Biology subjects

Bhattacharjee, A.

Publications and source records attributed to Bhattacharjee, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Inhibiting nociceptor endocytosis reduces MIA-induced osteoarthritic pain behavior

Introduction: Osteoarthritis (OA) is a degenerative joint condition characterized by chronic pain and the need for pain management. Locally targeting the endocytotic AP2 complex in nociceptors presents a potential strategy for providing sustained pain relief in individuals with OA. Objective: We investigated whether pain behavior associated with OA can be mitigated by genetically silencing the AP2alpha2 subunit of the AP2 complex in nociceptors and by pharmacologically inhibiting the AP2 complex through the intraarticular administration of a small lipidated decoy peptide. Method: Monoiodoacetate (MIA) was employed to induce knee joint OA in mice and rats. Pain behavior was assessed using dynamic weight-bearing and von Frey filaments. Upon confirmation of established OA pain behavior, in vivo AP2alpha2 genetic knockdown in mice was achieved through sciatic nerve transfection of a targeting AP2alpha2 short hairpin RNA (shRNA). To pharmacologically target endocytosis, a single intraarticular injection of peptide was administered into the arthritic knee of rats. The injection contained either the AP2 inhibitor peptide or a scrambled peptide control. Results: Pain behavior was significantly reduced after both genetic and pharmacological disruption of AP2-driven endocytosis. Animals treated with the Ap2 inhibitor peptide exhibited reduced pain behavior throughout the 28-day assay period. Following the completion of behavioral testing, arthritic knee joints and contralateral healthy knee joints were subsequently collected to assess the impact of the treatment on disease progression. Micro-computed tomography analysis revealed a preservation of bone volume in the arthritic joints that received the AP2 inhibitor peptide treatment, in contrast to the scrambled peptide group. Conclusion: These findings demonstrate that the inhibition of nociceptor endocytosis by a small lipidated peptide presents a promising approach to provide sustained relief from joint pain in individuals with arthritis.

pharmacology and toxicology↗

bioRxiv2026

Saprotrophic soil fungus dissolves lithium lepidolite through inositol rescue metabolism

Microbial weathering of minerals represents a key biogeochemical process through which microorganisms access essential nutrients locked within rock and ore substrates. In this study, we investigated the metabolic response of a model fungus during growth on lithium (Li) ore to elucidate the mechanisms underpinning biologically mediated mineral weathering and subsequent metal mobilization. Our results revealed a distinct metabolic shift in the fungus when cultivated on Li ore, characterized by altered patterns of organic acid production and energy metabolism. This shift coincided with measurable weathering of the Li ore matrix and the consequent release of soluble Li into the surrounding environment, demonstrating a direct link between fungal metabolic reprogramming and mineral breakdown. Importantly, these observations are consistent with metabolic shifts documented in previous studies of mineral weathering by this fungus, suggesting that such responses constitute a conserved and reproducible strategy employed during the colonization of mineral substrates. Although the present work was conducted using a single model microorganism under controlled conditions, the findings carry broader ecological implications. Natural microbial communities inhabiting mineral-rich environments may undergo analogous metabolic shifts when weathering minerals to acquire limiting nutrients, thereby contributing to large-scale elemental cycling and metal release. Understanding these processes not only advances fundamental knowledge of microbe-mineral interactions but also informs emerging applications in biomining and bio-based recovery of critical metals such as lithium. Collectively, this study highlights the central role of microbial metabolism in driving mineral weathering and offers a framework for predicting and harnessing similar processes within complex microbial communities. IMPORTANCEThe model fungus exhibits a distinct, reproducible shift in metabolism--particularly in organic acid production and energy pathways--when grown on Li ore, directly linking cellular metabolism to mineral breakdown. This metabolic shift promotes weathering of the ore matrix and the release of soluble lithium, demonstrating a biological route for liberating a critical metal from its mineral host. Because similar shifts occur across different minerals, natural microbial communities likely employ comparable strategies to weather minerals and acquire limiting nutrients, contributing to global elemental cycling. These findings provide a foundation for sustainable biomining and bio-based recovery of lithium and other critical metals, offering a lower-impact alternative to conventional extraction methods.

microbiology↗

bioRxiv2026

Copper-transporting ATPase ATP7B and the lysosomal exocytosis pathway synergise to detoxify cadmium

Cadmium, being a highly toxic metal, perturbs cellular homeostasis by forming stable complexes with numerous thiol-active proteins, ultimately leading to severe liver and lung damage. Despite its well-documented toxicity, the molecular mechanisms governing cadmium export remain poorly understood. Given the chemical similarity between cadmium and copper, we investigated whether the canonical copper-exporting ATPases, ATP7A and ATP7B participate in cadmium handling. Upon Cd treatment in hepatocytes, ATP7B undergoes trafficking to lysosomes via the retromer complex, as also observed in the case of elevated copper, accompanied by the upregulation of acidic lysosomal populations. In contrast, ATP7A expressed in lung adenocarcinoma cells, though exhibit vesicular redistribution upon Cd exposure, does not mediate lysosomal sequestration, suggesting distinct deployment of late secretory pathways by the two copper ATPases in response to cadmium. We have also observed that ATP7B-/- hepatocytes exhibit increased sensitivity to Cd exposure compared to wild-type cells. Whereas, overexpressing the ATP7B amino-terminal copper-binding domain in bacteria alleviates cadmium-induced stress, indicating its capacity to sequester Cd. Caenorhabditis elegans lacking copper-ATPase cua-1, displayed increased Cd sensitivity, while mutants (glo-1-/-), deficient in lysosome-related organelles (LRO), and (lmp-1-/-), deficient in lysosomal membrane glycoprotein, showed reduced resistance to cadmium toxicity. Treatment of the worm with cadmium increases the abundance of lysosomes marked by elevation in lysosomal biogenesis and functional genes, reinforcing the importance of lysosomal pathways in cadmium detoxification. To summarise, we delineated the non-canonical role of copper ATPases and lysosomes in cadmium-induced cellular toxicity.

cell biology↗

bioRxiv2026

Structure-Guided Design and Dynamic Evaluation of VP4-Targeting siRNAs Against Rotavirus A

Rotavirus is a major cause of severe diarrheal disease in children under the age of five, with reduced vaccine effectiveness in low-resource settings causing substantial morbidity and mortality. In the absence of approved antiviral therapeutics, treatment is largely supportive, urging the need for targeted and precision-based interventions. VP4 protein plays an essential role in viral attachment, entry, and infectivity, making it a suitable target for targeted therapy. In this context, RNA interference is a specific method for inhibiting viral gene expression with its efficacy depending on sequence conservation, target accessibility, and compatibility with the RISC-loading machinery. In the present study, an integrative in silico approach was employed to design and evaluate siRNAs targeting conserved regions of the VP4 gene across six geographically diverse countries. Candidate siRNAs were screened using established design rules and regression-based scoring with off-target filtering. Three optimized siRNAs were further assessed through structural modeling, molecular docking, and molecular dynamics simulations to examine interactions with human Dicer, TRBP, and Argonaute-2. Comparative dynamic analyses identified one siRNA with enhanced structural compatibility, reduced conformational fluctuations, and stable interactions with RISC-loading proteins. These findings provide a rational computational basis for VP4-targeted siRNA development, facilitating experimental validation.

bioinformatics↗

bioRxiv2026

Characterization of the biofilm landscape of Bacillus subtilis by spatial microproteomics

Bulk proteomics has been demonstrated to differentiate subpopulations based on molecular phenotypes within bacterial colonies, yet advanced analyses by mass spectrometry imaging (MSI) hold even greater promise for the future. This technology can enable high-throughput spatial phenotyping that can directly visualize distinct components of various biomolecular mechanisms with high mass resolving power in high spatial resolution analyses. Here, we applied MSI for intact protein imaging directly from thin cross sections of a biofilm of Bacillus subtilis and after minimal preparation we detected more than 285 unique isotopic envelopes corresponding to unique proteoforms. We paired our MSI analyses with bulk top-down proteomics (TDP) to form extensive experimental libraries, which provided us with high confidence MSI annotations based upon isotopic matching to validated post-translational modifications (PTMs) and truncations. This joint application of MSI and TDP allowed us to describe the microscal e spatial proteomic landscape within the B. subtilis biofilm. This study further demonstrated the feasibility of detecting differentiated subpopulations of cells through the identification of proteoforms of cannibalistic protein toxins as well as those involved in active sporulation to highly localized areas within the central and outermost periphery of the biofilm. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/702398v4_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@3fcd38org.highwire.dtl.DTLVardef@ba314dorg.highwire.dtl.DTLVardef@1faf52dorg.highwire.dtl.DTLVardef@f68974_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Copy number of the blaNDM-1 gene (New Delhi metallo-β-lactamase-1) and meropenem susceptibility in Enterobacterales: Consideration for treatment with meropenem?

Some Enterobacterales carrying blaNDM were still susceptible to meropenem, exhibiting meropenem minimum inhibitory concentration (MIC) values below the clinical breakpoint. As this phenomenon is a rare observation, this study investigated the underlying regulatory mechanisms contributing to the low MIC values and evaluated the efficacy of meropenem as a therapeutic preference for such isolates. Six clinical blaNDM-positive Enterobacterales exhibited meropenem MICs between 0.5-2.0 mg/L. Successful transmission of blaNDM into recipient E. coli J53 indicated its presence on plasmids. Conventional Sanger and whole-genome sequencing revealed that no truncation or deletion was observed within blaNDM or its core promoter region up to 120 bp upstream. Quantitative real-time PCR of blaNDM showed significantly lower expression levels of blaNDM, i.e., 0.2-0.5 in study isolates, compared to a clinical blaNDM-possessing isolate (expression=1) exhibiting a high meropenem MIC value (64 mg/L). Droplet digital PCR (ddPCR) further demonstrated that these isolates carried a lower copy number of the blaNDM gene, compared to the blaNDM-possessing isolate with high meropenem MIC (64 mg/L). Furthermore, the in vitro time-kill assay exhibited bactericidal efficacy of meropenem >3 log10 decrease in cfu/mL over the 24 hours from the starting inoculum. Administration of meropenem in in vivo neutropenic mice produced a 4-log cfu reduction compared to untreated controls at the start of dosing. Our data suggest that a reduction in blaNDM gene dosage, reflecting lower expression of blaNDM, correlates with lower meropenem MIC values. Meropenem is effective against these isolates when the meropenem MICs for the isolates are 0.5-2.0 mg/L. ImportanceThe production of NDM by Enterobacterales poses one of the most urgent global public health threats due to its plasmid-mediated spread, leading to treatment failure by exhibiting high MICs against a broad-spectrum of antibiotics. However, in rare instances, blaNDM-1-positive clinical Enterobacterales with unexpectedly low meropenem MICs (0.5-2.0 mg/L) raise a further question of reconsidering meropenem as a potential therapeutic option in these specific cases. This study identified that low MICs were associated with reduced expression and lower copy number of the plasmid-mediated blaNDM gene, despite intact promoter regions. Both in vitro and in vivo assays validated the bactericidal activity of meropenem against these isolates. The study raised an argument about the potential limitations of relying solely on genotypic detection of resistance genes for therapeutic decision-making, which emphasises the need for further investigation. As a safe medication, repurposing meropenem for neonatal treatment may eliminate the need for other toxic drugs.

microbiology↗

bioRxiv2025

Repurposing Melatonin in dual-mode for Wilson disease therapy as a Copper Chelator and an antioxidant agent

Loss-of-function mutations in copper-ATPase ATP7B underlie Wilson disease (WD), a disorder characterized by hepatic copper accumulation and severe hepato-neuropathology. Existing chelation therapeutics remove excess copper but lack intrinsic antioxidant capacity and frequently cause systemic toxicity. Here we evaluate melatonin, an FDA-approved indoleamine with antioxidant and putative metal-chelating activity, as a candidate therapeutic for WD. In ATP7B-/- hepatocytes, melatonin restored copper-induced reactive oxygen species (ROS) to basal levels, reduced apoptosis twofold, and attenuated Nrf2 nuclear translocation leading to reduction of Hemoxygenase-1 abundance. Live-cell ratiometric analysis of GSSG/GSH using GRX1-roGFP2 expressed in melatonin-treated ATP7B-/- hepatocytes revealed a significant reduction in intensity-ratio, indicating an effective mitigation of copper-induced glutathione oxidation. Isothermal calorimetric titration revealed moderate Cu2+ affinity (K ITC=4.54 x 103 M-{superscript 1}), rationalized by MD-simulations showing an interaction energy of 18.5 x 10-3 kcal{middle dot}mol-{superscript 1} via amide-Cu{superscript 2} coordination. In-cellulo studies also revealed that copper-induced vesicularized ATP7B reinstates to Golgi in melatonin-treated hepatocytes. In vivo, melatonin treatment reduced copper-induced oxidative stress in zebrafish embryos and lowered copper burden in Caenorhabditis elegans WD model. Our studies revealed that encapsulation of melatonin within an engineered polymeric nanocapsules having dithiol linkers, susceptible to cleavage by GSH, extended melatonins circulatory half-life ten-fold and enhanced its ROS-scavenging efficacy three-fold relative to free melatonin. This work introduces a unique dual-function therapeutic strategy that integrates antioxidant activity with copper chelation, simultaneously addressing copper overload and redox imbalance. Repurposing melatonin, with its established clinical safety, offers rapid and cost-effective translational pathway toward WD-therapy while providing a generalizable platform for redox- and metal-associated disorders.

cell biology↗

bioRxiv2025

Linking Genomic Landscape to Disease Mechanism: Core Genetic Factors Underlying Pathogenesis and Antimicrobial Resistance in Diarrheal Pathogens

BackgroundDiarrheal diseases remain a major global health burden, as they severely affect children, particularly in Bangladesh. After decades of research, the molecular mechanisms of diarrheal pathogens for disease pathogenesis and antibiotic resistance are still unknown, notably in Gram-negative bacteria. This pilot study fills the gap by employing whole genome sequencing and pan-genome analysis to analyze Bangladeshi diarrheal pathogens to identify genetic variables that cause disease pathogenesis and antibiotic resistance. ResultsHence, we investigated the genetic diversity of bacterial isolates from 31 clinical stool samples by a combination of whole-genome sequencing (WGS) and pan-genomic analysis. A core group of 50 genes, conserved across a significant number of strains, was identified via pan-genomic analysis, with considerable variation in accessory genes. This signifies a significant degree of genetic flexibility. Gene ontology analysis yielded substantial insights into prospective therapeutic targets by emphasizing the critical function of these core genes in bacterial survival and pathogenicity. Furthermore, the findings of the antimicrobial susceptibility test (AST) revealed concerning resistance trends, particularly to fluoroquinolones and beta-lactams, underscoring the necessity for enhanced surveillance and alternative therapeutic approaches. ConclusionThis study provides a comprehensive genetic framework to improve understanding of the complexity of diarrheal infections and the mechanisms underlying their resistance, fostering opportunities for potential therapeutic advancements.

microbiology↗

bioRxiv2025

APDeeM: A machine Learning strategy towards Effective Peptide Vaccine Candidates Identification against Different Types of Viruses

Viral infections pose significant global health challenges, underscoring the urgent need for improved medications. Nevertheless, traditional medicinal approaches depend significantly on labor-intensive laboratory tests, which impede efficient identification and prolong vaccine development, particularly when screening a huge number of samples. To address these obstacles, we present a comprehensive Antiviral Peptide (AVP) Detection Dataset, comprising 14 unique features to improve the characterization of antiviral and non-antiviral peptides. Subsequently, we introduce the Antiviral Peptide detection enhanced by Ensemble Machine Learning (APDeeM) system. This advanced computational framework considerably reduces the time required for AVP detection by utilizing ensemble learning methodologies. The APDeeM system incorporates Gradient Boosting, Random Forest, K-Nearest Neighbors (KNN), and AdaBoost algorithms to facilitate the swift selection of AVP candidates without requiring urgent laboratory testing. Our proposed ensemble methodology showed superior performance, with an accuracy of 85.99%, F1 score of 87.60%, recall of 88.91%, and precision of 86.32%, exceeding the efficacy of all tested antiviral peptide prediction models in this research. The APDeeM approach signifies a substantial improvement over conventional detection techniques, expediting the identification of prospective vaccine candidates and facilitating the advancement of more effective antiviral peptides. The most promising AVP candidates may urge laboratory validation, optimize resources, and accelerate vaccine development.

bioinformatics↗

bioRxiv2025

Development of ultrasound molecular contrast agents by site-specific conjugation of gas vesicles to antibodies

Ultrasound technology is a powerful tool for medical imaging and diagnosis especially when used in conjunction with a contrast agent to target proteins of interest. However, current ultrasound contrast agents are lacking the combination of specificity, stability, and size optimization. In this study we introduce and confirm the feasibility of using nanometer sized gas vesicles (GV) chemically click conjugated to antibodies (mAb) to make the first site-specific mAb-GV conjugates as a durable cancer cell targeting ultrasound molecular contrast agents. Protein expression of human epidermal growth factor receptor 2 (HER2) and programmed death-ligand 1 (PD-L1) were tested along with the antibody targeting efficiency using cancer cell lines and primary cells isolated from tumor bearing mice. The mAb conjugation was optimized to a site-specific method using the mAb glycans and tested with the addition of a clinically used mAb to target trophoblast cell surface antigen 2 (Trop-2). The developed contrast agents utilize the stability of GVs and the specificity of antibodies to label cancer biomarkers in various types of tumors for ultrasound imaging.

bioengineering↗

bioRxiv2025

Signal Detection of Point Targets Using Eigen-Images for Super-Resolution Ultrasound Imaging and Gas Vesicle Localization

Accurate signal detection of ultrasound contrast agents, such as microbubble (MB) and gas vesicle (GV), in the presence of clutter and noise is essential to increase image quality in super-resolution ultrasound imaging (SRUS) and achieve precise GV localization. We developed and evaluated an eigen-image based signal detection method using singular value decomposition (SVD) and changepoint detection to automatically segment the data that are closely related to physical events such as MB flow and GV collapse. Eigen-image based method was compared with the elbow point and hard thresholding method when selecting MB signals after SVD of raw data, acquired from phantom and in vivo experiments. Image reconstructed by eigen-image based method was also compared with unregistered difference image for GV localization when moving GVs in a phantom were collapsed by ultrafast plane waves. The eigen-image based MB signal detection method resulted in higher vessel density (VD) visualization in both the phantom and in vivo mouse tumor. It also achieved increased signal-to-noise ratio (SNR) in both cases. Moreover, this method localized moving GVs more efficiently than the difference imaging method, without requiring pixel registration based on landmarks. The eigenimage based method offers a reliable and automated approach to MB and GV signal detection for both SRUS and point target localization. This approach is a valuable tool for medical imaging providing high-quality vessel images along with accurate locations of moving ultrasound contrast agents, which can be potentially translatable to clinical diagnosis and pre-clinical research. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/662077v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@d03b0corg.highwire.dtl.DTLVardef@d4b318org.highwire.dtl.DTLVardef@3a2894org.highwire.dtl.DTLVardef@3e2962_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAn approach to efficiently detect point targets including microbubbles and gas vesicles is developed using eigenimages that describe the changes of point targets over time for super-resolution ultrasound imaging and gas vesicle localization. C_LIO_LISignals from point targets were automatically identified from clutter and noise by the changepoint detection method without prior Information. C_LIO_LIThis approach enhances microvasculature visualization of tumors in mice and improves the localization of gas vesicles in a phantom. C_LI

bioengineering↗

bioRxiv2025

Pathogenic BRCA1 mutations disrupt allosteric control by BARD1

Mechanistic insight into biophysical perturbations caused by pathogenic missense mutations is highly valuable information for the rational design of therapeutics. For hereditary breast and ovarian cancer, multiple pathogenic mutations in the N-terminal domain of BRCA1 have been reported in patients. How exactly these mutations disrupt the catalytic activity of BRCA1, and thereby lead to oncogenesis, is unknown. Here, we posit that the mechanism of pathogenesis is tied to how binding of BARD1 activates BRCA1 for E3 ligase activity. We use atomistic molecular dynamics simulations and Markov state modeling to uncover how BARD1 selects for active conformational states of BRCA1. We show that the helix bundle, where BARD1 binds, is allosterically coupled to the E2 interface. Furthermore, we show that BARD1 selects for conformational states that are pre-organized for E3 activity. Lastly, we show that pathogenic mutations allosterically destabilize active states, whereas hyperactive mutations constitutively increase their likelihood. These results provide a concrete strategy supported by mechanistic insight for the design of restorative small molecules targeting BRCA1.

biophysics↗

bioRxiv2025

Localization of AP2α2, TRPV1 and PIEZO2 to the Large Dense Core Vesicles of Human Dorsal Root Ganglion Neurons

Dorsal Root Ganglia (DRG) consist of both peptidergic and non-peptidergic nociceptive neurons. CGRP, an inflammatory neuropeptide, is a classical marker of peptidergic nociceptors and CGRP is stored within the large dense core vesicles (LDCVs) of these neurons. In addition to storing large peptide neurotransmitters, LDCVs might also serve to transport key membrane proteins to the peripheral terminals. This immunohistochemical study investigated the localization of different membrane proteins to the LDCVs of human DRG neurons. Previously validated antibodies against the endocytotic subunit AP22, the heat-activated channel TRPV1 and the mechanosensitive channel PIEZO2 were used in conjunction with an antibody against CGRP on sections of intact human DRG isolated from de-identified human subjects. Immunohistochemical studies were also performed on human synovial tissue to examine peripheral terminals. High magnification confocal microscopy was used to determine the co-localization signal of these membrane proteins with CGRP. We observed a strong co-localization of AP22 with the CGRP containing LDCVs signifying its role in membrane recycling. Moreover, we also observed a strong colocalization of TRPV1 and PIEZO2 with CGRP suggesting that LDCV release controls the trafficking of these channels to the membrane. It is likely that during injury, bulk exocytosis of CGRP will concomitantly increase the surface expression of TRPV1 and PIEZO2 channels enhancing the responsiveness of these neurons to painful stimuli. This model suggests that neurons that co-localize TRPV1 and PIEZO2 to CGRP containing LDCVs are likely silent nociceptors.

neuroscience↗

bioRxiv2025

A small lipidated peptide targeting NaV1.8 channels attenuates osteoarthritic pain behavior and prevents bone erosion

Chronic pain is a major concern for patients with osteoarthritis (OA). Current treatments for OA-related pain often fail and may worsen the disease. The sodium channel subtype NaV1.8 has emerged as a potential target for treating pain, leading to the development of NaV1.8 inhibitors in clinical trials. We previously identified Magi-1, a WW domain-containing scaffold protein, as a regulator of NaV1.8 at the plasma membrane of nociceptive neurons. Disrupting the interaction between NaV1.8 and Magi-1 facilitated channel degradation in neurons, reducing pain behavior in multiple animal models. In this study, we investigated the impact of disrupting NaV1.8 scaffolding on an animal model of OA pain using genetic and pharmacological approaches. Genetic Magi-1 knockdown effectively attenuated established OA pain in mice. Pharmacological targeting of the NaV1.8-Magi-1 interaction in rats with a lipidated NaV1.8 WW binding domain decoy peptide inhibited pain behavior for multiple weeks. MicroCT imaging revealed minimal alterations in subchondral bone remodeling in animals injected with the lipidated decoy peptide compared to those receiving scrambled peptide-control animals. This suggested that the NaV1.8 peptidomimetic not only alleviated OA pain but also delayed joint degeneration. Our preclinical studies indicate that intraarticular injection of lipidated peptides capable of disrupting ion channel scaffolding in neurons can provide effective and sustained analgesia for several weeks after a single administration.

pharmacology and toxicology↗

bioRxiv2024

Sulfatide deficiency-induced astrogliosis and myelin lipid dyshomeostasis are independent of Trem2-mediated microglial activation

Disrupted lipid homeostasis and neuroinflammation often co-exist in neurodegenerative disorders including Alzheimers disease (AD). However, the intrinsic connection and causal relationship between these deficits remain elusive. Our previous studies show that the loss of sulfatide (ST), a class of myelin-enriched lipids, causes AD-like neuroinflammatory responses, cognitive impairment, bladder enlargement, as well as lipid dyshomeostasis. To better understand the relationship between neuroinflammation and lipid disruption induced by ST deficiency, we established a ST-deficient mouse model with constitutive Trem2 knockout and studied the impact of Trem2 in regulating ST deficiency-induced microglia-mediated neuroinflammation, astrocyte activation and lipid disruption. Our study demonstrates that Trem2 regulates ST deficiency-induced microglia-mediated neuroinflammatory pathways and astrogliosis at the transcriptomic level, but not astrocyte activation at the protein level, suggesting that Trem2 is indispensable for ST deficiency-induced microglia-mediated neuroinflammation but not astrogliosis. Meanwhile, ST loss-induced lipidome disruption and free water retention were consistently observed in the absence of Trem2. Collectively, these results emphasize the essential role of Trem2 in mediating lipid loss-associated microglia-mediated neuroinflammation, but not both astrogliosis and myelin lipid disruption. Moreover, we demonstrated that attenuating neuroinflammation has a limited impact on brain ST loss-induced lipidome alteration or AD-like peripheral disorders. Our findings suggest that preserving lipidome and astrocyte balance may be crucial in decelerating the progression of AD.

neuroscience↗

bioRxiv2024

Dissecting Breast Cancer Heterogeneity Through Transcriptomics Insights of Diverse Etiological Factors for Common Biomarker Discovery

Breast cancer has many different causes, and the key to finding effective treatments is understanding the diseases heterogeneity. The present study used three gene expression datasets from 110 female samples related to stress, drug and hormonal imbalance, diet and nutrition, and physical activity and light exposure at night to predict differential gene expression. Interestingly, all gene expression datasets shared 22 upregulated and 4 downregulated genes, regardless of etiology. This suggests these genes share the core molecular mechanism and the biological pathway that causes breast cancer. Notably, these genes were significantly enriched in some important pathways, including cycle regulation, endoplasmic reticulum stress, and transcriptional regulation, demonstrating their potential as therapeutic targets. Further, we found UBE2J2 from upregulated genes and ZCCHC7 from downregulated genes as the top hub and bottleneck genes, which may help network connectivity and functional gene interactions. Computational study further asserted the strong binding affinity of drug-target complexes. Later, molecular dynamics simulations confirmed the predicted drug-target complexes stability and dynamic behavior, demonstrating these two genes as potential therapeutic targets. The findings from this analysis provide the molecular basis into the complex interplay between diverse etiologic factors and breast cancer pathogenesis, paving the way for innovative biomarker-targeted therapies.

bioinformatics↗

bioRxiv2024

Mapping the PTEN Mutation Landscape: Structural and Functional Drivers of Lung Cancer

Lung cancer is the predominant form of cancer globally, arising from the dysfunction of genetic mutations. Although PTEN mutation is crucial in the aetiology of lung cancer, the mapping of these major drivers has to be determined. We leverage computational algorithms on 43,855 SNPs of PTEN to discover the mutational impact contributing to lung cancer. Fifteen variations were identified as detrimental, and no pertinent studies have previously addressed their structural and functional aspects. Notably, seven variations were identified as the most significant contributors to lethal effects in functional aberration, as demonstrated by the computational assessment. Subsequently, molecular simulation elucidated the structural instability associated with these alterations. Furthermore, drug binding experiments at the mutational site corroborated the destabilization experiments by demonstrating the conformational alteration of the structure, resulting in varied amino acid interactions. In summary, the present study elucidates the influence of mutations in PTEN structure on its functional architecture.

cancer biology↗

bioRxiv2024

In vivo CRISPR base editing for treatment of Huntington's disease

Huntingtons disease (HD) is an inherited and ultimately fatal neurodegenerative disorder caused by an expanded polyglutamine-encoding CAG repeat within exon 1 of the huntingtin (HTT) gene, which produces a mutant protein that destroys striatal and cortical neurons. Importantly, a critical event in the pathogenesis of HD is the proteolytic cleavage of the mutant HTT protein by caspase-6, which generates fragments of the N-terminal domain of the protein that form highly toxic aggregates. Given the role that proteolysis of the mutant HTT protein plays in HD, strategies for preventing this process hold potential for treating the disorder. By screening 141 CRISPR base editor variants targeting splice elements in the HTT gene, we identified platforms capable of producing HTT protein isoforms resistant to caspase-6-mediated proteolysis via editing of the splice acceptor sequence for exon 13. When delivered to the striatum of a rodent HD model, these base editors induced efficient exon skipping and decreased the formation of the N-terminal fragments, which in turn reduced HTT protein aggregation and attenuated striatal and cortical atrophy. Collectively, these results illustrate the potential for CRISPR base editing to decrease the toxicity of the mutant HTT protein for HD.

bioengineering↗