Biology subjects

Dubey, N.

Publications and source records attributed to Dubey, N..

9 recordsLinked to original sources

bioRxiv2026

Experimental evolution reveals temporally opposing roles for Csu pili during Acinetobacter baumannii respiratory infection

Multidrug-resistant (MDR) Acinetobacter baumannii is an opportunistic pathogen responsible for a wide range of infections, including ventilator-associated pneumonia, bloodstream infections, and urinary tract infections. Most studies investigating A. baumannii pulmonary pathogenesis rely on acute pneumonia models that use high bacterial inocula and do not recapitulate the prolonged infections observed in some patients. Recently, our laboratory developed a murine model of chronic pulmonary infection that enabled the identification of virulence factors specifically required for long-term lung persistence. To investigate how A. baumannii adapts during chronic pulmonary infection, we performed an experimental evolution study using this model. This approach revealed an unexpected role for the archaic chaperone-usher (Csu) pili in A. baumannii pathogenesis. At early time points, Csu expression reduced bacterial burdens in both acute and chronic pneumonia models, an effect associated with enhanced host inflammatory responses. In contrast, at later stages of chronic infection, Csu promoted bacterial persistence, potentially by facilitating adhesion to pulmonary epithelial cells. These opposing effects were conserved across two distinct A. baumannii clinical isolates. We also found that Csu contributes to bacterial colonization in a catheter-associated urinary tract infection (CAUTI) model in a strain-dependent manner. Together, these findings reveal an infection-stage-dependent role for Csu in A. baumannii pathogenesis, demonstrating that a bacterial surface structure can impair early colonization while promoting long-term persistence.

microbiology↗

bioRxiv2026

Integrative Multi-Tissue Analysis Identifies Synaptic Gene Networks Specific to Major Depressive Disorder in Women

Major Depressive Disorder (MDD) shows marked gender differences in prevalence and molecular signatures. Transcriptomic studies of post-mortem human brain tissue have reported alterations in the expression of synapse-related genes in MDD, including gender-specific patterns. But it remains unclear whether transcriptional changes observed in the brains of women with MDD are detectable in peripheral blood and conserved in experimental stress models. Whole-blood RNA sequencing was performed in women with MDD (n = 6) and matched healthy controls (n = 4). Differentially expressed genes (DEGs) were compared with previously reported female-specific blood and post-mortem brain transcriptomic datasets where selected overlapping synapse-associated genes were evaluated in the hippocampus and prefrontal cortex of female mice exposed to Chronic Variable Mild Stress (CVMS). Peripheral blood analysis identified DEGs enriched for synaptic organization, neuronal structure, and ion transport pathways. A substantial proportion of DEGs overlapped with previously reported datasets from peripheral blood, female MDD brain transcriptomic studies, and genes showing exclusive/enriched expression in the normal human brain. Network-based prioritization identified seven synapse-associated genes (SHANK2, SHANK3, CACNG8, GPHN, PICK1, NRXN2 and DNM2) for further analysis. In the female CVMS model, several of these genes showed altered expression in the hippocampus and/or prefrontal cortex, alongside behavioural changes and reduced dendritic spine density. These findings highlight shared transcriptional signals across human blood and human brain datasets, as well as in the mouse brain. However, larger studies are required to confirm and validate these observations.

neuroscience↗

bioRxiv2024

Explainable models using transcription factor binding and epigenome patterns at promoters reveal disease-associated genes and their regulators in the context of cell-types

Understanding genome-wide epigenetic regulation of diseases is important in establishing pathogenic factors and could aid in disease diagnosis, prognosis, and therapeutics. In this study, we have utilized transcription factors (TFs) and co-factor profiles (n=823) as features in machine learning models to link them to various diseases. Further, along with TFs and co-factor profiles, histone modifications ChIP-seq (n = 621), cap analysis gene expression (CAGE) tags (n = 255), and DNase hypersensitivity profiles (n = 255) as features allowed for the modeling of association of coding and non-coding genes to diseases. Such predicted associations could be independently validated using genome-wide association data and survival analysis. However, the unique aspect of our approach is that it highlights the link between TF binding patterns and diseases in the context of cell types. Besides highlighting relevant TF-binding in known cell-types associated with diseases, it also provided their surprising link with TFs expressed in immune cells and other seemingly non-related cells. Further investigation revealed such links to be genuine and potentially useful for prognosis, further revealing the need to deconvolve a set of known genes associated with diseases.

bioinformatics↗

bioRxiv2023

Type I IFN signaling in the absence of IRGM1 promotes M. tuberculosis replication in immune cells by suppressing T cell responses

Polymorphisms in the IRGM gene are associated with susceptibility to tuberculosis in humans. A murine ortholog of Irgm, Irgm1, is also essential for controlling Mycobacterium tuberculosis (Mtb) infection in mice. Multiple processes have been associated with IRGM1 activity that could impact the host response to Mtb infection, including roles in autophagy-mediated pathogen clearance and expansion of activated T cells. However, what IRGM1-mediated pathway is necessary to control Mtb infection in vivo and the mechanistic basis for this control remains unknown. We dissected the contribution of IRGM1 to immune control of Mtb pathogenesis in vivo and found that Irgm1 deletion leads to higher levels of IRGM3-dependent type I interferon signaling. The increased type I interferon signaling precludes T cell expansion during Mtb infection. The absence of Mtb-specific T cell expansion in Irgm1-/- mice results in uncontrolled Mtb infection in neutrophils and alveolar macrophages, which directly contributes to susceptibility to infection. Together, our studies reveal that IRGM1 is required to promote T cell-mediated control of Mtb infection in neutrophils, which is essential for the survival of Mtb-infected mice. These studies also uncover new ways type I interferon signaling can impact TH1 immune responses.

immunology↗

bioRxiv2023

Unmasking Crucial Residues in Adipose Triglyceride Lipase (ATGL) for Co-Activation with Comparative Gene Identification-58 (CGI-58)

Lipolysis is an essential metabolic process that releases unesterified fatty acids from neutral lipid stores to maintain energy homeostasis in living organisms. Adipose triglyceride lipase (ATGL) plays a key role in intracellular lipolysis and can be co-activated upon interaction with the protein comparative gene identification-58 (CGI-58). The underlying molecular mechanism of ATGL stimulation by CGI-58 is incompletely understood. Based on analysis of evolutionary conservation, we used site directed mutagenesis to study a C-terminally truncated variant and full-length mouse ATGL providing insights in the protein co-activation on a per-residue level. We identified the region from residues N209-N215 in mouse ATGL as essential for co-activation by mouse CGI-58. ATGL variants with amino-acids exchanges in this region were still able to hydrolyze triacylglycerol at the basal level and to interact with CGI-58, yet could not be activated by CGI-58. Our studies also demonstrate that full-length mouse ATGL showed higher tolerance to specific single amino acid exchanges in the N209-N215 region upon CGI-58 co-activation compared to C-terminally truncated ATGL variants. The region is either directly involved in protein-protein interaction or essential for conformational changes required in the co-activation process. Three-dimensional models of the ATGL/CGI-58 complex with the artificial intelligence software AlphaFold demonstrated that a large surface area is involved in the protein-protein interaction. Mapping important amino acids for co-activation of both proteins, ATGL and CGI-58, onto the 3D model of the complex locates these essential amino acids at the predicted ATGL/CGI-58 interface thus strongly corroborating the significance of these residues in CGI-58 mediated co-activation of ATGL.

biochemistry↗

bioRxiv2023

Autophagy functions in lung macrophages and dendritic cells to suppress TH17 responses and neutrophil accumulation during allergic airway inflammation

Asthma affects 260 million people worldwide, with severe asthma cases that are associated with TH17/TH1 responses and neutrophil dominated inflammation being the most difficult to treat due to corticosteroid insensitivity. Single nucleotide polymorphisms in the ATG5 gene, which encodes for a protein required for the cellular recycling process of autophagy, are associated with higher risk for developing severe asthma. However, the role for ATG5 during allergic inflammation remains mostly unknown. We have identified an autophagy-dependent role for ATG5 in lung macrophages and dendritic cells (DCs) for suppressing TH17 responses and neutrophil accumulation in house dust mite (HDM)-challenged mice, a TH17/TH1 dominated model for allergic airway inflammation due to contamination of the HDM with lipopolysaccharide. In contrast, autophagy was required to promote eosinophil accumulation in the TH2-dominated ovalbumin model of allergic airway inflammation, supporting a model where autophagy functions in lung macrophages and DCs to suppress TH17 responses and promote TH2 responses in an allergen-dependent manner. In addition, we discover that autophagy is also required in macrophages exposed to HDM to suppress the secretion of cytokines and chemokines that would otherwise recruit neutrophils to the lungs, independent of T cell responses. Together, our data identify multiple roles for autophagy in suppressing the neutrophil accumulation in lungs that is associated with severe asthma.

immunology↗

bioRxiv2022

Autophagy protects against high-dose Mycobacterium tuberculosis infection

Host autophagy had been associated with the control of Mycobacterium tuberculosis (Mtb) infection due to its ability to sequesters microorganisms through a process termed "xenophagy"1-4. Xenophagy purportedly limits Mtb replication within infected macrophages1-4. However, studies in mice using a standard low-dose infection model demonstrated that xenophagy in infected phagocytes is not required to control Mtb pathogenesis5,6. Instead, an autophagy-independent function of ATG5 in myeloid cells controls low-dose Mtb infection through limiting neutrophilic inflammation5. Hitherto, an in vivo role for autophagy during Mtb infection remained to be elucidated. We report herein that autophagy in myeloid cells mediates protection against high-dose Mtb infection, providing the first evidence for a role for autophagy in myeloid cells during Mtb infection in vivo. With the exception of ATG5, the autophagy proteins required to control high-dose Mtb infection are dispensable for host defense against a standard low-dose Mtb infection. Specifically, autophagy is required in CD11c+ cells, but is dispensable in neutrophils, to control a high-dose Mtb infection in the lung. The role for autophagy is not to directly degrade Mtb in macrophages through xenophagy, but mainly to limit myeloid-derived suppressor cell accumulation and to promote sustained protective T cell responses. Together, our data highlight a novel role for autophagy in controlling Mtb infection, distinct from that of Atg5 during low-dose Mtb infection, or any previously reported roles for autophagy. In addition, our finding that the result of a pathogen-plus-susceptibility gene interaction is dependent on pathogen burden has important implications on our understanding of how Mtb infection in humans can lead to a spectrum of outcomes, the variables that contribute to autophagy gene function during infection and inflammation, and the potential use of autophagy modulators in clinical medicine.

microbiology↗

bioRxiv2022

DIP2 is a unique regulator of diacylglycerol lipid homeostasis in eukaryotes

Chain-length specific subsets of diacylglycerol (DAG) lipids are proposed to regulate differential physiological responses ranging from signal transduction to modulation of the membrane properties. However, the mechanism or molecular players regulating the subsets of DAG species remains unknown. Here, we uncover the role of a conserved eukaryotic protein family, DISCO-interacting protein 2 (DIP2) as a homeostatic regulator of a chemically distinct subset of DAGs using yeast, fly and mouse models. Genetic and chemical screens along with lipidomics analysis in yeast reveal that DIP2 prevents the toxic accumulation of specific DAGs in the logarithmic growth phase, which otherwise leads to endoplasmic reticulum stress. We also show that the fatty acyl-AMP ligase-like domains of DIP2 are essential for the redirection of the flux of DAG subspecies to storage lipid, triacylglycerols. Such modulation of selective DAG abundance by DIP2 is found to be crucial for optimal vacuole-membrane fusion and consequently osmoadaptation in yeast. Thus, the study illuminates an unprecedented DAG metabolism route and provides new insights on how cell fine-tunes DAG subspecies for cellular homeostasis and environmental adaptation.

biochemistry↗

bioRxiv2021

A universal pocket in FAALs ensures redirection of fatty acid pool away from CoA-based activation

Fatty acyl-AMP ligases (FAALs) channelize fatty acids towards biosynthesis of virulent lipids in mycobacteria and other pharmaceutically or ecologically important polyketides and lipopeptides in other microbes. They do so by bypassing the ubiquitous coenzyme A-dependent activation and rely on the acyl carrier protein-tethered 4-phosphopantetheine (holo-ACP). The molecular basis of how FAALs strictly reject chemically identical and abundant acceptors like coenzyme A (CoA) and accept holo-ACP unlike other members of the ANL superfamily remains elusive. We show FAALs have plugged the promiscuous canonical CoA-binding pockets and utilize highly selective alternative binding sites. These alternative pockets can distinguish adenosine 3, 5-bisphosphate-containing CoA from holo-ACP and thus FAALs can distinguish between CoA and holo-ACP. These exclusive features helped identify the omnipresence of FAAL-like proteins and their emergence in plants, fungi, and animals with unconventional domain organisations. The universal distribution of FAALs suggests they are parallelly evolved with FACLs for ensuring a CoA-independent activation and redirection of fatty acids towards lipidic metabolites.

biochemistry↗