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Liu, X.

Publications and source records attributed to Liu, X..

At least 271 records · Page 15Linked to original sources

Decades of dreams coming true: capillary zone electrophoresis-mass spectrometry for reproducible multi-level proteomics

Capillary zone electrophoresis (CZE)-mass spectrometry (MS) has been proposed as a powerful analytical tool for bottom-up, top-down, and native proteomics (multi-level proteomics) decades ago to analyze complex biological samples at the levels of peptides (bottom-up), proteoforms (top-down), and complexoforms (native). However, its broad adoption has been impeded by the limited robustness and reproducibility. Here, we present multi-level proteomics data from nearly 170 CZE-MS runs ([~]170 hours of instrument time), demonstrating qualitatively (i.e., the number of identified peptides and proteoforms, the number of detected complexoforms, and their migration time) and quantitatively (i.e., peptide, proteoform, and complexoform intensity) reproducible measurement of complex samples with varying levels of complexity, i.e., Escherichia coli cells, HeLa cells, and human plasma. CZE-MS-based native proteomics enabled the detection of hundreds of complexoforms up to 800 kDa from the complex systems via consuming only nanograms of protein material. The results indicate that CZE-MS is sensitive and reproducible enough for broad adoption for multi-level proteomics-based biomedical research.

systems biology↗

A Large-Scale Concordance Study of Toxicity Findings Across Preclinical Species and Humans for Small Molecules and Biologics in Drug Development

Translating preclinical safety findings into reliable insights for human risk assessment remains a fundamental challenge in drug development. Prior preclinical-clinical concordance studies have been constrained by limited drug coverage, reliance on identical-term matching for adverse events (AEs), and insufficient consideration of species, modality, exposure, and biological or mechanistic context. To address these gaps, we assembled a large cross-species concordance dataset, integrating standardized preclinical and clinical safety data for 7,565 marketed and investigational drugs from PharmaPendium and OFF-X. Our framework employs likelihood ratios to reduce prevalence bias and extends concordance assessment beyond identical-term matches to include semantically and mechanistically related AE pairs. Stratified analyses by species, modality, and exposure-matched subsets further refined translational relevance, while integration of on- and off-target annotations supports mechanistic interpretation and potential screening. Using this approach, we identified 850 significant identical-term AEs and 2,833 additional unique endpoints from cross-term associations. To promote reproducibility and transparency in animal research, we provide open access to the analytic code and statistical results via an interactive web application. An accompanying multi-agent AI system (ToxAgents) enables standardized querying and interpretation of concordance results. Together, these resources extend previous foundational efforts and establish a shared, data-driven platform to advance translational safety science, support evidence-based study design aligned with the 3Rs, and ultimately contribute to the development of safer medicines to improve human health.

bioinformatics↗

Intramuscular Adipose Tissue Accumulation is a Key Determinant of Limb Function in Peripheral Artery Disease

BackgroundPeripheral artery disease (PAD) and its severe form, chronic limb-threatening ischemia (CLTI), significantly impair blood flow to the lower extremities, affecting millions of adults globally. Intramuscular adipose tissue (IMAT) and fibrosis accumulation distinguish patients with CLTI from those with mild PAD, suggesting a role in CLTI pathobiology. However, the functional consequences of IMAT in CLTI remain unclear. MethodsWe compared gastrocnemius muscle samples from patients with PAD/CLTI, intermittent claudication, and non-PAD individuals. We analyzed bulk RNA sequencing, proteomic, lipidomic, and single-cell/nucleus RNA sequencing datasets. Additionally, we used murine models of hindlimb ischemia (HLI) with genetic manipulation of Ppar{gamma}, a key adipogenic transcription factor, specifically in fibro-adipogenic progenitor cells (FAPs), the cellular source of IMAT, to modulate IMAT formation and assessed the impact on limb function and pathology. ResultsPatients with CLTI exhibited significantly elevated expression of adipogenic genes and proteins in muscle specimens when compared to non-PAD controls. Murine models showed that increasing IMAT formation significantly worsened ischemic limb muscle strength and work output. In contrast, preventing IMAT formation significantly improved ischemic limb muscle strength and work output. These findings were consistent across both male and female mice, although females had greater tendency to form IMAT compared with male mice. ConclusionsIMAT accumulation is a key determinant of limb function in PAD/CLTI. Our studies demonstrate that targeting IMAT formation could improve limb function in mice with experimental PAD. Together, these findings suggest that developing strategies to limit or reduce IMAT may improve limb function and walking performance in patients with PAD/CLTI, providing a novel therapeutic avenue to address a critical unmet need. CLINICAL PERSPECTIVEO_ST_ABSWhat is new?C_ST_ABSO_LIIntramuscular adipose tissue accumulation (IMAT) distinguishes patients with chronic limb-threatening ischemia from those with milder peripheral artery disease or those without PAD and directly impairs ischemic limb muscle function. C_LIO_LIGenetic gain- and loss-of-function mouse models demonstrate that increasing IMAT worsens, while preventing IMAT formation improves, ischemic limb strength and performance independent of perfusion. C_LIO_LIAdipogenic signatures in human calf muscle negatively correlates with muscle strength and disease severity, identifying IMAT as a functional biomarker and modifiable target in PAD/CLTI. C_LI What are the clinical implications?O_LIIMAT accumulation represents an underappreciated, non-vascular mechanism contributing to leg dysfunction in PAD/CLTI. C_LIO_LITherapies aimed at limiting or reversing IMAT formation may improve leg strength and walking performance in patients with PAD/CLTI, addressing a critical unmet clinical need. C_LIO_LIIdentifying and targeting cellular pathways regulating IMAT formation from fibro-adipogenic progenitors may complement vascular interventions to enhance functional recovery after revascularization. C_LI

physiology↗

Global Proteomic Analysis of Colorectal Cancers Stratified by Microsatellite Instability Subtype Reveals Protein Differences

Lynch syndrome, historically known as hereditary nonpolyposis colorectal cancer, is caused by germline mutations in the DNA mismatch repair (MMR) genes, MLH1, MSH2 (EPCAM), MSH6, and PMS2. While the genetic changes associated with Lynch Syndrome have previously been characterized, there have not been studies of the associated proteomic alterations, in part because of the limited availability of primary samples and the absence of in vitro model systems. In this study, the first large-scale tissue proteomic assessment of Lynch Syndrome samples as well as three other subtypes of colorectal cancer was completed with specimens from the Ohio Colorectal Cancer Prevention Initiative. The cohort contained three groups of microsatellite unstable (MSI-high) CRC patients (Lynch syndrome, double somatic MMR mutation, and MLH1 hypermethylation) and a group of microsatellite stable (MSS) CRC patients. A total of 122 tumor and complimentary normal mucosa samples from 61 patients were evaluated using label-free bottom-up proteomic analysis. Hierarchical clustering analysis of the global proteome showed that the MSS group was significantly different than the three MSI-high groups. Of the 1,084 proteins found to be dysregulated across all four colorectal cancer subtypes, there were age at diagnosis associated shifts in proteins correlated with tumor proliferation and immune regulation for the Lynch syndrome and Double Somatic samples. The proteins TPD52, GMDS, and DSP showed increased protein abundance correlated with older age at diagnosis. In addition, the Lynch syndrome samples showed substantial sex-based differences in immune and inflammatory pathways, for example, downregulation of ZG16, DIS3, and WDR43. This study fills a critical gap as the first proteomic characterization of Lynch syndrome samples to date. Data are available via ProteomeXchange with identifier PXD073693. TeaserThis is the first study of the global proteomic differences between Lynch Syndrome and other forms of colorectal cancer.

cancer biology↗

A general and extensible algorithmic framework to biological sequence alignment across scales and applications

Sequence alignment underpins nearly every facet of modern genomics, from genetic testing and cancer profiling to functional genome annotation. Yet, despite decades of algorithmic innovation, most existing aligners remain narrowly optimized for specific tasks, fragmenting analytical workflows and limiting reproducibility. Here we introduce the Versatile Alignment Toolkit (VAT), a unified algorithmic framework that generalizes existing seeding and genome-indexing strategies within a single, transparent architecture. VAT employs a novel multi-view indexing scheme that integrates multiple seeding strategies and supports run-time seed-length parameterization without reindexing. A radix clustering algorithm based on hardware-efficient in-register bitonic sort accelerates multi-view table construction, ensuring scalability across large datasets. VAT delivers consistently high performance across diverse alignment tasks, including short- and long-read mapping, homology search, and whole-genome alignment, while maintaining algorithmic simplicity and adaptability. By bridging previously isolated alignment paradigms, VAT substantially reduces workflow complexity, enhances computational efficiency, and establishes an extensible foundation for future sequencing technologies. We anticipate this unification will set a new standard for flexible and reproducible sequence alignment in biomedical research and clinical genomics.

bioinformatics↗

GmEBS7a-E2 complex dissociation hyperactivates ERAD to impair plant immunity against Phytophthora pathogens

Endoplasmic reticulum-associated degradation (ERAD) pathways are crucial for maintaining plant development and stress responses. While ERAD has been extensively studied for its role in regulating responses to abiotic stress, its specific manipulation by eukaryotic pathogens stress remains unclear. Here, we reported that soybean GmEBS7a, a plant-specific ERAD component, is targeted and stabilized by a transmembrane domain-containing effector Avh131 from Phytophthora sojae. GmEBS7a enhances plant disease susceptibility by increasing ERAD efficiency and ER stress sensitivity. Mechanistically, Avh131 competitively disrupts the interaction with GmEBS7a and the ubiquitin-conjugating enzyme GmUBC32, reducing ubiquitination of GmEBS7a and subsequent inhibition of its degradation. These findings demonstrate that excessive ERAD triggered by stabilized GmEBS7a and its partnering E3 ligase impairs the plants response to biotic stress. Our study uncovers a fine-tuning of the ER protein-folding capacity to promote infection, thereby expanding our understanding of ER-centered immunity during plant-pathogen interactions.

immunology↗

Small brown planthopper infestation enhances it reproduction and insecticide tolerance by manipulating glucose distribution and levels in rice

The evolutionary arms race between plants and insects involves not only direct defense and counter-defense but also sophisticated resource manipulation. However, how herbivorous insects respond to host nutritional signals to modulate their fitness traits remains unclear. This study investigates how the small brown planthopper (SBPH, Laodelphax striatellus) manipulates host plant carbohydrate allocation, and to elucidate the molecular mechanisms by which the acquired glucose enhances SBPH fecundity and insecticide tolerance. Using molecular, pharmacological, and biochemical approaches, we found that SBPH infestation induced systemic carbohydrate reallocation in rice, elevating whole-plant glucose levels by promoting aerial accumulation while depleting root reserves. Host-derived glucose enhanced SBPH fecundity by activating the target of rapamycin (TOR) pathway, upregulating juvenile hormone (JH) signaling, and increasing vitellogenin production. For imidacloprid tolerance, glucose boosted glutathione S-transferase (GST) activity via two synergistic mechanisms: by upregulating glutamate cysteine ligase (GCL) to increase glutathione synthesis, and transcriptionally via the glucose-TOR-JH axis to induce LsGSTe1 (SBPH epsilon class GST) and LsGSTo1 (SBPH omega class GST) expression. Our findings establish host-derived glucose as a central signaling molecule that SBPH utilizes to modulate conserved pathways for simultaneous optimization of reproduction and insecticide resistance. This reveals a multifaceted nutrient-responsive mechanism in insect pests and identifies the glucose-TOR-JH axis as critical molecular targets for developing nutrient-based pest control strategies, such as disrupting insect nutrient-sensing pathways or modulating host carbohydrate metabolism. HighlightsO_LISBPH infestation elevates whole-plant glucose levels by promoting aerial accumulation while suppressing root abundance. C_LIO_LISBPH-induced glucose in the rice aerial tissues boosts reproduction of SBPH via TOR-JH-Vg pathway. C_LIO_LISBPH-induced glucose in the rice aerial tissues enhances imidacloprid tolerance of SBPH through GCL-GSH-GST and TOR-JH-GST axis. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/701313v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@39e084org.highwire.dtl.DTLVardef@1c310cborg.highwire.dtl.DTLVardef@1838575org.highwire.dtl.DTLVardef@1aedebe_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Global brain activity links subcortical degeneration to cortical tau progressively across Braak regions over early Alzheimer disease stages

Alzheimers disease (AD) is characterized by early tau pathology in subcortical neuromodulatory nuclei, followed by progressive cortical tau accumulation; however, the mechanisms linking subcortical dysfunction to cortical tau pathology remain unclear. Using multimodal neuroimaging data from the ADNI cohort, we examined how infra-slow (< 0.1 Hz) global brain (i.e., gBOLD) activity is related to the volume of the nucleus basalis of Meynert (NbM) and cortical tau accumulations in the early stages of AD. NbM degeneration was associated with reduced gBOLD activity and spatially co-localized tau accumulation, appearing in early Braak regions during the preclinical stage, i.e., cognitively unimpaired participants with abnormal CSF markers, and extending to more advanced Braak areas during the prodromal stage, i.e., mild cognitive impairment (MCI) subjects. Our findings suggest that infra-slow gBOLD activity serves as a functional neural mediator linking subcortical degeneration to cortical tau pathology, highlighting a potential functional pathway linking subcortical and cortical pathology in early AD.

neuroscience↗

Smooth Muscle Dysfunction Drives Cerebrovascular Reserve Failure and End-Organ Brain Injury

BackgroundFailure of cerebrovascular reserve is a fundamental determinant of ischemic vulnerability, yet the mechanisms by which vascular smooth muscle dysfunction compromises reserve and predisposes the brain to injury remain incompletely defined. We therefore tested whether a pathogenic smooth muscle mutation produces a baseline failure of cerebrovascular reserve sufficient to render the brain vulnerable to hypoperfusion, even in the absence of fixed arterial occlusion. MethodsWe examined cerebrovascular structure, hemodynamics, and reserve in a genetically defined mouse model of ACTA2-associated multisystemic smooth muscle dysfunction syndrome with systemic or brain-restricted expression of the mutant allele. Cerebral artery morphology was assessed using magnetic resonance angiography and black ink angiography. Vascular smooth muscle phenotype was evaluated by immunohistochemistry and proliferation assays. Blood pressure reactivity and cerebral blood flow (CBF) were measured simultaneously using femoral arterial catheterization and laser speckle flowmetry during vasoactive challenges and controlled hypotension. Cerebrovascular stress responses were tested using unilateral common carotid artery occlusion. Downstream brain effects were assessed by histology, resting state functional connectivity imaging, and behavioral testing. ResultsImpaired smooth muscle contractility drove rectification and narrowing of major cerebral arteries, downregulation of contractile markers, and increased vascular cell proliferation. These structural changes produced a distinct physiological phenotype: mutant mice exhibited blunted vasoreactivity, diminished spontaneous vasodynamic activity, and a downward shift in the blood pressure-CBF relationship across a wide range of arterial pressures, consistent with loss of cerebrovascular reserve. As a result, CBF was reduced at baseline and could not be maintained during hypotension or acute vascular stress. During carotid occlusion, mutant mice showed impaired compensatory perfusion, greater physiological instability, and worse behavioral outcomes. Chronic reserve failure coincided with white matter loss, reduced neuronal density, disrupted large-scale functional connectivity, and deficits in locomotion, anxiety-related behavior, and working memory. ConclusionsPathogenic smooth muscle dysfunction caused by ACTA2 mutation produces a baseline failure of cerebrovascular reserve that renders the brain vulnerable to hypoperfusion and stress-induced ischemic injury. These findings establish cerebrovascular reserve failure as a central physiological mechanism linking vascular dysfunction to end-organ brain injury and identify reserve preservation as a critical, potentially actionable determinant of brain health in hypotension-prone vascular disease. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABS- ACTA2 smooth muscle dysfunction produces baseline cerebrovascular reserve impairment, with reduced cerebral blood flow and a downward-shifted pressure-flow relationship in the absence of critical large-vessel occlusion. - Vascular tone dysregulation is coupled to end-organ brain injury, including white matter and neuronal loss, disrupted functional connectivity, and behavioral deficits. - The results support complementary disease mechanisms in ACTA2 vasculopathy: baseline reserve limitation and injury-provoked occlusive remodeling. Clinical Implications- Patients with ACTA2 vasculopathy may be vulnerable to ischemic brain injury during hypotension or systemic stress despite the absence of critical stenosis or occlusion on routine imaging. - Peri-procedural and acute-care management should emphasize preserving perfusion pressure and cerebrovascular reserve (e.g., during anesthesia, dehydration, or systemic illness). - More broadly, cerebrovascular reserve is a clinically relevant, potentially modifiable determinant of brain health in hypotension-prone vasculopathies and conditions characterized by impaired vascular reactivity.

physiology↗

PRDX6 Modulates Immune Checkpoint Inhibitor Response by Antagonizing Ferroptosis Induced By HDAC Inhibitors

Therapeutic resistance limits the efficacy of histone deacetylase (HDAC) inhibitors and immune checkpoint therapies in cancer. While HDAC inhibitors can induce ferroptosis, tumor cells often evade this cell death via antioxidant defenses. Here we identify peroxiredoxin 6 (PRDX6) as a critical modulator of resistance to HDAC inhibitor largazole by suppressing ferroptosis through its phospholipase A2 activity and maintaining GPX4 expression. Using genome-wide CRISPR activation screening, biochemical assays, and syngeneic tumor models, we show that PRDX6 depletion enhances largazole-induced lipid peroxidation, ferroptotic stress, and reshapes the tumor microenvironment to promote T-cell infiltration and inflammatory cytokine release. Importantly, combining PRDX6 knockdown with HDAC inhibition potentiates anti-PD-L1 immunotherapy efficacy and prolongs survival in vivo. These findings reveal PRDX6 as a redox gatekeeper linking ferroptosis resistance to immune evasion and suggest that co-targeting PRDX6 and HDAC pathways may improve responses to cancer immunotherapy.

cancer biology↗

The heteromeric Plasmodium falciparum pantothenate kinase has only one active site and does not require Pf14-3-3I for activity

Coenzyme A (CoA) is an essential molecule for the intraerythrocytic stage of Plasmodium falciparum. Pantothenate kinase (PanK) catalyses the first step of the CoA biosynthesis pathway and functions as a homodimer in most organisms investigated thus far. P. falciparum possesses a novel heteromeric PanK complex composed of PfPanK1, PfPanK2 and Pf14-3-3I. Using a mutagenesis approach, we generated 10 PfPanK mutants and demonstrate that the PfPanK complex has only one functional active site, with both PfPanK1 and PfPanK2 required for activity by the complex. We also show that PfPanK2 is essential for normal intraerythrocytic parasite proliferation using a conditional knockdown system. 14-3-3 binding motifs generally contain a phosphoserine/threonine residue. Mass spectrometry analyses of phospho-peptide enriched, immunoprecipitated PfPanK samples revealed phosphorylation sites in both PfPanK1 and PfPanK2 that were additional to the previously reported sites. To investigate the role of specific sites in PfPanK1 and PfPanK2 that may be involved in Pf14-3-3I binding, five additional mutants were generated. Mutagenesis of four predicted Pf14-3-3I binding sites in PfPanK1 resulted in a significant reduction in the amount of Pf14-3-3I bound to the PfPanK complex, with S334 being the most likely binding site. Heterologous expression of the PfPanK complex in an insect cell system yielded a small amount of soluble protein that assembled in situ into a functional complex. Combined results from heterologous expression and P. falciparum mutagenesis suggest that Pf14-3-3I may not be essential for PfPanK activity but may be important for stabilising the PfPanK complex.

biochemistry↗

Construction and Immunogenicity Detection of Canine Parvovirus-like Particles Fusion with Canine Febrile Antigen Epitopes

This study aimed to design and evaluate the immunogenicity of a dual-valent virus-like particles (VLP) vaccine that can simultaneously target Canine distemper virus (CDV) and Ca nine parvovirus virus (CPV).By bioinformatic analysis, conserved antigen epitopes of the three major functional proteins of CDV were screened and inserted into CPV-VP2 proteins by two different methods to construct recombinant expression plasmids CDPV1 versus CDPV2.Thr ee-dimensional structure, hydrophobicity and stability predictions of the two recombinant proteins showed that their hydrophobicity were 0.233 and 0.251, and their structural stability scores were 0.77 and 0.78, respectively.Recombinant plasmids were co-transformed with molecular chaperone pTf16 to be expressed in E. coli BL21(DE3), respectively, and the optimal expression conditions were determined after optimization: 0.25 mmol/L IPTG, 2 g/L L-arabinose in duction, and culture at 25{degrees}C for 16 h.Purified recombinant proteins can self-assemble in vitro to form VLPs about 23.5 nm in diameter with a hemagglutination titer of 1:29.The mouse immune test showed that the hemagglutination inhibition titer peaked on the 7th day after the third immunization, and the neutralizing Antibody level could reach up to 1:28.The CPV VLP s constructed in this institute carrying CDV antigen epitopes were able to successfully assemble in vitro and were well immunogenic, providing experimental basis for the development of a canine polyvalent vaccine.

immunology↗

Medication and Developmental Stage Shape the Brain-Age Gap in ADHD

Identifying robust biomarkers for Attention-Deficit/Hyperactivity Disorder (ADHD) remains challenging. The brain-age gap (BAG), which is the difference between predicted biological brain age and chronological age, has been proposed as a marker of atypical neurodevelopment, yet findings have been inconsistent across studies, limiting its clinical translation. We hypothesized that two major sources of heterogeneity, medication status and developmental stage, contribute to these discrepancies. To test this, we analyzed structural MRI data from a large multi-site cohort (N = 947; ages 7-26 years). Individuals with ADHD were stratified by medication history (medicated vs. unmedicated) and developmental stage (childhood vs. adolescence) and compared with matched typically developing controls. We estimated global- and network-level BAG using publicly available pretrained models. Our results revealed that BAG differences were contingent on medication status, with abnormalities predominantly observed in unmedicated individuals. Developmental stage further moderated the presence of this effect: BAG abnormalities were present significantly in children with ADHD but not in adolescents. Network-level analyses demonstrated spatial specificity, with significant effects in visual, ventral attention, and dorsal attention networks. Together, these findings provide compelling evidence that BAG in ADHD is both medication- and development-dependent, highlighting the need to account for treatment exposure and developmental stage when evaluating BAG as a biomarker and further underscoring the importance of early intervention during childhood.

neuroscience↗

Programmed Double-stranded RNA Formation Enables Meiotic Stage Transitions

Cell fate transitions rely on extensive transcriptional activation mediated by transcription factors, yet the equally important processes that ensure the selective removal of pre-existing mRNAs remain elusive. We uncover widespread formation of double-stranded RNA (dsRNA) during early-to-middle meiosis using quantitative RNA structure analysis, and validate hundreds of natural antisense transcripts (NATs) through long-read sequencing. These NATs are induced by meiosis-specific transcription factors, including Ndt80p, and pair with sense mRNAs to drive cytoplasmic aggregation of the resulting dsRNAs. These dsRNA aggregates are subsequently transported to the vacuole for clearance, likely via autophagy. This pathway selectively eliminates mRNAs before metaphase I, including NDJ1, which encodes a meiotic cohesion protein that would otherwise block chromosome segregation. Our study reveals a physiological role for large-scale dsRNA formation, and highlights a simple but powerful model: the same transcription factors that activate mRNAs required for a specific developmental stage also program the synthesis of NATs that promote removal of transcripts from the preceding stage, thereby driving bidirectional transcriptome reprogramming.

cell biology↗

THIK-1 channel mediates microglial glucose sensing and modulates AgRP neurons

Microglia play essential roles in maintaining energy homeostasis, and their dysfunction contributes to metabolic disease. Although high-fat diet (HFD) exposure induces microglial activation, the underlying mechanisms remain poorly defined. Here, we identified a previously unrecognized role for THIK-1 channel in mediating glucose sensing of microglia in arcuate nucleus of the hypothalamus (ARH), during HFD-induced obesity. Pharmacological inhibition of THIK-1 channel with tetrapentylammonium (TPA) suppresses feeding and attenuates body-weight gain in diet induced obese mice. Mechanistically, inhibition of agouti-related peptide (AgRP) neurons is indispensable for TPA-induced hypophagia. Moreover, THIK-1 inhibition promotes microglial phagocytosis of perineuronal nets (PNNs), leading to reduced AgRP neuronal activity and feeding suppression. Together, these findings establish THIK-1 as a critical glucose sensor in hypothalamic microglia and uncover a microglia-dependent pathway through which overnutrition modulates AgRP neuronal activity via PNN remodeling to regulate energy balance, highlighting THIK-1 as a potential therapeutic target for treatment of diet-induced obesity.

neuroscience↗

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↗

When CycloneSEQ meets Oxford Nanopore Technologies: a performance comparison of contemporary nanopore DNA sequencing platforms

Nanopore sequencing enables direct analysis of native DNA modifications, but these modifications can also introduce systematic basecalling errors. Here, we investigated how bacterial DNA methylation contributes to nanopore substitution errors using matched native whole-genome sequencing (WGS) and methylation-depleted whole-genome amplification (WGA) datasets from six bacterial species across CycloneSEQ (CS) and Oxford Nanopore Technologies platforms (ONT). Adenine-to-guanine (A2G) and guanine-to-adenine (G2A) substitutions were consistently enriched across species, nanopore platforms, sequencing configurations, and basecalling models, indicating a shared nanopore-associated substitution bias. This enrichment remained detectable in WGA reads, whereas native WGS reads showed a further increase. Using independent PacBio methylation profiling, we found that the WGS-associated substitution excess was strongly concentrated around bacterial methylation motifs and was minimal in non-motif regions. The magnitude and substitution pattern of these errors varied among motifs and sequencing platforms. At a subset of motif-associated positions, alternative-base fractions exceeded 50%, producing SNP-like signals. In ONT data, 28 WGS-specific calls survived the applied SNP-calling filters, all within PacBio-supported methylation contexts, and most showed significant strand imbalance. Together, these results identify a shared A2G/G2A substitution bias in all nanopore datasets and support a methylation-associated increase in these errors near bacterial methylation motifs, with some loci producing SNP-like artifacts.

bioinformatics↗

Python metabolomics uncovers a conserved postprandial metabolite and gut-brain feeding pathway

Most mammals consume small and frequent meals. By contrast, pythons are ambush predators that exhibit extreme feeding and fasting patterns and provide a unique model for uncovering molecular mediators of the postprandial response1-3. Using untargeted metabolomics, here we show that circulating levels of the metabolite para-tyramine-O-sulfate (pTOS) are increased >1,000-fold in pythons after a single meal. In pythons, pTOS production occurs in a microbiome-dependent manner via sequential decarboxylation and sulfation of dietary tyrosine. In both pythons and mice, pTOS administration activates a neural population in the ventromedial hypothalamus (VMH). In mice, these VMH neurons are required for the anorexigenic effects of pTOS. Chronic administration of pTOS to diet-induced obese male mice suppresses food intake and body weight. pTOS is also present in human blood, where its levels are increased after a meal. Together, these data uncover a conserved postprandial anorexigenic metabolite that links nutrient intake to energy balance.

physiology↗