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Results for “Pathology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 991 records · Page 55Linked to original sources

bioRxiv2024

HCM-associated mutations in MYH6/7 drive pathologic expression of TGF-β1 in cardiomyocytes within weeks of developmental specification

Hypertrophic cardiomyopathy (HCM) is characterized by myocyte hypertrophy, sarcomere disarray, and myocardial fibrosis, leading to significant morbidity and mortality. As the most common inherited cardiomyopathy, HCM largely results from mutations in sarcomeric protein genes. Current treatments for HCM primarily focus on alleviating late-stage symptoms, with a critical gap in the detailed understanding of early-stage deficiencies that drive disease progression. We recently showed, in monolayers of cardiomyocytes derived from human induced pluripotent stem cells (hiPSCs) with MYH7 R723C and MYH6 R725C mutations, altered expression of several extracellular matrix (ECM)-related genes with associated defects in cardiomyocyte-ECM adhesion. To better evaluate the cardiomyocyte-ECM interface and pathological ECM dynamics in early-stage HCM, here we adopted a 3D engineered heart tissue (EHT) model containing both cardiomyocytes and fibroblasts, the primary contributor to ECM remodeling. Mutant EHTs showed aberrant cardiomyocyte distribution, augmented calcium handling, and force generation compared to controls. Altered proteoglycan deposition and increased phosphorylated focal adhesion kinase (pFAK) further indicated changes in ECM composition and connectivity. Elevated transforming growth factor beta-1 (TGF-{beta}1) secretion and a higher proportion of activated fibroblasts were identified in mutant EHTs, along with sustained TGF-{beta}1 transcription specifically in mutant cardiomyocytes. Remarkably, blocking TGF-{beta}1 receptor signaling reduced fibroblast activation and contraction force to control levels. This study underscores the early interplay of mutant hiPSC-CMs with fibroblasts, wherein mutant cardiomyocytes initiate fibroblast activation via TGF-{beta}1 overexpression, independent of the immune system. These findings provide a promising foundation for developing and implementing novel strategies to treat HCM well before the manifestation of clinically detectable fibrosis and cardiac dysfunction.

bioengineering↗

bioRxiv2024

Genetic analysis of retinal cell types reveals synaptic pathology in schizophrenia

ImportanceAs an accessible part of the central nervous system, the retina provides a unique window to study pathophysiological mechanisms of brain disorders in humans. Imaging and electrophysiological studies have revealed retinal alterations across several neuropsychiatric and neurological disorders. However, it remains largely unclear whether primary disease mechanisms within the retina contribute to the observed retinal alterations and which specific retinal cell types and biological mechanisms are involved. ObjectiveTo determine whether specific retinal cell types are affected by genomic risk for neuropsychiatric and neurological disorders and to explore the mechanisms through which genomic risk converges in these cell types. Design, Setting, and ParticipantsIn this study, we combined findings from genome-wide association studies in schizophrenia, bipolar disorder, major depressive disorder, multiple sclerosis, Parkinson disease, Alzheimer disease, and stroke with retinal single-cell transcriptomic data sets from humans, macaques, and mice. To identify susceptible cell types, we applied MAGMA cell type enrichment analyses and performed subsequent pathway analyses. Furthermore, we translated the cellular top hit to the structural level by using retinal optical coherence tomography and genotyping data in the large population-based UK Biobank cohort (n = 36,349). Main Outcomes and MeasuresCell type-specific enrichment of genetic risk loading for neuropsychiatric and neurological disorder traits in the gene expression profiles of retinal cells. ResultsAmacrine cells (interneurons within the retina) were robustly enriched in schizophrenia genetic risk across mammalian species and in different developmental stages. This enrichment was primarily driven by genes involved in synapse biology. On the structural level, higher polygenic risk for schizophrenia was associated with thinning of the ganglion cell-inner plexiform layer, which contains dendrites and synaptic connections of amacrine cells. Moreover, retinal immune cell populations were enriched in multiple sclerosis genetic risk. No consistent cell type associations were found for bipolar disorder, major depressive disorder, Parkinson and Alzheimer disease, or stroke. Conclusions and RelevanceThis study provides novel insights into the cellular underpinnings of retinal alterations in neuropsychiatric and neurological disorders and highlights the retina as a potential proxy to study synaptic pathology in schizophrenia.

neuroscience↗

bioRxiv2024

Myo-inositol and total NAA in the hippocampus are linked to CSF tau pathology in cognitively normal older adults

INTRODUCTIONUnderstanding relationships between in vivo neurometabolic changes and Alzheimers disease (AD) pathology in the hippocampus, a region vulnerable to early changes in AD, will support early diagnosis. METHODSTwo studies using 1H-MRS examined concentrations of myo-inositol (MI), total creatine (tCr) and total NAA (tNAA) in the hippocampus. The first study compared hippocampal metabolite concentrations in healthy young and older adults and the second study assessed relationships between hippocampal metabolites and cerebrospinal fluid (CSF) measurements of A{beta}42, phosphotau 181 (pTau181), and total tau (t-Tau) while adjusting for demographic covariates and spectral characteristics (linewidth, signal- to-noise ratio) in a separate group of older adults ranging from cognitively normal (CN) to AD-dementia. RESULTSHippocampal MI, but not tCr or tNAA, was increased in cognitively normal older versus young adults. Within the second older adult group, MI and tNAA, but not tCr, were linked to increases in CSF pTau181 and t-Tau, but not A{beta}42. DISCUSSIONTau deposition in cognitively normal individuals is associated with biochemical changes related to glial reactivity and neural integrity in the hippocampus.

neuroscience↗

bioRxiv2024

A Human Brain-Chip for modelling brain pathologies and screening of BBB crossing therapeutic strategies

The limited translatability of preclinical experimental findings to human patients remains an obstacle for successful treatment of brain diseases. Relevant models to elucidate mechanisms behind brain pathogenesis, such as human cell-based systems, and support successful targeting and prediction of drug responses in humans are in urgent need given the species differences in brain and blood-brain barrier (BBB) functions. Here, we examined and advanced a Brain-Chip which recapitulates aspects of the human cortical parenchyma and the BBB in one model. We utilized human primary astrocytes and pericytes, hiPSC-derived cortical neurons, hiPSC-derived brain microvascular endothelial-like cells, and included for the first time on chip hiPSC-derived microglia. Using TNF to emulate neuroinflammation, we demonstrate that our model recapitulates in vivo-relevant responses. Importantly, we show microglia-derived responses, highlighting the ability of the model to capture cell-specific contributions in human disease associated pathology. We next tested BBB crossing of human transferrin receptor antibodies and conjugated adeno-associated viruses, and demonstrate successful in vitro/in vivo correlation in identifying crossing differences. These findings highlight the potential of the Brain-Chip as a time-saving and reliable model to support therapeutic development for brain diseases.

bioengineering↗

bioRxiv2024

Temporally resolved single-cell RNA sequencing reveals protective and pathological responses during herpes simplex virus 1 CNS infection

Herpes Simplex Virus 1 (HSV-1) is a common human neurotropic virus with the majority of adults harboring latent-recurrent infections. In rare cases, HSV-1 infection can access the central nervous system through the neuronal route and develop into life-threatening encephalitis. Here, we used a mouse model for HSV-1 infection to describe the transcriptomic profile of the infected brain stem at the single-cell level and with temporal resolution. Among resident brain cells, microglia increased in proportion during the course of infection, while astrocytes, pericytes, and endothelial cell levels decrease. At the levels of peripheral immune cells, we found notably monocytes to strongly influx the infected brain. Large dynamic changes were found in the abundance of subpopulations of the different cell types following virus infection. For instance, we identify one subpopulation of microglia exhibiting very high type I interferon and chemokine expression early during infection. This population was also enriched for viral transcripts, suggesting localization at foci of infection, and orchestrating recruitment of other immune cells. In contrast, for the infiltrating monocytes, we identified a larger panel of unique subpopulations with antiviral and inflammatory phenotypes, and found not all of these being highly positive for viral transcripts, thus indicating monocyte activities beyond the infected brain areas. Finally, investigation of endothelial cell cross-talk with other cell types revealed that cytokines derived from microglia and monocyte, but also T cells, contribute to disturbance of the blood brain barrier. Our work thus reveals for the first time the complex nature of the cellular response in the virus-infected brain, which seeks to eliminate infection but can also prime for pathological changes.

immunology↗

bioRxiv2024

Towards Digital Quantification of Ploidy from Pan-Cancer Digital Pathology Slides using Deep Learning

Abnormal DNA ploidy, found in numerous cancers, is increasingly being recognized as a contributor in driving chromosomal instability, genome evolution, and the heterogeneity that fuels cancer cell progression. Furthermore, it has been linked with poor prognosis of cancer patients. While next-generation sequencing can be used to approximate tumor ploidy, it has a high error rate for near-euploid states, a high cost and is time consuming, motivating alternative rapid quantification methods. We introduce PloiViT, a transformer-based model for tumor ploidy quantification that outperforms traditional machine learning models, enabling rapid and cost-effective quantification directly from pathology slides. We trained PloiViT on a dataset of fifteen cancer types from The Cancer Genome Atlas and validated its performance in multiple independent cohorts. Additionally, we explored the impact of self-supervised feature extraction on performance. PloiViT, using self-supervised features, achieved the lowest prediction error in multiple independent cohorts, exhibiting better generalization capabilities. Our findings demonstrate that PloiViT predicts higher ploidy values in aggressive cancer groups and patients with specific mutations, validating PloiViT potential as complementary for ploidy assessment to next-generation sequencing data. To further promote its use, we release our models as a user-friendly inference application and a Python package for easy adoption and use.

bioinformatics↗

bioRxiv2024

Mitochondrial complex III-derived ROS amplify immunometabolic changes in astrocytes and promote dementia pathology

Neurodegenerative disorders alter mitochondrial functions, including the production of reactive oxygen species (ROS). Mitochondrial complex III (CIII) generates ROS implicated in redox signaling, but its triggers, targets, and disease relevance are not clear. Using site-selective suppressors and genetic manipulations together with mitochondrial ROS imaging and multiomic profiling, we found that CIII is the dominant source of ROS production in astrocytes exposed to neuropathology-related stimuli. Astrocytic CIII-ROS production was dependent on nuclear factor-{kappa}B (NF-{kappa}B) and the mitochondrial sodium-calcium exchanger (NCLX) and caused oxidation of select cysteines within immune and metabolism-associated proteins linked to neurological disease. CIII-ROS amplified metabolomic and pathology-associated transcriptional changes in astrocytes, with STAT3 activity as a major mediator, and facilitated neuronal toxicity in a non-cell- autonomous manner. As proof-of-concept, suppression of CIII-ROS in mice decreased dementia-linked tauopathy and neuroimmune cascades and extended lifespan. Our findings establish CIII-ROS as an important immunometabolic signal transducer and tractable therapeutic target in neurodegenerative disease.

neuroscience↗

bioRxiv2024

Divergent macrophage induced lung pathology occurs between infants and adults during respiratory viral infection

Young children, especially those aged 4 months to 2 years of age, frequently exhibit severe morbidity during respiratory viral infections. For influenza infections, macrophages/monocytes serve as front line defenses against early viral replication in the lungs until the adaptive immune system arrives to clear virus. However, infiltrating inflammatory monocytes are a significant cause of influenza induced lung pathology/morbidity. We utilized a young murine model of respiratory viral infections using 21-day-old mice to investigate the mechanisms driving the heightened influenza induced morbidity observed in human young children. We hypothesized that macrophages/monocytes responses to influenza would diverge between young and older mice despite our evidence that macrophages from both groups appear to control viral replication at similar rates. While inflammatory monocyte infiltration contributed to influenza induced morbidity/lung inflammation in adults, they did not appear to contribute to morbidity in young mice. Instead, young mice appeared to develop lung inflammation through a lack of interferon gamma (IFN{psi}) and infection of macrophage populations. In contrast, adult mice controlled early viral replication through macrophage populations (alveolar, interstitial, and inflammatory) and inflammatory monocytes. While intrinsic limitations in anti-viral cytokine responses, especially IFN{psi}, characterized the macrophage response to viral infection in young mice, the innate immune response to infection appears diminished compared to adults. This study highlights the intrinsic limitations in macrophage effector functions that may arise in young children but that also contribute to disease pathology.

immunology↗

bioRxiv2024

Modulating NLRP3 splicing with antisense oligonucleotides to control pathological inflammation

Inflammation has an essential role in healing. However, over-active inflammation disrupts normal cellular functions and can be life-threatening when not resolved. The NLR family pyrin domain-containing 3 (NLRP3) inflammasome, a component of the innate immune system, is an intracellular multiprotein complex that senses stress-associated signals, and, for this reason is a promising therapeutic target for treating unresolved, pathogenic inflammation. Alternative splicing of NLRP3 RNA has been suggested as a regulatory mechanism for inflammasome activation, as some spliced isoforms encode NLRP3 proteins with compromised function. Here, we take advantage of this natural regulatory mechanism and devise a way to control pathogenic inflammation using splice-switching antisense oligonucleotides (ASOs). To identify and induce NLRP3 isoforms lacking inflammatory activity, we tested a series of ASOs, each targeting a different exon, to determine the most effective strategy for down-regulating NLRP3. We identify several ASOs that modulate NLRP3 splicing, reduce NLRP3 protein, and decrease inflammasome signaling in vitro. The most effective ASO suppresses systemic inflammation in vivo in mouse models of acute inflammation and cryopyrin-associated periodic syndrome (CAPS). Overall, these results demonstrate how ASOs can be used to systematically engineer proteins with modified functions and treat pathological inflammation in mice by reducing functional NLRP3.

molecular biology↗

bioRxiv2024

Robust CRISPR/dCas13 RNA blockers specifically perturb miRNA-target interactions and rescue type 1 myotonic dystrophy pathology

While RNA-targeting strategies are powerful tools for disease therapy, challenges, including low target engagement and off-target collateral effects, currently limit their efficacy. Here, we report the engineering and optimisation of a CRISPR/dCas13 RNA steric blocker (CRISPR-Lock) that prevents mRNA translation, shields mRNAs from miRNA-mediated silencing, and blocks RNA-protein interactions. By tuning the spatial resolution and mismatch tolerance of CRISPR-Lock, we develop a high-resolution perturbation approach that employs genetically encoded CRISPR-Lock as a miRNA target protector. This system enables precise spatiotemporal control of miRNA:mRNA interactions, offering broader applicability compared to phosphorodiamidate mor-pholino (PMO) target protectors. Moreover, we demonstrate the potential therapeutic application of CRISPR-Lock for blocking pathological RNA-protein interactions in type 1 myotonic dystro-phy (DM1). Optimising CRISPR-Lock to target expanded repeat RNAs corrects approximately 85% of clinically relevant splicing biomarkers in patient-derived myotubes and significantly out-performs third-generation PMO antisense oligonucleotides. Finally, by delivering a miniaturised AAV-encoded CRISPR-Lock system into an established DM1 mouse model, we demonstrate the dose-dependent correction of intranuclear foci and splicing dysregulation, underscoring the potential therapeutic application of this technology.

bioengineering↗

bioRxiv2024

Sca-1 expression depicts pro-inflammatory murine neutrophils under steady state and pathological conditions

Neutrophils play a crucial role in various pathophysiological conditions, yet targeting them for therapeutic intervention has been discouraged due to the associated risk of infections. Thus, identification of neutrophil subsets and their involvement in inflammatory conditions is warranted for targeted therapeutic strategies. This study, through screening of surface proteins on neutrophils isolated from different tissue microenvironments, identified a distinct neutrophil subset, CD11b+Ly6G+Sca1+ neutrophils, expressing Stem cell antigen-1 (Sca-1). Interestingly, these Sca1pos neutrophils were more abundant in the liver than BM, blood, and lungs. Further analysis revealed that Sca1pos neutrophils are mature and activated with enhanced effector functions, including superoxide generation, phagocytosis, degranulation, and NETosis. Tracing studies demonstrated ageing-independent characteristics of Sca1pos neutrophils. Remarkably, Sca1pos pro-inflammatory neutrophils promote T cell proliferation through ROS, while inhibition of Sca-1 restores T cell proliferation and ROS generation. Intriguingly, inflammatory as well as metabolic cues induce the transition of conventional neutrophils (Sca1neg) to Sca1pos neutrophils and differentiation of progenitors (granulocyte monocyte progenitors, GMPs) into Sca1pos neutrophils. Furthermore, in vivo models of acute inflammation, peritonitis, and chronic inflammatory condition, non-alcoholic steatohepatitis (NASH), exhibit an increase of Sca1pos neutrophils at inflammatory sites, while the pharmacological approach using NAC specifically mitigates the expansion of these pro-inflammatory neutrophils. Collectively, our findings unveil a novel subset of Sca1pos neutrophils with implications for inflammation. Significance StatementNeutrophilic inflammation remains the leading driver in infectious and inflammatory diseases. Targeting neutrophil populations remained un-recommended due to hampering the immunological functions of neutrophils. The heterogeneity of neutrophils provides the perspective to target altered neutrophil subsets, but subtle changes defining neutrophil subsets make it complex and ambiguous. Our study identified abundant expression of Sca1on distinct neutrophils under steady state and inflammation. Thus, we reported previously undefined Sca1pos pro-inflammatory neutrophil subsets and elucidated their regulation. This study further established their involvement in acute and chronic inflammatory conditions. This understanding may further pave the way toward targeting specific neutrophil subsets in pathologies characterized by neutrophilic inflammation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/613221v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@62f3eaorg.highwire.dtl.DTLVardef@7baed3org.highwire.dtl.DTLVardef@12da63org.highwire.dtl.DTLVardef@1bfcce9_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICD11b+Ly6G+Sca1+ neutrophil subset identified with <1% presence in BM and >40% frequency in the liver. C_LIO_LIThese neutrophils are mature and activated, demonstrating enhanced effector functions. C_LIO_LISca1pos neutrophils promote T cell proliferation and display pro-inflammatory characteristics. C_LIO_LIConventional Sca1neg neutrophils transition into Sca1pos neutrophils in response to inflammatory signals, while progenitors undergo differentiation. C_LIO_LIBoth acute and chronic inflammatory models show the expansion of CD11b+Ly6G+Sca1+ neutrophils. C_LI

immunology↗

bioRxiv2024

Synthetic chaperone based on Hsp90-Tau interaction inhibits pathological Tau aggregation and rescues physiological Tau-Microtubule interaction

The accumulation of intracellular aggregates of Tau protein is one main hallmark of Alzheimers disease (AD) and is the consequence of Tau conformational changes, increased phosphorylation, and self-association to form fibrillar aggregates. This pathological process prevents the physiological interaction of Tau with microtubules to the detriment of the structural integrity of neurons. In healthy cells, aberrant protein misfolding and aggregation are counteracted by chaperone proteins whose protective capacity decreases with age. The role of the chaperone Hsp90 and the mechanism by which it can prevent Tau aggregation toxicity are controversial. The innovative strategy of mimicking Hsp90 through the design of the {beta}-hairpin like peptidomimetic {beta}-Hsp90, inspired by two Hsp90/Tau interaction sequences, is presented here. {beta}-Hsp90 inhibits Tau aggregation both in vitro and in cells, restoring Taus physiological interaction with microtubules. {beta}-Hsp90, which interacts with the P1 region of Tau, is more effective than individual peptide sequences from the chaperone HSP90 and another {beta}-hairpin mimic based on Tau sequences. Moreover, {beta}-Hsp90 dramatically reduces AD-associated A{beta}1-42 aggregation, offering the development of a dual inhibitor. This work paves the way for the design of new drugs targeting devastating untreated amyloid diseases, by mimicking physiological chaperones with small synthetic peptide drugs.

pharmacology and toxicology↗

bioRxiv2024

The Unique Role of Intracellular Perinuclear β-Adrenergic Receptors in defining Signaling Compartmentation and Pathological Cardiac Remodeling

The {beta}-adrenergic receptor is a prototypical G-protein coupled receptor that initiates signaling from the plasma membrane. However, active receptors have been detected within intracellular compartments. The functional significance of these intracellular receptors remains unclear, including whether they regulate distinct cellular processes or function independently of plasma membrane receptors. We show using live cell imaging of primary cardiomyocytes that {beta}-adrenergic receptors localized to Golgi apparatus opposing the outer nuclear membrane are sufficient and necessary for the stimulation of cAMP and calcium signaling within a nanometer scale compartment independent of receptors at other sites. Using compartment-specific activators and inhibitors, we show Golgi {beta}-adrenergic receptors associated with the scaffold protein AKAP6{beta} and the outer nuclear membrane protein nesprin-1 are responsible for pathological gene transcription and the induction of cardiomyocyte hypertrophy. The functional significance of Golgi-localized receptors is demonstrated in mice models of cardiomyopathy, providing proof-of-concept for a compartment-specific therapeutic intervention in Dilated Cardiomyopathy.

cell biology↗

bioRxiv2024

Targeting the acetyltransferase NAT10 corrects pathologies in human frontotemporal neurons and extends lifespan in an in vivo Drosophila tauopathy model

Disruption of the neuronal nuclear membrane and perturbation of nucleocytoplasmic transport are features of neurodegenerative diseases, including Alzheimers disease, that involve the microtubule-associated protein tau (MAPT). We previously identified that missense and splicing mutations in the MAPT gene, causal for frontotemporal dementia, result in nuclear envelope deformation and disrupted nucleocytoplasmic transport in human neurons. This is most likely due to microtubule mechanical stress, similar to that observed in Hutchinson-Gilford Progeria Syndrome (HGPS). A small molecule inhibitor of the acetyltransferase NAT10 has been shown to correct nuclear membrane defects in HGPS by modulating microtubule dynamics. We report here that NAT10 inhibition alters microtubule dynamics and corrects nuclear lamina defects and aberrant nucleocytoplasmic transport in human iPSC-derived FTD-MAPT neurons. Similarly, NAT10 inhibition and haploinsufficiency correct neuronal nuclear shape defects and extend lifespan in vivo in a Drosophila model of tauopathy. Our results show that NAT10 mediates neuronal pathologies in tauopathies and is a promising new therapeutic target in these diseases.

neuroscience↗

bioRxiv2024

Adiponectin-receptor agonism prevents right ventricular tissue pathology in a mouse model of Duchenne muscular dystrophy

Cardiac fibrosis during Duchenne muscular dystrophy (DMD) arises from cellular damage and inflammation and is associated with myofibre hypertrophy and metabolic dysfunction. However, the extent to which these relationships develop across all 4 cardiac chambers, particularly during early-stage disease, remains unknown. Here, we discovered that very young D2.mdx mice exhibit fibrosis exclusively in the right ventricle (RV) and left atrium. Concurrent cardiomyocyte hypertrophy and disorganization in the RV were related to a highly specific inflammatory signature of increased infiltrating pro-inflammatory macrophages (CD11b+CD45+CD64+F4/80+CCR2+), myofibre mitochondrial-linked apoptosis, and reduced carbohydrate and fat oxidation. This relationship did not occur in the left ventricle. Short-term daily administration of a peptidomimetic adiponectin receptor agonist, ALY688, completely prevented RV fibrosis, myofibre hypertrophy, infiltrating macrophages and mitochondrial stress as well as left atrial fibrosis. Our discoveries demonstrate early-stage cardiac tissue pathology occurs in a chamber-specific manner and is prevented by adiponectin receptor agonism, thereby opening a new direction for developing therapies that prevent tissue remodeling during DMD. TeaserHeterogeneous distribution of fibrosis, inflammation and metabolic dysfunction across the heart is prevented by adiponectin receptor agonism in a mouse model of Duchenne muscular dystrophy.

physiology↗

bioRxiv2024

Mapping DNA Methylation to Cardiac Pathologies Induced by Beta-Adrenergic Stimulation in a Large Panel of Mice

BackgroundHeart failure (HF) is a leading cause of morbidity and mortality worldwide, with over 18 million deaths annually. Despite extensive research, genetic and environmental factors contributing to HF remain complex and poorly understood. Recent studies suggest that epigenetic modifications, such as DNA methylation, may play a crucial role in regulating HF-associated phenotypes. In this study, we leverage the Hybrid Mouse Diversity Panel (HMDP), a cohort of over 100 inbred mouse strains, to investigate the role of DNA methylation in HF progression. ObjectiveWe aim to identify epigenetic modifications associated with HF by integrating DNA methylation data with gene expression and phenotypic traits. Using isoproterenol (ISO)-induced cardiac hypertrophy and failure in HMDP mice, we explore the relationship between methylation patterns and HF susceptibility. MethodsWe performed reduced representational bisulfite sequencing (RRBS) to capture DNA methylation at single-nucleotide resolution in the left ventricles of 90 HMDP mouse strains under both control and ISO-treated conditions. We identified differentially methylated regions (DMRs) and performed an epigenome-wide association study (EWAS) using the MACAU algorithm. We identified likely candidate genes within each locus through integration of our results with previously reported sequence variation, gene expression, and HF-related phenotypes. In vitro approaches were employed to validate key findings, including gene knockdown experiments in neonatal rat ventricular myocytes (NRVMs). We also examined the effects of preventing DNA methyltransferase activity on HF progression. ResultsOur EWAS identified 56 CpG loci significantly associated with HF phenotypes, including 18 loci where baseline DNA methylation predicted post-ISO HF progression. Key candidate genes, such as Prkag2, Anks1, and Mospd3, were identified based on their epigenetic regulation and association with HF traits. In vitro follow-up on a number of genes confirmed that knockdown of Anks1 and Mospd3 in NRVMs resulted in significant alterations in cell size and blunting of ISO-induced hypertrophy, demonstrating their functional relevance in HF pathology. Furthermore, treatment with the DNA methyltransferase inhibitor RG108 in ISO-treated BTBRT mice significantly reduced cardiac hypertrophy and preserved ejection fraction compared to mice only treated with ISO, highlighting the therapeutic potential of targeting DNA methylation in HF. Differential expression analysis revealed that RG108 treatment restored the expression of several methylation-sensitive genes, further supporting the role of epigenetic regulation in HF. ConclusionOur study demonstrates a clear interplay between DNA methylation, gene expression, and HF-associated phenotypes. We identified several novel epigenetic loci and candidate genes that contribute to HF progression, offering new insights into the molecular mechanisms of HF. These findings underscore the importance of epigenetic regulation in cardiac disease and suggest potential therapeutic strategies for modifying HF outcomes through targeting DNA methylation.

genomics↗

bioRxiv2024

Artificial intelligence networks combining histopathology and machine learning can extract axon pathology in autism spectrum disorder

Axon features that underlie the structural and functional organization of cortical pathways have distinct patterns in the brains of neurotypical controls (CTR) compared to individuals with Autism Spectrum Disorder (ASD). However, detailed axon study demands labor-intensive surveys and time-consuming analysis of microscopic sections from post-mortem human brain tissue, making it challenging to systematically examine large regions of the brain. To address these challenges, we developed an approach that uses machine learning to automatically classify microscopic sections from ASD and CTR brains, while also considering different white matter regions: superficial white matter (SWM), which contains a majority of axons that connect nearby cortical areas, and deep white matter (DWM), which is comprised exclusively by axons that participate in long-range pathways. The result was a deep neural network that can successfully classify the white matter below the anterior cingulate cortex (ACC) of ASD and CTR groups with 98% accuracy, while also distinguishing between DWM and SWM pathway composition with high average accuracy, up to 80%. Multidimensional scaling analysis and sensitivity maps further underscored the reliability of ASD vs CTR classification, based on the consistency of axon pathology, while highlighting the important role of white matter location that constrains pathway dysfunction, based on several shared anatomical markers. Large datasets that can be used to expand training, validation, and testing of this network have the potential to automate high-resolution microscopic analysis of post-mortem brain tissue, so that it can be used to systematically study white matter across brain regions in health and disease. One Sentence StatementHistopathology-trained AI can identify ASD network disruptions and guide development of diagnostics and targeted therapeutics.

neuroscience↗

bioRxiv2024

Alzheimer's Disease Patient Brain Extracts Induce Multiple Pathologies in Vascularized Neuroimmune Organoids for Disease Modeling and Drug Discovery

Alzheimers Disease (AD) is the most common cause of dementia afflicting 55 million individuals worldwide, with limited treatment available. Current AD models mainly focus on familial AD (fAD), which is due to genetic mutations. However, models for studying sporadic AD (sAD), which represents over 95% of AD cases without specific genetic mutations, are severely limited. Moreover, the fundamental species differences between humans and animals might significantly contribute to clinical failures for AD therapeutics that have shown success in animal models, highlighting the urgency to develop more translational human models for studying AD, particularly sAD. In this study, we developed a complex human pluripotent stem cell (hPSC)-based vascularized neuroimmune organoid model, which contains multiple cell types affected in human AD brains, including human neurons, microglia, astrocytes, and blood vessels. Importantly, we demonstrated that brain extracts from individuals with sAD can effectively induce multiple AD pathologies in organoids four weeks post-exposure, including amyloid beta (A{beta}) plaques-like aggregates, tau tangles-like aggregates, neuroinflammation, elevated microglial synaptic pruning, synapse/neuronal loss, and impaired neural network. Furthermore, after treatment with Lecanemab, an FDA-approved drug targeting A{beta}, AD brain extract exposed organoids showed a significant reduction of amyloid burden. Thus, the neuroimmune organoid model provides a unique opportunity to study AD, particularly sAD under a pathophysiological relevant three-dimensional (3D) human cell environment. It also holds great promise to facilitate AD drug development, particularly for immunotherapies.

neuroscience↗