bioRxiv - Molecular Biology最新文献

{"title":"A universal limit for mammalian lifespan revealed by epigenetic entropy","authors":"Juan Jose Alba-Linares, Juan Ramon Tejedor, Agustin F. Fernandez, Raul F. Perez, Mario F. Fraga","doi":"10.1101/2024.09.06.611669","DOIUrl":"https://doi.org/10.1101/2024.09.06.611669","url":null,"abstract":"Age-associated DNA methylation patterns have shown strong associations with species lifespan. However, it remains unclear whether epigenetic noise levels can account for the observed differences between mammalian species. In this study, we examined the rate of loss of epigenetic information with age by measuring entropy at mammalian conserved CpG sites across a diverse range of species. Longer-lived mammals tend to gain fewer noisy CpGs with age, irrespective of whether these originate from hyper- or hypomethylation processes. Importantly, we found that the rate of epigenetic entropy gain declines in a linear fashion with species maximum lifespan, pointing to the existence of a universal limit for mammalian lifespan in the vicinity of 220 years.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"110 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142212667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative Multi-Omics Analysis of IFNγ-induced Macrophages and Atherosclerotic Plaques Reveals Macrophage-dependent STAT1-Driven Transcription in Atherosclerosis","authors":"Mahdi Eskandarian Boroujeni, Natalia Lopacinska, Aleksandra Antonczyk, Katarzyna Kluzek, Joanna Wesoly, Hans AR Bluyssen","doi":"10.1101/2024.09.06.611606","DOIUrl":"https://doi.org/10.1101/2024.09.06.611606","url":null,"abstract":"This study investigates the role of STAT1-mediated IFNγ signaling in atherosclerosis progression through multi-omics integration and analysis of human and mouse models of atherosclerotic lesions. By integrating ATAC-seq, ChIP-seq, and RNA-seq data from IFNγ-treated bone marrow-derived macrophages, we identified 1139 STAT1-dependent integrative genes that show chromatin accessibility, differential epigenetic marks (H3K27ac, H3K4me1, H3K4me3), prominent transcription factor binding patterns (STAT1 and PU.1), and active transcription. These genes were also enriched for lipid metabolism and atherosclerosis-related pathways. We then validated our findings by tracing the expression of these genes in human atherosclerotic lesions and in ApoE-/- and LDLr-/- mouse models, revealing significant correlations with LDL cholesterol and diseased vessel traits. Single-cell RNA-seq of human and mouse atherosclerotic samples showed dynamic changes in macrophage subtypes, with foamy and tissue-resident macrophages displaying increased STAT1 activity. This comprehensive multi-omics approach provides new insights into the transcriptional regulation of atherosclerosis progression mediated by STAT1-PU.1 co-binding and IFNγ signaling. Moreover, our data delineates a STAT1-dependent gene signature, highlighting the potential of these integrative genes as biomarkers and therapeutic targets in atherosclerosis.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142212666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transfer RNA levels are tuned to support differentiation during Drosophila neurogenesis","authors":"Rhondene Wint, Michael D. Cleary","doi":"10.1101/2024.09.06.611608","DOIUrl":"https://doi.org/10.1101/2024.09.06.611608","url":null,"abstract":"Neural differentiation requires a multifaceted program to alter gene expression along the proliferation to differentiation axis. While critical changes occur at the level of transcription, post-transcriptional mechanisms allow fine-tuning of protein output. We investigated the role of tRNAs in regulating gene expression during neural differentiation by quantifying tRNA abundance in neural progenitor-biased and neuron-biased Drosophila larval brains. We found that tRNA profiles are largely consistent between progenitor-biased and neuron-biased brains but significant variation occurs for 10 cytoplasmic isodecoders (individual tRNA genes) and this establishes differential tRNA levels for 8 anticodon groups. We used these tRNA data to investigate relationships between tRNA abundance, codon optimality-mediated mRNA decay, and translation efficiency in progenitors and neurons. Our data reveal that tRNA levels strongly correlate with codon optimality-mediated mRNA decay within each cell type but generally do not explain differences in stabilizing versus destabilizing codons between cell types. Regarding translation efficiency, we found that tRNA expression in neural progenitors preferentially supports translation of mRNAs whose products are in high demand in progenitors, such as those associated with protein synthesis. In neurons, tRNA expression shifts to disfavor translation of proliferation-related transcripts and preferentially support translation of transcripts tied to neuron-specific functions like axon pathfinding and synapse formation. Overall, our analyses reveal that changes in tRNA levels along the neural differentiation axis support optimal gene expression in progenitors and neurons.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142212668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GelGenie: an AI-powered framework for gel electrophoresis image analysis","authors":"Matthew Aquilina, Nathan J.W. Wu, Kiros Kwan, Filip Busic, James Dodd, Laura Nicolas-Saenz, Alan O'Callaghan, Peter Bankhead, Katherine E Dunn","doi":"10.1101/2024.09.06.611479","DOIUrl":"https://doi.org/10.1101/2024.09.06.611479","url":null,"abstract":"Gel electrophoresis is a ubiquitous laboratory method for the separation and semi-quantitative analysis of biomolecules. However, gel image analysis principles have barely advanced for decades, in stark contrast to other fields where AI has revolutionised data processing. Here, we show that an AI-based system can automatically identify gel bands in seconds for a wide range of experimental conditions, far surpassing the capabilities of current software. We used a dataset containing 500+ images of manually-labelled gels to train various U-Nets to accurately identify bands through segmentation, i.e. classifying pixels as 'band' or 'background'. When applied to gel electrophoresis data from other laboratories, our system generated results that quantitatively matched those of the original authors. We have publicly released our models through GelGenie, an open-source application that allows users to extract bands from gel images on their own devices, with no expert knowledge or experience required.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142212669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ER stress relief drives beta cell proliferation","authors":"Stephanie Bourgeois, Annelore Van Mulders, Yves Heremans, Gunter Leuckx, Lien Willems, Sophie Coenen, Laure Degroote, Julie Pierreux, Daliya Kancheva, Isabelle Scheyltjens, Kiavash Movahedi, Francoise Carlotti, Eelco de Koning, Xiaoyan Yi, Chiara Vinci, Yue Tong, Miriam Cnop, Harry Heimberg, Nico De Leu, Willem Staels","doi":"10.1101/2024.09.06.611615","DOIUrl":"https://doi.org/10.1101/2024.09.06.611615","url":null,"abstract":"Regenerating endogenous pancreatic beta cells is a potentially curative yet currently elusive strategy for diabetes therapy. Mimicking the microenvironment of the developing pancreas and leveraging vascular signals that support pancreatic endocrinogenesis may promote beta cell regeneration. We aimed to investigate whether recovery from experimental hypovascularization of the endocrine pancreas, achieved by modulating the transgenic production of a VEGF-A blocker in beta cells, could trigger mouse beta cell proliferation. Serendipitously, we found that transgene overexpression in beta cells induces endoplasmic reticulum (ER) stress and that subsequent relief from this stress stimulates beta cell proliferation independent of vessel recovery. Transient GFP overexpression in vivo and chemical induction of ER stress in vitro replicated this beta cell cycling response. Our findings highlight the potential side effects of ER stress due to transgene overexpression in beta cells and assert that ER stress relief serves as a potent regenerative stimulus.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142212670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeting Specific Kinase Substrates Rescues Increased Colitis Severity Induced by the Crohn's Disease-Linked LRRK2-N2081D Variant","authors":"George R Heaton, Xianting Li, Xiaoting Zhou, Yuanxi Zhang, Duc Tung Vu, Marc Oeller, Ozge Karayel, Quyen Q Hoang, Meltem Ece Kars, Minghui Wang, Leonid Tarassishin, Matthias Mann, Inga Peter, Zhenyu Yue","doi":"10.1101/2024.09.05.611530","DOIUrl":"https://doi.org/10.1101/2024.09.05.611530","url":null,"abstract":"LRRK2 contains a kinase domain where both the N2081D Crohn's disease (CD) risk and the G2019S Parkinson's disease (PD)-pathogenic variants are located. The mechanisms by which the N2081D variant increase CD risk, and how these adjacent mutations result in distinct diseases, remain unclear. To investigate the pathophysiology of the CD-linked LRRK2 N2081D variant, we generated a knock-in (KI) mouse model and compared its effects to those of the LRRK2-G2019S mutation. We find that Lrrk2-N2081D KI mice demonstrate heightened sensitivity to induced colitis, resulting in more severe inflammation and intestinal damage than Lrrk2-G2019S KI and wild-type mice. Analysis of Colon tissue revealed distinct mutation-dependent LRRK2 RAB substrate phosphorylation, with significantly elevated phosphorylated RAB10 levels in Lrrk2-N2081D mice. In cells, we demonstrate that the N2081D mutation activates LRRK2 through a mechanism distinct from that of LRRK2-G2019S. We further find that proinflammatory stimulation enhances LRRK2 kinase activity, leading to mutation-dependent differences in RAB phosphorylation and inflammatory responses in dendritic cells. Finally, we show that genetic knockout of Rab12, but not pharmacological LRRK2 kinase inhibition, significantly reduced colitis severity in Lrrk2-N2081D mice. Our study characterizes the pathogenic mechanisms of LRRK2-linked CD, highlights important structural and functional differences between disease-associated LRRK2 variants, and suggests RAB proteins as promising therapeutic targets for modulating LRRK2 activity in CD treatment.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"273 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142212673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ADAR1 orchestrates the ZBP1-mediated PANoptosis and heart transplant rejection","authors":"Haitao Lu, Jifu Jiang, Xuyan Huang, Aaron Haig, Lakshman Gunaratnam, Anthony Jevnikar, Zhu-Xu Zhang","doi":"10.1101/2024.09.05.611429","DOIUrl":"https://doi.org/10.1101/2024.09.05.611429","url":null,"abstract":"Background: PANoptosis is an integrated form of cell death that combines features of pyroptosis, apoptosis, and necroptosis and is regulated by a complex network of signaling proteins. The roles of ADAR1 (adenosine deaminase acting on RNA 1) and RIPK1 (receptor-interacting serine/threonine-protein kinase 1) in orchestrating the ZBP1 (Z-DNA binding protein 1)-RIPK3 complex to mediate PANoptosis is not fully understood, particularly in the context of heart transplantation.\u0000Objective: This study investigated how ADAR1 and RIPK1 coordinate the activation of the ZBP1-RIPK3 complex to mediate PANoptosis and its implications in mouse heart transplantation.\u0000Methods: Using both in vitro and in vivo models, we analyzed the interactions between ADAR1, RIPK1, ZBP1, and RIPK3. We employed western blotting, and siRNA to elucidate the dynamics of these interactions. Additionally, we assessed the impact of ZBP1 on mouse heart transplantation outcomes.\u0000Results: Our studies revealed that ADAR1 regulates the activation of the ZBP1-RIPK3 complex for PANoptosis. The interaction of ADAR1 with ZBP1 protected against Z-DNA-induced cell death by limiting activations of ZBP1 and RIPK3. In mouse heart transplantation study, we found that ZBP1 and its ligand Z-DNA/Z-RNA were significantly increased in the graft post-transplantation. Furthermore, ZBP1 deficiency in the heart graft inhibited cardiac PANoptosis, attenuated acute graft injury, and induced long-term graft survival. Conclusion: This study elucidates the role of ADAR1 in ZBP1-mediated PANoptosis. Inhibition of ZBP1 can prevent heart graft injury and rejection. Understanding these mechanisms provides valuable insights into the regulation of cell death and may inform the development of novel therapeutic strategies to improve transplant outcomes.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142212671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The curse of the red pearl: a fibroblast specific pearl-necklace mitochondrial phenotype caused by phototoxicity","authors":"Irene MGM Hemel, Kèvin Knoops, Carmen López-Iglesias, Mike Gerards","doi":"10.1101/2024.09.05.611420","DOIUrl":"https://doi.org/10.1101/2024.09.05.611420","url":null,"abstract":"The dynamic nature of mitochondria makes live cell imaging an important tool in mitochondrial research. Although imaging using fluorescent probes is the golden standard in studying mitochondrial morphology, these probes might introduce a-specific features. In this study, live cell fluorescent imaging was applied to investigate a pearl-necklace shaped mitochondrial phenotype that arises when mitochondrial fission is restricted. In this fibroblast specific pearl-necklace phenotype, constricted and expanded mitochondrial regions alternate. Imaging studies revealed that the formation time of this pearl-necklace phenotype differs between laser scanning confocal, widefield and spinning disk confocal microscopy. We found that the phenotype formation correlates with the excitation of the fluorescent probe and is the result of phototoxicity. Interestingly, the phenotype only arises in cells stained with red mitochondrial dyes. Serial section electron tomography pearl-necklace mitochondria revealed that the mitochondrial membranes remained intact, while the cristae structure was altered. Furthermore, filaments and ER were present at the constricted sites. This study illustrates the importance of considering experimental conditions for live cell imaging to prevent imaging artefacts that can have a major impact on the obtained results.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"100 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142212672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A DNA barcode library for Culex mosquitoes (Diptera: Culicidae) of South America with the description of two cryptic species of subgenus Melanoconion","authors":"Stanislas Talaga, Amandine Guidez, Benoît de Thoisy, Anne Lavergne, Romuald Carinci, Pascal Gaborit, Jean Issaly, Isabelle Dusfour, Jean-Bernard Duchemin","doi":"10.1101/2024.09.04.611342","DOIUrl":"https://doi.org/10.1101/2024.09.04.611342","url":null,"abstract":"The genus Culex is one of the most diverse in the world and includes numerous known vector species of parasites and viruses to humans. Morphological identification of Culex species is notoriously difficult and rely mostly on the examination of properly dissected male genitalia which largely prevents female and immature identification during entomological, ecological or arboviral surveys. The aims of this study were (i) to establish a DNA barcode library for Culex mosquitoes of French Guiana based on the mitochondrial gene cytochrome c oxidase I (COI) marker, (ii) to compare three approaches of molecular delimitation of species to morphological identification, and (iii) to test the effectiveness of the COI marker at a broader geographical scale across South America. Mosquitoes used in this study were sampled in French Guiana between 2013 and 2023. We provide 246 COI sequences for 90 morphologically identified species of Culex, including five new country records and two newly described species. Overall, congruence between morphological identification and molecular delimitations using the COI barcode were high. The Barcode of Life Data clustering approach into Barcode Index Numbers gives the best result in terms of species delimitation, followed by the muti-rate Poisson Tree Processes and the Assemble Species by Automatic Partitioning methods. Inconsistencies between morphological identification and molecular delimitation can be explained by introgression, incomplete lineage sorting, imperfect taxonomy or the effect of the geographical scale of sampling. This increases by almost two-fold the number of mosquito species for which a DNA barcode is available in French Guiana, including 75% of the species of Culex currently known in the territory. Finally, this study confirms the usefulness of the COI barcode in identifying Culex mosquitoes of South America, but also points the limits of this marker for some groups of species within the subgenera Culex and Melanoconion.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142212674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondrial topoisomerase I (Top1MT) prevents the onset of metabolic dysfunction-associated steatohepatitis (MASH) in mice","authors":"Simone A Baechler, Liton Kumar Saha, Valentina M Factor, Chaitali Chitinis, Anjali Dhall, Diana Becker, Jens U Marquardt, Yves Pommier","doi":"10.1101/2024.09.05.611454","DOIUrl":"https://doi.org/10.1101/2024.09.05.611454","url":null,"abstract":"High fat (HF) diet is a major factor in the development of metabolic dysfunction-associated steatotic liver disease (MASLD) and steatohepatis (MASH), and mitochondria have been proposed to play a role in the pathogenesis of HF diet-induced MASH. Because Mitochondrial topoisomerase I (Top1MT) is exclusively present in mitochondria and Top1MT knock-out mice are viable, we were able to assess the role of Top1MT in the development of MASH. We show that after 16 weeks of HF diet, mice lacking Top1MT are prone to the development of severe MASH characterized by liver steatosis, lobular inflammation and hepatocyte damage. Mice lacking Top1MT also show prominent mitochondrial dysfunction, ROS production and mitochondrial DNA (mtDNA) release, accompanied by hepatic inflammation and fibrosis. In summary, our study demonstrates the importance of Top1MT in sustaining hepatocyte functions and suppressing MASH.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"52 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142212675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}