Biology subjects

Ghosh, S.

Publications and source records attributed to Ghosh, S..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Concomitant suppression of COX-1 and COX-2 is insufficient to induce enteropathy associated with chronic NSAID use

Nonsteroidal anti-inflammatory drugs (NSAIDs) are the most widely used medications for the management of chronic pain; however, they are associated with numerous gastrointestinal (GI) adverse events. Although many mechanisms have been suggested, NSAID-induced enteropathy has been thought to be primarily due to inhibition of both cyclooxygenases (COX) -1 and -2, which results in suppression of prostaglandin synthesis. Yet surprisingly, we found that concomitant postnatal deletion of Cox-1 and -2 over 10 months failed to cause intestinal injury in mice unless they were treated with naproxen or its structural analog, phenylpropionic acid, which is not a COX inhibitor. Cox double knockout mice exhibit a distinct gut microbiome composition and cohousing them with controls rescues their dysbiosis and delays the onset of NSAID-induced GI bleeding. In both the UK Biobank and All of Us human cohorts, coadministration of antibiotics with NSAIDs is associated with an increased frequency of GI bleeding. These results show that prostaglandin suppression plays a trivial role in NSAID-induced enteropathy. However, Cox deletion causes dysbiosis of the gut microbiome that amplifies the enteropathic response to NSAIDs.

pharmacology and toxicology↗

bioRxiv2024

The Synergy between Topography and Lipid Domains in the Plasma Membrane of Mast Cells Controls the Localization of Signaling Proteins and Facilitates their Coordinated Activation

Similar to T cells and B cells, mast cell surfaces are dominated by microvilli, and like these other immune cells we showed with microvillar cartography (MVC) that key signaling proteins for RBL mast cells localize to these topographical features. Although stabilization of ordered lipid nanodomains around antigen-crosslinked IgE-Fc{varepsilon}RI is known to facilitate necessary coupling with Lyn tyrosine kinase to initiate transmembrane signaling in these mast cells, the relationship of ordered-lipid nanodomains to membrane topography had not been determined. With nanoscale resolution provided by MVC, SEM and co-localization probability (CP) analysis, we found that Fc{varepsilon}RI and Lyn kinase are positioned primarily on the microvilli of resting mast cells in separate nano-assemblies. Upon antigen-activation, Fc{varepsilon}RI and Lyn merge into overlapping populations together with the LAT scaffold protein, accompanied by merger of microvilli into ridge-like ruffles. With selective lipid probes, we further found that ordered-lipid nanodomains preferentially occupy microvillar membranes, contrasting with localization of disordered lipids to flatter regions. With this proximity of signaling proteins and ordered lipid nanodomains in microvilli, the mast cells are poised to respond sensitively and efficiently to antigen but only in the presence of this stimulus. Use of a short chain ceramide to disrupt ordered-lipid regions of the plasma membrane and evaluation with MVC, CP, and flow cytometry provided strong evidence that the microvillar selective localization of signaling proteins and membrane environments is facilitated by the interplay between ordered-lipid nanodomains and actin attachment proteins, ERM (ezrin, radixin, moesin) and cofilin. Significance StatementParticipation of ordered-lipid nanodomains (aka "rafts") to target immune signaling in the plasma membrane has been established. Separately, membrane topography, specifically microvilli, has also emerged as a participant. Here, we show how these features are coordinated in mast cells that serve as gatekeepers for antigen-triggered, receptor-mediated immune responses, including allergies and inflammation. We found that these specific antigen receptors and a key kinase, together with ordered-lipid nanodomains, localize to microvilli in resting cells, forming separated nano-assemblies. Antigen causes the merger of microvilli into ruffles where receptors and kinases couple to initiate transmembrane signaling. Selective pre-organization of signaling proteins and targeting lipid domains in microvilli and their coordinated redistribution upon antigen stimulation facilitates sensitive and efficient immune responses.

immunology↗

bioRxiv2024

UV-Induced DNA Repair Mechanisms and Their Effects on Mutagenesis and Culturability in Escherichia coli

Ultraviolet-B (UV-B) radiation, intensified by ozone depletion, induces DNA damage and promotes mutagenesis, shaping evolution. While UV-induced SOS responses are well characterized in bacteria, the cellular consequences of prolonged UV-B exposure remain less clear. Prolonged UV-B exposure disrupts translation and RecA-mediated SOS induction without major changes in membrane permeability or reactive oxygen species. This impairs mutagenesis and induces a reversible loss of culturability. Genetic analysis reveals both redundant and differential roles for DNA repair pathways: homologous recombination (RecA, RecB), nucleotide excision repair (UvrA), and translesion synthesis (UmuC/D) are essential for maintaining mutagenesis and culturability, while others (RecN, RmuC) have limited impact. Notably, deletion of UvrD (a repair-associated helicase) intensifies transient non-culturability without affecting mutagenesis, underscoring complexity in repair networks. Overall, our findings reveal a dose-dependent trade-off: moderate UV-B promotes mutagenesis with minimal viability loss, whereas prolonged exposure suppresses mutagenesis via transient dormancy, reflecting an adaptive strategy with significant evolutionary implications.

microbiology↗

bioRxiv2024

Telmisartan impedes JEV infection predominately via AT1/PPARγ axis

Japanese encephalitis, caused by Japanese encephalitis virus (JEV) is a vector born disease for which no specific therapeutics are available yet. Binding of angiotensin II (Ang II) to angiotensin II type 1 (AT1) receptor induces release of inflammatory cytokines associated with viral encephalitis. Accordingly, Ang II receptor blockers (ARBs) have been proposed to manage encephalitis. Since Telmisartan (TM, antagonist of AT1 and agonist of PPAR{gamma}) has relatively better brain access than other ARBs, this investigation aims to evaluate its anti-JEV efficacy in vitro and in vivo. TM reduced JEV titer, RNA and protein (NS3) significantly in the BHK-21 cells with IC50 of 24.68M and CC50 of >350 M (Selectivity Index >14.18) indicating its potential of repurposing against JEV. The anti-JEV efficacy of TM was further observed in macrophages (RAW264.7) and neuronal (SH-SY5Y) cells. Interestingly, the viral load was reduced significantly in pre, co and post-treatment conditions of TM, however most efficiently (80%) in post treatment. In presence of GW (PPAR{gamma} antagonist) and AG (AT1 agonist), viral infection was increased remarkably while AT1 was upregulated and PPAR{gamma} was downregulated. Whereas, TM treatment reversed the levels of AT1 and PPAR{gamma} during infection. Further, reduction of inflammatory markers like p-IRF-3, COX-2 and p-NF-{kappa}B was observed after TM treatment in RAW264.7 cells suggesting its immunomodulation through the AT1/PPAR{gamma} axis. Finally, the anti-JEV potential of TM was validated in mice model through the reduction of disease score, viral protein and histological changes. Thus, the preclinical efficacy of TM suggests its suitability for repurposing against JEV.

microbiology↗

bioRxiv2024

Nanomaterials trigger functional responses in primary human immune cells

Targeting the immune system with nanoparticles (NPs) to deliver immunomodulatory molecules emerged as a solution to address intra-tumoral immunosuppression and enhance therapeutic response. While the potential of nanoimmunotherapies in reactivating immune cells has been evaluated in several preclinical studies, the impact of drug-free nanomaterials on the immune system remains unknown. Here, we characterize the molecular and functional response of human NK cells and pan T cells to a selection of five NPs that are commonly used in biomedical applications. After a pre-screen to evaluate the toxicity of these nanomaterials on immune cells, we selected ultrasmall silica-based gadolinium (Si-Gd) NPs and poly(lactic-co-glycolic acid) (PLGA) NPs for further investigation. Bulk RNA-sequencing and flow cytometry analysis showcase that PLGA NPs trigger a transcriptional priming towards activation in NK and pan T cells. While PLGA NPs improved NK cells anti-tumoral functions in cytokines-deprived environment, Si-Gd NPs significantly impaired T cells activation as well as functional responses to a polyclonal antigenic stimulation. Altogether, we identified PLGAs NPs as suitable and promising candidates for further targeting approaches aiming to reactivate the immune system of cancer patients.

immunology↗

bioRxiv2024

Polyphenol-rich fraction of Bergenia ligulata (Wall.) Engl. sensitizes colon and breast cancer metastasis in vivo: Evidence of cell-type specific mechanism

BackgroundColon and breast cancer are one of the leading causes of mortality worldwide. Limited efficacies of present treatments highlighted an urgent need for improvement. Bergenia ligulata is known for its anticancer properties in Indian traditional and folk medicine though the molecular basis of its effects, particularly its anti-metastatic properties, is not well understood. Anti-prostate cancer activity of a LCMS defined polyphenol-rich fraction from Bergenia ligulata (PFBL) rhizome extract has already been published showing promising results in preclinical models. PurposeThe present study aims to explore anti-cancer activity and anti-metastatic potentials of PFBL against colon and breast cancers in both in vitro and preclinical settings. Study design and methodsPFBL alone or in synergy with standard chemotherapeutic drugs was tasted in CT26 and 4T1 subcutaneous solid tumors in BALB/c mice. The effect of PFBL was analyzed in terms of changes in tumor mass and different molecular marker levels. Anti-metastatic potential of PFBL was evaluated in CT26 and 4T1 lung metastasis model in mice focusing on the number of lung nodules and lung size. ResultsOur results evidenced that PFBL efficiently regressed both CT26 and 4T1-induced solid tumors alone and in combination with 5FU/doxorubicin without affecting the health of normal host. Notably, PFBL suppressed lung metastasis of 4T1 and CT26 cells in mice with great efficacy. Analysis of tumor and cell extracts suggested that colon cancer cells died by autophagy, while breast cancer cells majorly died by caspase-dependent apoptosis. PFBL actions involved AMPK-dependent inhibition of mTORC1 and subsequent increase in LC3II, PARP1, CDK4 and Cyclin D1 levels in both HCT116 and MCF7 cells; an elevation of intracellular ROS level was the major cause of death in both the cancer types. PFBL treatment also reversed the EMT marker expressions in in vivo and in vitro. ConclusionPFBL regressed colon and breast cancer metastasis through distinct mechanisms with little effect on healthy mice. The present study underscored PFBL as a novel anti-tumor and anti-metastasis candidate warranting further testing in clinical settings.

cancer biology↗

bioRxiv2024

Limitations of the radiotheranostic concept in neuroendocrine tumors due to lineage-dependent somatostatin receptor expression on hematopoietic stem and progenitor cells

Radiopharmaceutical therapy (RPT) has become an effective treatment option for neuroendocrine tumors (NETs) and castration-resistant prostate cancer and is in clinical development for a growing number of indications. One of the major advantages of theranostic RPT is that the distribution of radiopharmaceuticals in the human body can be imaged, and radiation doses to the patients organs can be calculated. However, accurate dosimetry may be fundamentally limited by microscopic heterogeneity of radiopharmaceutical distribution. We developed fluorescent analogs of somatostatin-receptor-subtype 2 (SSTR2) targeting Lutetium-177 labelled radiopharmaceuticals that are clinically used in patients with neuroendocrine tumors (NETs) and studied their uptake by hematopoietic stem and progenitor cells (HSPC). Hematopoietic stem cells (HSCs) and multipotent progenitor cells (MPPs) showed high and specific SSTR2-ligand uptake, which was at similar levels as neuroendocrine tumor cells. Furthermore, they displayed a several-fold higher uptake of SSTR2-antagonists than of SSTR2-agonists. HSPC treatment with a 177Lu-labelled antagonist and agonist showed a stronger reduction of HSC proliferation by the antagonist. Due to the scarcity of HSCs and MPPs, their contribution to total bone marrow uptake of SSTR2-ligands is not detectable in imaging-based dosimetry studies. This likely explains why SSTR2-antagonists caused pancytopenia in clinical trials despite safe dosimetry estimates. In conclusion, target expression heterogeneity can lead to underestimation of radiopharmaceutical toxicity and should be considered when designing clinical trials for new radiopharmaceuticals. The implications of our findings go beyond somatostatin receptor-targeted radiopharmaceuticals and suggest more generally that first-in-human studies should not only be guided by radiation dosimetry from imaging studies but should also include careful escalation of the administered therapeutic activity. The MMC technology is modular and can be applied to other peptide or protein-based radiopharmaceuticals to study cellular distribution and potential bone marrow uptake prior to clinical testing.

cancer biology↗

bioRxiv2024

Deep Mining of the Human Antibody Repertoire Identifies Frequent and Immunogenetically Diverse CDRH3 Topologies Targetable by Vaccination

Germline targeting vaccination strategies against highly variable pathogens such as HIV aim to elicit broadly neutralizing antibodies (bnAbs) with particular immunogenetic or structural features. The V2 apex of the HIV Env protein is a promising target for a class of bnAbs that contain conserved structural motifs in the heavy chain complementarity determining region 3 (CDRH3). Here, we show that these structural motifs are targetable by vaccination by characterizing V2 apex axe-like CDRH3s in the human repertoire and developing new immunogens capable of engaging them. We determined the frequency and diversity of axe-like CDHR3s in healthy human donors using a series of structural informatics approaches, finding these precursors in nearly 90% of donors. Axe-targeting immunogens based on the HIV Env Q23.17 bound axe-like precursors in cryo-EM structures, induced V2 apex-specific antibody responses in humanized mice, and induced axe-like heterologous neutralizing antibodies in rhesus macaques infected with a germline-targeted simian-human immunodeficiency virus. These results illustrate a new structure-guided immunoinformatic vaccine design paradigm that can be employed to elicit immunogenetically diverse yet structurally conserved classes of antibodies. Significance StatementMany broadly neutralizing antibodies (bnAbs) utilize modes of epitope recognition dominated by the antibody complementarity determining region 3 (CDRH3). The CDRH3 is the most diverse part of the antibody, posing a challenge for germline targeting vaccine designs that aim to elicit antibodies with particular immunogenetic features. Vaccine design strategies that accommodate CDRH3 variability are therefore needed. Many HIV Env V2 apex bnAbs share "axe-like" CDRH3 microfolds that arise from diverse immunogenetic origins. Here we determined the frequency in humans of B cells with such CDRH3 topologies and designed immunogens to engage their precursors. This work opens a path toward vaccines that engage specific structural classes of B cells, thereby advancing the rational design of immunogens for HIV and other pathogens.

immunology↗

bioRxiv2024

Deciphering shared molecular dysregulation across Parkinson's disease variants using a multi-modal network-based data integration and analysis

Parkinsons disease (PD) is a progressive neurodegenerative disorder with no effective treatment. Advances in neuroscience and systems biomedicine now enable the use of complex patient-specific in vitro disease models and cutting-edge computational tools for data integration, enhancing our understanding of complex PD mechanisms. To explore common biomedical features across monogenic PD forms, we developed a knowledge graph (KG) by integrating previously published high-content imaging and RNA sequencing data of PD patient-specific midbrain organoids harbouring LRRK2-G2019S, SNCA triplication, GBA-N370S or MIRO1-R272Q mutations with publicly available biological data. Furthermore, we generated a single-cell RNA sequencing dataset of midbrain organoids derived fromidiopathic PD patients (IPD) to stratify IPD patients towards genetic forms of PD. Despite high PD heterogeneity, we found that common transcriptomic dysregulation in monogenic PD forms is reflected in IPD glial cells. In addition, dysregulation in ROBO signalling might be involved in shared pathophysiology between monogenic PD and IPD cases.

systems biology↗

bioRxiv2024

Cyclooxygenase-2 disruption predisposes to heart failure with preserved ejection fraction

Heart failure (HF) is one of the most strongly associated adverse cardiovascular events linked to the use of cyclooxygenase (COX)-2 selective and non-selective nonsteroidal anti-inflammatory drug (NSAID). Nevertheless, it remains uncertain whether NSAID exposure is more likely to lead to heart failure with reduced ejection fraction (HFrEF) or preserved ejection fraction (HFpEF). In adult mice, postnatal genetic deletion or pharmacological inhibition of COX-2 did not affect cardiac function. In contrast, aged female inducible COX-2 (iCOX-2) knockout (KO) mice displayed diastolic dysfunction, cardiac hypertrophy, pulmonary congestion, and elevated levels of plasma N-terminal pro B-type natriuretic peptide (BNP) when compared to age- and sex- matched controls, while their ejection fraction (EF) remained preserved ([≥] 50%). No such phenotype was observed in aged male iCox-2 KO mice. Aged female iCox-2 KO mice showed a shift from prostanoid to leukotriene biosynthesis, along with changes in the expression of mitochondrial genes and calcium-handling proteins in the myocardium. The ratio of phospholamban to SERCA2a was increased, indicating an inhibitory effect on SERCA2a activity, which may contribute to impaired myocardial relaxation. In larval zebrafish, COX-2 inhibition by celecoxib caused a modest yet significant reduction in heart rate and diastolic function, while EF was preserved. Additionally, celecoxib increased BNP expression and ventricular calcium transient amplitude. Diabetic patients in the Harvard-Partners electronic medical record exposed to NSAIDs selective for COX-2 inhibition were more strongly associated with an increased risk of HFpEF compared to HFrEF. Collectively, these findings indicate that COX-2 deletion or inhibition does not impair systolic cardiac function but instead leads to an HFpEF phenotype in mice, zebrafish, and humans. An imbalance in calcium handling may mediate the impairment of myocardial relaxation following COX-2 suppression. SummaryGenetic deletion or pharmacological inhibition of COX-2 results in heart failure with preserved ejection fraction across zebrafish, mice, and humans.

pharmacology and toxicology↗

bioRxiv2024

Membrane-tethered cadherin substrates reveal actin architecture at adherens junctions

Adherens junctions (AJs) are E-cadherin-based adhesions at cell-cell contacts that connect the actin cytoskeleton of epithelial cells. Formation and maturation of these junctions is important in development, e.g. for the generation of epithelial tissues, and loss of adherens junctions is linked to metastasis in cancer. It is well established that AJ formation is a mechano-sensitive process involving cis and trans clustering of E-cadherin and the mechanotransducive activation of -catenin that connects E-cadherin with the actin cytoskeleton. However, how mobility of E-cadherin in the cell membrane and their local density influences actin polymerisation is less well understood due to limitations in controlling physical properties of cell membranes and performing high-resolution microscopy in model organisms or cell-monolayers. Here we have created a biomimetic system enabling super-resolution microscopy of AJs by placing MCF7 cells, labelled with fluorescent actin, E-cadherin and -catenin, on fluid supported lipid bilayers (SLB) containing the extracellular domain of E-cadherin. We found that MCF7 cells were able to attach and spread on these substrates, recruiting E-cadherin and -catenin to form AJs that can mature and are mobile. Interestingly, we found that depending on E-cadherin mobility within the SLB, distinct types of actin architecture emerge. Low mobility substrates support formin-based linear actin polymerisation while high mobility substrates support Arp2/3-based branched actin network polymerisation. These polymerising actin structures are spatially confined to regions of low E-cadherin density suggesting they may play a role in AJ repair. Following how these actin structures at the cell-SLB interface evolve over time indicates regions of both linear and branched actin being present at mature cell-cell contacts.

cell biology↗

bioRxiv2024

Protein degradation by small tag artificial bacterial E3 ligase

Targeting of proteins for degradation in a reversible manner is a powerful approach to decipher gene function and mimic drug effects, with great potential for drug target discovery and validation. A generalized approach is to tag a protein of interest and then use this tag to recruit an endogenously or exogenously expressed E3 ligase for its polyubiquitination and subsequent degradation via 26S proteasome. However, the often bulky size of the tag and the great variability of substrate-dependent degradation efficiency of mammalian E3 ligases pose great challenges in practice. Here we show that small tags (10-15 amino acids) can be used to efficiently tag endogenous proteins for degradation when coupled with an exogenously expressed artificial bacterial E3 ligase (ABEL) consisting of a tag-interacting moiety and the catalytic domain of the bacterial E3 ligase IpaH9.8. We name this versatile and efficient platform degradation by small tag ABEL (DESTABEL). Furthermore, we show that an ABEL containing a nanobody against human -synuclein mediates efficient degradation in primary neurons as well as in the adult mouse brain. Taken together, our data show that tag-dependent and independent ABELs are powerful yet flexible tools for studies of protein function and drug target validation.

molecular biology↗

bioRxiv2024

Optimizing Digital PCR Assays for Multiplexed Microbial Source Tracking in Surface Waters

Digital PCR (dPCR) shows great promise for precise, sensitive, and inhibition-resilient measurement of nucleic acids in surface water, providing an advantage for applications such as microbial source tracking (MST). Herein, we describe our empirical optimization of two triplex format dPCR reactions (Triplex 1 - Cow M2, Rum2Bac, Cow M3; Triplex 2 - HF183/BacR287, Pig2Bac, Entero1a) on the QIAcuity One system for MST. Each triplex produced gene copy measurements similar to single-plex format assays for a standard reference material (SRM 2917) at a fixed concentration and along a concentration gradient. For achieved water samples previously tested by single-plex assays, each triplex also produced MST marker measurements comparable to the single-plex results. The triplexes described here can be directly adopted for MST on the QIAcuity, or the optimization protocol we demonstrate can be used to develop additional multiplex assays on the QIAcuity system.

molecular biology↗

bioRxiv2024

Enhancing efficacy of the MEK inhibitor trametinib with paclitaxel in KRAS-mutated colorectal cancer

BackgroundKRAS is frequently mutated in the tumors of patients with metastatic colorectal cancer (mCRC) and thus represents a valid target for therapy. However, the strategies of targeting KRAS directly and targeting the downstream effector mitogen-activated protein kinase kinase (MEK) via monotherapies have shown limited efficacy. Thus, there is a strong need for novel, effective combination therapies to improve MEK-inhibitor efficacy in patients with KRAS-mutated mCRC. ObjectiveOur objective was to identify novel drug combinations that enhance MEK-inhibitor efficacy in patients with KRAS-mutated mCRC. DesignIn this study, we performed unbiased high-throughput screening (HTS) to identify drugs that enhance the efficacy of MEK inhibitors in vitro, and we validated the efficacy of the drugs in vivo. MethodsHTS was performed using 3-dimensional CRC spheroids. Trametinib, the anchor drug, was probed with 2 clinically ready libraries of 252 drugs to identify effective drug combinations. The effects of the drug combinations on CRC cell proliferation and apoptosis were further validated using cell growth assays, flow cytometry, and biochemical assays. Proteomic and immunostaining studies were performed to determine the effects of the drugs on molecular signaling and cell division. The effects of the drug combinations were examined in vivo using CRC patient-derived xenografts. ResultsHTS identified paclitaxel as being synergistic with trametinib. In vitro validation showed that, compared with monotherapies, this drug combination demonstrated strong inhibition of cell growth, reduced colony formation, and enhanced apoptosis in multiple KRAS-mutated CRC cell lines. Mechanistically, combining trametinib with paclitaxel led to alterations in signaling mediators that block cell cycle progression and increases in microtubule stability that resulted in significantly higher defects in the mitosis. Finally, the combination of trametinib with paclitaxel exhibited significant inhibition of tumor growth in several KRAS-mutant patient-derived xenograft mouse models. ConclusionOur data provide evidence supporting clinical trials of trametinib with paclitaxel as a novel therapeutic option for patients with KRAS-mutated, metastatic CRC.

cancer biology↗

bioRxiv2024

A hepatocyte-specific cytochrome c oxidase deficiency in mice leads to a lymphopenia owing to deficiencies in bone marrow progenitors

Mutations that negatively impact mitochondrial function are highly prevalent in humans and lead to disorders with a wide spectrum of disease phenotypes, including deficiencies in immune cell development and/or function. Previous analyses of mice with a hepatocyte-specific cytochrome c oxidase (COX) deficiency revealed an unexpected peripheral blood leukopenia associated with splenic and thymic atrophy. Here, we use mice with a hepatocyte-specific deletion of the COX assembly factor Sco1 to show that metabolic defects extrinsic to the hematopoietic compartment lead to a pan-lymphopenia represented by severe losses in both B and T cells. We further demonstrate that immune defects in these mice are associated with the loss of bone marrow lymphoid progenitors common to both lineages and early signs of autoantibody-mediated autoimmunity. Our findings collectively point to a significant role for hepatocyte dysfunction as an instigator of immunodeficiency in patients with congenital mitochondrial defects who suffer from chronic or recurrent infections.

immunology↗

bioRxiv2024

FAIR assessment of MINERVA as an opportunity to foster open science and scientific crowdsourcing in systems biomedicine

1The Disease Maps Project (https://disease-maps.org) focuses on the development of diseasespecific comprehensive structured knowledge repositories supporting translational medicine research. These disease maps require continuous interdisciplinary collaboration and should be reusable and interoperable. Adhering to the Findable, Accessible, Interoperable and Reusable (FAIR) principles enhances the utility of such digital assets. We used the RDA FAIR Data Maturity Model and assessed the FAIRness of the Molecular Interaction NEtwoRk VisuAlization (MINERVA) Platform. MINERVA is a standalone webserver that allows users to manage, explore and analyse disease maps and their related data manually or programmatically. We exemplify the FAIR assessment on the Parkinsons Disease Map (PD map) and the COVID-19 Disease Map, which are large-scale projects under the umbrella of the Disease Maps Project, aiming to investigate molecular mechanisms of the Parkinsons disease and SARS-CoV-2 infection, respectively. We discuss the FAIR features supported by the MINERVA Platform and we outline steps to further improve the MINERVA FAIRness and to better connect this resource to other ongoing scientific initiatives supporting FAIR in computational systems biomedicine.

systems biology↗

bioRxiv2024

Prenatal glyphosate exposure disrupts the gut-brain axis across several generations in mice.

Glyphosate, a widely used herbicide in North America, has become prevalent in the food supply, raising concerns about potential health impacts. In this exploratory study, male and female F0 mice were exposed to glyphosate through drinking water during mating and gestation. We investigated whether prenatal exposure at dietary-relevant levels (0.01 mg/kg/day, Average American Diet, [AAD]) or the U.S. EPAs acceptable daily intake (1.75 mg/kg/day, [EPA upper limit]) altered gut, metabolic, and behavioral outcomes across two generations in mice with or without genetic susceptibility to colitis (Muc2+/- and Muc2-/-, respectively). Healthy (Muc2+/-) offspring of glyphosate-exposed mice exhibited colonic goblet cell depletion, reduced mucin-2 expression, and pro-inflammatory cytokine profiles in both F1 and F2 generations. These healthy (Muc2+/-) offspring also developed metabolic dysfunction, including impaired glucose tolerance, insulin resistance, and reduced GLP-1 in serum. Behavioral deficits were also observed in healthy (Muc+/-) mice including reduced locomotion and working memory, and these changes were associated with altered microbiome composition and gut-brain mediators. These findings suggest that prenatal glyphosate exposure, even below regulatory thresholds, may disrupt multiple physiological systems across generations, highlighting the need for further research and regulatory consideration.

pharmacology and toxicology↗

bioRxiv2024

Genomic loci for sclerotinia stem rot resistance and chlorophyll stability in Brassica napus: integrating GWAS with microbiome insights

Sclerotinia Stem Rot (SSR) disease is one of the most serious diseases affecting the yield and quality of oilseed rape (Brassica napus). Understanding the genetic basis of the resistance trait in oilseed rape to SSR and microbiome composition for enhanced resistance is crucial for developing resistant varieties and sustainably mitigate the impact of the disease. In this study, in a panel of 168 oilseed rape accessions, most resistant (NGB 13503 and NGB 13834) and susceptible (NGB 13497 and NGB 13897) accessions are identified. A Genome-wide association study (GWAS) identified 47 SNPs linked to the SSR lesion length, lesion area, and lesion relative to the leaf area. Among the SNPs significantly linked to lesion length were Bn-A04-p10555408, Bn-A07-p12487549, Bn-A09-p4652268, Bn-A09-p4916858 and to our knowledge, these SNPs have not been previously linked to SSR resistance in oilseed rape. Moreover, the study identified 24 SNPs linked with chlorophyll content before SSR inoculation (SPADH), after the SSR inoculation (SPADI), and chlorophyll index (CI). Maintaining the chlorophyll level is correlated with the SSR resistance. Furthermore, bacterial taxa (e.g. Pseudomonas, Methylobacterium, and Aquabacterium) and fungal taxa (e.g. Mycosphaerellales, Thelebolales, and Akanthomyces) were enriched in the resistant compared to in the susceptible oilseed rape accessions. The SNPs linked to lesion length showed consistent haplotype variation between these selected accessions. Given the absence of complete resistance against SSR, the study provides insights into the significance of maintaining chlorophyll levels and considering microbiome composition for enhancing the level of existing partial resistance to SSR in oilseed rape.

plant biology↗