bioRxiv : the preprint server for biology最新文献

筛选
英文 中文
MPAC: a computational framework for inferring pathway activities from multi-omic data. MPAC:从多组学数据推断癌症通路活动的计算框架。
bioRxiv : the preprint server for biology Pub Date : 2025-06-14 DOI: 10.1101/2024.06.15.599113
Peng Liu, David Page, Paul Ahlquist, Irene M Ong, Anthony Gitter
{"title":"MPAC: a computational framework for inferring pathway activities from multi-omic data.","authors":"Peng Liu, David Page, Paul Ahlquist, Irene M Ong, Anthony Gitter","doi":"10.1101/2024.06.15.599113","DOIUrl":"10.1101/2024.06.15.599113","url":null,"abstract":"<p><p>Fully capturing cellular state requires examining genomic, epigenomic, transcriptomic, proteomic, and other assays for a biological sample and comprehensive computational modeling to reason with the complex and sometimes conflicting measurements. Modeling these so-called multi-omic data is especially beneficial in disease analysis, where observations across omic data types may reveal unexpected patient groupings and inform clinical outcomes and treatments. We present Multi-omic Pathway Analysis of Cells (MPAC), a computational framework that interprets multi-omic data through prior knowledge from biological pathways. MPAC leverages network relationships encoded in pathways through a factor graph to infer consensus activity levels for proteins and associated pathway entities from multi-omic data, runs permutation testing to eliminate spurious activity predictions, and groups biological samples by pathway activities to allow identifying and prioritizing proteins with potential clinical relevance, e.g., associated with patient prognosis. Using DNA copy number alteration and RNA-seq data from head and neck squamous cell carcinoma patients from The Cancer Genome Atlas as an example, we demonstrate that MPAC predicts a patient subgroup related to immune responses not identified by analysis with either input omic data type alone. Key proteins identified via this subgroup have pathway activities related to clinical outcome as well as immune cell compositions. Our MPAC R package, available at https://bioconductor.org/packages/MPAC, enables similar multi-omic analyses on new datasets.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11212914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141474583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells. GraphVelo允许推断多模态单细胞速度和分子机制。
bioRxiv : the preprint server for biology Pub Date : 2025-06-14 DOI: 10.1101/2024.12.03.626638
Yuhao Chen, Yan Zhang, Jiaqi Gan, Ke Ni, Ming Chen, Ivet Bahar, Jianhua Xing
{"title":"GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells.","authors":"Yuhao Chen, Yan Zhang, Jiaqi Gan, Ke Ni, Ming Chen, Ivet Bahar, Jianhua Xing","doi":"10.1101/2024.12.03.626638","DOIUrl":"10.1101/2024.12.03.626638","url":null,"abstract":"<p><p>RNA velocities and generalizations emerge as powerful approaches for extracting time-resolved information from high-throughput snapshot single-cell data. Yet, several inherent limitations restrict applying the approaches to genes not suitable for RNA velocity inference due to complex transcriptional dynamics, low expression, or lacking splicing dynamics, or data of non-transcriptomic modality. Here, we present GraphVelo, a graph-based machine learning procedure that uses as input the RNA velocities inferred from existing methods and infers velocity vectors lying in the tangent space of the low-dimensional manifold formed by the single cell data. GraphVelo preserves vector magnitude and direction information during transformations across different data representations. Tests on synthetic and experimental single-cell data including viral-host interactome, multi-omics, and spatial genomics datasets demonstrate that GraphVelo, together with downstream generalized dynamo analyses, extends RNA velocities to multi-modal data and reveals quantitative nonlinear regulation relations between genes, virus and host cells, and different layers of gene regulation.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11642879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142831809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Brain Reward Circuit Inhibited By Next-Generation Weight Loss Drugs. 新一代减肥药抑制大脑奖赏回路
bioRxiv : the preprint server for biology Pub Date : 2025-06-14 DOI: 10.1101/2024.12.12.628169
Elizabeth N Godschall, Taha Bugra Gungul, Isabelle R Sajonia, Aleyna K Buyukaksakal, Orien Dong-Ang Li, Sophia Ogilvie, Austin B Keeler, Guilian Tian, Omar Koita, Yu Shi, Tyler C J Deutsch, Maisie Crook, YuChen Zhang, Nicholas J Conley, Addison N Webster, O Yipkin Calhan, Weile Liu, Amani Akkoub, Karan Malik, Kaleigh I West, Sara Michel-Le, Arun Karthikeyan, Grace van Gerven, Kevin T Beier, Larry S Zweifel, Manoj K Patel, John N Campbell, Christopher D Deppmann, Ali D Güler
{"title":"A Brain Reward Circuit Inhibited By Next-Generation Weight Loss Drugs.","authors":"Elizabeth N Godschall, Taha Bugra Gungul, Isabelle R Sajonia, Aleyna K Buyukaksakal, Orien Dong-Ang Li, Sophia Ogilvie, Austin B Keeler, Guilian Tian, Omar Koita, Yu Shi, Tyler C J Deutsch, Maisie Crook, YuChen Zhang, Nicholas J Conley, Addison N Webster, O Yipkin Calhan, Weile Liu, Amani Akkoub, Karan Malik, Kaleigh I West, Sara Michel-Le, Arun Karthikeyan, Grace van Gerven, Kevin T Beier, Larry S Zweifel, Manoj K Patel, John N Campbell, Christopher D Deppmann, Ali D Güler","doi":"10.1101/2024.12.12.628169","DOIUrl":"https://doi.org/10.1101/2024.12.12.628169","url":null,"abstract":"<p><p>Glucagon-like peptide-1 receptor agonists (GLP1RAs) effectively reduce body weight and improve metabolic outcomes, yet established peptide-based therapies require injections and complex manufacturing. Small-molecule GLP1RAs promise oral bioavailability and scalable manufacturing, but their selective binding to human versus rodent receptors has limited mechanistic studies. Here, we developed humanized GLP1R mouse models to investigate how small-molecule GLP1RAs influence feeding behavior. This approach revealed that these compounds regulate both homeostatic and hedonic feeding through parallel neural circuits. Beyond engaging canonical hypothalamic and hindbrain networks that control metabolic homeostasis, GLP1RAs recruit a discrete population of Glp1r-expressing neurons in the central amygdala, which selectively suppress the consumption of palatable foods by reducing dopamine release in the nucleus accumbens. Stimulating these central amygdalar neurons curtail hedonic feeding, whereas targeted deletion of the receptor in this cell population specifically diminishes the anorectic efficacy of GLP1RAs for reward-driven intake. These findings reveal a dedicated neural circuit through which small molecule GLP1RAs modulate reward processing, suggesting broad therapeutic potential in conditions of dysregulated dopamine signaling including substance use disorder and binge eating.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11702550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rhagovelia uses interfacial run-and-tumble locomotion to improve food capture in flowing environments. Rhagovelia在流动的环境中利用奔跑和翻滚的界面运动来提高猎物的捕获能力。
bioRxiv : the preprint server for biology Pub Date : 2025-06-14 DOI: 10.1101/2025.04.03.647112
Ishant Tiwari, Nithil Nagappan, Jacob S Harrison, Saad Bhamla
{"title":"Rhagovelia uses interfacial run-and-tumble locomotion to improve food capture in flowing environments.","authors":"Ishant Tiwari, Nithil Nagappan, Jacob S Harrison, Saad Bhamla","doi":"10.1101/2025.04.03.647112","DOIUrl":"10.1101/2025.04.03.647112","url":null,"abstract":"<p><p><i>Rhagovelia oriander</i> is a freshwater water strider native to the rivers and streams of North and South America, known for its distinctive skating movement on the water's surface. This movement resembles the correlated random-walk pattern seen in microorganisms such as <i>Escherichia coli</i> . Previous studies have primarily focused on limb adaptations and biomechanics, leaving the ecological significance inadequately addressed. We combine field observations with controlled laboratory experiments using a flow mill to investigate the dynamics of <i>R. oriander</i> under typical flow conditions. Our findings indicate that this insect exhibits a two-dimensional run-and-tumble motion, often incorporating lateral tumbles following straight runs (run distance: 30.7 ± 9.3 mm). We find that this behavior is resilient to changes in flow speed. In-silico simulations of particle interception demonstrated that this locomotion method enhances encounter rates compared to linear movement, particularly when the simulated food particle is following a rapid flow field. Our results document run-and-tumble locomotion in a millimeter-scale organism, showcasing a unique example of convergent behavior across diverse taxonomic groups and providing valuable insights into locomotion ecology while serving as a source of inspiration for bioinspired robotics and environmental exploration algorithms.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12026581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144059674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mechanistic insights into Down syndrome comorbidities via convergent RNA-seq and TWAS signals. 通过聚合RNA-seq和TWAS信号对唐氏综合症合并症的机制见解。
bioRxiv : the preprint server for biology Pub Date : 2025-06-12 DOI: 10.1101/2025.06.05.658129
Marc Subirana-Granés, Haoyu Zhang, Prashant Gupta, Milton Pividori
{"title":"Mechanistic insights into Down syndrome comorbidities via convergent RNA-seq and TWAS signals.","authors":"Marc Subirana-Granés, Haoyu Zhang, Prashant Gupta, Milton Pividori","doi":"10.1101/2025.06.05.658129","DOIUrl":"10.1101/2025.06.05.658129","url":null,"abstract":"<p><p>Down syndrome (DS) is caused by trisomy of chromosome 21 and is associated with diverse clinical manifestations, yet the molecular pathways linking chromosome-21 dosage effects to DS comorbidities remain poorly defined. Here we address this gap by applying a network-based, integrative framework that combines whole-blood transcriptomic data with gene-trait associations to uncover mechanistic insights into DS-associated conditions. First, we performed matrix factorization using PLIER on Human Trisome Project (HTP) RNA-Seq profiles from 304 trisomy-21 (T21) and 95 euploid (D21) individuals, deriving 156 biologically interpretable gene modules. We then identified 92 modules whose activity differed significantly between T21 and D21 and annotated these with prior-knowledge and KEGG pathways. To connect modules to clinical traits, we integrated PrediXcan-derived TWAS results from the UK Biobank, revealing 25 T21-specific modules with significant gene-trait associations (FDR < 0.1), including modules linked to cardiovascular, hematological, immune, metabolic, and neurological phenotypes relevant to DS. Using HTP clinical records as a replication cohort, 13 of these modules reliably predicted comorbidity status (AUC > 0.65, mAPS > 0.65). Most notably module 37, an interferon-stimulated gene network, whose elevated expression robustly distinguished DS individuals with pulmonary hypertension (AUC = 0.76, mAPS = 0.73). Overall, our study demonstrates that integrating blood-derived gene modules with population-scale genetic data uncovers coherent molecular signatures underlying DS comorbidities, identifies candidate biomarkers and therapeutic targets (e.g., <i>ISG15, IFITs, MX1</i> ), and highlights the power of combining transcriptomic and genetic evidence to elucidate complex disease mechanisms.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12157637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Direct RNA nanopore sequencing reveals rapid RNA modification changes following glucose stimulation of human pancreatic beta-cell lines. 直接RNA纳米孔测序揭示了葡萄糖刺激人类胰腺β细胞系后快速RNA修饰的变化。
bioRxiv : the preprint server for biology Pub Date : 2025-06-12 DOI: 10.1101/2025.06.12.659352
Logan Mulroney, Henry J Taylor, Angela Lee, Amy J Swift, Mihail Zdravkov, Lori L Bonnycastle, Shelise Y Brooks, Brian N Lee, Tomas Fitzgerald, Narisu Narisu, Leslie G Biesecker, Michael R Erdos, Francesco Nicassio, Ewan Birney, Francis S Collins, D Leland Taylor
{"title":"Direct RNA nanopore sequencing reveals rapid RNA modification changes following glucose stimulation of human pancreatic beta-cell lines.","authors":"Logan Mulroney, Henry J Taylor, Angela Lee, Amy J Swift, Mihail Zdravkov, Lori L Bonnycastle, Shelise Y Brooks, Brian N Lee, Tomas Fitzgerald, Narisu Narisu, Leslie G Biesecker, Michael R Erdos, Francesco Nicassio, Ewan Birney, Francis S Collins, D Leland Taylor","doi":"10.1101/2025.06.12.659352","DOIUrl":"https://doi.org/10.1101/2025.06.12.659352","url":null,"abstract":"<p><p>RNA modifications are critical regulators of gene expression and cellular processes; however, the epitranscriptome is less well studied than the epigenome. Here, we studied transcriptome-wide changes in RNA modifications and expression levels in two human pancreatic beta-cell lines, EndoC-BH1 and EndoC-BH3, after one hour of glucose stimulation. Using direct RNA nanopore sequencing (dRNA-seq), we measured N6-methyladenosine (m6A), 5-methylcytosine (m5C), inosine, and pseudouridine concurrently across the transcriptome. We developed a differential RNA modification method and identified 1,697 differentially modified sites (DMSs) across all modifications. These DMSs were largely independent of changes in gene expression levels and enriched in transcripts for type 2 diabetes (T2D) genes. Our study demonstrates how dRNA-seq can be used to detect and quantify RNA modification changes in response to cellular stimuli at the single-nucleotide level and provides new insights into RNA-mediated mechanisms that may contribute to normal beta-cell response and potential dysfunction in T2D.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12190750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144500150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Thiopurine-like Mutagenic Process Defines TGCT Subtypes. 硫嘌呤样诱变过程定义TGCT亚型。
bioRxiv : the preprint server for biology Pub Date : 2025-06-12 DOI: 10.1101/2025.06.12.655573
Kevin M Brown, Jun Zhong, Adriana Morales Miranda, Mengyan Zhang, Joycelyn Williams, Jacob Williams, Haoyu Zhang, Cheng Liang, Wenbo Li, Bin Zhu, Stephen J Chanock, Katherine L Nathanson, Tongwu Zhang
{"title":"A Thiopurine-like Mutagenic Process Defines TGCT Subtypes.","authors":"Kevin M Brown, Jun Zhong, Adriana Morales Miranda, Mengyan Zhang, Joycelyn Williams, Jacob Williams, Haoyu Zhang, Cheng Liang, Wenbo Li, Bin Zhu, Stephen J Chanock, Katherine L Nathanson, Tongwu Zhang","doi":"10.1101/2025.06.12.655573","DOIUrl":"https://doi.org/10.1101/2025.06.12.655573","url":null,"abstract":"<p><p>Testicular germ cell tumors (TGCTs) are the most common malignancy in young men, exhibit a unique developmental origin and exceptional chemosensitivity. However, the molecular distinctions between TGCT subtypes remain poorly understood. Here we present a comprehensive genomic analysis of 252 treatment-naive primary TGCTs, integrating deep whole-genome sequencing with matched transcriptomic and epigenomic data. We identify new driver genes and uncover defining features of TGCTs, including pervasive chromosome X amplification with subtype-specific X chromosome inactivation, and a germ cell-like transcriptional program. Although previously reported, whole genome doubling (WGD) in TGCTs is further characterized here as ubiquitous, developmentally early, and associated with age at onset. Seminomas are enriched for early driver mutations, secondary WGD events, sustained <i>XIST</i> expression and replication stress-associated indel mutational signatures, while non-seminomas show greater structural complexity, subclonal diversity, relatively earlier-onset WGD, extended tumor latency, and telomere elongation. Moreover, we identify a mutational signature, SBS87, that is exceptionally rare across cancers with exception of thiopurine-treated leukemia, but strikingly prevalent in TGCT, especially non-seminomas. SBS87 is linked to extended tumor latency and telomere elongation, implicating possible environmental or endogenous processes that mimic thiopurine-induced DNA damage in TGCT pathogenesis. Collectively, our findings define TGCTs as molecularly distinct tumors shaped by early genomic instability and highlight SBS87 as a novel mutational footprint with potential etiologic and clinical relevance.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12191103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144500104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Neural coding of choice and outcome are modulated by uncertainty in orbitofrontal but not secondary motor cortex. 选择和结果的神经编码受眶额叶不确定性的调节,但不受次级运动皮层的调节。
bioRxiv : the preprint server for biology Pub Date : 2025-06-12 DOI: 10.1101/2024.11.05.622092
Juan Luis Romero-Sosa, Alex Yeghikian, Andrew M Wikenheiser, Hugh T Blair, Alicia Izquierdo
{"title":"Neural coding of choice and outcome are modulated by uncertainty in orbitofrontal but not secondary motor cortex.","authors":"Juan Luis Romero-Sosa, Alex Yeghikian, Andrew M Wikenheiser, Hugh T Blair, Alicia Izquierdo","doi":"10.1101/2024.11.05.622092","DOIUrl":"10.1101/2024.11.05.622092","url":null,"abstract":"<p><p>Orbitofrontal cortex (OFC) and secondary motor cortex (M2) are both implicated in flexible reward learning but the conditions that differentially recruit these regions are not fully understood. We imaged calcium activity from single neurons in OFC or M2 during <i>de novo</i> learning of increasingly uncertain reward probability schedules. Predictions of choice were decoded from M2 neurons with high accuracy under all certainty conditions, but were more accurately decoded from OFC neurons under greater uncertainty. The number of choice- and reward-selective neurons was significantly higher in M2 than in OFC across schedules, but these proportions increased across levels of uncertainty only in OFC. Decoding accuracy of choice and outcome was predicted by behavioral strategies Win-Stay and Lose-Shift in OFC, but not M2. We also tested causal involvement of these regions with chemogenetic perturbation as rats learned increasing and then decreasing uncertainty schedules. Whereas inhibition of OFC neurons attenuated learning across all schedules, M2 neurons were found to support learning in the most certain reward schedule. Thus, OFC neurons preferentially encode choices and outcomes that foster a greater reliance on adaptive strategies under uncertainty. This reveals a novel functional heterogeneity within frontal cortex in support of flexible learning.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11580916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142690469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Single-nucleus analysis reveals oxidative stress in Down syndrome basal forebrain neurons at birth. 单核分析揭示出生时唐氏综合征基底前脑氧化磷酸化失调。
bioRxiv : the preprint server for biology Pub Date : 2025-06-12 DOI: 10.1101/2025.02.05.636750
Nicole R West, Kalpana Hanthanan Arachchilage, Sara Knaack, Shawn MacGregor, Masoumeh Hosseini, Ryan D Risgaard, Pubudu Kumarage, Jose L Martinez, Su-Chun Zhang, Daifeng Wang, Andre M M Sousa, Anita Bhattacharyya
{"title":"Single-nucleus analysis reveals oxidative stress in Down syndrome basal forebrain neurons at birth.","authors":"Nicole R West, Kalpana Hanthanan Arachchilage, Sara Knaack, Shawn MacGregor, Masoumeh Hosseini, Ryan D Risgaard, Pubudu Kumarage, Jose L Martinez, Su-Chun Zhang, Daifeng Wang, Andre M M Sousa, Anita Bhattacharyya","doi":"10.1101/2025.02.05.636750","DOIUrl":"10.1101/2025.02.05.636750","url":null,"abstract":"<p><strong>Introduction: </strong>Basal forebrain cholinergic neurons (BFCNs) are integral to learning, attention, and memory, and are prone to degeneration in Down syndrome (DS), Alzheimer's disease, and other neurodegenerative diseases. However, the mechanisms that lead to the degeneration of these neurons are not known.</p><p><strong>Methods: </strong>Single-nucleus gene expression and ATAC sequencing were performed on postmortem human basal forebrain from unaffected control and DS tissue samples at 0-2 years of age (n=4 each).</p><p><strong>Results: </strong>Sequencing analysis of postmortem human basal forebrain identifies gene expression differences in DS early in life. Genes encoding proteins associated with energy metabolism pathways, specifically oxidative phosphorylation and glycolysis, and genes encoding antioxidant enzymes are upregulated in DS BFCNs.</p><p><strong>Discussion: </strong>Multiomic analyses reveal that energy metabolism may be disrupted in DS BFCNs by birth. Increased oxidative phosphorylation and the accumulation of reactive oxygen species byproducts may be early contributors to DS BFCN neurodegeneration.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11839037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143461761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Measuring renal cortical cell-specific mitochondrial metabolism. 肾皮质细胞特异性氧化代谢。
bioRxiv : the preprint server for biology Pub Date : 2025-06-12 DOI: 10.1101/2024.11.24.622516
Kyle Feola, Andrea H Venable, Mina Rasouli, Julie Do, Tatyana McCoy, Claire B Llamas, Dana Straus, Prashant Mishra, Behzad Najafian, Sarah C Huen
{"title":"Measuring renal cortical cell-specific mitochondrial metabolism.","authors":"Kyle Feola, Andrea H Venable, Mina Rasouli, Julie Do, Tatyana McCoy, Claire B Llamas, Dana Straus, Prashant Mishra, Behzad Najafian, Sarah C Huen","doi":"10.1101/2024.11.24.622516","DOIUrl":"10.1101/2024.11.24.622516","url":null,"abstract":"<p><p>The metabolic health of the kidney is a primary determinant of the risk of progressive kidney disease. Our understanding of the metabolic processes that fuel kidney functions is limited by the kidney's structural and functional heterogeneity. As the kidney contains many different cell types, we sought to determine the intra-renal mitochondrial heterogeneity that contributes to cell-specific metabolism. To interrogate this, we utilized a recently developed mitochondrial tagging technique to isolate kidney cell-type specific mitochondria. Here, we investigate mitochondrial functional capacities and the metabolomes of the early and late proximal tubule (PT) and the distal convoluted tubule (DCT). The conditional MITO-Tag transgene was combined with <i>Slc34a1-CreERT2</i> , <i>Ggt1-Cre</i> , or <i>Pvalb-Cre</i> transgenes to generate mouse models capable of cell-specific isolation of hemagglutinin (HA)-tagged mitochondria from the early PT, late PT, or the DCT, respectively. Functional assays measuring mitochondrial respiratory and fatty acid oxidation (FAO) capacities and metabolomics were performed on anti-HA immunoprecipitated mitochondria from kidneys of ad libitum fed and 24-hour fasted male mice. The renal MITO-Tag models targeting the early PT, late PT, and DCT revealed differential mitochondrial respiratory and FAO capacities which dynamically changed during fasting conditions. The renal MITO-Tag model captured differential mitochondrial metabolism and functional capacities across the early PT, late PT, and DCT at baseline and in response to fasting.</p><p><strong>New & noteworthy: </strong>This study described the generation and utilization of mouse models capable of interrogating kidney tubular epithelial cell-specific mitochondrial metabolism. Applying the MITO-Tag system in the kidney, we have for the first time defined the mitochondrial metabolic heterogeneity of renal cortical tubular epithelium and discovered differential mitochondrial functional capacities in response to an acute metabolic stress such as fasting.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142804160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信