Biology subjects

Gao, Y.

Publications and source records attributed to Gao, Y..

At least 235 records · Page 13Linked to original sources

bioRxiv2024

Varying recombination landscapes between individuals are driven by polymorphic transposable elements

AbstractsMeiotic recombination is a prominent force shaping genome evolution, and understanding the causes for varying recombination landscapes within and between species has remained a central, though challenging, question. Recombination rates are widely observed to negatively associate with the abundance of transposable elements (TEs), selfish genetic elements that move between genomic locations. While such associations are usually interpreted as recombination influencing the efficacy of selection at removing TEs, accumulating findings suggest that TEs could instead be the cause rather than the consequence. To test this prediction, we formally investigated the influence of polymorphic, putatively active TEs on recombination rates. We developed and benchmarked a novel approach that uses PacBio long-read sequencing to efficiently, accurately, and cost-effectively identify crossovers (COs), a key recombination product, among large numbers of pooled recombinant individuals. By applying this approach to Drosophila strains with distinct TE insertion profiles, we found that polymorphic TEs, especially RNA-based TEs and TEs with local enrichment of repressive marks, reduce the occurrence of COs. Such an effect leads to different CO frequencies between homologous sequences with and without TEs, contributing to varying CO maps between individuals. The suppressive effect of TEs on CO is further supported by two orthogonal approaches-analyzing the distributions of COs in panels of recombinant inbred lines in relation to TE polymorphism and applying marker-assisted estimations of CO frequencies to isogenic strains with and without transgenically inserted TEs. Our investigations reveal how the constantly changing mobilome can actively modify recombination landscapes, shaping genome evolution within and between species.

genomics↗

bioRxiv2024

Viral fragments in the urine proteome: New clues to the cause of fever

[Background]Fever of unknown origin refers to a medical condition where the cause of the fever is not yet clear. This condition is common in various potential diseases and usually requires detailed examination and testing to determine the specific cause. No one has ever looked for the cause of fever in urine proteomics, and this study provides clues and diagnostic evidence for patients with fever of unknown origin through urine proteomics analysis. [Methods]We attempted virus-wide database searching for the first time in urine samples, using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyze urine proteins from febrile patients. Virus protein fragments were identified and retrieved. [Results]In urine samples, we detected specific peptide segments from various viruses including monkeypox virus, saliva virus A, human herpesvirus 8 type P, Middle East respiratory syndrome-related coronavirus, rotavirus A, foot-and-mouth disease virus (strain NZ2), human herpesvirus 2 (strain HG52), human adenovirus E serotype 4, influenza A virus, human coronavirus NL63, influenza B virus (strain W3), Nipah virus, and hepatitis C virus genotype 2k (isolate VAT96), among others. Several viruses showed significantly higher detection levels in febrile patients compared to controls, with saliva virus A showing an increase by over 4200-fold, and multiple virus proteins increased by more than 20-fold. It is noteworthy that the overall protein retrieval error rate was less than 1%, and the individual protein retrieval error rate for each sample was less than 5%, ensuring highly reliable protein retrieval results with a probability of error across all proteins of only 1.2xe-17. [Conclusion]Reliable virus protein fragments can be retrieved from urine proteomics, providing clues for febrile patient investigation and potentially applicable to the exploration of any unknown diseases. By adopting our method, there is no need to know in advance what specific viruses are contained in the sample, as long as the information of these viruses has been stored in the virus database, comprehensive and extensive virus retrieval can be achieved. This method significantly expands the coverage of virus detection and improves the flexibility and efficiency of detection.

molecular biology↗

bioRxiv2024

Cholesterol binding to VCAM-1 promotes vascular inflammation

Hypercholesterolemia has long been implicated in endothelial cell (EC) dysfunction, but the mechanisms by which excess cholesterol causes vascular pathology are incompletely understood. Here we used a cholesterol-mimetic probe to map cholesterol-protein interactions in primary human ECs and discovered that cholesterol binds to and stabilizes the adhesion molecule VCAM-1. We show that accessible plasma membrane (PM) cholesterol in ECs is acutely responsive to inflammatory stimuli and that the nonvesicular cholesterol transporter Aster-A regulates VCAM-1 stability in activated ECs by controlling the size of this pool. Deletion of Aster-A in ECs increases VCAM-1 protein, promotes immune cell recruitment to vessels, and impairs pulmonary immune homeostasis. Conversely, depleting cholesterol from the endothelium in vivo dampens VCAM-1 induction in response to inflammatory stimuli. These findings identify cholesterol binding to VCAM-1 as a key step during EC activation and provide a biochemical explanation for the ability of excess membrane cholesterol to promote immune cell recruitment to the endothelium.

physiology↗

bioRxiv2024

Spontaneously regenerative corticospinal neurons in mice

The spinal cord receives inputs from the cortex via corticospinal neurons (CSNs). While predominantly a contralateral projection, a less-investigated minority of its axons terminate in the ipsilateral spinal cord. We analyzed the spatial and molecular properties of these ipsilateral axons and their post-synaptic targets in mice and found they project primarily to the ventral horn, including directly to motor neurons. Barcode-based reconstruction of the ipsilateral axons revealed a class of primarily bilaterally-projecting CSNs with a distinct cortical distribution. The molecular properties of these ipsilaterally-projecting CSNs (IP-CSNs) are strikingly similar to the previously described molecular signature of embryonic-like regenerating CSNs. Finally, we show that IP-CSNs are spontaneously regenerative after spinal cord injury. The discovery of a class of spontaneously regenerative CSNs may prove valuable to the study of spinal cord injury. Additionally, this work suggests that the retention of juvenile-like characteristics may be a widespread phenomenon in adult nervous systems.

neuroscience↗

bioRxiv2024

eProbe: a capture probe design toolkit for genetic diversity reconstructions from ancient environmental DNA

Ancient environmental DNA (aeDNA) is now commonly used in paleoecology and evolutionary ecology, yet due to difficulties in gaining sufficient genome coverage on individual species from metagenome data, its genetic perspectives remain largely uninvestigated. Hybridization capture has proven as an effective approach for enriching the DNA of target species, thus increasing the genome coverage of sequencing data and enabling population and evolutionary genetics analysis. However, to date there is no tool available for designing capture probe sets tailored for aeDNA based population genetics. Here we present eProbe, an efficient, flexible and easy-to-use program toolkit that provides a complete workflow for capture probe design, assessment and validation. By benchmarking a probe set for foxtail millet, an annual grass, made by the eProbe workflow, we demonstrate a remarkable increase of capturing efficiency, with the target taxa recovery rate improved by 577-fold, and the genome coverage achieved by soil capture-sequencing data even higher than data directly shotgun sequenced from the plant tissues. Probes that underwent our filtering panels show notably higher efficiency. The capture sequencing data enabled accurate population and evolutionary genetic analysis, by effectively inferring the fine-scale genetic structures and patterns, as well as the genotypes on functional genes.

bioinformatics↗

bioRxiv2024

Whole-brain dynamics of articulatory, acoustic and semantic speech representations

Speech production is a complex process that traverses several representations, from the meaning of spoken words (semantic), through the movement of articulatory muscles (articulatory) and, finally, to the produced audio waveform (acoustic). In our study, we aimed to identify how these different representations of speech are spatially and temporally distributed throughout the depth of the brain. By considering multiple representations from the same exact data, we can limit potential con-founders to better understand the different aspects of speech production and acquire crucial complementary information for speech brain-computer interfaces (BCIs). Intracranial speech production data was collected of 15 participants, recorded from 1647 electrode contacts, while they overtly spoke 100 unique words. The electrodes were distributed across the entire brain, including sulci and subcortical areas. We found a bilateral spatial distribution for all three representations, although there was a stronger tuning in the left hemisphere with a more widespread and temporally dynamic distribution than in the right hemisphere. The articulatory and acoustic representations share a similar spatial distribution surrounding the Sylvian fissure, while the semantic representation appears to be widely distributed across the brain in a mostly distinct network. These results highlight the distributed nature of the speech production process and the potential of non-motor representations for speech BCIs.

neuroscience↗

bioRxiv2024

Evidence for S331-G-S-L within the amyloid core of myocilin olfactomedin domain fibrils based on low-resolution 3D solid-state NMR spectra

Myocilin-associated glaucoma is a protein-conformational disorder associated with formation of a toxic amyloid-like aggregate. Numerous destabilizing single point variants, distributed across the myocilin olfactomedin {beta}-propeller (OLF, myocilin residues 245-504, 30 kDa) are associated with accelerated disease progression. In vitro, wild type (WT) OLF can be promoted to form thioflavin T (ThT)-positive fibrils under mildly destabilizing (37{degrees}C, pH 7.2) conditions. Consistent with the notion that only a small number of residues within a protein are responsible for amyloid formation, 3D 13C-13C solid-state NMR spectra show that OLF fibrils are likely to be composed of only about one third of the overall sequence. Here, we probe the residue composition of fibrils formed de novo from purified full-length OLF. We were able to make sequential assignments consistent with the sequence S331-G-S-L334. This sequence appears once within a previously identified amyloid-prone region (P1, G326AVVYSGSLYFQ) internal to OLF. Since nearly half of the pairs of adjacent residues (di-peptides) in OLF occur only once in the primary structure and almost all the 3-residue sequences (tri-peptides) are unique, remarkably few sequential assignments are necessary to uniquely identify specific regions of the amyloid core. This assignment approach could be applied to other systems to expand our molecular comprehension of how folded proteins undergo fibrillization. TOC GRAPHIC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/606901v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@ff42feorg.highwire.dtl.DTLVardef@875722org.highwire.dtl.DTLVardef@169b1deorg.highwire.dtl.DTLVardef@1ca311_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Nascent flagellar basal bodies are immobilized by rod assembly in Bacillus subtilis

Flagella are complex, trans-envelope nanomachines that localize to species- specific cellular addresses. Here we study the localization dynamics of the earliest stage of basal body formation in Bacillus subtilis using a fluorescent fusion to the C-ring protein FliM. We find that B. subtilis basal bodies do not exhibit dynamic subunit exchange and are largely stationary at steady state, consistent with flagellar assembly through the peptidoglycan. Rare basal bodies were observed to be mobile however, and the frequency of basal body mobility is elevated both early in basal body assembly and when the rod is mutated. Thus, basal body mobility is a precursor to patterning and we propose that rod polymerization probes the peptidoglycan superstructure for pores of sufficient diameter that permit rod completion. Furthermore, mutation of the rod also disrupts basal body patterning in a way that phenocopies mutation of the cytoplasmic flagellar patterning protein FlhF. We infer that conformational changes in the basal body exchange information between rod synthesis and the cytoplasmic patterning proteins to restrict assembly at certain pores established by a grid-like pattern pre-existent in the peptidoglycan itself. IMPORTANCEBacteria insert flagella in a species-specific pattern on the cell body, but how patterns are achieved is poorly understood. In bacteria with a single polar flagellum, a marker protein localizes to the cell pole and nucleates the assembly of the flagellum at that site. Bacillus subtilis assembles [~]15 flagella over the length of the cell body in a grid-like pattern and lacks all proteins associated with targeted assembly in polarly flagellated bacteria. Here we show that B. subtilis basal bodies are mobile soon after assembly and become immobilized when the flagellar rod transits the peptidoglycan wall. Moreover, defects in the flagellar rod lead to an asymmetric distribution of flagella with respect to the midcell. We conclude that the patterning of flagella is different in B. subtilis, and we infer that the B. subtilis rod probes the peptidoglycan for holes that can accommodate the machine.

cell biology↗

bioRxiv2024

Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque

Experimental access to cell types within the mammalian spinal cord is severely limited by the availability of genetic tools. To enable access to lower motor neurons (LMNs) and LMN subtypes, we generated single cell multiome datasets from mouse and macaque spinal cords and discovered putative enhancers for each neuronal population. We cloned these enhancers into adeno-associated viral vectors (AAVs) driving a reporter fluorophore and functionally screened them in mouse. We extensively characterized the most promising candidate enhancers in rat and macaque and developed an optimized pan LMN enhancer virus. Additionally, we generated derivative viruses expressing iCre297T recombinase or ChR2-EYFP for labeling and functional studies, and we created a single vector with combined enhancer elements to achieve simultaneous labeling of layer 5 extratelencephalic projecting (ET) neurons and LMNs. This unprecedented LMN toolkit will enable future investigations of cell type function across species and potential therapeutic interventions for human neurodegenerative diseases.

neuroscience↗

bioRxiv2024

Successive pattern in winter wheat main stem structure modeling

1.With the rise of research on functional structural plant models (FSPMs), it is particularly important to realistically describe the structural traits of a plant. In 3D FSPMs, the true structural information of the canopy can make the models estimation of functional traits more accurate. Since canopy is the medium of the crop stands that sense and respond to the external environment, accurate estimation of detailed organ sizes in crop canopy is crucial, and current FSPMs still need to be improved. Here the structure of wheat (Triticum aestivum) was measured in detail at the phytomer level. Dataset was built which covers a set of [~]100 cultivars and 11 site-year under various field managements such as sowing density, inter-row, nitrogen fertilizer and sowing date. The relationships of successive phytomer sizes were quantified and the variance was analyzed for each independent experiment, only site was found as a significant impact factor. A conceptual model based on the successive pattern was proposed and validated for detailed final phytomer sizes. Then we coupled the meteorology data - the ratio of average daily gross radiation and temperature during the emergence and architecture mature with the model. The validation has taken place three times to emphasize models independent of cultivars, sites dependent and the ability of model parameters deriving from environmental factors, respectively. The results revealed the feasibility of the newly built wheat main stem structure model with the R2 higher than 0.85. Compared with ADEL-Wheat and Sirius Quality, the model achieved better performance in blade width and blade area estimation. According to the concise and easily acquired parameters of this model, it has potential for high throughput phenotyping detail wheat canopy structure. Previous work on the relationship between blade width and circumference of apex shoot in maize illustrated that the cell number was the most likely explanation for this pattern, which means the same work holds for similar crops.

developmental biology↗

bioRxiv2024

SSRI antidepressant citalopram reverses the Warburg effect to inhibit hepatocellular carcinoma by directly targeting GLUT1

Although there is growing appreciation for effective repurposing of selective serotonin reuptake inhibitors (SSRIs) for cancer therapy, particularly hepatocellular carcinoma (HCC), efforts are hampered by limited knowledge of their molecular targets and mechanism of action. Global inverse gene-expression profiling method, drug affinity responsive target stability assay, and in silico molecular docking analysis was performed to identify the targets of SSRIs. Murine subcutaneous, orthotopic models, and patient-derived xenograft were employed to explore the therapeutic effects and underlying mechanisms of SSRIs in HCC. The clinical relevance of SSRI use was verified with real world data. SSRIs exhibit significant anti-HCC effects independent of their known target serotonin reuptake transporter. The glucose transporter 1 (GLUT1) is identified as a new target of SSRIs. Citalopram binds to and antagonizes GLUT1, resulting in reduced glycolytic flux and ATP generation. Mutant GLUT1 in the binding site E380 of citalopram compromises the inhibitory effects of citalopram on the Warburg effect and tumor growth. In preclinical models, citalopram dampens the growth kinetics of GLUT1high liver tumors and displays a synergistic effect with anti-PD-1 therapy. Retrospective analysis of health records found that SSRIs use is associated with a lower risk of metastasis among HCC patients. Our study reveals an unprecedented role of SSRIs in cancer metabolism, and establishes a rationale for repurposing SSRIs as potential anticancer drugs for HCC.

cancer biology↗

bioRxiv2024

Systematically investigating and identifying unmodified bacteriocins in the human gut microbiome

Human gut microbiota produces unmodified bacteriocins, natural antimicrobial peptides that protect against pathogens and regulate host physiology. However, current bioinformatic tools limit the comprehensive investigation of bacteriocins biosynthesis, obstructing research into their biological functions. Here, we introduce IIBacFinder, a superior analysis pipeline for identifying unmodified class II bacteriocins. Through large-scale bioinformatic analysis and experimental validation, we demonstrate their widespread distribution across the bacterial kingdom, with being niche-specific and enriched in the human microbiome. Analyzing over 280,000 bacterial genomes, we reveal the diverse potential of human gut bacteria to produce these bacteriocins. Guided by meta-omics analysis, we synthesized 26 hypothetical bacteriocins from gut commensal species, with 16 showing antibacterial activities. Further ex vivo tests show minimal impact of narrow-spectrum bacteriocins on human fecal microbiota. Our study highlights the huge biosynthetic potential of unmodified bacteriocins in the human gut, paving the way for understanding their biological functions and health implications.

microbiology↗

bioRxiv2024

Ultra-resolution Deconvolution of Spatial Transcriptomics Unveils Spatiotemporal Cellular Dynamics in Complex Microenvironments

Immune cells infiltrate tissues in response to exogenous pathogens or spontaneous tumors, generating protective immunity to safeguard tissues. Despite advancements in spatial transcriptomics (ST), the precise spatial distribution and functional specialization of immune cells within tissue microenvironments remain elusive. Here, we introduce an ultra-precision ST deconvolution algorithm (UCASpatial) that enhances the mapping of cell subpopulations to spatial locations by leveraging the contribution of genes indicative of cell identity through entropy-based weighting. Using both in silico and real ST datasets, we demonstrate that UCASpatial improves the robustness and accuracy in identifying low-abundant cell subpopulations and distinguishing transcriptionally heterogeneous cell subpopulations. Applying UCASpatial to human colorectal cancer (CRC), we link genomic alterations in individual cancer clones to multi-cellular characteristics of the tumor immune microenvironment (TIME) and reveal the co-evolution of tumor cells and TIME at a clonal resolution. We show that the copy number gain on chromosome 20q (chr20q-gain) in tumor cells orchestrates a T cell-excluded TIME, indicative of resistance to immunotherapy in CRC, and is associated with tumor-intrinsic human endogenous retrovirus subfamily H (HERV-H) silencing and impaired type I interferon response. In murine wound healing models, we illuminate the spatiotemporal dynamics of individual cell subsets across various stages of the healing process. We discovered that the scarring-healing mice (C57BL/6) exhibited a replacement of Prg4+ chondrogenic progenitors to Igfbp5+ chondrocytes in the wound bed at the regeneration stage, a change not observed in the regenerative strain (MRL/MpJ). The Igfbp5+ chondrocyte, spatially coordinating with Cd36+ Gpnmb+ Il1b- macrophage and Fmod+ fibroblast, forms a pro-fibrotic community associated with regeneration failure. The cell-cell interactions within this three-cell cluster, mediated by the IL11-IL11RA axis, drive the pro-fibrotic community formation and limit regeneration in C57BL/6 mice. Our findings present UCASpatial as a versatile tool for deciphering fine-grained cellular landscapes in ST and exploring intercellular mechanisms in complex and dynamic microenvironments.

bioinformatics↗

bioRxiv2024

GeneLLM: A Large cfRNA Language Model for Cancer Screening from Raw Reads

We present GeneLLM, a novel large language model that offers a transformative approach to non-invasive cancer detection and biomarker discovery by directly interpreting plasma cell-free RNA (cfRNA) sequences. Unlike traditional annotation-dependent methods, GeneLLM operates without prior knowledge, achieving significantly improved multi-cancer detection accuracy. Critically, GeneLLM identifies novel cfRNAs ( pseudo-biomarkers) originating from previously unannotated genomic regions-overlooked by existing methods-offering new therapeutic targets and insights into intercellular communication. This innovative, cost-effective approach bypasses traditional bioinformatics tools, generating novel pseudo-biomarkers that outperform existing methods even with low-depth sequencing data. Consequently, GeneLLM opens new avenues for biomarker discovery and expands our understanding of the extracellular transcriptomes role in cancer development.

bioinformatics↗

bioRxiv2024

Detecting branching rate heterogeneity in multifurcating trees with applications in lineage tracing data

Understanding variation in cellular growth rates among cells in tumors is crucial for predicting cancer progression and interpreting tumor-derived genetic data. Advances in lineage tracing technologies enable the reconstruction of high-resolution, single-cell phylogenies of cancer cell populations, but methods to detect cellular growth rate differences on these phylogenies remain limited. Tree balance statistics offer a way forward, but it is unknown if and how these statistics are distorted when applied to phylogenetic reconstructions built from lineage tracing data, and if these distortions limit the utility of tree balance statistics to distinguish between evolutionary scenarios characterized by variable or homogeneous cellular growth rates. Here, we examined two tree balance statistics, J1 and the Sackin index, and benchmarked their performance in distinguishing lineage tracing trees derived from populations with and without variable cellular growth rates. We found that when tumor population sizes and lineage tracing editing rates are approximately known and in favorable ranges, J1 detects departures from homogenous growth rates just as well on lineage tracing trees as on true genealogical trees, while the Sackin index loses most of its power even under the most favorable conditions. We applied our J1-based test to data derived from cancer lineage tracing experiments and found widespread signals of growth rate heterogeneity in murine autochthonous lung cancers, and lung and PDAC xenograft experiments in mice. Our results demonstrate the potential and challenges of tree balance statistics in analyzing growth dynamics in lineage tracing data. Significance statementAlthough tree balance statistics are increasingly applied to examine tumor growth dynamics in trees built from bulk sequencing data, their application in tumor lineage tracing studies remains limited. In this study, we benchmarked J1 and the Sackin indexs potential to distinguish between tumor populations with and without varying growth rates among concurrent lineages using trees reconstructed from lineage tracing experiments. We describe conditions under which J1 can detect deviations from homogenous growth rates in lineage tracing trees, and find that the Sackin index is not well-suited to this objective. Our findings provide a first look at the complications associated with using tree balance statistics on trees reconstructed from lineage tracing data, and provide a practical guide for the application of these balance statistics in future lineage tracing studies.

evolutionary biology↗

bioRxiv2024

Deficiency of m6A RNA methylation promotes ZBP1-mediated cell death

m6A RNA methylation suppresses the immunostimulatory potential of endogenous RNA. Deficiency of m6A provokes inflammatory responses and cell death, but the underlying mechanisms remain elusive. Here we showed that the noncoding RNA 7SK gains immunostimulatory potential upon m6A depletion and subsequently activates the RIG-I/MAVS axis to spark interferon (IFN) signaling cascades. Concomitant excess of IFN and m6A deficiency synergistically facilitate the formation of RNA G-quadruplexes (rG4) to promote ZBP1-mediated necroptotic cell death. Collectively, our findings delineate a hitherto uncharacterized mechanism that links m6A dysregulation with ZBP1 activity in triggering inflammatory cell death.

molecular biology↗

bioRxiv2024

RSG-YOLO: Detection of rice seed germination rate based on enhanced YOLOv8 and multi-scale attention feature fusion

The lack of obvious difference between germinated seeds and non-germinated seeds will cause the low accuracy of detecting rice seed germination rate, remains a challenging issue in the field. In view of this, a new model named Rice Seed Germination-YOLO (RSG-YOLO) is proposed in this paper. This model initially incorporates CSPDenseNet to streamline computational processes while preserving accuracy. Furthermore, the BRA, a dynamic and sparse attention mechanism is integrated to highlight critical features while minimizing redundancy. The third advancement is the employment of a structured feature fusion network, based on GFPN, aiming to reconfigure the original Neck component of YOLOv8, thus enabling efficient feature fusion across varying levels. An additional detection head is introduced, improving detection performance through the integration of variable anchor box scales and the optimization of regression losses. This paper also explores the influence of various attention mechanisms, feature fusion techniques, and detection head architectures on the precision of rice seed germination rate detection. Experimental results indicate that RSG-YOLO achieves a mAP50 of 0.981, marking a 4% enhancement over the mAP50 of YOLOv8 and setting a new benchmark on the RiceSeedGermination dataset for the detection of rice seed germination rate.

plant biology↗

bioRxiv2024

ATP-dependent citrate lyase Drives Left Ventricular Dysfunction by Metabolic Remodeling of the Heart

BackgroundMetabolic remodeling is a hallmark of the failing heart. Oncometabolic stress during cancer increases the activity and abundance of the ATP-dependent citrate lyase (ACL, Acly), which promotes histone acetylation and cardiac adaptation. ACL is critical for the de novo synthesis of lipids, but how these metabolic alterations contribute to cardiac structural and functional changes remains unclear. MethodsWe utilized human heart tissue samples from healthy donor hearts and patients with hypertrophic cardiomyopathy. Further, we used CRISPR/Cas9 gene editing to inactivate Acly in cardiomyocytes of MyH6-Cas9 mice. In vivo, positron emission tomography and ex vivo stable isotope tracer labeling were used to quantify metabolic flux changes in response to the loss of ACL. We conducted a multi-omics analysis using RNA-sequencing and mass spectrometry-based metabolomics and proteomics. Experimental data were integrated into computational modeling using the metabolic network CardioNet to identify significantly dysregulated metabolic processes at a systems level. ResultsHere, we show that in mice, ACL drives metabolic adaptation in the heart to sustain contractile function, histone acetylation, and lipid modulation. Notably, we show that loss of ACL increases glucose oxidation while maintaining fatty acid oxidation. Ex vivo isotope tracing experiments revealed a reduced efflux of glucose-derived citrate from the mitochondria into the cytosol, confirming that citrate is required for reductive metabolism in the heart. We demonstrate that YAP inactivation facilitates ACL deficiency. Computational flux analysis and integrative multi-omics analysis indicate that loss of ACL induces alternative isocitrate dehydrogenase 1 flux to compensate. ConclusionsThis study mechanistically delineates how cardiac metabolism compensates for suppressed citrate metabolism in response to ACL loss and uncovers metabolic vulnerabilities in the heart.

molecular biology↗