Biology subjects

Gao, Y.

Publications and source records attributed to Gao, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Container-less Acoustic Levitation Expands Plasma Extracellular Vesicle Proteome Coverage by Mitigating Size-Dependent Peptide Loss

Proteomic profiling of plasma-derived extracellular vesicles (EVs) is limited in part by adsorptive loss of peptides and proteins to container walls during sample preparation. Here we apply an automated, environment-controlled acoustic levitation platform (Levcell) to the tryptic digestion of small EVs (sEVs) isolated from pooled breast cancer patient plasma, and compare it directly with digestion in low-bind microcentrifuge tubes. Across three parallel technical replicates per method, container-less digestion identified 309 {+/-} 22 protein groups versus 261 {+/-} 6 for tubes (+18.4%; Welch t-test p = 0.053), with equivalent or better quantitative reproducibility (median CV 12.0% vs 14.4%). The gain was strongly asymmetric: 66 protein groups were recovered only under levitation while 10 were recovered only in tubes (exact McNemar p = 3 x 10-11). Peptides recovered exclusively by levitation were longer and heavier than those exclusive to tubes (median 14 vs 12 residues, 1611 vs 1358 Da; p < 2 x 10-6; Cliffs {delta} {approx} 0.19-0.20), whereas the total peptide pools were indistinguishable and mean missed-cleavage rates were equivalent (0.276 vs 0.263, p = 0.41), excluding differential digestion efficiency as an explanation. No systematic difference in hydropathy, isoelectric point or hydrophobic residue frequency was detected. The levitation-rescued sub-proteome was enriched for ribosomal, proteasomal, chaperonin and RNA-binding complexes -- canonical sEV luminal cargo (MYC targets 16/19, odds ratio 31.7, q = 5.6 x 10-8) -- and covered 33 of the 100 ExoCarta reference markers versus 22 for tubes, gaining 14 markers while losing three (a single ezrin/moesin/radixin protein group; McNemar p = 9.8 x 10-4). We also report two findings that temper the approach: levitated samples carried an approximately 3.7-fold higher keratin burden, consistent with airborne contamination in an open chamber, and no individual marker showed a significant abundance difference after correction for multiple testing. Container-less processing therefore offers a reproducible gain in sEV proteome coverage attributable to reduced size-dependent peptide loss, provided that contamination control is addressed.

biochemistry↗

bioRxiv2026

Nutrient flux governs osteogenic fate commitment through the SLC3A1-cystine Axis

Skeletal and mesenchymal cells have limited bone-forming potential due to their rarity, tendency for senescence and/or unstable osteogenic lineage commitment. We previously identified an osteopotent CXCR4 stem cell population with unclear mechanism for its differentiation potential. Here, we found that the cystine transporter SLC3A1 was selectively enriched in CXCR4+ stem cells, uncovering a role for amino acid transport in regulating osteogenic fate commitment. Enforced SLC3A1 expression reprogrammed mesenchymal cells toward a stable osteogenic state while suppressing adipogenic differentiation. Mechanistically, SLC3A1-mediated cystine flux established a glutathione-dependent metabolic program that preserved mitochondrial fitness and restrained stem cell senescence. SLC3A1 also stabilized IGF-1 through suppression of ZMYND8-mediated ubiquitination, uncovering ZMYND8 as a previously unrecognized E3 ligase regulating osteogenic commitment. Cystine supplementation phenocopied the effects of SLC3A1 activation, promoting osteogenic differentiation and skeletal regeneration without genetic manipulation. In vivo, cystine administration accelerated bone regeneration and attenuated ovariectomy-induced bone loss, while analyses of a human osteoporosis cohort, osteoporotic specimens, and single-cell transcriptomic datasets revealed coordinated suppression of the SLC3A1-cystine-IGF-1 pathway in osteoporotic mesenchymal cells. Taken together, these findings establish SLC3A1-mediated cystine transport as a programmable metabolic determinant of osteogenic fate commitment and identify cystine metabolism as a therapeutically targetable axis for skeletal regeneration and osteoporosis.

cell biology↗

bioRxiv2026

ChatGEM: An Agentic Architecture Enabling Interactive Simulation of Genome-Scale Metabolic Models

Genome-scale metabolic models (GEMs) are powerful tools for predicting cellular phenotypes and guiding microbial strain engineering, yet broad adoption remains challenging due to the computational expertise required. To overcome that, we present ChatGEM, an agentic platform that enables interactive GEM simulation through natural language. Built on the multi-agent ADEPT framework, ChatGEM integrates COBRApy within a retrieval-augmented generation (RAG) architecture that coordinates code generation and execution through specialized agents. Benchmarking across three tasks of increasing complexity showed that RAG-enabled code generation improved the mean overall performance score from 2.63 to 4.20 while reducing the execution time significantly starting from routine to complex tasks. Application of ChatGEM using an enzyme-constrained GEM (ecGEM) for four engineered Pseudomonas putida KT2440 strains identified the constitutive strain as the optimal chassis for succinate overproduction using a succinate leakage index - a prediction observed experimentally. Therefore, ChatGEM democratizes metabolic modeling by enabling researchers without computational expertise to perform sophisticated GEM-based analyses through natural language, and, hence, accelerating scientific discovery.

systems biology↗

bioRxiv2026

Elucidating the half-site reactivity mechanism of Salmonella enterica FraB deglycase using native mass spectrometry

Inter-subunit communication and allosteric regulation are central to the function of oligomeric enzymes, yet these features remain difficult to characterize. Conventional kinetic and structural methods typically yield ensemble averages or static snapshots, thus making it difficult to uncover the dynamic cross-subunit cooperation obligatory for multi-site catalysis by oligomeric enzymes. Here, we investigate Salmonella FraB--a homodimeric deglycase and a potential drug target--to showcase the value of an integrated approach combining native mass spectrometry (nMS), surface-induced dissociation (SID), and kinetic studies to gain insights into catalytic intermediates and inter-subunit communication. By resolving substrate-, product-, and mixed-occupancy species, nMS revealed that both inter-subunit active sites in FraB bind substrate even though only one catalytic center generates the product at any given time. To characterize each active site independently, we designed heterodimers with a mutation that changes the general base or acid in only one active site. Kinetic studies with these mutants indicate that although the two active sites are likely coupled, they do not concomitantly perform cleavage. Consistent with the conformational asymmetry observed in apo-FraB crystal structures, our findings establish a half-site reactivity mechanism in which post-binding conformational changes across the dimer interface restrict substrate cleavage to one active site even though both protomers are able to bind substrate. Importantly, this nMS-based workflow offers a broadly applicable framework for resolving the catalytic states and inter-site communication of oligomeric enzymes that are otherwise difficult to uncover by conventional structural methods.

biochemistry↗

bioRxiv2026

Decoding the oxytocinergic and behavioral signatures of milk ejection

Oxytocin-mediated milk ejection (ME) is pivotal to effective breastfeeding and productive health, yet behaviorally decoding and revealing neural mechanisms of ME remains challenging. Here, we combined in vivo calcium imaging and intramammary pressure recording to uncover the temporal connections between episodic activity of oxytocin neurons and ME in conscious lactating rats. Leveraging the association and behavioral responses in dam and pup, we developed a supervised machine learning framework (ME Decoder) to enable automated analyses of ME. Inspired by its interpretable features, we defined the activity-coupled dam-pup interactions (ADPI), manifested by high kyphosis of the dam followed by pup treading and stretch, as the behavioral signatures of ME. By ME Decoder and ADPI analyses, we detected reduced ME but unaffected activity of oxytocinergic neurons after systemic blockade of oxytocin receptor. Our study uncovers the oxytocinergic and behavioral signatures of ME and provides a generalizable approach for further investigation.

neuroscience↗

bioRxiv2026

A consensus atlas of human brain development defines cell type-specific maturation trajectories across the lifespan

Human neurodevelopment is a continuous process that begins prenatally and extends into postnatal life. Current transcriptomic datasets are limited, fragmented across analytical frameworks, precluding comprehensive reconstruction of cellular trajectories linking developmental states to mature cell types. Here we present a consolidated cellular-resolution transcriptomic atlas of human brain development from the onset of neurogenesis to adulthood, covering [~]2.2 million cells from 156 donors across nine studies. All data were reprocessed from raw sequencing reads and annotated within a unified cell-type taxonomy, enabling reliable mapping across the lifespan. Cell types were highly replicable across heterogeneous datasets, enabling us to chart their maturation and cortical layer localization over time. We identify dynamic gene programs predictive of cell-type maturation, validate gene modules tracking known fate transitions, and leverage our atlas scale to characterize rare populations, including microglia. This resource establishes a standardized reference of human brain development and maturation gene modules for future comparisons across model systems, species, and disease states.

neuroscience↗

bioRxiv2026

Integrated Interactomics Reveals Novel Protein Associations: The FOXA1-PBX1 Complex as a Case Study

Protein-protein interactions (PPIs) are fundamental to cellular signaling networks, yet many remain undetected due to technical limitations of individual affinity purification approaches. To address this, we systematically mapped the interaction landscapes of six regulatory proteins involved in cell proliferation, immunity, and inflammation, including three transcription factors (TFs) and three kinases. We implemented an integrated proteomics workflow that combined four complementary affinity purification strategies: native immunoprecipitation, two crosslinking-assisted capture methods, and proximity labeling. Combining these approaches revealed distinct yet overlapping interaction profiles, uncovered numerous previously unreported interactors not reliably detected by individual methods, and robustly recovered known interactions while substantially extending PPI networks. Despite method-specific differences at the protein level, functional enrichment analyses showed strong convergence on coherent biological pathways. Biochemical approaches validated most of the previously unreported interactions, including putative weak and transient complexes stabilized by crosslinking. Functional assays revealed a previously unrecognized physical interaction between FOXA1 and PBX1 TFs and demonstrated their cooperative regulation of transcriptional programs and cell fitness in estrogen receptor (ER) positive breast cells. We propose that the FOXA1-PBX1 complex could represent a higher-order regulatory node integrating chromatin accessibility and ER-driven transcriptional output. HIGHLIGHTSO_LIComplementary affinity purification strategies uncover putative weak and transient protein-protein interactions C_LIO_LIFunctional pathway convergence validates biologically coherent interactome expansion C_LIO_LIBiochemical validations confirm unreported interactions C_LIO_LIFunctional validation studies identify a FOXA1-PBX1 pioneer factor complex that regulates estrogen receptor transcriptional programs C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/738938v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@193cc1borg.highwire.dtl.DTLVardef@3d068dorg.highwire.dtl.DTLVardef@791d5corg.highwire.dtl.DTLVardef@1769ce7_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Dynamic Changes in the Urinary Proteome of Normal Pregnant Women and Their Correlation with Fetal Developmental Progression - A Methodological Exploration Based on "One-versus-Many" Urinary Proteomic Comparative Analysis

This study employed a "one-versus-many" (a single pregnant woman compared with multiple non-pregnant women) urinary proteomic comparative framework to examine whether fetal development-related signals can be captured through changes in the urinary proteome under conditions of limited sample size. The experimental group consisted of urinary proteomic data from three women with normal pregnancies (R6, R15, R16) at three gestational time points ([~]6-8 weeks, 22-24 weeks, and 32-34 weeks; Wang et al., 2022), while the control group consisted of urinary proteomic data from six healthy non-pregnant women (Bao & Gao, ChinaXiv: 202302.00108v2). A total of nine independent "1 vs. 6" differential protein analyses and DAVID GO Biological Process enrichment analyses (P < 0.05) were performed. The results showed that all three pregnant women exhibited a large number of differentially expressed proteins at each time point, and all enriched GO BP terms highly relevant to concurrent fetal organ development (nervous system, lung, eye, ear, kidney, etc.). This suggests that the pregnancy urinary proteome can reflect fetal development signals, corroborating the findings reported by Wang et al. (2025) in a rat model. This study demonstrates that the one-versus-many comparative approach maintains high sensitivity under small-sample conditions and can provide a methodological reference for personalized pregnancy medicine.

biochemistry↗

bioRxiv2026

Overcoming protocatechuate and catechol accumulation in muconic acid production via adaptive laboratory evolution and metabolic engineering in Pseudomonas putida

Muconic acid is an industrially valuable molecule that can be biologically produced from diverse biogenic and waste-derived feedstocks, including sugars and lignin- and plastic-derived aromatic compounds. However, accumulation of protocatechuate (PCA) has been observed in multiple microbes engineered for muconate production when the PCA decarboxylase, AroY, is used. This raises the question of whether PCA decarboxylation represents a rate-limiting step and how this bottleneck might be alleviated, especially given the toxicity and reactivity of PCA and catechol intermediates. To address this, we performed adaptive laboratory evolution (ALE) on a strain of Pseudomonas putida originally engineered for muconate production from aromatic compounds, but with catBC restored, to select for improved conversion of PCA and, in separate lineages, 4-hydroxybenzoate. Contrary to our expectations, the predominant beneficial mutations localized to the catA1 cassette encoding catechol 1,2-dioxygenase, rather than aroY or its associated cofactor biosynthesis genes. Transcriptomic analysis revealed elevated catA1 expression in evolved isolates from ALE, and introduction of these mutations improved productivity in strains designed for muconate production from both aromatic and sugar substrates. Quantitative proteomics and biochemical assays demonstrated that the mutations also led to increased CatA1 protein abundance and modest enhancements in catalytic efficiency, respectively, with strain phenotypes largely driven by high CatA1 levels and potentially synergistic kinetic improvements. Additional reverse-engineering studies identified variants with modest effects on muconate accumulation, including those with potential to enhance biosynthesis of the prenylated FMN cofactor of AroY. Collectively, these results indicate that catechol, not PCA, is the principal bottleneck in muconate production via the PCA decarboxylation route originally demonstrated by Draths et al., refining our understanding of pathway limitations and offering new strategies for improving rate, yield, and strain resilience in muconate bioproduction. HighlightsO_LIAccumulation of metabolic intermediates was alleviated by adaptive laboratory evolution C_LIO_LISequencing, proteomics, and enzyme kinetics revealed mechanisms for adaptation C_LIO_LIIncreased CatA1 expression reduced bottlenecks and improved muconate production C_LI

synthetic biology↗

bioRxiv2026

An integrative single-cell and spatial transcriptomics atlas highlights candidate regulatory factors in the development of gerbera capitulum

In Asteraceae species, the capitulum is a compact inflorescence, featuring a characteristic reproductive structure. Despite the identification of a few key regulatory factors, the transcriptome-level information on the developing capitulum remains limited. Here, we applied single-cell and spatial transcriptome sequencing to investigate the developing Gerbera hybridas capitulum during floret differentiation. We obtained a transcriptomics atlas encompassing different stages of the Gerbera capitulum and analyzed the cellular and spatial dynamics of gene expression. Using marker gene expression and GO enrichment of cluster-specific DEGs, we annotated putative cell types and described changes in gene expression across sampled stages, potentially associated with ongoing developmental processes. We detected activity of previously undescribed MADS-box genes and defined their spatial expression patterns. Notably, the MADS-box gene GAGL12 was found to be enriched in the putative capitulum phloem cells. The GAGL12 protein was shown in yeast two-hybrid assays to interact with several other MADS-domain proteins with hypothesized functions in vasculature development, and further detailed in silico analyses supported a candidate role in the development of capitulum vasculature. Altogether, we provide integrative and dynamic transcriptomic insight into capitulum and floret development and lay a basis for future functional studies of the control and development of this intriguing reproductive structure.

plant biology↗

bioRxiv2026

Linguistic Analysis of Chinese Oral Performance in Different Tasks of Chinese Second Language Learners and Native Speakers

This study investigated how different forms of task influence the oral performance of Chinese second-language learners and native speakers. By analyzing data from 40 Chinese second-language learners and 40 native speakers through picture description tasks, formal and informal questions, and questions with different emotions (happy and unhappy), it was found that different task characteristics significantly affected language performance. Short picture tasks led to higher communication efficiency and noun rates but more errors, while long story tasks showed higher verb rates, function word rates, etc. Formal questions had more characters and nouns but lower communication efficiency compared to informal ones. Also, happy emotion questions resulted in fewer characters, sentences, and errors than unhappy emotion questions. These findings contribute to the theoretical understanding of task-based language performance in Chinese as a second language and offer practical implications for teaching, textbook compilation, and student evaluation.

scientific communication and education↗

bioRxiv2026

Effect of CSFV on Differential Genes of Histone Lactylation at H3K18 in the PI3K-AKT Signaling Pathway

Classical swine fever (CSF) is a highly contagious disease caused by Classical swine fever virus (CSFV), posing a serious threat to the global swine industry. This study aimed to investigate the effect of CSFV on differential genes of histone lactylation at the H3K18 site in the PI3K-AKT signaling pathway. The site with the most significant change in histone lactylation antibody level was screened by Western blot. Omics analysis was performed using CUT&Tag technology to identify differential genes in the PI3K-AKT pathway between the CSFV-infected group and the mock group, followed by validation using RT-qPCR. Functional analysis of significantly differential proteins was conducted, and the protein expression level of THBS4 was detected by Western blot. The results showed that after CSFV infection of 3D4/21 cells, the H3K18la site exhibited the most significant difference in antibody level. A total of 8,859 differential genes at the H3K18la site were identified by CUT&Tag analysis, including 6,349 up-regulated genes and 2,510 down-regulated genes. Further focusing on the PI3K-AKT signaling pathway, 10 differential genes were identified, comprising 6 up-regulated genes and 4 down-regulated genes. Compared with the control group, the mRNA expression levels of CD19, LAMA1, PDGFRA, BDNF, ANGPT4, and THBS4 were up-regulated in the CSFV-infected group, while FOXO3 and NRTN were down-regulated. Western blot results showed that the protein expression level of THBS4 increased after CSFV infection. These findings lay an important foundation for understanding the molecular mechanisms regulating viral replication and immune evasion, and have significant scientific implications and potential application value.

microbiology↗

bioRxiv2026

Focal astrocyte Kir4.1 loss drives seizures, spreading depolarizations and postictal impairments

Astrocytic dysfunction is increasingly recognised as an important contributor to epileptogenesis and seizure dynamics. Kir4.1 potassium channels expressed in astrocytes play a critical role in activity-dependent extracellular potassium buffering, and their loss may impair network stability and promote pathological hyperexcitability. In epilepsy, seizures can be accompanied by spreading depolarizations (SDs), propagating waves of neuronal and glial depolarization. While seizure-associated SDs have been proposed to terminate seizures and limit seizure spread, they have also been implicated in postictal dysfunction and sudden unexpected death in epilepsy (SUDEP), and their significance in chronic epilepsy remains unclear. Here, we tested whether focal loss of astrocytic Kir4.1 in the adult hippocampus is sufficient to disrupt potassium buffering, generate spontaneous seizures, and promote seizure-associated SDs. Using astrocyte-targeted viral vector Cre recombinase in adult Kir4.1-floxed mice, we induced focal hippocampal reduction of Kir4.1 expression. This impaired activity-dependent potassium buffering, producing enhanced stimulation-evoked extracellular potassium accumulation and larger DC shifts in hippocampal slices. Chronic wireless EEG recordings demonstrated that focal astrocytic Kir4.1 loss was sufficient to induce spontaneous recurrent seizures and interictal epileptiform activity. To investigate seizure-associated SDs, we combined optogenetic stimulation with graphene-based micro-transistor recordings capable of stable full-bandwidth DC electrophysiology in awake head-fixed mice. Focal hippocampal loss of astrocytic Kir4.1 markedly increased susceptibility to evoked seizures accompanied by SDs. We used chronic wireless DC-coupled video-telemetry recordings to continuously monitor seizure and SD dynamics in freely moving mice. SDs occurred frequently during generalized seizures and were first detected in cortical channels. Seizures accompanied by SDs exhibited greater spectral power, longer duration, and prolonged postictal depression compared with seizures alone. Behaviourally, seizures accompanied by SDs were linked to postictal impairment characterised by behavioural arrest and abnormal motor behaviours. These findings highlight the utility of graphene micro-transistor arrays and chronic DC-coupled telemetry for resolving infraslow (<0.1 Hz) epileptic dynamics that are largely inaccessible using conventional electrophysiological approaches. Ground-truth DC-coupled recordings enabled identification of AC-band electrographic signatures that segregated seizures with SDs from seizures alone, raising the possibility that SD-associated seizures may be retrospectively inferred from conventional AC-coupled epilepsy datasets. We demonstrate that focal astrocytic Kir4.1 loss in the adult brain impairs potassium buffering and is sufficient to drive spontaneous seizures, supporting astrocytic potassium dysregulation as a determinant of seizure and spreading depolarization susceptibility in epilepsy. Furthermore, seizure-associated SDs are strongly linked to increased postictal impairments, supporting the concept that SDs are major determinants of pathological postictal states.

neuroscience↗

bioRxiv2026

The nucleolar complex FAN-FIP1 mediates ribosome biogenesis in Arabidopsis and is critical for BR signaling and heat tolerance

Ribosome biogenesis is critical for plant development and environmental responses. A large number of ribosomal proteins (RPs) and ribosomal biogenesis factors (RBFs) are required for ribosome biogenesis, many of which remain uncharacterized in plants. We report here the identification of Arabidopsis RBF FAN and its interacting partner FAN-INTERACTING PROTEIN 1 (FIP1). As their human and yeast orthologues, FAN-FIP1 interact. Both FAN and FIP1 participate in the processing of pre-rRNAs. Functional loss of FAN or FIP1 knock-down results in developmental retardation and hypersensitivity to heat stresses. We demonstrate that FAN-FIP1 positively mediates brassinosteroid (BR) signaling by ensuring the translation efficiency of the BR receptor-coding gene BRASSINOSTEROID INSENSITIVE 1 (BRI1) through the presence of its upstream open reading frame (uORF). Importantly, BR signaling positively mediates the processing of pre-rRNAs, which may be critical not only for development but also for heat tolerance.

plant biology↗

bioRxiv2026

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets

Large-scale clinical and biomedical datasets increasingly contain both diverse subgroup attributes (e.g., demographic or clinical subgroups) and multiple prediction targets. Although various machine learning approaches can address subgroup differences or multi-target prediction, they often consider these aspects independently rather than jointly. To more effectively capture the shared and subgroup-specific information in such complex datasets, we propose the Integrative Transfer Network (ITN), a deep neural network designed to leverage data across subgroups and multiple related outcomes simultaneously. In extensive experiments, including time-to-event and classification tasks where demographic subgroups and multiple disease end-points are prevalent, ITN demonstrates consistent improvements in subgroup-specific prediction by borrowing strength from other subgroups and outcomes. We envision ITN as a unified frame-work for learning from heterogeneous datasets where subgroup-specific insights are critical.

bioinformatics↗

bioRxiv2026

Structural Basis of Nidovirus Replication Organelle Evolution Revealed by the Arterivirus DMV Pore Complex

Positive-strand RNA viruses of the order Nidovirales - which include coronaviruses and arteriviruses - remodel host membranes into double-membrane vesicles (DMVs) as replication organelle to shield viral RNA synthesis from immune sensors. In coronaviruses, newly synthesized RNA is exported to the cytoplasm through a massive DMV pore complex formed by viral non-structural proteins (nsps). However, it remains unknown whether this elaborate architecture is unique to large-genome coronaviruses or a universal hallmark of the order. Here, we integrate in situ cryo-electron tomography and single-particle cryo-electron microscopy to resolve the atomic structure of DMV pore complex within its native membrane environment, from Equine Arteritis Virus (EAV), a prototype arterivirus with small genome. Despite lacking obvious sequence homology, the minimal EAV pore shares conserved architectural principles with its elaborate coronavirus counterpart. EAV pore complex is formed by a 12:12 stoichiometry of nsp2 and nsp3 protomers organized into four stacked concentric rings on double-membrane, yet generating pronounced structure symmetry mismatch. Functionally, the complex displays a distinct pore profile while preserving a positively charged central channel, essential for viral replication and transport. These findings demonstrate that, despite diversity in genome size and virion morphology, nidovirus replication organelles exhibit striking evolutionary conservation at the atomic structural level. Collectively, we propose that the order Nidovirales can be unified at the ultrastructural level by this conserved signature pore complex on the DMV-based replication organelle.

microbiology↗

bioRxiv2026

Conserved Cell Type Signatures Across the Brainstem and Spinal Cord in the Mouse Central Nervous System

Understanding how cell types are organized across the central nervous system (CNS) is key to uncovering neural function. Here, we integrate single-nucleus Multiome (RNA+ATAC) sequencing, spatial transcriptomics, and computational analyses to map conserved cell type signatures in the adult mouse brainstem and spinal cord. We identify a shared core of neuronal and non-neuronal cell types, alongside region-specific specializations reflecting distinct functions. Spatial data reveal conserved cellular niches across the brainstem-spinal cord boundary, indicating a continuous organizational logic. Cross-region comparisons uncover recurrent gene expression modules and signaling programs that may support shared circuit features. Chromatin accessibility profiling highlights cell-type-specific regulatory programs and implicates Hox transcription factors in positional identity. Notably, cell-type and positional identities are largely orthogonal, with varying regional influence across neuronal classes: motor neurons show strong positional coupling, whereas glutamatergic and GABAergic interneurons show minimal entrainment. This work provides a reference for the shared molecular architecture of these CNS regions.

neuroscience↗

bioRxiv2026

Reductive carboxylation via isocitrate dehydrogenase 1 supports cardiac metabolic adaptation during oncometabolic stress.

BackgroundCardiovascular disease and cancer are the two leading causes of morbidity and mortality worldwide. Metabolic dysregulation of cancer cells extends beyond the tumor microenvironment and increases the risk for cardiovascular diseases. One common somatic mutation in cancer cells affects isocitrate dehydrogenase (IDH) 1 and 2, which catalyzes the oxidative decarboxylation of isocitrate to alpha-ketoglutarate in the cytosol and mitochondria, respectively. IDH1 and 2 mutations cause the production of the oncometabolite D-2-hydroxyglutarate (D2-HG), which allosterically inhibits -ketoglutarate dehydrogenase (-KGDH) and is associated with reduced cardiac contractile function. MethodsWe combined stable isotope tracer studies with computational modeling to investigate the fundamental role of IDH isoforms in cardiac adaptation under oncometabolic stress. ResultsWe uncovered an unexpected cardiac phenotype that expands the role of IDH1 in the heart beyond oxidative metabolism. We quantified the stable isotopomer distributions from glucose and glutamine in perfused working rat hearts and isolated adult ventricular cardiomyocytes using mass spectrometry-based metabolomics. Our analysis revealed that defective mitochondrial metabolism causes the redirection of carbon flux from oxidative towards reductive pathways. Reductive carboxylation of -KGDH increases glutamine uptake and glutamine-derived citrate formation in working rat heart perfusions and cultured adult mouse ventricular cardiomyocytes. To identify which IDH isoform is responsible for redirecting carbon flux, we developed knockout models of IDH1, IDH2, and IDH3 in adult mouse ventricular cardiomyocytes. Loss of IDH1 expression impaired the reductive formation of citrate and caused functional defects in cardiomyocytes. Lastly, epigenetic analyses of histone marks revealed that IDH1 induces widespread alterations in histone acetylation and tri-methylation. ConclusionOur results highlight a novel role for IDH1 in cardiac metabolism and transcriptional control of metabolic adaptation to tumor-mediated stress and provide evidence that reductive-citrate formation may induce epigenetic modifications in the heart.

systems biology↗