bioRxiv - Molecular Biology最新文献

{"title":"Tracing Endometriosis: Coupling deeply phenotyped, single-cell based Endometrial Differences and AI for disease pathology and prediction","authors":"Lea Duempelmann, Shaoline Sheppard, Angelo Duo, Jitka Skrabalova, Brett McKinnon, Thomas Andrieu, Dennis Goehlsdorf, Sukalp Muzumdar, Cinzia Donato, Ryan Lusby, Wiebke Solass, Hans Bosmuller, Peter Nestorov, Michael Mueller","doi":"10.1101/2024.08.09.606959","DOIUrl":"https://doi.org/10.1101/2024.08.09.606959","url":null,"abstract":"Endometriosis, affecting 1 in 9 women, presents treatment and diagnostic challenges. To address these issues, we generated the biggest single-cell atlas of endometrial tissue to date, comprising 466,371 cells from 35 endometriosis and 25 non-endometriosis patients without exogenous hormonal treatment. Detailed analysis reveals significant gene expression changes and altered receptor-ligand interactions present in the endometrium of endometriosis patients, including increased inflammation, adhesion, proliferation, cell survival, and angiogenesis in various cell types. These alterations may enhance endometriosis lesion formation and offer novel therapeutic targets. Using ScaiVision, we developed neural network models predicting endometriosis of varying disease severity (median AUC = 0.83), including an 11-gene signature-based model (median AUC = 0.83) for hypothesis-generation without external validation. In conclusion, our findings illuminate numerous pathway and ligand-receptor changes in the endometrium of endometriosis patients, offering insights into pathophysiology, targets for novel treatments, and diagnostic models for enhanced outcomes in endometriosis management.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941653","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":"Uncoupling de novo pyrimidine biosynthesis from mitochondrial electron transport by ectopic expression of cytosolic DHODH","authors":"Andrea Curtabbi, Rocio Sanz-Cortes, Jose Antonio Enriquez","doi":"10.1101/2024.08.09.607333","DOIUrl":"https://doi.org/10.1101/2024.08.09.607333","url":null,"abstract":"Dihydroorotate dehydrogenase (DHODH) is an enzyme involved in the biosynthesis of pyrimidine nucleotides. In most eukaryotes, this enzyme is bound to the inner mitochondrial membrane, where it couples the synthesis of orotate with the reduction of ubiquinone. As ubiquinone must be regenerated by respiratory complex III, pyrimidine biosynthesis and cellular respiration are tightly coupled. Consequently, inhibition of respiration leads to cessation of DNA synthesis and impairs cell proliferation. We show that expression of Saccharomyces cerevisiae URA1 gene (ScURA) in mammalian cells uncouples biosynthesis of pyrimidines from mitochondrial electron transport. ScURA forms a homodimer in the cytosol that uses fumarate instead of ubiquinone as the electron acceptor, enabling oxygen-independent pyrimidine biosynthesis. Cells expressing ScURA are resistant to drugs that inhibit complex III and the mitochondrial ribosome. ScURA enables the growth of mtDNA-lacking ρ0 cells in uridine-deficient medium and ameliorates the phenotype of cellular models of mitochondrial diseases. This genetic tool uncovers the contribution of pyrimidine biosynthesis to the phenotypes arising from electron transport chain defects.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"135 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941440","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 ameliorative effect of C-Kit pos hepatic endothelial Mertk deficiency on nonalcoholic steatohepatitis","authors":"Seng-Wang Fu, Yu-Xuan Gao, Hui-Yi Li, Yi-Fan Ren, Jun-Cheng Wu, Zheng-Hong Li, Mingyi Xu","doi":"10.1101/2024.08.08.607275","DOIUrl":"https://doi.org/10.1101/2024.08.08.607275","url":null,"abstract":"Recently, Mer tyrosine kinase (Mertk) and KIT proto-oncogene (C-Kit) were reported play a role in liver sinusoidal endothelial cells (LSECs) in patients with nonalcoholic steatohepatitis (NASH). In this study, lower levels of C-Kit and higher levels of Mertk/p-Mertk were confirmed in steatotic LSECs and in the livers of patients and mice with NASH. C-Kit was suggested to negatively regulate Mertk signaling in steatotic LSECs. The steatotic LSECs in which Mertk was knocked down displayed high fenestration and reduced expression of procapillarized CD31/VN; showed antiangiogenic features and decreased expression of proangiogenic VEGF/ERK1/2; and exhibited intact mitophagy and upregulation of the Pink1/Parkin pathway. Bone marrow transplantation (BMT) of C-Kitpos-BMCssh-Mertk to MCD mice could equivalently protect endothelial functions. Steatotic hepatocytes (HCs) or hepatic stellate cells (HSCs) cocultured with LSECssh-Mertk exhibited diminished lipid deposition; decreased expression of prolipogenic LXR/SREBP-1c, proinflammatory TNF-alpha/IL-6 and profibrotic alpha-SMA/ColI; and increased expression of prolipolytic FXR/ADPN. Similarly, the BMT of C-Kitpos-BMCssh-Mertk to MCD mice ameliorated NASH. C-Kitpos-LSECs that underwent Mertk cleavage were found to limit NASH progression. Therefore, Mertk deficiency should be a novel therapeutic agent for restoring LSECs in patients with NASH.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"2012 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941658","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":"Biogenesis, engineering and function of membranes in the CO2-fixing pyrenoid","authors":"Jessica H Hennacy, Nicky Atkinson, Angelo Kayser-Browne, Sabrina L Ergun, Eric Franklin, Lianyong Wang, Moshe Kafri, Friedrich Fauser, Josep Vilarrasa-Blasi, Robert E Jinkerson, Alistair J McCormick, Martin C Jonikas","doi":"10.1101/2024.08.08.603944","DOIUrl":"https://doi.org/10.1101/2024.08.08.603944","url":null,"abstract":"Approximately one-third of global CO2 assimilation is performed by the pyrenoid, a liquid-like organelle found in most algae and some plants. Specialized membranes are hypothesized to drive CO2 assimilation in the pyrenoid by delivering concentrated CO2, but their biogenesis and function have not been experimentally characterized. Here, we show that homologous proteins SAGA1 and MITH1 mediate the biogenesis of the pyrenoid membrane tubules in the model alga Chlamydomonas reinhardtii and are sufficient to reconstitute pyrenoid-traversing membranes in a heterologous system, the plant Arabidopsis thaliana. SAGA1 localizes to the regions where thylakoid membranes transition into tubules and is necessary to initiate tubule formation. MITH1 localizes to the tubules and is necessary for their extension through the pyrenoid. Tubule-deficient mutants exhibit growth defects under CO2-limiting conditions, providing evidence for the function of membrane tubules in CO2 delivery to the pyrenoid. Furthermore, these mutants form multiple aberrant condensates of pyrenoid matrix, indicating that a normal tubule network promotes the coalescence of a single pyrenoid. The reconstitution of pyrenoid-traversing membranes in a plant represents a key milestone toward engineering a functional pyrenoid into crops for improving crop yields. More broadly, our study demonstrates the functional importance of pyrenoid membranes, identifies key biogenesis factors, and paves the way for the molecular characterization of pyrenoid membranes across the tree of life.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"99 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941442","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":"FACT-(H3-H4) complex stimulates Pol α activity to coordinate DNA synthesis with nucleosome assembly","authors":"Wenshuo Zhang, Jiawei Xu, Jiayi Yang, Guojun Shi, Jiale Wu, Ning Gao, Jianxun Feng, Qing Li","doi":"10.1101/2024.08.08.607175","DOIUrl":"https://doi.org/10.1101/2024.08.08.607175","url":null,"abstract":"Deficiencies in replication-coupled (RC) nucleosome assembly often lead to reduced DNA replication rate, but the precise mechanism underlying this process remains unsolved. Here, we discovered that H3-H4, but not H2A-H2B, mediates the interaction between FACT and the primase-polymerase complex DNA Pol α. This interaction stimulates the DNA polymerase activity of Pol α, and is indispensable for Okazaki fragment synthesis and replication fork progression. Moreover, the Pol1-N domain of Pol α provides a specific binding site for FACT and H3-H4. Furthermore, CAF-1 and Rtt106-mediated replication-coupled nucleosome assembly pathways regulate this interaction. Together, we propose that the FACT-(H3-H4)-Pol α interaction acts as a “Pre-Warning System” that regulates DNA replication, ensuring proper coordination between DNA synthesis and nucleosome assembly.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941446","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":"Biallelic Loss of Molecular Chaperone Molecule AIP Results in a Novel Severe Multisystem Disease Defined by Defective Proteostasis","authors":"Marta Korbonits, Xian Wang, Sayka Barry, Chung Lim, Oniz Suleyman, Stefano De-Tito, Nazia Begum, Maria Lillina Vignola, Charlotte Hall, Laura Perna, Paul Chapple, Sian Henson, Valle Morales, Katiuscia Bianchi, Vidar Orn Edvardsson, Kristjan Ari Ragnarsson, Viktoria Eir Kristinsdottir, Anne Debeer, Yoeri Sleyp, Rena Zinchenko, Glenn Anderson, Michael Duchen, Kritarth Singh, Chih-Yao Chung, Yu Yuan, Sandip Patel, Ezra Aksoy, Artem O Borovikov, Hans Tomas Bjornsson, Hilde Van Esch, Gabor Czibik, Sharon Tooze, Caroline Helen Brennan, Oliver Haworth","doi":"10.1101/2024.08.08.604602","DOIUrl":"https://doi.org/10.1101/2024.08.08.604602","url":null,"abstract":"Children born with deleterious biallelic variants of the chaperone aryl hydrocarbon receptor interacting protein (AIP) have a novel pediatric metabolic disease presenting a severe, complex clinical phenotype characterized by failure to develop following birth. Analysis of Aip knockout mouse embryonic fibroblasts and patient-derived dermal fibroblasts revealed that AIP was required to support proteostasis; including proteasome activity, induction of autophagy and lysosome function. aip knockout zebrafish, recapitulated the phenotype of the children; dying at an early stage of development when autophagy is required to adapt to periods of starvation. Our results demonstrate that AIP plays a crucial role in initiating autophagy and maintaining proteostasis in vitro and in vivo.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"63 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941444","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":"Clostridioides difficile Toxins Unhinged: Allosterically Switchable Network Orients β-flap","authors":"Lauren Marie Finn, Rebecca Cummer, Bastien Castagner, Bettina G. Keller","doi":"10.1101/2024.08.08.607137","DOIUrl":"https://doi.org/10.1101/2024.08.08.607137","url":null,"abstract":"Allosteric proteins exhibit a functional response upon ligand binding far from the active site. <em>Clostridioides difficile</em> toxins use allosteric binding by an endogenous co-factor to orchestrate self-cleavage from within the target cell. This binding event induces a conformational shift, primarily effecting a lever-like \"β-flap\" region, with two known orientations. We uncovered a mechanism for this allosteric transition using extensive atomistic MD simulations and computational and experimental mutagenesis. The mechanism relies on a switchable interaction network. The most prominent interaction pair is K600–E743, with K600 interactions explaining ~70% of the allosteric effect. Rather than gradually morphing between two end states, the interaction network adopts two mutually exclusive configurations in the active and inactive state. Similar switchable networks may explain allostery more broadly. This mechanism in particular could aid in drug development targeting the <em>Clostridioides difficile</em> toxins autoproteolysis.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941443","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":"Histone variant H3.3 mediates cGAS-STING pathway activation via telomere deprotection","authors":"Chiao-Ming Huang, Liuh-Yow Chen","doi":"10.1101/2024.08.07.606966","DOIUrl":"https://doi.org/10.1101/2024.08.07.606966","url":null,"abstract":"Telomeric deposition of histone variant H3.3 is controlled by ATRX, DAXX, HIRA, and ASF1 proteins. Point mutations of H3.3 and defective mutants of ATRX are associated with cancers that utilize the alternative lengthening of telomeres (ALT) pathway to protect and maintain chromosome ends. Here, we identify a cascade of events following the expression of a TRF2 dominant negative mutant, TRF2ΔBΔM, which are regulated by H3.3 expression. H3.3 regulates the formation of damaged foci at telomeres and subsequent telomere-to-telomere fusion events controlled by the DNA repair pathway. Telomere fusion events also contributes to the formation of micronuclei and abnormal segregation. Micronuclei formation triggers activation of the cGAS-STING mediated innate immune response to intracellular DNA and inhibits cell growth. All of these phenotypes are controlled by the expression of H3.3. Additionally, disruption of ATRX, DAXX, HIRA, or ASF1 elicits an impairment phenotype similar to that is caused by H3.3 inhibition. Our results indicate that cGAS-STING-mediated cellular senescence is triggered by deprotected telomeres and is controlled by the expression and deposition of H3.3 on telomeres.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"99 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941650","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":"Mass spectrometric profiling of estrogen and estrogen metabolites in human stool and plasma partially elucidates the role of the gut microbiome in estrogen recycling","authors":"Vince W. Li, Tien S. Dong, Diana Funes, Laura Hernandez, Srinivasa T. Reddy, Emeran Mayer, Lin Chang, David Meriwether","doi":"10.1101/2024.08.07.606543","DOIUrl":"https://doi.org/10.1101/2024.08.07.606543","url":null,"abstract":"Estrogen and estrogen metabolites are commonly measured in human plasma and serum, but there exist almost no reports of estrogen measured in human stool. This methodological limitation in turn limits our understanding of the relationship between systemic and intestinal estrogen. We thus developed a highly sensitive liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) method for measuring free and conjugated forms of 15 estrogens and estrogen metabolites in human stool and plasma. We first investigated human stool and plasma estrogen in healthy control males; follicular and luteal phase premenopausal females; and postmenopausal females. Most estrogens were present in the plasma and stool of all groups, and plasma estrogen levels correlated with stool estrogen levels. In stool, estrogens were higher in premenopausal females, with estrogen levels rising across the menstrual cycle. We further combined these measures with shotgun metagenomic sequencing of the stool microbiomes. The level of estrogen deconjugation enzyme gene copy number (beta-glucuronidase + arylsulfatase) was higher in premenopausal females; while the gene copy numbers of beta-glucuronidase + arylsulfatase, but not beta-glucuronidase alone, correlated with reactivated stool estrogen in all groups. Moreover, deconjugation enzyme gene copy number correlated with plasma total estrogen in males and with individual plasma estrogen metabolites in all groups. These results support the hypothesis that gut microbial beta-glucuronidase and arylsulfatase control the reactivation of gut estrogen while modulating systemic levels through the uptake and recirculation of reactivated estrogen.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941451","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":"DROSHA, DICER and Damage-Induced long ncRNA control BMI1-dependent transcriptional repression at DNA double-strand break","authors":"Francesca Esposito, Ilaria Capozzo, Stefania Modafferi, Ubaldo Gioia, Letizia Manfredi, Fabio Iannelli, Alessio Colantoni, Adelaide Riccardi, Alessia di Lillo, Sara Tavella, Matteo Cabrini, Fabrizio d’Adda di Fagagna, Sofia Francia","doi":"10.1101/2024.08.07.606960","DOIUrl":"https://doi.org/10.1101/2024.08.07.606960","url":null,"abstract":"Genome integrity is safeguarded by the DNA damage response (DDR). Controlled transcriptional dampening of genes surrounding DNA double-strand breaks (DSBs) has been shown to facilitate DNA repair. This phenomenon, defined as DSB-induced silencing in <em>cis</em> (DISC), involves the DDR apical kinase ATM and the Polycomb Repressive Complex 1 (PRC1). Conversely, DSBs have also been reported to induce <em>de novo</em> transcription of damaged-induced long non-coding RNAs (dilncRNAs) in a MRE11-RAD50-NBS1 (MNR) complex-dependent manner. MRN also controls the recruitment to DSB of the ribonuclease DROSHA, which together with DICER, stimulates DDR signaling and DNA repair. Here, we reconcile these apparently contrasting observations by showing that dilncRNA, together with DROSHA and DICER, but not GW182-like proteins required for miRNA-mediated gene silencing, controls DISC. Indeed, similarly to ATM, MRN inhibition abolishes DISC while pharmacological enhancement of DICER ribonuclease activity by Enoxacin improves DISC. Importantly, Enoxacin administration restores DISC upon ATM inhibition, demonstrating that DICER promotes DISC independently from ATM. Differently, Enoxacin does not restore DISC upon MRN inhibition, suggesting that DICER acts downstream to dilncRNA biogenesis and DROSHA recruitment. Mechanistically, we show that DROSHA and DICER control the recruitment of the PRC1 component BMI1 at DSBs and the consequent H2A-K119 ubiquitination. Upon DSBs formation, BMI1 and DROSHA interact in an RNA-dependent manner. Indeed, BMI1 associates to dilncRNA and do so in a DROSHA- and DICER-dependent manner. Importantly, inhibition of dilncRNA function by antisense oligonucleotides or Cas13-mediated targeting is sufficient to reduce BMI1 recruitment and DISC at individual loci. We propose that dilncRNAs together with DROSHA and DICER control DISC at genomic DSB by supporting PRC1 recruitment and chromatin ubiquitination.","PeriodicalId":501108,"journal":{"name":"bioRxiv - Molecular Biology","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941651","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}