from source cells can spread to neighbouring capture locations, reducing cell-type specificity and biasing downstream analyses. Here we developed SPARKLE (Spatial Ambient RNA Kernel-based Leakage Estimator), a cell-level correction method that uses capture locations outside cell-segmentation masks as within-sample spatial evidence of leakage. SPARKLE fits sparse spatial kernels to out-of-mask observations to estimate a sample-level propagation scale and gene-specific leakage coefficients. It corrects only genes supported by out-of-mask goodness of fit and uses expression-dependent conservative shrinkage to protect highly expressing source cells. In ten simulated scenarios, SPARKLE achieved the highest cell-wise concordance in eight and the lowest RMSE in nine. In axolotl brain, mouse brain and human ovarian cancer, SPARKLE removed ectopic marker signal from neighbouring cells while retaining source-cell expression, improved agreement with independent single-cell and single-nucleus references, and recovered an inferred fibroblast-to-tumor COL1A2-SDC4 communication route that was obscured by ectopic COL1A2 expression. Conclusions remained stable across plausible spatial scales and background-bin sizes. Runtime scaled near-linearly with tissue-window area and was further accelerated on GPU. SPARKLE is therefore a reference-free, fast and scalable method for correcting local RNA leakage from evidence contained within each sample, improving the reliability of cell-type localization, tissue-compartment identification and cell-cell communication inference.

bioinformatics↗

A cross-modal generative model for incomplete and degradedprostate MRI with multicentre clinical validation

Missing or degraded sequences can limit prostate multiparametric MRI. We developed MSCNet, a sequence-conditioned cross-modal generative framework for reconstructing unavailable contrasts and restoring degraded acquisitions. Across ten completion tasks, task-specific MSCNet achieved mean structural similarity of 0.818 versus 0.798 for the strongest task-matched comparators; matched-capacity analyses showed larger differences in lesion fidelity and boundary preservation. In a blinded 1,000-case reader study, overall image quality met the prespecified non-inferiority criterion for DWI, ADC and T2W completion, but not T1W. In a separate 200-case diagnostic assessment, AUCs for clinically significant cancer were 0.860 with acquired images, 0.841 with MSCNet and 0.797 with baseline-generated images. A locked 186-case three-hospital cohort supported multicentre transportability. These retrospective results support quality-controlled cross-modal reconstruction as an adjunct to acquired prostate MRI.

bioengineering↗

NET1 mRNA localization to the midbody is required for ARP2/3-dependent initiation of mitotic abscission

The recruitment and activation of abscission machinery following mitosis is tightly regulated in time and space, yet the mechanisms controlling this process are poorly understood. We find that RNA localization and local translation at the midbody regulates when and where abscission-regulating proteins are expressed. The 3'UTR of NET1 mRNA contains an element that is necessary and sufficient for RNA targeting to the midbody. Mislocalization of NET1 mRNA results in a loss of NET1 protein, a Rho family GEF, throughout the intercellular bridge as well as slower cell proliferation and delayed abscission. This leads to a loss of Arp2/3 at the abscission site and is dependent upon NET1 binding to Rho family GTPases. These findings establish midbody RNA localization and local translation as a key layer of regulation over abscission timing and identify a role for NET1 as a regulator of Arp2/3-mediated branched actin accumulation at the abscission site.

molecular biology↗

RNA m6A demethylase ALKBH4 governs whitefly development

N6-methyladenosine (m6A) modification is the most predominant and ubiquitous internal modification of RNA in eukaryotes, serving as a key post-transcriptional regulator of gene expression that is dynamically modulated by methyltransferases (writers) and demethylases (erasers). However, while the functions of m6A methylases have been partially elucidated in insects, the identity of m6A erasers in arthropods and their chemical catalytic mechanisms, as well as biological functions, remains largely enigmatic. Here, we uncovered 2499 putative methylase genes and 1148 putative demethylase genes in 266 insect genomes, and demonstrated that ALKBH4 functions as an m6A demethylase in the whitefly, Bemisia tabaci, catalyzing the oxidative reversal of mRNA m6A modifications both in vitro and in vivo. Furthermore, we established that ALKBH4, in coordination with other core components of the m6A pathway, fulfills an essential function in regulating the transcript stability of Imaginal Disk Growth Factor 1 (IDGF1) during whitefly development. Collectively, our findings expand the evolutionary scope of the eukaryotic m6A modification system, and reveal a conserved yet insect-specific epitranscriptomic regulatory mechanism governing fundamental physiological processes and adaptive phenotypes. Significance statementThe addition of a methyl group to the N6-position of adenosine (m6A) is a highly abundant chemical modification of RNA. However, the functional role of m6A in insects and the key enzymes that regulate its levels remains poorly understood. In this study, we explored putative methylase genes and demethylase genes in hundreds insect genomes, and identified an m6A RNA demethylase, ALKBH4, in the whitefly, Bemisia tabaci. We demonstrate that ALKBH4 oxidatively reverses mRNA methylation in vivo and in vitro, in combination with other components of the m6A pathway, plays an important role in whitefly development. These findings provide new insight into m6A methylation system of insect.

zoology↗

The linker histone H1.4 condenses chromatin in maturing postmitotic neurons

H1 histones are abundant nuclear proteins that bind to linker DNA at the entry and exit points of nucleosomes. Although individual H1 family members play partially redundant roles in chromatin organization, the discovery of disease-associated mutations in H1 genes has raised interest in their cell-type specific functions. Heterozygous, de novo frameshift mutations in H1-4 cause the neurodevelopmental disorder Rahman Syndrome, which is characterized by mild to severe intellectual disability along with other neurological and morphological features. H1.4 has mostly been studied in dividing cells, and its expression in the brain was poorly understood. Here we characterized the expression of H1f4 mRNA and H1.4 protein in the brains of male and female mice across postnatal development. Using an epitope-tagged H1f4 knockin mouse, we show that this linker histone is robustly expressed throughout the brain including in mature, post-mitotic neurons of adult mice. By chromatin immunoprecipitation, we observe that H1.4 binds broadly across the genome in neural progenitors and accumulates in heterochromatin over the course of neuronal maturation. Finally we show that developmental maturation of chromatin compaction in cerebellar granule neurons is disrupted in H1f2/H1f4 double knockout mice. These data raise the possibility that the neurological changes in Rahman Syndrome may arise from disrupted functions of histone H1.4 in neurons.

cell biology↗

Health-associated gut bacteriocins target TLR4 to suppress intestinal inflammation

The human microbiome maintains host immune homeostasis by secreting bioactive metabolites. However, extending beyond well-characterized metabolites, the functions of most microbiome-encoded peptides remain poorly defined. In this study, we developed a multi-cohort metagenomic framework to profile protective class II bacteriocins--unmodified, ribosomally synthesized peptides--that are enriched in healthy individuals but depleted in patients with inflammatory bowel disease (IBD). We have designated these health-associated bacteriocins as gutcins. Two gutcins, which lack canonical antimicrobial activity, potently attenuate intestinal inflammation in murine models. Cryo-electron microscopy (cryo-EM) reveals that one gutcin, named gutcin 03, directly engages the C-terminus of TLR4, blocking its dimerization and downstream inflammatory signaling. Guided by this structural interface, we generated truncated variants with enhanced potency, demonstrating the amenability of these simple peptides to rational optimization. Collectively, our findings reposition class II bacteriocins from antimicrobial agents to endogenous immunomodulatory effectors and establish a structural and mechanistic foundation for their development as next-generation therapeutics for inflammatory intestinal disorders.

microbiology↗

Ribonucleotide Reductase Inhibition Overcomes FLT3 Inhibitor Resistance in Acute Myeloid Leukemia

Internal tandem duplication mutations in FLT3 (FLT3ITD) occur in approximately 30% of patients with acute myeloid leukemia (AML) and are among the most common genetic alterations in this disease. FLT3ITD is a major driver of AML and is associated with poor clinical outcomes. Although FLT3 inhibitors (FLT3is) have significantly improved outcomes for patients with FLT3ITD+ AML, acquired resistance remains a major barrier to durable clinical benefit. Reactivation of RAS/MAPK signaling, often driven by activating NRAS mutations, is a major mechanism of FLT3i resistance in AML; however, effective strategies to overcome this resistance remain lacking. Here, we identify ribonucleotide reductase (RNR) as a critical therapeutic vulnerability in NRAS-driven FLT3i-resistant FLT3ITD+ AML. Activation of RAS signaling through SPRY3 loss or oncogenic NRAS mutations confers robust resistance to FLT3is, whereas pharmacologic inhibition of RNR with multiple inhibitors, as well as siRNA-mediated RNR suppression, reverses FLT3i resistance and restores FLT3i sensitivity across multiple FLT3ITD+ AML models in vitro. In vivo, clofarabine, an FDA-approved RNR inhibitor (RNRi), significantly overcomes NRAS mutation-driven FLT3i resistance. In combination with FLT3 inhibition, clofarabine markedly suppresses the progression of FLT3i-resistant AML and significantly prolongs survival in cell line-derived xenograft (CDX) models. Importantly, the therapeutic efficacy of the gilteritinib/clofarabine combination was independently validated in two genetically distinct patient-derived xenograft (PDX) models harboring different NRAS mutations, demonstrating robust reduction of leukemia burden and confirming the generalizability of RNR inhibition in primary FLT3i-resistant AML. Together, these findings identify a previously unrecognized therapeutic vulnerability in FLT3i-resistant FLT3mut+ AML and establish RNR inhibition as an effective strategy to overcome FLT3i resistance, providing a strong rationale for the clinical evaluation of RNRis in combination with FLT3is in patients with resistant AML. SignificanceAlthough FLT3 inhibitors (FLT3i) are an important therapeutic advance in FLT3ITD+ AML, resistance commonly develops. We identified ribonucleotide reductase (RNR) as a new key vulnerability in NRAS-driven FLT3i-resistant AML and demonstrated that multiple RNRis, including the FDA-approved agent clofarabine, restore FLT3i sensitivity and enhance antileukemic activity, supporting a clinically actionable combination strategy.

cancer biology↗