bioRxiv : the preprint server for biology最新文献

{"title":"Cell-type specific profiling of human entorhinal cortex at the onset of Alzheimer's disease neuropathology.","authors":"Patricia Rodriguez-Rodriguez, Wei Wang, Christina Tsagkogianni, Irena Feng, Ana Morello-Megias, Kaahini Jain, Vilma Alanko, Han-Ali Kahvecioglu, Elyas Mohammadi, Xiaofei Li, Marc Flajolet, Anna Sandebring-Matton, Silvia Maioli, Noemi Vidal, Ana Milosevic, Jean-Pierre Roussarie","doi":"10.1101/2024.12.31.630881","DOIUrl":"10.1101/2024.12.31.630881","url":null,"abstract":"<p><p>Neurons located in layer II of the entorhinal cortex (ECII) are the primary site of pathological tau accumulation and neurodegeneration at preclinical stages of Alzheimer's disease (AD). Exploring the alterations that underlie the early degeneration of these cells is essential to develop therapies that curb the disease before symptom onset. Here we performed cell-type specific profiling of human EC at the onset of AD neuropathology. We identify an early response to amyloid pathology by microglia and oligodendrocytes. Importantly, we provide the first insight into neuronal alterations that coincide with incipient tau pathology: the signaling pathway for Reelin, recently shown to be a major AD resilience gene is dysregulated in ECII neurons, while the secreted synaptic organizer molecules NPTX2 and CBLN4, emerging AD biomarkers, are downregulated in surrounding neurons. By uncovering the complex multicellular landscape of EC at these early AD stages, this study paves the way for detailed characterization of the mechanisms governing NFT formation and opens long-needed novel therapeutic avenues.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11722323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142974390","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}

{"title":"Study design and the sampling of deleterious rare variants in biobank-scale datasets.","authors":"Margaret C Steiner, Daniel P Rice, Arjun Biddanda, Mariadaria K Ianni-Ravn, Christian Porras, John Novembre","doi":"10.1101/2024.12.02.626424","DOIUrl":"10.1101/2024.12.02.626424","url":null,"abstract":"<p><p>One key component of study design in population genetics is the \"geographic breadth\" of a sample (i.e., how broad a region across which individuals are sampled). How the geographic breadth of a sample impacts observations of rare, deleterious variants is unclear, even though such variants are of particular interest for biomedical and evolutionary applications. Here, in order to gain insight into the effects of sample design on ascertained genetic variants, we formulate a stochastic model of dispersal, genetic drift, selection, mutation, and geographically concentrated sampling. We use this model to understand the effects of the geographic breadth of sampling effort on the discovery of negatively selected variants. We find that samples which are more geographically broad will discover a greater number variants as compared geographically narrow samples (an effect we label \"discovery\"); though the variants will be detected at lower average frequency than in narrow samples (e.g. as singletons, an effect we label \"dilution\"). Importantly, these effects are amplified for larger sample sizes and moderated by the magnitude of fitness effects. We validate these results using both population genetic simulations and empirical analyses in the UK Biobank. Our results are particularly important in two contexts: the association of large-effect rare variants with particular phenotypes and the inference of negative selection from allele frequency data. Overall, our findings emphasize the importance of considering geographic breadth when designing and carrying out genetic studies, especially at biobank scale.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11642817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142831833","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}

{"title":"A Bi-Specific T Cell-Engaging Antibody Shows Potent Activity, Specificity, and Tumor Microenvironment Remodeling in Experimental Syngeneic and Genetically Engineered Models of GBM.","authors":"Markella Z Zannikou, Joseph T Duffy, Daniele Procissi, Hinda Najem, Rebecca N Levine, Dolores Hambardzumyan, Catalina Lee-Chang, Lara Leoni, Bin Zhang, Amy B Heimberger, Jason Miska, Irina V Balyasnikova","doi":"10.1101/2024.12.18.628714","DOIUrl":"https://doi.org/10.1101/2024.12.18.628714","url":null,"abstract":"<p><strong>Background: </strong>Bispecific T cell-engagers (BTEs) are engineered antibodies that redirect T cells to target antigen-expressing tumors. BTEs targeting tumor-specific antigens such as interleukin 13 receptor alpha 2 (IL13Rα2) and EGFRvIII have been developed for glioblastoma (GBM). However, there is limited mechanistic understanding of the action of BTE since prior studies were mostly conducted in immunocompromised animal models. To close this gap, the function of BTEs was assessed in the immunosuppressive glioma microenvironment (TME) of orthotopic and genetically engineered mouse models (GEMM) with intact immune systems.</p><p><strong>Methods: </strong>A BTE that bridges CD3 epsilon on murine T cells to IL13Rα2-positive GBM cells was developed and the therapeutic mechanism investigated in immunocompetent mouse models of GBM. Multi-color flow cytometry, single-cell RNA sequencing (scRNA-Seq), multiplex immunofluorescence, and multiparametric magnetic resonance imaging (MRI) across multiple pre-clinical models of GBM were used to evaluate the mechanism and action and response.</p><p><strong>Results: </strong>BTE-mediated interactions between murine T cells and GBM cells triggered T cell activation and antigen-dependent killing of GBM cells. BTE treatment significantly extended the survival of mice bearing IL13Rα2-expressing orthotopic glioma and de novo forming GBM in the GEMM. Quantified parametric MR imaging validated the survival data showing a reduction in glioma volume and decreased glioma viability. Flow cytometric and scRNA-seq analyses of the TME revealed robust increases in activated and memory T cells and decreases in immunosuppressive myeloid cells in the brains of mice following BTE treatment.</p><p><strong>Conclusions: </strong>Our data demonstrate that the survival benefits of BTEs in preclinical models of glioma are due to the ability to engage the host immune system in direct killing, induction of immunological memory, and modulation of the TME. These findings provide a deeper insight into the mechanism of BTE actions in GBM.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11702671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070639","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}

{"title":"Epigenetic trajectory predicts development of clinical rheumatoid arthritis in ACPA+ individuals: Targeting Immune Responses for Prevention of Rheumatoid Arthritis (TIP-RA).","authors":"E Barton Prideaux, David L Boyle, Eunice Choi, Jane H Buckner, William H Robinson, V Michael Holers, Kevin D Deane, Gary S Firestein, Wei Wang","doi":"10.1101/2024.10.15.618490","DOIUrl":"10.1101/2024.10.15.618490","url":null,"abstract":"<p><strong>Objective: </strong>The presence of autoantibodies to citrullinated protein antigens (ACPAs) in the absence of clinically-apparent inflammatory arthritis (IA) identifies individuals at-risk for developing future clinical rheumatoid arthritis (RA). However, it is unclear why some ACPA+ individuals convert to clinical RA while others do not. We explored the possibility in the Targeting Immune Responses for Prevention of Rheumatoid Arthritis (TIP-RA) study that epigenetic remodeling is part of the trajectory from an at-risk state to clinical disease and identifies novel biomarkers associated with conversion to clinical RA.</p><p><strong>Methods: </strong>ACPA- Controls, ACPA+ At-Risk, and Early RA individuals were followed for up to 5 years, including obtaining blood samples annually and at RA diagnosis. Peripheral blood mononuclear cells (PBMCs) were separated into CD19+ B cells, memory CD4+ T cells, and naive CD4+ T cells using antibodies and magnetic beads. Genome-wide methylation within each cell lineage was assayed using the Illumina MethylationEPIC v1.0 beadchip. ACPA+ At-Risk participants who did or did not develop RA were designated Pre-RA or Non-converters, respectively. Differentially methylated loci (DML) were selected using the Limma software package. Using the Caret package, we constructed machine learning models in test and validation cohorts and identified the most predictive loci of clinical RA conversion.</p><p><strong>Results: </strong>Cross-sectional differential methylation analysis at baseline revealed DMLs that distinguish the Pre-RA methylome from ACPA+ Non-converters, the latter which closely resembled ACPA- Controls. Genes overlapping these DMLs correspond to aberrant NOTCH signaling and DNA repair pathways in B cells. Longitudinal analysis showed that ACPA- Control and ACPA+ Non-converter methylomes are relatively constant. In contrast, the Pre-RA methylome remodeled along a dynamic RA methylome trajectory characterized by epigenetic changes in active regulatory elements. Clinical conversion to RA, defined based on diagnosis, marked an epigenetic inflection point for cell cycle pathways in B cells and adaptive immunity pathways in naive T cells. Machine learning revealed individual loci associated with RA conversion. This model significantly outperformed autoantibodies plus acute phase reactants as predictors of RA conversion.</p><p><strong>Conclusion: </strong>DNA methylation is a dynamic process in ACPA+ individuals at-risk for developing RA that eventually transition to clinical disease. In contrast, non-converters and controls have stable methylomes. The accumulation of epigenetic marks over time prior to conversion to clinical RA conforms to pathways that are associated with immunity and can be used to identify potential pathogenic pathways for therapeutic targeting and/or use as prognostic biomarkers.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11507690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142516045","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}

{"title":"Failure to resolve inflammation contributes to juvenile onset cardiac damage in a mouse model of Duchenne Muscular Dystrophy.","authors":"James S Novak, Amy Lischin, Prech Uapinyoying, Ravi Hindupur, Young Jae Moon, Surajit Bhattacharya, Sarah Tiufekchiev, Victoria Barone, Davi Ag Mazala, Iteoluwakishi H Gamu, Gabriela Walters, Jyoti K Jaiswal","doi":"10.1101/2024.08.15.607998","DOIUrl":"10.1101/2024.08.15.607998","url":null,"abstract":"<p><p>Absence of dystrophin protein causes cardiac dysfunction in patients with Duchenne muscular dystrophy (DMD). Unlike boys with DMD, the common mouse model of DMD (B10-mdx) does not manifest cardiac deficits until late adulthood. This has limited our understanding of the mechanism and therapeutic approaches to target the pediatric onset of cardiac pathology in DMD. Here we show that the mdx mouse model on the DBA/2J genetic background (D2-mdx) displays juvenile-onset cardiac degeneration. Molecular and histological analysis revealed that cardiac damage in this model is linked to increased leukocyte chemotactic signaling and an inability to resolve inflammation. These deficiencies result in chronic inflammation and fibrotic conversion of the extracellular matrix (ECM) in the juvenile D2-mdx heart. To address these pathologies, we tested the utility of pro-resolution therapy to clear chronic cardiac inflammation. Use of an N-formyl peptide receptor (FPR) agonist helped physiologically resolve inflammation and mitigate the downstream events that lead to fibrotic degeneration of cardiomyocytes, preventing juvenile onset cardiac muscle loss. These results establish the utility of D2-mdx model to study events associated with pediatric-onset cardiac damage and demonstrates pro-resolution therapy as an alternate to anti-inflammatory therapy for treating cardiac degenerative pathology responsible for cardiomyopathy in DMD patients.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11343189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057835","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}

{"title":"Behavioral and genetic markers of susceptibility to escalate fentanyl intake.","authors":"Jack Keady, Richard Charnigo, Jakob D Shaykin, Emily R Prantzalos, Mengfan Xia, Emily Denehy, Cody Bumgardner, Justin Miller, Pavel Ortinski, Michael Bardo, Jill R Turner","doi":"10.1101/2024.12.06.627259","DOIUrl":"10.1101/2024.12.06.627259","url":null,"abstract":"<p><strong>Background: </strong>The ″loss of control″ over drug consumption, present in opioid use disorder (OUD) and known as escalation of intake, is well-established in preclinical rodent models. However, little is known about how antecedent behavioral characteristics, such as valuation of hedonic reinforcers prior to drug use, may impact the trajectory of fentanyl intake over time. Moreover, it is unclear if distinct escalation phenotypes may be driven by genetic markers predictive of OUD susceptibility.</p><p><strong>Methods: </strong>Male and female Sprague-Dawley rats (n=63) were trained in a sucrose reinforcement task using a progressive ratio schedule. Individual differences in responsivity to sucrose were hypothesized to predict escalation of fentanyl intake. Rats underwent daily 1-h acquisition sessions for i.v. fentanyl self-administration (2.5 μ g/kg; FR1) for 7 days, followed by 21 6-h escalation sessions, then tissue from prefrontal cortex was collected for RNA sequencing and qPCR. Latent growth curve and group-based trajectory modeling were used, respectively, to evaluate the association between sucrose reinforcement and fentanyl self-administration and to identify whether distinct escalation phenotypes can be linked to gene expression patterns.</p><p><strong>Results: </strong>Sucrose breakpoints were not predictive of fentanyl acquisition nor change during escalation, but did predict fentanyl intake on the first day of extended access to fentanyl. Permutation analyses did not identify associations between behavior and single gene expression when evaluated overall, or between our ascertained phenotypes. However, weighted genome correlation network analysis (WGCNA) and gene set enrichment analysis (GSEA) determined several gene modules linked to escalated fentanyl intake, including genes coding for voltage-gated potassium channels, calcium channels, and genes involved in excitatory synaptic signaling. Transcription factor analyses identified EZH2 and JARID2 as potential transcriptional regulators associated with escalated fentanyl intake. Genome-wide association study (GWAS) term categories were also generated and positively associated with terms relating to substance use disorders.</p><p><strong>Discussion: </strong>Escalation of opioid intake is largely distinct from motivation for natural reward, such as sucrose. Further, the gene networks associated with fentanyl escalation suggest that engagement of select molecular pathways distinguish individuals with ″addiction prone″ behavioral endophenotypes, potentially representing druggable targets for opioid use disorder. Our extended in silico identification of SNPs and transcription factors associated with the ″addiction prone″ high escalating rats highlights the importance of integrating findings from translational preclinical models. Through a precision medicine approach, our results may aid in the development of patient-centered treatment options for those with OUD.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879359","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}

{"title":"Mutations that prevent phosphorylation of the BMP4 prodomain impair proteolytic maturation of homodimers leading to lethality in mice.","authors":"Hyung-Seok Kim, Mary L Sanchez, Joshua Silva, Heidi L Schubert, Rebecca Dennis, Christopher P Hill, Jan L Christian","doi":"10.1101/2024.10.08.617306","DOIUrl":"10.1101/2024.10.08.617306","url":null,"abstract":"<p><p>Bone morphogenetic protein4 (BMP4) plays numerous roles during embryogenesis and can signal either alone as a homodimer, or together with BMP7 as a more active heterodimer. BMPs are generated as inactive precursor proteins that dimerize and are cleaved to generate the bioactive ligand and inactive prodomain fragments. In humans, heterozygous mutations within the prodomain of BMP4 are associated with birth defects. We studied the effect of two of these mutations (p.S91C and p.E93G), which disrupt a conserved FAM20C phosphorylation motif, on ligand activity. We compared the activity of ligands generated from BMP4, BMP4S91C or BMP4E93G in Xenopus embryos and found that these mutations reduce the activity of BMP4 homodimers but not BMP4/7 heterodimers. We generated Bmp4S91C and Bmp4E93G knock-in mice and found that Bmp4S91C/S91C mice die by E11.5 and display reduced BMP activity in multiple tissues including the heart. Most Bmp4E93G/E93G mice die before weaning and Bmp4-/E93G mutants die prenatally with reduced or absent eyes, heart and ventral body wall closure defects. Mouse embryonic fibroblasts (MEFs) isolated from Bmp4S91C and Bmp4E93G embryos show accumulation of BMP4 precursor protein, reduced levels of cleaved BMP ligand and reduced BMP activity relative to MEFs from wild type littermates. Because Bmp7 is not expressed in MEFs, the accumulation of unprocessed BMP4 precursor protein in mice carrying these mutations most likely reflects an inability to cleave BMP4 homodimers, leading to reduced levels of ligand and BMP activity in vivo. Our results suggest that phosphorylation of the BMP4 prodomain is required for proteolytic activation of BMP4 homodimers, but not heterodimers.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11482978/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485498","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}

{"title":"Helical transition of the bridge helix of Cas12a is an allosteric regulator of R-loop formation and RuvC activation.","authors":"Chhandosee Ganguly, Lindsie Martin, Swarmistha Aribam, Leonard M Thomas, Rakhi Rajan","doi":"10.1101/2025.01.09.632262","DOIUrl":"10.1101/2025.01.09.632262","url":null,"abstract":"<p><p>CRISPR-Cas12a is widely used for genome editing and biomarker detection since it can create targeted double-stranded DNA breaks and promote non-specific DNA cleavage after identifying specific DNA. To mitigate the off-target DNA cleavage of Cas12a, we previously developed a <i>Francisella novicida</i> Cas12a variant (FnoCas12a ^KD2P ) by introducing double proline substitutions (K969P/D970P) in a conserved helix called the bridge helix (BH). In this work, we used cryogenic electron microscopy (cryoEM) to understand the molecular mechanisms of BH-mediated activation of Cas12a. We captured five structures of FnoCas12a ^KD2P at different states of conformational activation. Comparison with wild-type (FnoCas12a ^WT ) structures unravels a mechanism where BH acts as a trigger that allosterically activates REC lobe movements by tracking the number of base pairs in the growing RNA-DNA hybrid to undergo a loop-to-helical transition and bending to latch onto the hybrid. The transition of the BH is coupled to the previously reported loop-to-helix transition of the \"lid\", essential for opening RuvC endonuclease, through direct interactions of residues of the BH and the lid. We also observe structural details of cooperativity of BH and \"helix-1\" of RuvC for activation, a previously proposed interaction. Overall, our study enables development of high-fidelity Cas12a and Cas9 variants by BH-modifications.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11741254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143019895","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}

{"title":"Pathogenetic mechanisms of muscle-specific ribosomes in dilated cardiomyopathy.","authors":"Michael R Murphy, Mythily Ganapathi, Teresa M Lee, Joshua M Fisher, Megha V Patel, Parul Jayakar, Amanda Buchanan, Alyssa L Rippert, Rebecca C Ahrens-Nicklas, Divya Nair, Rajesh K Soni, Yue Yin, Feiyue Yang, Muredach P Reilly, Wendy K Chung, Xuebing Wu","doi":"10.1101/2025.01.02.630345","DOIUrl":"10.1101/2025.01.02.630345","url":null,"abstract":"<p><p>The heart employs a specialized ribosome in its muscle cells to translate genetic information into proteins, a fundamental adaptation with an elusive physiological role ^1-3 . Its significance is underscored by the discovery of neonatal patients suffering from often fatal heart failure caused by severe dilated cardiomyopathy when both copies of the gene <i>RPL3L</i> are mutated ^4-9 . RPL3L is a muscle-specific paralog ^1-3 of the ubiquitous ribosomal protein L3 (RPL3), which makes the closest contact of any protein to the ribosome's RNA-based catalytic center ¹⁰ . <i>RPL3L</i> -linked heart failure represents the only known human disease associated with tissue-specific ribosomes, yet the underlying pathogenetic mechanisms remain poorly understood. Intriguingly, disease is linked to a large number of mostly missense variants in <i>RPL3L</i> , and <i>RPL3L</i> -knockout resulted in no severe heart defect in either human or mice ^{3, 11-13} , challenging the prevailing view that autosomal recessive diseases are caused by loss-of-function mutations. Here, we report three new cases of <i>RPL3L</i> -linked severe neonatal heart failure and present a unifying pathogenetic mechanism by which a large number of variants in the muscle-specific ribosome led to disease. Specifically, affected families often carry one of two recurrent toxic gain-of-function variants alongside a family-specific putative loss-of-function variant. While the non-recurrent variants often trigger partial compensation of <i>RPL3</i> similar to <i>Rpl3l</i> -knockout mice, both recurrent variants exhibit increased affinity for the RPL3/RPL3L chaperone GRWD1 ^14-16 and 60S biogenesis factors, sequester 28S rRNA in the nucleus, disrupt ribosome biogenesis, and trigger severe cellular toxicity that extends beyond the loss of ribosomes. These findings provide critical insights for genetic screening and therapeutic development of neonatal heart failure. Our results suggest that gain-of-toxicity mechanisms may be more prevalent in autosomal recessive diseases, and a combination of gain-of-toxicity and loss-of-function mechanisms could underlie many diseases involving genes with paralogs.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11722222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973519","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}

{"title":"7-ketocholesterol contributes to microglia-driven increases in astrocyte reactive oxygen species in Alzheimer's disease.","authors":"Kayalvizhi Radhakrishnan, Yiyu Zhang, Oluwaseun Mustapha, Thaddeus K Weigel, Clint M Upchurch, Xiaodong Tian, Franklin Herbert, Wenyuan Huang, Norbert Leitinger, Ukpong Bassey Eyo, Huiwang Ai, Heather A Ferris","doi":"10.1101/2025.01.19.633810","DOIUrl":"10.1101/2025.01.19.633810","url":null,"abstract":"<p><p>Oxidative stress is a prominent feature of Alzheimer's disease. Within this context, cholesterol undergoes oxidation, producing the pro-inflammatory product 7-ketocholesterol (7-KC). In this study, we observe elevated levels of 7-KC in the brains of the 3xTg mouse model of AD. To further understand the contribution of 7-KC on the oxidative environment, we developed a method to express a genetically encoded fluorescent hydrogen peroxide (H2O2) sensor in astrocytes, the primary source of cholesterol in the brain. With this sensor, we discovered that 7-KC increases H2O2 levels in astrocytes in vivo, but not when directly applied to astrocytes in vitro. Interestingly, when 7-KC was applied to a microglia cell line alone or mixed astrocyte and microglia cultures, it resulted in microglia activation and increased oxidative stress in astrocytes. Depletion of microglia from 3xTg mice resulted in reduced 7-KC in the brains of these mice. Taken together, these findings suggest that 7-KC, acting through microglia, contributes to increased astrocyte oxidative stress in AD. This study sheds light on the complex interplay between cholesterol oxidation, microglia activation, and astrocyte oxidative stress in the pathogenesis of AD.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761689/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049459","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}