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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 595 records · Page 33Linked to original sources

bioRxiv2022

Closed-loop brain stimulation to reduce pathologic fear

Maladaptive processing of trauma related memory engrams leads to dysregulated fear reactions. In post-traumatic stress disorder (PTSD), dysfunctional extinction learning prevents discretization of trauma-related memory engrams and leads to generalized fear responses. PTSD is postulated as a mnemonic-based disorder, but we lack markers or treatments targeting pathological fear memory processing. Hippocampal sharp wave-ripples (SWRs) and concurrent neocortical oscillations are scaffolds to consolidate contextual memory, but their role during fear processing remains poorly understood. We demonstrate that closed-loop SWRs triggered neuromodulation of the medial forebrain bundle (MFB) can enhance the consolidation of fear extinction. It modified fear memories that became resistant to induced recall (i.e., renewal and reinstatement) and did not reemerge spontaneously as a PTSD-like phenotype. The effects are mediated by D2 receptor signaling induced synaptic remodeling in the basolateral amygdala. These results suggest that SWRs help consolidating fear extinction memories. Furthermore, enhancing the consolidation of extinction engrams by SWR-triggered induction of reward signals can alleviate pathologic fear reactions in a rodent model of PSTD. No adverse effects were seen, suggesting this potential therapy for PTSD and anxiety disorders.

neuroscience↗

bioRxiv2022

Synthesizing Images of Tau Pathology from Cross-modal Neuroimaging using Deep Learning

Given the prevalence of dementia and the development of pathology-specific disease modifying therapies, high-value biomarker strategies to inform medical decision making are critical. In-vivo tau positron emission tomography (PET) is an ideal target as a biomarker for Alzheimers disease diagnosis and treatment outcome measure. However, tau PET is not currently widely accessible to patients compared to other neuroimaging methods. In this study, we present a convolutional neural network (CNN) model that impute tau PET images from more widely-available cross-modality imaging inputs. Participants (n=1,192) with brain MRI, fluorodeoxyglucose (FDG) PET, amyloid PET, and tau PET were included. We found that a CNN model can impute tau PET images with high accuracy, the highest being for the FDG-based model followed by amyloid PET and MRI. In testing implications of AI-imputed tau PET, only the FDG-based model showed a significant improvement of performance in classifying tau positivity and diagnostic groups compared to the original input data, suggesting that application of the model could enhance the utility of the metabolic images. The interpretability experiment revealed that the FDG- and MRI-based models utilized the non-local input from physically remote ROIs to estimate the tau PET, but this was not the case for the PiB-based model. This implies that the model can learn the distinct biological relationship between FDG PET, MRI, and tau PET from the relationship between amyloid PET and tau PET. Our study suggests that extending neuroimagings use with artificial intelligence to predict protein specific pathologies has great potential to inform emerging care models.

bioengineering↗

bioRxiv2022

APOE ε4 gene dose effect on imaging and blood biomarkers of glial reactivity and β-amyloid pathology

Increased reactivity of microglia and astrocytes is known to be present at various stages of the Alzheimers continuum but their relationship with core Alzheimers disease pathology in the preclinical stages is less clear. We investigated glial reactivity and {beta}-amyloid pathology in cognitively unimpaired APOE {varepsilon}4 homozygotes, heterozygotes and non-carriers using 11C-PK11195 PET (targeting 18-kDa translocator protein), 11C-PiB PET (targeting {beta}-amyloid), brain MRI, and a preclinical cognitive composite (APCC). Plasma glial fibrillary acidic protein (GFAP) by and plasma A{beta}1-42/1-40 were measured using single molecule array and immunoprecipitation combined with mass spectrometry, respectively. We observed that (i) 11C-PiB-binding was significantly higher in APOE {varepsilon}4 homozygotes compared with non-carriers in all evaluated regions, (ii) regional 11C-PK11195-binding did not differ between the APOE {varepsilon}4 gene doses or between A{beta}-positive and -negative individuals, and (iii) higher 11C-PK11195-binding and plasma GFAP were associated with lower hippocampal volume, and elevated 11C-PiB-binding and plasma GFAP concentration with lower APCC scores. Increased glial reactivity might emerge in later stages of preclinical Alzheimers disease in parallel with early neurodegenerative changes.

neuroscience↗

bioRxiv2022

Biochemical and metabolic maladaption defines pathological niches in progressive multiple sclerosis

Progressive multiple sclerosis (MS) is driven by demyelination, neuroaxonal loss, and mitochondrial damage occurring behind a closed blood-brain barrier (BBB).1,2 Patients with progressive MS typically fail to respond to available immunomodulatory drugs that reduce relapses in early disease.2 This indicates a dire need to identify non-canonical therapeutic avenues to limit neurodegeneration and promote protection and repair.3 Here, we have employed high-resolution multiomic profiling to characterise the biochemical and metabolic adaptations underpinning MS pathology, as these have been incompletely described but critically, may be amenable to BBB-permeable drug targeting. Using synchrotron radiation (SR)- and focal plane array (FPA)-based Fourier transform infrared microspectroscopy (FTIR), we spatially mapped the biochemical features present in human progressive MS and control post-mortem brain and rare spinal cord tissue. By employing single-nuclear RNA sequencing (snRNA-seq), 10x Genomics Visium spatial transcriptomics and spatial proteomics to resolve their cellular context, we found that these biochemical features provide a uniquely and highly disease-specific barcode for distinct pathological niches within the tissue. Characterisation of the metabolic processes underpinning these niches revealed an associated re-organisation of the astrocytic landscape in the grey and white matter, with implications for the treatment of progressive MS.

neuroscience↗

bioRxiv2022

On a mechanistic impact of transmembrane tetramerization in pathological activation of RTKs

Constitutive activation of receptor tyrosine kinases (RTKs) via different mutation has a strong impact into development of severe human disorders, including cancer. While pathological effect of such mutations can be common on the phenotypical level, mechanistic understanding of their contribution into the receptor activation depends on the exact molecular context. Mutations in transmembrane (TM) domains represent an interesting class of pathological modifications since they can directly affect a signal transduction pathway from the receptor to the kinase domains of RTKs. Here we propose a putative activation scenario of RTK, whereby TM mutations can also promote higher order oligomerization of the receptors that leads to the subsequent ligand-free activation. To illustrate this model with all-atom resolution for a previously characterized oncogenic TM mutation V536E in platelet-derived growth factor receptor alpha (PDGFRA), we use a computational modeling framework including sequence-based structure prediction and all-atom 1 {micro}s molecular dynamics (MD) simulations in a model membrane for the predicted configuration of the PDGFRA TM tetramers. We show that in the course of MD simulations the mutant tetramer retains stable and compact configuration, which is strengthened by tight protein-protein interactions. In contrast, the wild type tetramer demonstrates looser packing and tendency to dissociate. Such a structural organization shapes the dynamics of TM helices in the oligomeric state. Specifically, the mutation affects the characteristic motions of mutated TM helical segments by introducing additional non-covalent crosslinks in the middle of the TM tetramer, which work as mechanical hinges. This leads to dynamic decoupling of the C-termini from the rigidified N-terminal parts and facilitates higher possible displacement between the C-termini of the mutant TM helical regions. This, in turn, can provide more freedom to downstream kinase domains in their mutual rearrangement. The observed structural and dynamic effects of the V536E mutations in the context of PDGFRA TM tetramer provide an interesting possibility that an effect of oncogenic TM mutations can go beyond alternating structure and dynamics of TM dimeric states and also promote formation of higher-order oligomers that may directly contribute into the ligand independent signaling of PDGFRA and other RTKs.

biophysics↗

bioRxiv2022

Brain DNA methylomic analysis of frontotemporal lobar degeneration reveals OTUD4 and CEBPZ in shared dysregulated signatures across pathological subtypes

Frontotemporal lobar degeneration (FTLD) is an umbrella term describing the neuropathology of a clinically, genetically and pathologically heterogeneous group of diseases, including frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP). Among the major FTLD pathological subgroups, FTLD with TDP-43 positive inclusions (FTLD-TDP) and FTLD with tau positive inclusions (FTLD-tau) are the most common, representing about 90% of the cases. Although alterations in DNA methylation have been consistently associated with neurodegenerative diseases, including Alzheimers disease and Parkinsons disease, little is known for FTLD and its heterogeneous subgroups and subtypes. The main goal of this study was to investigate DNA methylation variation in FTLD-TDP and FTLD-tau. We used frontal cortex genome-wide DNA methylation profiles from three FTLD cohorts (234 individuals), generated using the Illumina 450K or EPIC microarray. We performed epigenome-wide association studies (EWAS) for each cohort followed by meta-analysis to identify shared differential methylated loci across FTLD subgroups/subtypes. Additionally, we used weighted gene correlation network analysis to identify co-methylation signatures associated with FTLD and other disease-related traits. Wherever possible, we also incorporated relevant gene/protein expression data. After accounting for a conservative Bonferroni multiple testing correction, the EWAS meta-analysis revealed two differentially methylated loci in FTLD, one annotated to OTUD4 (5UTR-shore) and the other to NFATC1 (gene body-island). Of these loci, OTUD4 showed consistent upregulation of mRNA and protein expression in FTLD. Additionally, in the three independent co-methylation networks, OTUD4-containing modules were enriched for EWAS meta-analysis top loci and were strongly associated with the FTLD status. These co-methylation modules were enriched for genes implicated in the ubiquitin system, RNA/stress granule formation and glutamatergic synaptic signalling. Altogether, our findings identified novel FTLD-associated loci, and support a role for DNA methylation as a mechanism involved in the dysregulation of biological processes relevant to FTLD, highlighting novel potential avenues for therapeutic development.

neuroscience↗

bioRxiv2022

A non-human primate model with Alzheimer's disease-like pathology induced by hippocampal overexpression of human tau

Alzheimers disease (AD) is one of the most burdening diseases of the century with no disease-modifying treatment yet. Non-human primates (NHPs) share genetic, anatomical and physiological similarities with humans, making them an ideal model for investigating the pathogenesis and therapeutics of AD. However, the applications of NHPs in AD research have been hindered by the paucity of spontaneous or induced monkey models for AD due to their long generation time, ethical considerations and technical challenges in making genetically modified monkeys. Here we developed an AD-like NHP model by overexpressing human tau in bilateral hippocampi of adult rhesus macaque monkeys. We evaluated the pathological features of these monkeys with immunostaining, cerebrospinal fluid (CSF) analysis, magnetic resonance imaging (MRI), positron emission tomography (PET) scan, and behavioral tests. We demonstrated that after hippocampal overexpression of human tau, the rhesus macaque monkeys displayed multiple pathological features of AD, including neurofibrillary tangle formation, neuronal loss, hippocampal atrophy, neuroinflammation, A{beta} clearance deficit, blood vessel damage and cognitive decline. This work establishes a human tau-induced AD-like NHP model that may facilitate mechanistic studies and therapeutic treatments for AD.

neuroscience↗

bioRxiv2022

Interferon-gamma Elicits Pathological Hallmarks of ALS in Human Motor Neurons

Neuroinflammation is an established factor contributing to amyotrophic lateral sclerosis (ALS) pathology, implicating the possible detrimental effects of inflammatory cytokines on motor neurons. The RNA/DNA-binding protein TDP-43 has emerged as a pivotal actor in ALS, because TDP-43 mutations cause familial ALS and loss of nuclear TDP-43, associated with its redistribution into cytoplasmic aggregates (TDP-43 proteinopathy) in motor neurons occurs in 97% of ALS cases. However, mechanisms linking neuroinflammation to TDP-43 mislocalization have not been described. Programmed death-ligand 1 (PD-L1) is an immune-modulatory protein, highly expressed on cell surfaces following acute inflammatory stress. To determine which inflammatory cytokines might impact motor neuron function, seven cytokines known to be elevated in ALS patients cerebrospinal fluid were tested for their effects on PD-L1 expression in human iPSC-derived motor neurons. Among the tested cytokines, only interferon-{gamma} (IFN-{gamma}) was found to strongly promote PD-L1 expression. Thus, we hypothesized that excessive exposure to IFN-{gamma} may contribute to motor neuron degeneration in ALS. We observed that neuronal populations exposed to IFN-{gamma} exhibited severe TDP-43 cytoplasmic aggregation and excitotoxic behavior correlated with impaired neural firing activity, hallmarks of ALS pathology, in both normal and ALS mutant (TARDB1K+/-) neurons. Single-cell RNA sequencing revealed possible mechanisms for these effects. Motor neurons exposed to IFN-{gamma} exhibited an extensive shift of their gene expression profile toward a neurodegenerative phenotype. Notably, IFN-{gamma} treatment induced aberrant expression levels for 70 genes that are listed in the recent literature as being dysregulated in various ALS subtypes. Additionally, we found that genes related to neuronal electrophysiology, protein aggregation, and TDP-43 misregulation were abnormally expressed in IFN-{gamma} treated cells. Moreover, IFN-{gamma} induced a significant reduction in the expression of genes that encode indispensable proteins for neuromuscular synapse development and maintenance, implying that the continuous cytokine exposure could directly impair signal transmission between motor axons and muscle membranes. Our findings suggest that IFN-{gamma} could be a potent upstream pathogenic driver of ALS and provide potential candidates for future therapeutic targets to treat sporadic forms of ALS, which account for roughly 90% of reported cases.

neuroscience↗

bioRxiv2022

Application of Physiological and Pathological Wall Shear Stress to Endocardial Endothelial Cells Triggers Complex Signaling Pathways

Discrete subaortic stenosis (DSS) is a congenital heart disease in which a fibrotic membrane forms below the aortic valve; the underlying cellular mechanisms are currently unknown. Since an elevated pressure gradient in the left ventricular outflow tract (LVOT) is a distinguishing feature of DSS, it is hypothesized that the membrane formation is caused by elevated wall shear stress applied to the endocardial endothelial cells (EECs) that line the LVOT, triggering fibrosis. To correlate shear stress to an EEC fibrotic phenotype, we applied fluid shear stress to EECs at physiological and pathological shear rates using a cone-and-plate device, designed to recapitulate physiological wall shear stress in a controlled in vitro environment. Controlled shear stress regimes were applied to EECs to replicate the conditions observed in DSS patients. We found that elevated shear stress triggered EEC alignment as well as endothelial-to-mesenchymal transformation (EndMT) signaling pathways driven by upregulation of SNAI1 gene expression. The EECs were then treated with a small molecule inhibitor of Snail1 protein, CYD19, to attempt to attenuate EndMT signaling, and subsequently subjected to pathological shear stress. The Snail1 inhibitor did downregulate selected markers of EndMT signaling, although only transiently. Interestingly, the application of shear stress had a greater effect on the EEC gene and protein expression than did the Snail1 inhibition. This investigation of EEC response to shear stress reveals the pronounced and complex effect of this mechanical stimulation on the EEC phenotype. Further study should reveal the mechanisms that drive fibrosis and the formation of the DSS membrane.

bioengineering↗

bioRxiv2023

LZTR1 polymerization provokes cardiac pathology in recessive Noonan syndrome

Noonan syndrome patients harboring causative variants in LZTR1 are particularly at risk to develop severe and early-onset hypertrophic cardiomyopathy. However, the underling disease mechanisms of LZTR1 missense variants driving the cardiac pathology are poorly understood. Hence, therapeutic options for Noonan syndrome patients are limited. In this study, we investigated the mechanistic consequences of a novel homozygous causative variant LZTR1L580Pby using patient-specific and CRISPR/Cas9-corrected iPSC-cardiomyocytes. Molecular, cellular, and functional phenotyping in combination with in silico prediction of protein complexes uncovered a unique LZTR1L580P-specific disease mechanism provoking the cardiac hypertrophy. The homozygous variant was predicted to alter the binding affinity of the dimerization domains facilitating the formation of linear LZTR1 polymer chains. The altered polymerization resulted in dysfunction of the LZTR1-cullin 3 ubiquitin ligase complexes and subsequently, in accumulation of RAS GTPases, thereby provoking global pathological changes of the proteomic landscape ultimately leading to cellular hypertrophy. Furthermore, our data showed that cardiomyocyte-specific MRAS degradation is mediated by LZTR1 via the autophagosome, whereas RIT1 degradation is mediated by both LZTR1-dependent and LZTR1-independent proteasomal pathways. Importantly, uni-or biallelic genetic correction of the LZTR1L580P missense variant rescued the molecular and cellular disease-associated phenotype, providing proof-of-concept for CRISPR-based gene therapies.

cell biology↗

bioRxiv2023

AnimalGAN: A Generative Adversarial Network Model Alternative to Animal Studies for Clinical Pathology Assessment

Animal studies are unavoidable in evaluating chemical and drug safety. Generative Adversarial Networks (GANs) can generate synthetic animal data by learning from the legacy animal study results, thus serving as an alternative approach to assess untested chemicals. AnimalGAN, a GAN method to simulate 38 rat clinical pathology measures, was developed with significant robustness even for the drugs that vary significantly from these used during training, both in terms of chemical structure, drug class, and the year of FDA approval. AnimalGAN showed a comparable performance in hepatotoxicity assessment as animal studies and outperformed the optimal prediction of 12 traditional regression approaches for almost all clinical pathology measures. Using AnimalGAN, a virtual experiment of 100,000 rats ranked hepatotoxicity of three similar drugs that correlated with the findings in human population. AnimalGAN represented a significant step with artificial intelligence towards the global effort in replacement, reduction, and refinement (3Rs) of animal use.

bioinformatics↗

bioRxiv2023

α-Melanocyte-Stimulating Hormone Regulates Pathological Cardiac Remodeling by Activating Melanocortin 5 Receptor in Cardiomyocytes

Background-Melanocyte-stimulating hormone (-MSH) regulates diverse physiological functions by activating melanocortin receptors (MC-R). -MSH is predominantly expressed in the pituitary gland, but it is also found in several peripheral tissues such as the skin and heart. However, the role of -MSH and its possible target receptors in the heart remain completely unknown. Therefore, we sought to investigate whether -MSH could be involved in the regulation of pathological cardiac remodeling. MethodsTissue -MSH concentrations and the effects of chronic -MSH administration were investigated in mice subjected to transverse aortic constriction (TAC). Rat H9c2 cells, neonatal mouse ventricular myocytes and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) were used to study the effects of -MSH and selective MC-R agonists. Inducible cardiomyocyte-specific melanocortin 5 receptor (MC5-R) knockout mouse model was engineered to investigate the role of MC5-R in cardiac hypertrophy. Results-MSH was highly expressed in the mouse heart, particularly in the ventricles, and its level was reduced in the left ventricles of TAC-operated mice. Administration of a stable -MSH analogue protected mice against TAC-induced cardiac hypertrophy and systolic dysfunction. In vitro experiments revealed that cardiomyocytes serve as effector cells for the -MSH mediated antihypertrophic signaling and that selective activation of MC5-R mimics the actions of -MSH. In keeping with these findings, MC5-R was downregulated in the failing mouse heart and stressed hiPSC-CMs. Silencing of MC5-R in mouse cardiomyocytes induced hypertrophy and fibrosis markers in vitro and aggravated TAC-induced cardiac hypertrophy and fibrosis in vivo. Conversely, pharmacological activation of MC5-R improved systolic function and reduced cardiac fibrosis in TAC-operated mice. Conclusions-MSH is expressed in the heart and protects against pathological cardiac remodeling by activating MC5-R in cardiomyocytes. These results suggest that analogues of naturally occurring -MSH, that have been recently approved for clinical use and have agonistic activity at MC5-R, may be of benefit in treating heart failure.

physiology↗

bioRxiv2023

Weakly supervised contrastive learning infers molecular subtypes and recurrence risk of breast cancer from pathology images

The deep learning-powered computational pathology has led to sig-nificant improvements in the speed and precise of tumor diagnosis,, while also exhibiting substantial potential to infer genetic mutations and gene expression levels. However,current studies remain limited in predicting molecular subtypes and recurrence risk in breast cancer. In this paper, we proposed a weakly supervised contrastive learning framework to address this challenge. Our framework first performed contrastive learning pretraining on large-scale unlabeled patches tiled from whole slide images (WSIs) to extract patch-level features. The gated attention mechanism was leveraged to aggregate patch-level features to produce slide feature that was then applied to various downstream tasks. To confirm the effectiveness of the proposed method, we have conducted extensive experiments on four independent cohorts of breast cancer. For gene expression prediction task, rather than one model per gene, we adopted multitask learning to infer the expression levels of 21 recurrence-related genes, and achieved remarkable performance and generalizability that were validated on an external cohort. Particularly, the predictive power to infer molecular subtypes and recurrence events was strongly validated by cross-cohort experiments. In addition, the learned patch-level attention scores enabled us to generate heatmaps that were highly consistent with pathologist annotations and spatial transcriptomic data. These findings demonstrated that our model effectively established the high-order genotype-phenotype associations, thereby enhances the potential of digital pathology in clinical applications.

bioinformatics↗

bioRxiv2023

Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis in Alzheimer's disease models

Alzheimers Disease (AD) is a progressive and irreversible neurodegenerative disorder, characterized by the accumulation of abeta-amyloid aggregates, which triggers tau hyperphosphorylation and neuronal loss. While the precise mechanisms underlying neurodegeneration in AD are not entirely understood, it is known that loss of proteostasis is implicated in this process. Maintaining neuronal proteostasis requires proper transfer RNA (tRNA) modifications, which are crucial for optimal translation. However, research into tRNA epitranscriptome in AD is limited, and it is not yet clear how alterations in tRNA modifying enzymes and tRNA modifications might contribute to disease progression. Here, we report that expression of the tRNA modifying enzyme ELP3 is reduced in the brain of AD patients and amyloid AD mouse models, suggesting ELP3 is implicated in proteostasis dysregulation observed in AD. To investigate the role of ELP3 specifically in neuronal proteostasis impairments in the context of amyloid pathology, we analyzed SH-SY5Y neuronal cells carrying the amyloidogenic Swedish familial AD mutation in the APP gene (SH-SWE) or the wild-type gene (SH-WT). Similarly to the amyloid mouse models, SH-SWE exhibited reduced levels of ELP3 which was associated with tRNA hypomodifications and reduced abundance, as well as proteostasis impairments. Furthermore, the knock-down of ELP3 in SH-WT recapitulated the proteostasis impairments observed in SH-SWE cells. Importantly, the correction of tRNA deficits due to ELP3 reduction rescued and reverted proteostasis impairments of SH-SWE and SH-WT knock-down for ELP3, respectively. Additionally, SH-WT exposed to the secretome of SH-SWE or synthetic amyloid aggregates recapitulate the SH-SWE phenotype, characterized by reduced ELP3 expression, tRNA hypomodification and increased protein aggregation. Taken together, our data suggest that amyloid pathology dysregulates neuronal proteostasis through the reduction of ELP3 and tRNA modifications. This study highlights the modulation of tRNA modifications as a potential therapeutic avenue to restore neuronal proteostasis in AD and preserve neuronal function. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/538928v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@ed5cf4org.highwire.dtl.DTLVardef@171b14aorg.highwire.dtl.DTLVardef@12eb19dorg.highwire.dtl.DTLVardef@8ed4ab_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Brain cell type specific proteomics approach to discover pathological mechanisms in the childhood CNS disorder mucolipidosis type IV

1 Mucolipidosis IV (MLIV) is an ultra-rare, recessively inherited lysosomal disorder resulting from inactivating mutations in MCOLN1, the gene encoding the lysosomal cation channel TRPML1. The disease primarily affects the central nervous system (CNS) and manifests in the first year with cognitive and motor developmental delay, followed by a gradual decline in neurological function across the second decade of life, blindness, and premature death in third or fourth decades. Brain pathology manifestations in MLIV are consistent with hypomyelinating leukodystrophy with brain iron accumulation. Presently, there are no approved or investigational therapies for MLIV, and pathogenic mechanisms remain largely unknown. The MLIV mouse model, Mcoln1-/- mice, recapitulates all major manifestations of the human disease. Here, to better understand the pathological mechanisms in the MLIV brain, we performed cell type specific LC-MS/MS proteomics analysis in the MLIV mouse model and reconstituted molecular signatures of the disease in either freshly isolated populations of neurons, astrocytes, oligodendrocytes, and neural stem cells, or whole tissue cortical homogenates from young adult symptomatic Mcoln1-/- mice. Our analysis confirmed on the molecular level major histopathological hallmarks of MLIV universally present in Mcoln1-/- tissue and brain cells, such as hypomyelination, lysosomal dysregulation, and impaired metabolism of lipids and polysaccharides. Importantly, pathway analysis in brain cells revealed mitochondria-related alterations in all Mcoln1-/- brain cells, except oligodendrocytes, that was not possible to resolve in whole tissue. We also report unique proteome signatures and dysregulated pathways for each brain cell population used in this study. These data shed new light on cell-intrinsic mechanisms of MLIV and provide new insights for biomarker discovery and validation to advance translational studies for this disease.

neuroscience↗

bioRxiv2023

Integrative mapping of spatial transcriptomic and amyloid pathology in Alzheimer's disease at single-cell resolution

Alzheimers disease (AD) is a complex neurodegenerative disorder that affects millions of people worldwide. Despite decades of research, the underlying molecular and cellular changes of AD remain unresolved, especially in terms of the spatial structure of gene expression changes that correlates with pathology, e.g. amyloid beta (A-beta) plaques. Recent advances in imaging-or sequencing-based single-cell spatial transcriptomics have allowed a systematic dissection of molecular and cell architectures in the brain and other tissues. In this study, we employed the recently developed Stereo-seq technology to spatially profile the whole-genome transcriptomics in the 5xFAD mouse model and established the methodology to analyze the specific neuronal transcriptomic changes spatially correlated with amyloid pathology at single cell resolution. More specifically, we developed a pipeline for integrative image- and non-image-based cell segmentation, VoxelMorph-based non-linear alignment, and Unet-based object detection to achieve reliable transcriptomics analysis at the single-cell resolution, and investigated the spatial relationship between diverse neuronal clusters and A-beta depositions. This work has demonstrated the potential of using the Stereo-seq technology as a powerful tool to investigate AD and other complex neurological disorders.

neuroscience↗

bioRxiv2023

Native-state proteomics of Parvalbumin interneurons identifies novel molecular signatures and metabolic vulnerabilities to early Alzheimer's disease pathology

One of the earliest pathophysiological perturbations in Alzheimers Disease (AD) may arise from dysfunction of fast-spiking parvalbumin (PV) interneurons (PV-INs). Defining early protein-level (proteomic) alterations in PV-INs can provide key biological and translationally relevant insights. Here, we use cell-type-specific in vivo biotinylation of proteins (CIBOP) coupled with mass spectrometry to obtain native-state proteomes of PV interneurons. PV-INs exhibited proteomic signatures of high metabolic, mitochondrial, and translational activity, with over-representation of causally linked AD genetic risk factors. Analyses of bulk brain proteomes indicated strong correlations between PV-IN proteins with cognitive decline in humans, and with progressive neuropathology in humans and mouse models of A{beta} pathology. Furthermore, PV-IN-specific proteomes revealed unique signatures of increased mitochondrial and metabolic proteins, but decreased synaptic and mTOR signaling proteins in response to early A{beta} pathology. PV-specific changes were not apparent in whole-brain proteomes. These findings showcase the first native state PV-IN proteomes in mammalian brain, revealing a molecular basis for their unique vulnerabilities in AD.

neuroscience↗

bioRxiv2023

Transcriptome analysis of peripheral blood of Schistosoma mansoni infected children from the Albert Nile region in Uganda reveals genes implicated in fibrosis pathology.

Over 290 million people are infected by schistosomes worldwide. Schistosomiasis control efforts focus on mass drug treatment with praziquantel (PZQ), a drug that kills the adult worm of all Schistosoma species. Nonetheless, re-infections have continued to be detected in endemic areas with individuals living in the same area presenting with varying infection intensities. Our objective was to characterize the transcriptome profiles in peripheral blood of children between 10 - 15 years with varying intensities of Schistosoma mansoni infection living along the Albert Nile in Uganda. RNA extracted from peripheral blood collected from 44 S. mansoni infected (34 high and 10 low by circulating anodic antigen [CAA] level) and 20 uninfected children was sequenced using Illumina NovaSeq S4 and the reads aligned to the GRCh38 human genome. Differential gene expression analysis was done using DESeq2 and enriched pathways in differentially expressed genes (DEGs) were identified using REACTOME. Principal component analysis revealed clustering of gene expression by gender when S. mansoni infected children were compared with uninfected children. In addition, we identified 14 DEGs between S. mansoni infected and uninfected individuals, 56 DEGs between children with high infection intensity and uninfected individuals, 33 DEGs between those with high infection intensity and low infection intensity and no DEGs between those with low infection and uninfected individuals. We also observed upregulation and downregulation of some DEGs that are associated with fibrosis and its regulation. These data suggest expression of fibrosis associated genes as well as genes that regulate fibrosis in S. mansoni infection. The relatively few significant DEGS observed in children with schistosomiasis suggests that chronic S. mansoni infection is a stealth infection that does not stimulate a strong immune response. Author SummarySchistosomiasis is a neglected tropical disease transmitted via an intermediate snail host through contact with contaminated fresh water. Even with routine Mass Drug Administration for treatment of the infection, re-infections are still common and variations in infection intensity and pathology are still observed in individuals in the same location. These may be due to differences in individuals response to S. mansoni infection. In this study, we used RNAseq to identify differentially expressed genes associated with S. mansoni infection in children between 10-15 years. We conducted comparisons between phenotypes including infection intensities measured by circulating anodic antigen, wasting by body mass index and stunting by height-for-age z score. Our data showed very low numbers of significant differentially expressed genes in all comparisons. Some of the few differentially expressed genes that were observed were associated with fibrosis which is the cause of pathology in humans and has been observed in late stages of S. mansoni infection in murine studies.

genomics↗