Biology subjects

Sanyal, A.

Publications and source records attributed to Sanyal, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Longitudinal single-cell modeling reveals monocyte reprogramming in juvenile systemic sclerosis following autologous stem cell transplantation

Juvenile systemic sclerosis (jSSc) is a rare autoimmune disease marked by skin fibrosis and multi-organ involvement. Autologous stem cell transplantation (ASCT) is an emerging therapy for severe, treatment-refractory jSSc, but its effects on immune cell dynamics remain poorly understood. PBMCs were collected from three patients with jSSc before ASCT and at 6, 12, and 24 months post-ASCT. Patient and healthy control samples were profiled using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). We focused on monocytes, given their role in fibrosis-promoting inflammation. To detect longitudinal trends, pseudobulked gene expression (log scale) was regressed against time since ASCT. This approach identified widespread changes in jSSc monocytes, including decreased expression of systemic sclerosis-linked genes, such as SERPINE1. On the pathway level, NF-{kappa}B-associated inflammatory signaling was elevated in jSSc monocytes at baseline relative to healthy controls and decreased progressively post-ASCT. Genes related to mitochondrial function and oxidative phosphorylation progressively increased in expression after ASCT, suggesting a shift in metabolic state. Compositional changes in monocyte subpopulations were also identified and may have contributed to longitudinal gene expression patterns. Together, these findings characterize the dynamic immune changes in jSSc following ASCT and highlight a widely applicable longitudinal modeling framework for single-cell data.

genomics↗

bioRxiv2026

The CYP27A1 - VDR Feedback Rheostat Controls Mitochondrial Protein Homeostasis and Preserves Hippocampal - Striatal Network Integrity to rescue Cognitive impairment in HD condition

Emerging evidence links vitamin D (VD) deficiency to cognitive and motor dysfunction in Huntingtons disease (HD), yet the underlying mechanism remains unclear. Here, we combine in vitro genetic and 3-nitropropionic acid (3-NP)-induced in vivo models of HD to define the mechanistic basis of VD-mediated neuroprotection. We demonstrate that VD supplementation restores cognitive and motor deficits while improving mitochondrial function and cellular survival. Mechanistically, VD enhances mitochondrial fusion and rescues complex II expression, a key defect in HD pathology. We identify the mitochondrial enzyme CYP27A1 as a critical mediator of this effect, as its expression is reduced in HD models but restored upon VD treatment. Overexpression of CYP27A1 recapitulates the protective effects of VD, confirming its central role in maintaining mitochondrial integrity. Furthermore, VD promotes vitamin D receptor (VDR)-dependent transcriptional activation of CYP27A1 and additional nuclear- and mitochondrial-encoded genes, establishing a regulatory feedback loop that supports mitochondrial biogenesis and function. VD supplementation also improves proteostasis via attenuating endoplasmic reticulum stress. Together, our findings uncover a previously unrecognized VD-CYP27A1 axis that links mitochondrial dysfunction to HD pathology and highlight CYP27A1 as a potential therapeutic target.

neuroscience↗

bioRxiv2026

Comparative Genomics of Two Chaetoceros muelleri Strains Reveals Structural and Functional Variation

Diatoms are major contributors to global primary production and biogeochemical cycling, yet high quality nuclear genome resources remain limited for ecologically dominant lineages such as Chaetoceros. Here, we present a highly contiguous nuclear genome assembly of Chaetoceros muelleri generated from living cells resurrected from resting spores preserved in Baltic Sea sediments and sequenced using PacBio HiFi long read technology. The resurrected BS20 assembly is highly contiguous and gapless, enabling robust resolution of genes, protein domain architecture, and transposable element (TE) landscapes that are poorly captured in fragmented assemblies. By directly comparing this resurrected genome with a contemporary laboratory strain (C. muelleri NMCA1316), we disentangle biological divergence from assembly-driven artefacts. Despite a strongly conserved core genome, the two strains differ markedly in repeat content, gene family copy number, and functional enrichment patterns. The resurrected genome harbors [~]38% repetitive DNA approximately 1.8-fold higher than the laboratory strain dominated by LTR retrotransposons and a large fraction of unclassified repeats, indicating extensive historical TE activity. Expanded orthogroups in the resurrected strain are enriched for retroelement-associated domains, nucleic-acid processing functions, and stress-responsive gene families, including small heat shock proteins, whereas apparent expansions in the laboratory strain largely reflect annotation inflation arising from assembly fragmentation. Spatial analyses further reveal widespread proximity between TEs, and genes involved in membrane transport and environmental responsiveness, suggesting a role for TE dynamics in regulatory and functional diversification. Together, our results demonstrate that assembly strategy and strain history critically shape genomic inference and highlight the value of resurrected genomes for accessing historical diversity. This study provides a foundational genomic resource for C. muelleri and establishes a genomic framework that explicitly accounts for strain level variation when investigating diatom genome evolution, TE mediated innovation, and long-term ecological adaptation.

evolutionary biology↗

bioRxiv2026

A High-Quality Genome Assembly of Chaetoceros muelleri Reveals Extensive Gene Duplication, Functional Diversification, and Unique Lineage-Specific Innovation

Diatoms are major contributors to marine primary production, yet high-quality nuclear genome resources remain scarce for ecologically dominant lineages such as Chaetoceros. Here, we present the first high-quality nuclear genome assembly of Chaetoceros muelleri, generated from living cells resurrected from resting spores preserved in Baltic Sea sediments and sequenced using PacBio HiFi long-read technology. The assembly is compact (43{square}Mb), highly contiguous (N50{square}={square}1.40{square}Mb), and highly complete (93% BUSCO). Comparative analyses across 14 diatom genomes revealed extensive lineage-specific and expanded gene families in C. muelleri, alongside a small, conserved core genome, reflecting rapid evolutionary turnover. Functional enrichment highlighted diversification of polysaccharide biosynthesis, vesicle-mediated trafficking, membrane remodelling, and transcriptional regulation, consistent with adaptations linked to frustule formation and environmental responsiveness. Transposable elements (TEs) strongly shape the genome, accounting for [~]18% of the assembly, with dominant LTR retrotransposons and a large fraction of unclassified repeats suggesting novel or highly diverged TE lineages. Enrichment of DNA replication, recombination, and repair functions further indicates compensatory genome maintenance associated with TE-driven structural dynamics. Direct comparison with C. tenuissimus revealed contrasting patterns of gene family expansion and regulatory innovation, underscoring divergent evolutionary strategies within Chaetoceros. By integrating resurrection ecology with long-read genomics, this study provides a foundational genomic resource for C. muelleri and highlights the role of TE-mediated genome plasticity in diatom evolution.

genomics↗

bioRxiv2026

PNPLA3I148M is a novel regulator of bone mass independent of MASLD

Metabolic-dysfunction associated steatotic liver disease (MASLD) is the most common chronic liver disease. Fracture risk is increased among people with MASLD, however, the genetic contribution to risk is undetermined. PNPLA3I148M is a common SNP which accounts for most MASLD heritability and increases MASLD morbidity and mortality. However, PNPLA3I148M impact on bone is unexplored. To bridge this gap, we used a validated murine model of MASLD (DIAMOND mice) which received human PNPLA3 transgenes via adeno-associated vector serotype 8 (AAV8) and assessed bone morphology, cellularity, and transcriptomics. PNPLA3I148M was expressed in bone and associated with bone loss, decreased bone formation, increased bone resorption, and increased bone marrow adiposity. PNPLA3I148M reprogrammed the transcriptome in bone, enriching expression of pathways associated with fatty acid metabolism and hampering bone turnover. Notably, these findings occurred in the absence of MASLD. These findings suggest PNPLA3I148M possesses an intrinsic deleterious skeletal role.

physiology↗

bioRxiv2026

Pathology of dose dependent inocula of H5N8 avian influenza viruses in experimentally infected chicken

In the present study, we assessed the pathogenicity of H5N8 avian influenza viruses belongs to the clade 2.3.4.4b in chicken. Birds of three different dose groups, 102, 104, and 106 EID50 were used in the study. No mortality was observed in 102 EID0 group. Percent cumulative mortality of 104 and 106 EID50 group was 66.67 and 100 %, respectively. Varying duration of MDT of 3.2 and 2 days was observed in 104 and 106 EID50 group, respectively. The CID50 of virus was found to be 104.5 EID50. High no. of viral RNA copies were found both in oropharyngeal and cloacal swabs and in various organs of birds infected in 104 and 106 EID50 group. Significant gross and histological changes and presence of viral antigen in various organs were observed in 104 and 106 EID50 group. So, the study concludes that Indian HPAI, H5N8 isolates are highly pathogenic in nature to chicken by affecting most organs systemically. CID50 of this H5N8 virus indicates poor adaption in chicken and it implies poor transmission possibility of this virus for host species in field condition. Though this virus is highly pathogenic in nature as that of HPAI, H5N1 viruses, absence of endothelial staining in most organ attributes variation in replication process and pathogenesis from HPAI, H5N1 viruses. Hence, further studies need to be done to elucidate the pathobiology of this virus in various bird species. HighlightsO_LIH5N8 virus belong to the clade 2.3.4.4b, Indian isolate is highly pathogenic in nature as that of HPAIV, H5N1. C_LIO_LIThe dose inocula, 102 EID50 is noninfectious to chicken. C_LIO_LIThe dose inocula, 104 and 106 EID50 had caused significant mortality in the inoculated chicken with MDT of 2 and 3.2 days, respectively. C_LIO_LIH5N8 virus was detected with high viral titres in clocal and oral shedding and in multiple organ with the dose inocula, 104 and 106 EID50. C_LIO_LI104 and 106 EID50 of H5N8 inocula virus caused significant gross and histological changes in multiple organs and viral antigens were detected in respective organs. C_LI

microbiology↗

bioRxiv2025

Anthropogenic habitats shape gut microbiome composition in Southern Indian bats

BackgroundAnthropogenic habitat modification and associated resources can exert selection pressures on wildlife and their microbiomes, altering their diversity, resulting in homogenization and making them resemble the human microbiome. Diet is an important predictor of the microbiomes of volant vertebrates, mainly for birds, but for bats, results remain inconclusive. In spite of Indias exceptional bat diversity, there is little understanding of how their microbiomes respond to anthropogenic habitats. Therefore, we investigated the trends of taxonomic and functional diversity and their relationships with host feeding-guild and phylogeny for six wide-ranging bat species across six anthropogenically modified sites in Southern India by generating 16S barcode sequences from their fecal samples. ResultsEubacteria dominated samples with diet-specific taxonomic composition. Frugivore microbiomes contained large proportions of Cyanobacteria, possibly sourced from consumed plant matter or polluted drinking-water sources, and Lactobacillales dominated insectivore microbiomes, while Gammaproteobacteria were abundant regardless of host feeding guild. We found human pathogens in our samples possibly transferred from polluted water to the guts of bats foraging in nearby areas. We observed diet-specific taxonomic, phylogenetic, and functional composition. However, functional composition incorporating abundances displayed a high degree of overlap across feeding-guilds, suggesting functional homogenisation of microbiomes across feeding guilds, possibly due to anthropogenicity. Sample-wise diversity indices were significantly different with respect to diet only when samples from the same roost were not pooled together. However, in all cases, microbiomes from the same diet types displayed significant taxonomic and phylogenetic similarity to each other. Lastly, we observed limited concordance of microbiome diversity with chiropteran phylogeny. ConclusionsBecause of these potential signatures of pollution on bat microbiomes such as pathogens, we recommend their monitoring, especially because Cyanobacteria play a known role in bat and human disease. Our study is one of the first to study microbiome composition and function from bat species common around human inhabitation in South India, and establishes baselines in this region.

evolutionary biology↗

bioRxiv2025

Tau seeding in neurons enabled by transient endolysosomal perforations are confined within endolysosomes

Pathogenic tau assemblies propagate by templated seeding. For endocytosed fibrils to initiate aggregation of endogenous tau, a breach must occur in the limiting membrane of an endosome or lysosome. To study the route by which internalized tau seeds access cytosolic monomers and to identify the site of aggregate growth, we imaged live human iPSC-derived neurons (iNs) expressing tau P301L-eGFP after exposure to recombinant tau pre-formed fibrils (PFFs) or Alzheimers disease (AD) brain-derived oligomers or fibrils. We detected seeded tau P301L- eGFP aggregation within late endosomes/lysosomes of iNs but not in undifferentiated iPSCs. Colocalization with a Dextran pH biosensor showed that the aggregates remained within the lumen of an intact, low-pH compartment. Reporters of endolysosomal injury and repair (endolysosomal recruitment cytosolic galectin-3 and the ESCRT-III component IST1) did not change during seeding. Volume focused-ion-beam scanning electron microscopy showed fibrillar material exclusively inside membrane-bounded endolysosomes, with no membrane discontinuities in the fibril-containing compartments and with no evidence of cytosolic aggregates. Because tau and -synuclein can cross-seed, we adapted a HaloTag pulse-chase assay to test for the persistence of trans-membrane access. AD fiber-containing endolysosomes progressively recruited cytosolic -synuclein-Halo over days, with heterogeneous incorporation histories consistent with recurrent, self-limited access events rather than persistent rupture or terminal sealing. Pharmacologic inhibition of the endolysosomal lipid kinase PIKfyve with apilimod suppressed seeded tau aggregation and prevented neuronal toxicity. These data indicate that templated conversion proceeds within acidic, membrane-intact endolysosomes; tau seeding in neurons is enabled by transient, self-limited endolysosomal perforations yet remains confined to the endolysosomal lumen, and it requires PIKfyve- dependent PI(3,5)P2.

neuroscience↗

bioRxiv2025

PEX11β-mediated improvement of mitochondrial dysfunction restores behavioral defect and cellular viability in neuropathological conditions

Peroxisomal biogenesis factor 11 beta (Pex11{beta}) is a key regulator of peroxisome proliferation, functioning in coordination with mitochondrial fission proteins. Recent human proteome co-regulation mapping has revealed a distinctive co-expression pattern between Pex11{beta} and components of the mitochondrial respiratory chain complex at the peroxisome-mitochondria interface. In neurodegenerative disorders, such as Huntingtons disease (HD) and Alzheimers disease (AD), mitochondrial dysfunction is primarily associated with impairments in the respiratory chain complexes, particularly Complex II. However, the role of Pex11{beta} in maintaining mitochondrial homeostasis in these two disease conditions remains largely unexplored. In this study, using both in vitro and in vivo models, we identify Pex11{beta} as a critical modulator of mitochondrial dynamics, influencing the balance between fission and fusion. Through targeted knockdown and overexpression experiments, we demonstrate a direct link between Pex11{beta} level and mitochondrial dysfunction, mediated by transcriptional dysregulation of nuclear-encoded Complex II and mitochondrial fusion genes. Restoration of Pex11{beta} expression, along with Complex II and fusion gene level in striatal brain via a peroxisome proliferator & chemical chaperone, significantly alleviates motor and cognitive deficits in 3-NP-induced HD mouse model indicating better mitochondrial health in striatal brain. Furthermore, in silico analysis and ChIP-qPCR reveal Yin Yang 1 (YY1) is a critical transcription factor governing the co-expression of Pex11{beta} and Complex II genes. This establishes a novel transcriptional axis that orchestrates inter-organellar communication. Collectively, our findings position Pex11{beta} as a pivotal mediator of mitochondrial fission-fusion dynamics, linking mitochondrial morphology and oxidative phosphorylation (OXPHOS) to behavioural outcomes, and offering mechanistic insights relevant to amyloid-associated neurodegenerative diseases.

neuroscience↗

bioRxiv2025

CTG clade-specific proteins of the RSC chromatin remodeling complex regulate cell cycle progression of a critical priority fungal pathogen, Candida albicans

The RSC and the homologous chromatin remodeling complexes are known to regulate cell cycle progression in various organisms, including Saccharomyces cerevisiae, Drosophila, and Homo sapiens. In this work, we characterized the role of two novel CTG clade-specific proteins (Nri1 and Nri2) of the RSC complex in the regulation of cell cycle progression in a critical priority fungal pathogen, Candida albicans. We observed that Nri1, alone or along with Nri2, regulates cell cycle progression at multiple stages. The nri1{Delta}/{Delta} and nri1{Delta}/{Delta} nri2{Delta}/{Delta} mutants exhibited transient cell cycle arrest, defective spindle morphology, and cytokinesis. Transcriptomic analysis supported these mutant phenotypes and indicated a broad role of Nri proteins in the cell cycle. From our results, we conclude that Nri proteins are crucial for C. albicans proliferation and fitness. ImportanceThe composition of the essential RSC chromatin remodeling complex exhibits species-specific divergence, harboring unique subunits with distinct functions. In this study, we report that two fungal CTG clade-specific proteins of the C. albicans RSC complex, namely Nri1 and Nri2 can promote C. albicans fitness through regulating its cell cycle progression at multiple stages. Fitness defect along with stressor sensitivity and differential expression of the genes regulating pathogenesis in the nri mutants indicate potentiality of the Nri proteins as anti-Candida drug targets.

cell biology↗

bioRxiv2025

Close-Up of vesicular ER Exit Sites by Volume Electron Imaging using FIB-SEM

Volume electron microscopy by high-pressure freeze substitution combined with block-face focused ion beam scanning electron microscopy (FIB-SEM) provides comprehensive 3D views of subcellular architecture, essential for understanding cellular activity in context. Aided by Automated Segmentation in Electron Microscopy (ASEM)--a 3D-Unet convolutional neural network trained with sparse annotations--we characterized the spatial organization of endoplasmic reticulum exit sites (ERES), the initial locations for membrane remodeling in protein secretion, in cells not overexpressing secretory cargo. The ASEM model, trained on 50-70 nm in diameter COPI vesicles, successfully identified vesicles adjacent to the Golgi apparatus of HeLa, SVG-A, and iPSC-derived neurons. It also revealed abundant vesicles of similar appearance, often within a group of [~]5-40 vesicles clustered within a 250 nm3 region adjacent to flattened endoplasmic reticulum (ER) domains, forming what we propose are COPII-mediated vesicular ER-exit sites. Elsewhere, similar assemblies appeared alongside tubular ER networks emerging from similarly enlarged ER domains previously reported as the only ERES in HeLa cells. These findings underscore the power of large-scale volume electron microscopy to resolve contradictions regarding membrane organization in vesicular trafficking. We encourage the scientific community to use our publicly accessible repository, containing open-source code, trained models, annotations, predictions, and FIB- SEM datasets, to facilitate continued advances in automated segmentation methods. SummaryNair et. al. show abundance of vesicular ERES in mammalian cells imaged by volume focused ion beam electron microscopy.

cell biology↗

bioRxiv2024

Sexual dimorphism of MASLD-driven bone loss

Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) is highly prevalent with major risk of progression to Metabolic Dysfunction-Associated Steatohepatitis (MASH) and Hepatocellular Carcinoma (HCC). Recently, osteoporosis and bone fracture have emerged as sexually-dimorphic comorbidities of MASLD yet the mechanisms of this bone loss are unknown. Herein, we address these knowledge gaps using DIAMOND mice which develop MASLD, MASH, and HCC via Western diet exposure. We examined the skeletal phenotype of male DIAMOND mice after 16, 36, and 48 weeks of exposure to Western or control diet. At 16 weeks, male DIAMOND mice with MASLD lose trabecular bone but retain mechanical bone integrity. At 48 weeks, males lose cortical bone and mechanical integrity, indicating severe skeletal weakening. Female DIAMOND mice were protected from cortical and trabecular MASLD-associated bone loss and skeletal fragility at all timepoints. Using NicheNet, a publicly available database of hepatic mRNA expression in DIAMOND mice, and a PTH-induced model of bone loss, we suggest Ctgf, Rarres2, Anxa2, Fgf21, and Mmp13 are liver-secreted ligands inducing bone resorption. This study is the first preclinical investigation of bone loss in MASLD, and the first to suggest the role of Ctgf, Rarrest2, Anxa2, Fgf21, and Mmp13 as drivers of this pathology.

physiology↗

bioRxiv2024

Identification of distinct rodent-associated adenovirus lineages from a mixed-use landscape in the Western Ghats biodiversity hotspot

Shifts in land-use patterns and increased human-livestock-wildlife interactions have generated numerous possibilities for pathogen spillover. This demands increased efforts of pathogen surveillance in wildlife, especially in changing landscapes with high biodiversity. We investigated adenovirus diversity in small mammals, an understudied host taxon, from a forest-plantation mosaic in the Western Ghats biodiversity hotspot. Using PCR-based screening followed by Sanger sequencing and phylogenetic analyses, we attempted to detect and characterize adenovirus diversity in seven species of small mammals. We observed high prevalence (up to 38.8%) and identified five lineages of adenoviruses with unique mutations in the endemic and dominant small mammal species, Rattus satarae. These lineages significantly differed from other known Murine adenoviruses (p-distance > 25%), indicating the likelihood of novel adenovirus diversity in this endemic small mammal. Collectively, our results highlight the potential for unexplored diversity of DNA viruses like adenovirus in poorly explored host taxa inhabiting human-used landscapes and its zoonotic implications.

evolutionary biology↗

bioRxiv2024

Evaluation of extraction solvents for untargeted metabolomics to decipher the DOM of Antarctic cryoconite holes

Cryoconite holes are biological hotspots with a high biogeochemical turnover rate, contributing significantly to the glacial ecosystems overall carbon cycles and net fluxes. Unfortunately, the information about the composition of low molecular weight molecules formed through the metabolic processes of cryoconite-dwelling microbes is scanty. These molecules constitute a substantial portion of the dissolved organic matter (DOM) within cryoconite holes. The present study investigated the composition of DOM in cryoconite holes using reverse-phase liquid chromatography (RP-LC) coupled with high-resolution tandem mass spectrometry. We evaluated various solvent combinations of water, methanol, and acetonitrile to extract chemically diverse polar and non-polar metabolites from the cryoconite holes. Among the single solvents, organic-rich MeOH: Water (70:30 v/v) and in parallel 2-single solvent combinations of MeOH: Water (70:30 v/v) and Acetonitrile: Methanol: Water (40:40:20 v/v) provided increased number and chemical diversity of extracted metabolites. Combining RP with the hydrophilic interaction liquid chromatography (HILIC) technique provided the highest number of unique metabolites. This dual-LC and ionization polarity combination increased the detection of metabolic features by 46.96% and 24.52% in single- and two-solvent combinations compared to RP alone. This study developed a simple untargeted metabolomics workflow that is highly sensitive and robust, detecting and potentially identifying a large number of chemically diverse molecules present in the DOM (extracellular) and microbes (intracellular) from the cryoconite holes environment. This method can better characterize DOMs chemical composition and, after integrating with other omics approaches, can be used to examine the link between metabolic pathways and microbial communities in global cryoconite holes or other similar ecosystems, revealing how these earthy systems and their microbial flora control carbon or nutrient storage or release in response to global climate change. Overall, the study presents a valuable methodology for studying the biogeochemistry of cryoconite holes.

microbiology↗

bioRxiv2024

Loss of TIM4-Dependent Efferocytosis in Kupffer CellsPromotes Liver Fibrosis in Nonalcoholic Steatohepatitis

Background and aimsHepatocyte apoptosis is a key feature of non-alcoholic steatohepatitis (NASH), but the fate of apoptotic hepatocytes in NASH is poorly understood. Herein we explore the hypothesis that impaired TIM4-mediated clearance of dead hepatocytes by liver macrophages (efferocytosis) is impaired in NASH and drives the progression to liver fibrosis. MethodsKupffer cell (KC)-TIM4 expression and efferocytosis were assayed in normal and NASH liver from humans and diet-induced NASH mice. The engulfment of human and mouse apoptotic hepatocytes by primary human and mouse liver KCs was assayed ex vivo. Causation was assessed in NASH mice using anti-TIM4 antibodies, KC-TIM4-knockout, or inducible KC-TIM4 expression, with analyses focused on efferocytosis of apoptotic hepatocytes by liver macrophages and liver fibrosis. ResultsIn human and mouse NASH liver, apoptotic hepatocytes accumulated and was associated with the loss of the KC efferocytosis receptor TIM4. Anti-TIM4 inhibited the engulfment of apoptotic hepatocytes by primary human and mouse liver KCs ex vivo, and anti-TIM4 administration to early NASH mice worsened liver macrophage efferocytosis and accelerated the progression to fibrotic NASH. A similar result was obtained by genetically deleting TIM4 in KCs in NASH mice. Most importantly, genetic restoration of macrophage TIM4 in NASH mice enhanced the clearance of apoptotic hepatocytes by liver macrophages and decreased liver fibrosis. ConclusionsThe loss of macrophage TIM4 that occurs during NASH progression impairs the clearance of apoptotic hepatocytes by liver macrophages, which subsequently promotes the progression to fibrotic NASH. This pathogenic sequence of events can be prevented by restoring macrophage TIM4, suggesting that future therapeutic approaches designed to boost TIM4 expression in liver macrophages could represent a novel strategy to prevent fibrotic NASH progression. Lay summaryNonalcoholic steatohepatitis (NASH) is emerging as the leading cause of liver disease, but the processes leading to liver fibrosis in NASH, which determines clinical outcome, are incompletely understood. Our study provides evidence impaired clearance of dead liver cells by liver macrophages in NASH, which is due to loss of a macrophage receptor called TIM4, contributes to liver fibrosis. Knowledge of this process may suggest new ways to bolster the clearance of dead liver cells in NASH and thereby prevent the progression to liver fibrosis and subsequent liver disease.

pathology↗

bioRxiv2024

Constitutive Endolysosomal Perforation in Neurons allows Induction of alpha-Synuclein Aggregation by Internalized Pre-Formed Fibrils

The endocytic pathway is both an essential route of molecular uptake in cells and a potential entry point for pathology-inducing cargo. The cell-to-cell spread of cytotoxic aggregates, such as those of -synuclein (-syn) in Parkinsons Disease (PD), exemplifies this duality. Here we used a human iPSC-derived induced neuronal model (iNs) prone to death mediated by aggregation in late endosomes and lysosomes of endogenous -syn, seeded by internalized pre-formed fibrils of -syn (PFFs). This PFF-mediated death was not observed with parental iPSCs or other non-neuronal cells. Using live-cell optical microscopy to visualize the read out of biosensors reporting endo-lysosome wounding, we discovered that up to about 10% of late endosomes and lysosomes in iNs exhibited spontaneous constitutive perforations, regardless of the presence of internalized PFFs. This wounding, absent in parental iPSCs and non-neuronal cells, corresponded to partial damage by nanopores in the limiting membranes of a subset of endolysosomes directly observed by volumetric focused ion beam scanning electron microscopy (FIB-SEM) in iNs and in CA1 pyramidal neurons from mouse brain, and not found in iPSCs or in other non-neuronal cells in culture or in mouse liver and skin. We suggest that the compromised limiting membranes in iNs and neurons in general are the primary conduit for cytosolic -syn to access PFFs entrapped within endo-lysosomal lumens, initiating PFF-mediated -syn aggregation. Significantly, eradicating the intrinsic endolysosomal perforations in iNs by inhibiting the endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase (PIKfyve kinase) using Apilimod or Vacuolin-1 markedly reduced PFF-induced -syn aggregation, despite PFFs continuing to enter the endolysosomal compartment. Crucially, this intervention also diminished iN death associated with PFF incubation. Our results reveal the surprising presence of intrinsically perforated endo-lysosomes in neurons, underscoring their crucial early involvement in the genesis of toxic -syn aggregates induced by internalized PFFs. This discovery offers a basis for employing PIKfyve kinase inhibition as a potential therapeutic strategy to counteract synucleinopathies.

cell biology↗

bioRxiv2023

Unraveling molecular basis for reduced neuraminidase inhibitors susceptibility in highly pathogenic avian influenza A (H5N1) viruses isolated from chickens in India

The increasing resistance cases in influenza viruses to different classes of antiviral drugs, necessitates the in-depth analysis of molecular interactions governing reduced susceptibility to these drugs. This study explores the molecular basis of neuraminidase inhibitors resistance in avian H5N1 influenza viruses identified in our previous research. Using comprehensive modeling and docking tools, we investigated two isolates--A/chicken/India/85459/2008 (N294S) and A/chicken/WestBengal/142121/2008 (E119A + I117V). The N294S mutation conferred oseltamivir resistance while retaining zanamivir susceptibility, whereas the E119A + I117V mutations led to zanamivir resistance while reducing oseltamivir susceptibility. Molecular interactions analysis unveiled varied fitness levels, hydrogen bonding, and affinity transitions associated with N294S and E119A + I117V mutations. This study provides crucial insights into molecular interactions responsible for reduced susceptibility to neuraminidase inhibitors, which is essential for optimizing antiviral strategies and pandemic preparedness.

microbiology↗

bioRxiv2023

Host-pathogen-vector continuum in a changing landscape: Drivers of Bartonella prevalence and evidence of historic spillover in a tropical multi-host community

Small mammals and their ectoparasites present a unique system to investigate the eco-epidemiology of multi-host vector-borne pathogens and identify specific bacterial spillover determinants. We applied ecological and evolutionary analyses in a rainforest-human-use mosaic to investigate Bartonella spp. across small mammal and ectoparasite communities. We observed substantial overlap among small mammal communities in different habitat types, predominantly driven by habitat generalists. Most ectoparasites were generalists, infecting multiple hosts. We observed high Bartonella prevalence at both study sites -a forest-plantation mosaic (47.4%) and a protected area (28.8%). Seven of the ten ectoparasite species sampled were also positive for Bartonella, following prevalence trends in their hosts. A generalised linear model revealed an independent association between aggregated ectoparasite load in hosts and Bartonella prevalence, implicating ectoparasites in transmission. Bartonella lineages from small mammals were host-specific, while ectoparasites carried Bartonella associated with other small mammal hosts, indicating the potential for cross-species transmission. Phylogenetic ancestral trait reconstruction of Bartonella haplotypes suggest historic spillover events in the small mammal community, validating the potential for contemporary spillover events. These results highlight the necessity to disentangle the complex relationship between hosts, ectoparasites, and pathogens to understand the zoonotic implications of undetected spillover events in such multi-host communities.

ecology↗