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Cai, F.

Publications and source records attributed to Cai, F..

At least 19 recordsLinked to original sources

Learning with interacting dendrites improves neuronal familiarity detection

Biological neurons can perform nonlinear computations within their dendrites and support branch-localized plasticity. This raises the possibility that single cells can store memories more efficiently and with less interference by confining synaptic modifications to specific dendrites. We study a parallel-dendrite model performing online familiarity detection and compare three dendrite-update rules during learning: (i) independent thresholding, (ii) an interacting rule that adapts the target local dendritic activation per item, and (iii) an interacting n-winners-take-all (WTA) rule that constrains the number of updated branches per item. The interacting rules substantially improve capacity by limiting variance in memory responses and decorrelating weights across branches -- even when inputs are strongly correlated. These results suggest that competition among dendrites, consistent with resource-limited plasticity mechanisms, can enhance single-cell memory beyond non-interacting schemes.

neuroscience↗

Rapid vaccine induction of macaque HIV-1 V2 Apex broadly neutralizing antibodies with immunogenetic signatures that are potentially translatable to humans

Due to the complex biology of HIV-1 broadly neutralizing antibodies (bnAbs), HIV-1 vaccines must target unmutated germline precursor antibodies with B cell receptors that have the appropriate specificity and genetic features to develop neutralization breadth. Previous work has shown that immunization or infection in macaques primes unmutated precursor antibodies that target the broadly neutralizing epitope composed of the second variable region and proximal glycans (termed V2-apex site) of HIV-1 envelope (Env). Macaque V2-apex bnAb precursors elicited thus far have homogeneous usage of the second reading frame of a diversity (D) gene found only in macaques, calling into question whether HIV-1 Env immunogens can elicit only this canonical, macaque-specific V2-apex antibody response, limiting human vaccination success. Here, we show that vaccination of rhesus macaques with Env conjugated to a ferritin nanoparticle (OPT4-scNP) rapidly elicited V2-apex bnAbs with distinct D gene segment usage and motifs that are not restricted only to macaques. After two priming immunizations, V2-apex antibodies with non-canonical HCDR3s exhibited greater neutralization potency and breadth than V2-apex antibodies with previously observed HCDR3 motifs. Following sequential boosting immunizations, a V2-apex bnAb lineage with a novel HCDR3-encoded EDGED motif increased its neutralization breadth, including neutralization of viral isolates bearing the N130 glycan, which shields the V2-apex from recognition. High-resolution structures of two members of this V2-apex bnAb lineage, called DH2050, defined a novel binding mode in which it used its EDGED motif to contact the C-strand peptide and the N160 glycan within the V2-apex site. Altogether, we define a novel bnAb binding mode to the V2 Apex and demonstrate that HIV-1 Env sequential vaccination elicits V2-apex bnAbs with immunogenetic signatures that are potentially translatable to the human immune system.

immunology↗

Continental-scale multi-omics reveals a distinct microbial-viral biome in sandy beach ecosystems structured by tidal zonation

Sandy beaches are dynamic coastal interfaces shaped by strong physical forcing and intense exchange between marine and terrestrial environments, yet their microbiomes remain poorly resolved at the genomic scale. Here we present a genome-resolved survey of microbial and viral communities across sandy beaches spanning a continental-scale latitudinal gradient along the Chinese coastline. By integrating cross-shore sampling, coastal geochemistry and large-scale multi-omics, we generated 978 metagenomes, 63 viromes and 72 metatranscriptomes, reconstructing 13,337 metagenome-assembled genomes and 38,255 viral populations. Sandy beach microbiomes exhibit exceptionally high genomic novelty, with more than 90% of species-level genomes representing previously undescribed taxa, suggesting that permeable coastal sediments constitute a distinct microbial and viral reservoir. Tidal zonation emerged as a dominant ecological driver structuring microbial diversity, metabolic strategies and virus-host interactions across cross-shore gradients. Genome-resolved analyses revealed systematic metabolic shifts from oxic heterotrophy in supratidal sediments toward increasingly chemolithotrophic and autotrophic pathways toward the low-intertidal and subtidal zone. Sandy beach microbiomes further encode broad potential for hydrocarbon and plastic transformation, together with diverse biosynthetic and antibiotic resistance repertoires that may mediate microbial chemical interactions. Together, these findings identify sandy beaches as a previously under-recognized microbial-viral biome shaped by tidal forcing, providing insight into microbiome evolution and coastal ecosystem resilience under increasing anthropogenic pressure.

microbiology↗

UFMylation of Pyruvate Dehydrogenase Regulates Mitochondrial Metabolism

The ubiquitin-fold modifier 1 (UFM1) post-translational modification (PTM), or UFMylation, regulates protein homeostasis and is essential for human development. Yet the roles of the de-UFMylase, UFM1-specific peptidase 2 (UFSP2), which removes UFM1 from UFMylated proteins, remain poorly characterized. Here, we demonstrate that UFMylation and UFSP2 regulate mitochondrial metabolism. Quantitative proteomics in UFSP2-deficient cells revealed the accumulation of many proteins previously unknown to be impacted by UFMylation. These included components of the mitochondrial ribosome, electron transport chain (ETC), and pyruvate dehydrogenase (PDH) complex. Functional analyses demonstrated that excessive UFMylation in UFSP2-deficient cells increases mitochondrial respiration, glucose oxidation in the tricarboxylic acid (TCA) cycle, and PDH enzymatic activity. We identified dihydrolipoamide S-acetyltransferase (DLAT), the E2 component of PDH, as a direct UFMylation substrate, with lysine 118 (K118) as the primary conjugation site. Mutating K118 to arginine (K118R) abolished DLAT UFMylation and reduced pyruvate oxidation, identifying this modification as an activator of PDH. These findings reveal a UFMylation-based regulatory mechanism that controls mitochondrial function by inducing utilization of pyruvate as a TCA cycle fuel.

biochemistry↗

Time-Resolved Tracking and Secretome Mapping of Intracellular, Cell Surface, and Extracellular Glycoconjugates with a Mini-Tetrazine N-Acetylglucosamine

Glycosylation is instrumental in governing essential biological processes that dictate health outcomes. Herein we describe a mini-tetrazine N-acetylglucosamine (HTz-GlcNAc) that is incorporated into N-linked glycans and through rapid live-cell labeling with trans-cyclooctene (TCO) reagents enables real-time visualization and evaluation of glycoconjugate trafficking in living cells. We utilize cell-permeable and impermeable TCO-fluorophores to perform time-resolved, multicolor live labeling of cell-surface glycoconjugates, as well as intracellular, and internalized glycoconjugates. We observe intracellular glycoconjugate trafficking throughout the secretory pathway of live cells in real-time, as well as cell surface glycan turnover and extracellular vesicle secretion across three days. In the toolkit of probes for metabolic oligosaccharide engineering, HTz-GlcNAc brings the capability of precise interrogation of intracellular and extracellular glycoconjugate trafficking, and selective tagging of intra-and-extracellular vesicles, while providing a handle for the purification and enrichment of glycans for immunoblot and proteomic analyses. TOC image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/682811v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@f65188org.highwire.dtl.DTLVardef@162c58corg.highwire.dtl.DTLVardef@1977b73org.highwire.dtl.DTLVardef@29e9ff_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Mass spectrometry-based proteomic and glycoproteomic drafts of fifteen human body fluids

The study of proteins and N-glycosylation in human body fluids (HBFs) is crucial for understanding both physiological and pathological states, offering valuable insights for disease diagnostics and monitoring. In this study, we present a comprehensive proteomics and glycoproteomics dataset featuring 15 types of precious HBFs (plasma (P), urine (U), cerebrospinal fluid (CSF), pleural fluid (PF), ascitic fluid (AF), synovial fluid (SF), pericardial fluid (PCF), peritoneal dialysis effluent (PDE), bile (B), gastric juice (GJ), seminal plasma (SP), saliva (SA), pancreatic juice (PJ), sweat (SW), and tear (T)). We also provide detailed protocols for protein processing specific to each type of HBF. The resulting peptides and enriched intact N-glycopeptides were analyzed via liquid chromatography-tandem mass spectrometry (LC-MS/MS) in data independent acquisition (DIA) and combined electron transfer/higher-energy collisional dissociation and stepped collision energy/higher-energy collisional dissociation (EThcD-sceHCD) mode, respectively. The resulting spectra and searched files have been uploaded to the online repository iProX (www.iprox.cn) and made easily accessible (PXD068799) to facilitate further research into HBF proteomics and glycoproteomics.

systems biology↗

Gliomas phenocopy an inborn error of metabolism to drive neuronal activity and tumor growth

The metabolic hallmarks of high-grade glioma (HGG) are not fully understood. Human brain tissue metabolomics revealed that the creatine synthesis pathway intermediate guanidinoacetate (GAA) accumulated [~]100-fold in HGGs relative to controls, which was caused by imbalanced activities of enzymes in this pathway. Glioma cells secreted GAA rather than using it to produce creatine, implicating an unexpected function. GAA accumulates in GAMT deficiency, an inborn error of metabolism, and elevates neuronal excitability. Neuronal excitability is also increased in glioma and drives tumor growth through neuron-glioma interactions. We hypothesized that glioma-generated GAA excites surrounding neurons. Indeed, GAA induced neuronal hyperactivity by activating GABAA receptors and causing depolarizing GABA currents in glioma-associated neurons with dysregulated chloride homeostasis. Depleting tumoral GAA decreased electrochemical activity, neuron-glioma interactions, and tumor aggressiveness. Our findings unveil a new mechanism linking cancer metabolism with cancer neuroscience and leverage human genetics to nominate GAA synthesis as a target in gliomas.

cancer biology↗

Mutant IDH silences GSX2 to reprogram neural progenitor cell fate and promote gliomagenesis

Isocitrate dehydrogenase (IDH) mutations arise early in gliomas and are associated with a defined neurodevelopmental cancer cell hierarchy. However, how mutant IDH contributes to this hierarchy and whether this interaction promotes gliomagenesis remain unclear. We captured the dynamics of IDH-mutant glioma initiation in genetically engineered mice through time-resolved, single-cell genomics. Mutant IDH activates and induces lineage switching of neural progenitor cells (NPCs). These actions expand oligodendrocyte precursor cells, the predominant cell-of-origin for these tumors, at the expense of interneurons. Lineage switching is mediated by promoter hypermethylation and silencing of Gsx2, a homeobox gene required for neurogenesis. Critically, Gsx2 ablation recapitulates NPC fate reprogramming by mutant IDH. We provide a new model of neural cell fate control by IDH oncogenes and insights into the developmental origins of glioma.

cancer biology↗

Hyper-Glycosylation as a Central Metabolic Driver of Alzheimers Disease

Alzheimers disease (AD) is a neurodegenerative disorder characterized by devastating degenerative decline. Metabolic disruptions are widely observed, yet their involvement in the molecular etiology of AD remains underexplored. Utilizing spatial metabolomics, lipidomics, and glycomics in both mouse models and human post-mortem samples, we identified a hyper-glycosylation phenotype as a hallmark of AD. To investigate the underlying mechanisms and whether the observed effect was a driver of the observed decline, we developed an advanced spatial isotopic tracing pulse-chase method to study the dynamics of N-linked glycans. Our analysis revealed enhanced glycan biosynthesis in AD mouse models. Based on these findings, we performed genetic and dietary interventions to modulate glycan biosynthesis. Genetic knockdown of glycan biosynthetic enzymes ameliorated the hyper-glycosylation and improved cognitive and behavioral outcomes in AD mice. In contrast, oral glucosamine supplementation drove hyper-glycosylation and exacerbated cognitive and behavioral deficits. To assess the clinical relevance of these findings, we conducted a retrospective analysis of a large population of patients with mild cognitive impairment (MCI), AD, and Alzheimers Disease Related Dementias (ADRD) stratified by glucosamine use, leveraging electronic health records. Consistently, glucosamine supplementation was associated with increased mortality in AD and ADRD patient cohorts, and significantly elevated progression from MCI to AD compared to age-matched controls. Collectively, our findings establish hyper-glycosylation as a pathological driver of AD and highlight glycan metabolism as an actional target in the fight against AD.

neuroscience↗

L-2-hydroxyglutarate impairs neuronal differentiation through epigenetic activation of MYC expression

High levels of L- and D-2-hydroxyglutarate, the reduced forms of -ketoglutarate (KG), are implicated in human neurodevelopmental disorders and cancer. Both enantiomers exert effects on epigenetics by modulating a family of KG-dependent dioxygenases involved in histone, DNA and RNA demethylation. L-2HG dehydrogenase (L2HGDH) converts L-2HG to KG. Its deficiency is a rare, autosomal recessive inborn error of metabolism (IEM) characterized by systemic elevations of L-2HG, progressive neurological disability and a high risk of malignancy in the brain. The mechanisms behind these aberrations are unknown. Here we used an isogenic, patient-derived induced pluripotent stem cell (iPSC) system to study the impact of L2HGDH deficiency on neural progenitor cell (NPC) function and neuronal differentiation. We demonstrate that L2HGDH deficiency causes accumulation of L-2HG, NPC hyperproliferation, increased clonogenicity, excessive growth, and defective neuronal differentiation in 2D cultures and cortical spheroids. Editing the L2HGDH locus to wild-type reverses these effects. Blocking L-2HG accumulation in NPCs with a glutaminase inhibitor also induces neuronal differentiation. L-2HG-dependent inhibition of KDM5 histone demethylases leads to widespread retention of H3K4me2 and H3K4me3, markers of active gene expression. These marks are prominently elevated at the MYC locus in L2HGDH-deficient cells, and consequently cells express high MYC both in 2D culture and in many distinct cell types within cortical spheroids. Although thousands of loci display altered histone methylation, genetically or pharmacologically normalizing MYC is sufficient to completely reverse defective neuronal differentiation. These data indicate that the primary metabolic disturbance in an iPSC IEM model activates the MYC oncogene, favoring stem cell self-renewal and suppressing lineage commitment to neurons.

genetics↗

NUDT5 regulates purine metabolism and thiopurine sensitivity by interacting with PPAT

Cells generate purine nucleotides through both de novo purine biosynthesis (DNPB) and purine salvage. Purine accumulation represses energetically costly DNPB through feedback inhibition of the enzymatic steps that produce the precursor phosphoribosylamine. Excessive DNPB is associated with human diseases including neurological dysfunction and hyperuricemia. However, the mechanisms explaining how cells balance DNPB and purine salvage are incompletely understood. Data from a genome-wide CRISPR loss-of-function screen and extensive stable isotope tracing identified Nudix hydrolase 5 (NUDT5) as a suppressor of DNPB during purine salvage. NUDT5 ablation allows DNPB to persist in the presence of either native purines or thiopurine drugs; this renders NUDT5-deficient cells insensitive to thiopurine treatment. Surprisingly, this regulation occurs independently of NUDT5s known function in hydrolyzing ADP-ribose to AMP and ribose-5-phosphate. Rather, NUDT5 interacts with phosphoribosyl pyrophosphate amidotransferase (PPAT), the rate-limiting enzyme in DNPB that generates phosphoribosylamine. Upon induction of purine salvage, the PPAT-NUDT5 interaction is required to trigger disassembly of the purinosome, a cytosolic metabolon involved in efficient DNPB. Mutations that disrupt NUDT5s interaction with PPAT but leave its catalytic activity intact permit excessive DNPB during purine salvage, inducing thiopurine resistance. Collectively, our findings identify NUDT5 as a regulator governing the balance between DNPB and purine salvage, underscoring its impact on nucleotide metabolism and efficacy of thiopurine treatment.

biochemistry↗

RAB1A is a novel vulnerability in uveal melanoma revealed by dual inhibition of MNK1/2 and mTOR.

Uveal melanoma (UM) is an eye cancer that is fatal upon metastasis to the liver. Most treatments trialed in UM fail to provide therapeutic benefit, thus there is an urgent need for novel treatment strategies. The MAPK and PI3K signaling pathways, key molecular drivers found to be hyper-activated in UM, converge on the MNK1/2-eIF4E and mTORC1/2-4EBP axes. Here, we demonstrate that the pharmacologic inhibition of MNK1/2 in combination with an mTOR inhibitor impairs clonogenic outgrowth and UM cell invasion. Using proteomic analyses, we reveal that combined MNK1/2 and mTOR inhibition disrupts Golgi homeostasis and protein vesicle trafficking mainly due to downregulated RAB1A expression, a master regulator of intracellular protein transport. We uncover that the knockdown of RAB1A blocks liver metastasis, a result that is recapitulated by combined pharmacologic inhibition of MNK1/2 and mTOR. Finally, we show that RAB1A expression reshapes the surfaceome by increasing the abundance of plasma membrane proteins associated with poor overall survival in UM, highlighting its potential as a biomarker. This study identifies protein vesicle transport as an unrecognized vulnerability in UM and supports a mechanistic rationale for targeting MNK1/2 and mTOR in metastatic UM.

cancer biology↗

CRAK-Velo: Chromatin Accessibility Kinetics integration improves RNA Velocity estimation

RNA velocity has recently emerged as a key tool in the analysis of single-cell transcriptomic data, yet connecting RNA velocity analyses to underlying regulatory processes has proved challenging. Here we propose CRAK-Velo, a semi-mechanistic model which integrates chromatin accessibility data in the estimation of RNA velocities. CRAK-Velo provides biologically consistent estimates of developmental flows and enables accurate cell-type deconvolution, while additionally shining light on regulatory processes at the level of interactions between genes and chromatin regions.

bioinformatics↗

Glycosaminoglycan-mediated lipoprotein uptake protects cancer cells from ferroptosis

Lipids are essential for tumours because of their structural, energetic, and signaling roles. While many cancer cells upregulate lipid synthesis, growing evidence suggests that tumours simultaneously intensify the uptake of circulating lipids carried by lipoproteins. Which mechanisms promote the uptake of extracellular lipids, and how this pool of lipids contributes to cancer progression, are poorly understood. Here, using functional genetic screens, we find that lipoprotein uptake confers resistance to lipid peroxidation and ferroptotic cell death. Lipoprotein supplementation robustly inhibits ferroptosis across numerous cancer types. Mechanistically, cancer cells take up lipoproteins through a pathway dependent on sulfated glycosaminoglycans (GAGs) linked to cell-surface proteoglycans. Tumour GAGs are a major determinant of the uptake of both low and high density lipoproteins. Impairment of glycosaminoglycan synthesis or acute degradation of surface GAGs decreases the uptake of lipoproteins, sensitizes cells to ferroptosis and reduces tumour growth in mice. We also find that human clear cell renal cell carcinomas, a distinctively lipid-rich tumour type, display elevated levels of lipoprotein-derived antioxidants and the GAG chondroitin sulfate than non-malignant human kidney. Altogether, our work identifies lipoprotein uptake as an essential anti-ferroptotic mechanism for cancer cells to overcome lipid oxidative stress in vivo, and reveals GAG biosynthesis as an unexpected mediator of this process.

cancer biology↗

An interactive web application for exploring human plasma and fibroblast metabolomics data from patients with inborn errors of metabolism

Metabolomic profiling is instrumental in understanding the systemic and cellular impact of inborn errors of metabolism (IEMs), monogenic disorders caused by pathogenic genomic variants in genes involved in metabolism. This study encompasses untargeted metabolomics analysis of plasma from 474 individuals and fibroblasts from 67 subjects, incorporating healthy controls, patients with 65 different monogenic diseases, and numerous undiagnosed cases. We introduce a web application designed for the in-depth exploration of this extensive metabolomics database. The application offers a user-friendly interface for data review, download, and detailed analysis of metabolic deviations linked to IEMs at the level of individual patients or groups of patients with the same diagnosis. It also provides interactive tools for investigating metabolic relationships and offers comparative analyses of plasma and fibroblast profiles. This tool emphasizes the metabolic interplay within and across biological matrices, enriching our understanding of metabolic regulation in health and disease. As a resource, the application provides broad utility in research, offering novel insights into metabolic pathways and their alterations in various disorders.

bioinformatics↗

Electron transport inhibition increases cellular dependence on purine transport and salvage

Cancer cells reprogram their metabolism to support cell growth and proliferation in harsh environments. While many studies have documented the importance of mitochondrial oxidative phosphorylation (OXPHOS) in tumor growth, some cancer cells experience conditions of reduced OXPHOS in vivo and induce alternative metabolic pathways to compensate. To assess how human cells respond to mitochondrial dysfunction, we performed metabolomics in fibroblasts and plasma from patients with inborn errors of mitochondrial metabolism, and in cancer cells subjected to inhibition of the electron transport chain (ETC). All these analyses revealed extensive perturbations in purine-related metabolites; in non-small cell lung cancer (NSCLC) cells, ETC blockade led to purine metabolite accumulation arising from a reduced cytosolic NAD+/NADH ratio (NADH reductive stress). Stable isotope tracing demonstrated that ETC deficiency suppressed de novo purine nucleotide synthesis while enhancing purine salvage. Analysis of NSCLC patients infused with [U-13C]glucose revealed that tumors with markers of low oxidative mitochondrial metabolism exhibited high expression of the purine salvage enzyme HPRT1 and abundant levels of the HPRT1 product inosine monophosphate (IMP). ETC blockade also induced production of ribose-5 phosphate (R5P) by the pentose phosphate pathway (PPP) and import of purine nucleobases. Blocking either HPRT1 or nucleoside transporters sensitized cancer cells to ETC inhibition, and overexpressing nucleoside transporters was sufficient to drive growth of NSCLC xenografts. Collectively, this study mechanistically delineates how cells compensate for suppressed purine metabolism in response to ETC blockade, and uncovers a new metabolic vulnerability in tumors experiencing NADH excess.

biochemistry↗

Somatic protospacer adjacent motifs are numerous and selectively targetable in cancers

Somatic mutations are desirable targets for selective elimination of cancer, yet most are found within the noncoding regions. We propose a novel, cancer-specific killing approach using CRISPR-Cas9 which exploits the requirement of a protospacer adjacent motif (PAM) for Cas9 activity. Through whole genome sequencing (WGS) of paired tumor minus normal (T-N) samples from three pancreatic cancer patients (Panc480, Panc504, and Panc1002), we identified an average of 417 somatic PAMs per tumor produced from single base substitutions. We analyzed 591 paired T-N samples from The International Cancer Genome Consortium and discovered medians of [~]455 somatic PAMs per tumor in pancreatic, [~]2800 in lung, and [~]3200 in esophageal cancer cohorts. Finally, we demonstrated >80% selective cell death of two targeted pancreatic cancer cell lines in co-cultures using 4-9 sgRNAs, targeting noncoding regions, designed from the somatic PAM discovery approach. We also showed no off-target activity from these tumor-specific sgRNAs through WGS. Statement of significanceThis study demonstrates the potential of CRISPR-Cas9 as a novel and selective anti-cancer strategy. It requires just a few targets to induce double strand breaks for significant cytotoxicity. Our findings markedly expand the repertoire of targetable mutations in cancers and support genetically targeting other adult solid tumor types.

cancer biology↗

Mechanism of delayed cell death following simultaneous CRISPR-Cas9 targeting in pancreatic cancers

While radiation is an effective oncologic therapy, killing cancer by inducing DNA double-strand breaks (DSBs), it lacks specificity for neoplastic cells. We have previously adapted the CRISPR-Cas9 gene-editing technology as a cancer-specific treatment modality targeting somatic mutations in pancreatic cancer (PC). However, its tumoricidal potential remains unclear, especially in comparison to therapeutic doses of radiation. Here, we demonstrate that CRISPR-Cas9-induced DSBs are more cytotoxic in PCs than a comparable number of radiation-induced DSBs. We observed >90% tumor growth inhibition by targeting 9 sites with cancer-specific single-guide RNAs (sgRNAs). Through both bioinformatics and cytogenetics analyses, we found that CRISPR-Cas9-induced DSBs triggered ongoing chromosomal rearrangements, with 87% of structural variants not directly produced from the initial CRISPR-Cas9-induced DSBs, and chromosomal instability (CIN) peaking before cell death. By comparing the cytotoxicity of CRISPR-Cas9- to radiation-induced DSBs, we demonstrate that the number of DSBs required to achieve equitoxic effects was [~]3 times higher for radiation than CRISPR-Cas9. Finally, we show that PC cells that had survived CRISPR-Cas9 targeting retained susceptibility to subsequent CRISPR-Cas9-induced DSBs at different genomic sites with >87% growth inhibition. Together, our data support the therapeutic potential of CRISPR-Cas9 as an anti-cancer strategy.

cancer biology↗