Biology subjects

Chandramouli, A.

Publications and source records attributed to Chandramouli, A..

9 recordsLinked to original sources

bioRxiv2026

Orthogonal Chemical Proteomic Strategies Reveal the Cholesteryl Ester Interactome in Mammalian Cells

Cholesteryl esters (CEs) are widely regarded as inert storage forms of cholesterol, yet their potential to directly engage cellular proteins remains largely unexplored. Here, we establish an integrated chemical proteomic platform to systematically define CE-protein interactions in mammalian cells. We developed and comparatively deployed three orthogonal photoaffinity labeling strategies: (i) metabolic assembly of a bifunctional CE probe through endogenous acyl-CoA:cholesterol acyltransferase activity, (ii) direct delivery of a structurally defined diazirine-alkyne CE analog, and (iii) fragment-assisted subtraction using sterol and fatty acyl control probes to resolve interactions dependent on the intact esterified scaffold. Each probe system was rigorously validated by lipidomics and UV-dependent crosslinking prior to quantitative proteomic analysis. Integration of these complementary modalities identified 495 CE-associated proteins spanning enzymes, transporters, scaffolding proteins, and canonical sterol-binding families. The limited overlap across strategies reveals that lipid-protein engagement is strongly conditioned by biosynthetic origin, probe topology, and intracellular routing. Functional and database annotations further demonstrate enrichment of druggable and disease-linked proteins, connecting CE interactions to metabolic, neurological, and cardiovascular pathways. Collectively, this work provides the first systems-level map of CE-protein interactions and establishes a generalizable, multimodal framework for chemically resolving lipid-protein interactomes.

biochemistry↗

bioRxiv2026

The Hunt for Cholesteryl Ester Hydrolases: Identification of Lipoprotein Lipase as a Cholesterylesterase

Cholesteryl esters (CEs) are central intermediates in cholesterol storage and transport, yet the enzymes responsible for their hydrolysis in mammals remain poorly defined. While lysosomal acid lipase is the only well-established acidic CE hydrolase, the molecular identity of physiologically relevant neutral CE hydrolases has remained unresolved. Here, we systematically profiled CE hydrolase activity across mouse tissues and blood using substrate-based LC-MS assays, tissue fractionation, and inhibitor screening. We observed robust CE hydrolase activity in multiple tissues and circulation, with activity predominantly enriched in membrane fractions and strongly sensitive to broad-spectrum metabolic serine hydrolase inhibitors. Pharmacological screening excluded previously proposed neutral CE hydrolases, including NCEH1 and LIPE, and identified tetrahydrolipstatin-sensitive lipoprotein lipase (LPL) as a candidate CE hydrolase. Competitive activity-based protein profiling analyses in RAW264.7 macrophages further supported selective enrichment and inhibition of LPL. Biochemical characterization demonstrated that recombinant wild-type LPL, but not the catalytic S159A variant, efficiently hydrolyzed CEs in vitro. Importantly, this activity required co-expression of the lipase maturation factor 1, indicating that LPL-mediated CE hydrolysis is dependent on proper enzymatic maturation. Together, these findings identify LPL as a previously unrecognized mammalian CE hydrolase and expand its functional role beyond triglyceride metabolism.

biochemistry↗

bioRxiv2026

Lysine specific demethylase 1 (LSD1) regulates host alpha-ketoglutarate levels to modulate lipid peroxidation during Mycobacterium tuberculosis infection

Mycobacterium tuberculosis (Mtb) subverts host immune responses via modulation of host epigenome and metabolism. In this study, we underscore a role for the epigenetic modifier, Lysine Specific Demethylase 1 (LSD1), in regulating macrophage metabolism to support mycobacterial pathogenesis. In ex vivo and in vivo infection models, LSD1 inhibition reduced mycobacterial CFU alleviating lung pathology. Metabolomic analysis of Mtb infected, LSD1 deficient macrophages revealed increased levels of alpha-ketoglutarate (AKG), a crucial TCA cycle metabolite via regulating genes implicated in glutamine breakdown. Moreover, exogenous addition of AKG resulted in reduced oxidative stress and attenuated lipid peroxidation (LPO) with a consequent decrease in Mtb survival. Blocking glutamine breakdown in LSD1 deficient macrophages failed to reduce LPO and promoted Mtb intracellular survival, highlighting the role of LSD1-AKG axis in this immunomodulation. Dietary supplementation of AKG to Mtb infected mice improved lung pathology, limited Mtb dissemination and reduced the levels of oxidative Malondialdehyde adducts. Therefore, we highlight a host protective role of AKG during Mtb pathogenesis through suppression of lipid peroxidation and uncover an epigenetic-metabolic axis exploited by Mtb, thereby positing dietary supplementation of AKG as a potential therapeutic strategy against Tuberculosis.

immunology↗

bioRxiv2025

A metabolic hierarchy directs cell cycle transition and morphogenesis

To optimize survival, cells must align differentiation and proliferation with metabolic status. Yet, how metabolic cues fine-tune cell cycle programs and morphogenesis remain unclear. Here, we show that cytosolic redox dynamics critically govern cell cycle transitions in Caulobacter crescentus. By integrating evolutionary genetics with fluxomics, we uncover temporally orchestrated shifts in core metabolic pathways that remodel cytosolic redox across the cell cycle. Early stages channel carbon flux toward unsaturated fatty-acid synthesis and a reverse-TCA to drive cytosolic oxidation-coupled G1-S transition. The later stages depend on an enhanced forward-TCA cycle that promote cytosolic reduction-driven proliferation. Strikingly, perturbing fatty-acid synthesis or reverse/forward-TCA uncouples growth from proliferation. Intriguingly, a biphasic glucose uptake program dictates the cell cycle-stage-specific metabolism. These findings reveal an unprecedented metabolic-redox circuitry coordinating morphogenesis with cell cycle progression in a carefully choreographed menage a trois.

microbiology↗

bioRxiv2025

Integrative lipidomics of brain and plasma uncovers sex-specific metabolic signatures in Parkinson's disease

Lipid dysregulation is increasingly recognized as a key feature of Parkinsons disease (PD). A central unresolved question, however, is whether lipidomic signatures identified in accessible peripheral biofluids faithfully recapitulate the pathogenic alterations within the central nervous system (CNS). This gap impedes the development of reliable biomarkers and constrains a comprehensive understanding of PD pathophysiology. To address this challenge, we employed a cross-species lipidomic approach. We modeled PD in both male and female mice by injecting human -synuclein preformed fibrils into the substantia nigra. Three months post-injection, lipidomic profiles of the midbrain and plasma were generated and compared. These findings were further validated in plasma from male and female PD patients and age-matched controls, enabling the identification of conserved alterations. We identified shared dysregulation of sphingolipids, glycerophospholipids, and fatty acids in the brains and plasma of diseased mice as well as in plasma from PD patients. Notably, lipids associated with lipid droplet biogenesis, including triacylglycerols and monoacylglycerols, were elevated in diseased mouse brains and patient plasma. These alterations coincided with a marked accumulation of lipid droplets in the mouse midbrain, and were further corroborated by increased lipid droplet abundance in macrophages derived from PD patients. Interestingly, lipid droplet accumulation exhibited sex-specific patterns: male mice displayed greater microglial accumulation, whereas female mice showed enhanced neuronal deposition. Together, these findings demonstrate that peripheral lipidomic signatures reflect CNS pathology in PD, highlighting new opportunities for biomarker discovery and therapeutic intervention. Furthermore, sex-specific lipid droplet accumulation in innate immune cells and neurons implicates these pathways as mechanistic contributors to PD and underscores the necessity of sex-stratified strategies in biomarker discovery and disease modeling.

neuroscience↗

bioRxiv2025

PE11 promotes intracellular persistence of Mycobacterium tuberculosis by inhibiting autophagy and lysosomal biogenesis by targeting the FLCN-lactate-TFEB signaling axis

Mycobacterium tuberculosis (Mtb) employs multiple virulence factors, including cell wall-associated proteins, to evade host immune responses. PE11, a cell wall-localized esterase, contributes to Mtb persistence by facilitating cell wall remodelling and resistance to acidic and antibiotic stress. Herein we describe a novel role of PE11 in subverting host autophagy through disruption of TFEB-mediated lysosomal function. PE11 promotes FLCN-dependent depletion of intracellular lactate to destabilize TFEB and thereby downregulate genes essential for autophagic flux and lysosomal acidification. Using a PE11-deficient Mtb strain, we demonstrate that PE11 targets the FLCN-lactate axis to regulate TFEB stability. Exogenous lactate supplementation restored TFEB stability, enhanced lysosomal acidification, and significantly reduced intracellular bacterial burden. Lactate also synergized with frontline anti-tubercular drugs to improve Mtb clearance. These findings establish PE11 as a key immune evasion factor and highlight lactate as a promising host-directed therapeutic to enhance bacterial killing and reduce antibiotic-associated toxicity.

microbiology↗

bioRxiv2024

A Facile LC-MS Method for Profiling Cholesterol and Cholesteryl Esters in Mammalian Cells and Tissues

Cholesterol is central to mammalian lipid metabolism and serves many critical functions in the regulation of diverse physiological processes. Dysregulation in cholesterol metabolism is causally linked to numerous human diseases, and therefore, in vivo, the concentrations and flux of cholesterol and cholesteryl esters (fatty acid esters of cholesterol) are tightly regulated. While mass spectrometry has been an analytical method of choice for detecting cholesterol and cholesteryl esters in biological samples, the hydrophobicity, chemically inert nature and poor ionization of these neutral lipids has often proved a challenge in developing lipidomics compatible liquid chromatography-mass spectrometry (LC-MS) methods to study them. To overcome this problem, here, we report a reverse-phase LC-MS method that is compatible with existing high-throughput lipidomics strategies, and capable of identifying and quantifying cholesterol and cholesteryl esters from mammalian cells and tissues. Using this sensitive yet robust LC-MS method, we profiled different mammalian cell lines and tissues, and provide a comprehensive picture of cholesterol and cholesteryl esters content in them. Specifically, amongst cholesteryl esters, we find that mammalian cells and tissues largely possess monounsaturated and polyunsaturated variants. Taken together, our lipidomics compatible LC-MS method to study this lipid class opens new avenues in understanding systemic and tissue-level cholesterol metabolism under various physiological conditions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/587668v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@badb0dorg.highwire.dtl.DTLVardef@1833f2aorg.highwire.dtl.DTLVardef@1a7e868org.highwire.dtl.DTLVardef@8b0ad9_HPS_FORMAT_FIGEXP M_FIG TOC Graphic C_FIG

biochemistry↗

bioRxiv2024

PPARγ mediated enhanced lipid biogenesis fuels Mycobacterium tuberculosis growth in hepatocytes.

Mycobacterium tuberculosis (Mtb) infection of the lungs, besides producing prolonged cough with mucus, also causes progressive fatigue and cachexia with debilitating loss of muscle mass. While anti-tuberculosis (TB) drug therapy is directed toward eliminating bacilli, the treatment regimen ignores the systemic pathogenic derailments that probably dictate TB-associated mortality and morbidity. Presently, it is not understood whether Mtb spreads to metabolic organs and brings about these impairments. Here we show that Mtb creates a replication-conducive milieu of lipid droplets in hepatocytes by upregulating transcription factor PPAR{gamma} and scavenging lipids from the host cells. In hepatocytes, Mtb shields itself against the common anti-TB drugs by inducing drug-metabolizing enzymes. Infection of the hepatocytes in the in vivo aerosol mice model can be consistently observed post-week 4 along with enhanced expression of PPAR{gamma} and drug-metabolizing enzymes. Moreover, histopathological analysis indeed shows the presence of Mtb in hepatocytes along with granuloma-like structures in human biopsied liver sections. Hepatotropism of Mtb during the chronic infectious cycle results in immuno-metabolic dysregulation that could magnify local and systemic pathogenicity, altering clinical presentations.

microbiology↗

bioRxiv2019

Human footprint differentially impacts genetic connectivity of four wide-ranging mammals in a fragmented landscape

AimMaintaining connectivity is critical for long-term persistence of wild carnivores in landscapes fragmented due to anthropogenic activity. We examined spatial genetic structure and the impact of landscape features on connectivity in four wide-spread species- jungle cat (Felis chaus), leopard (Panthera pardus), sloth bear (Melursus ursinus) and tiger (Panthera tigris). Location Our study was carried out in the central Indian landscape, a stronghold in terms of distribution and abundance of large mammals. The landscape comprises fragmented forests embedded in a heterogeneous matrix of multiple land-use types.\n\nMethodsMicrosatellite data from non-invasively sampled individuals (90 jungle cats, 82 leopards, 104 sloth bears and 117 tigers) were used to investigate genetic differentiation. Impact of landscape features on gene flow was inferred using a multi-model landscape resistance optimization approach.\n\nResultsAll four study species revealed significant isolation by distance (IBD). The correlation between genetic and geographic distance was significant only over a short distance for jungle cat, followed by longer distances for sloth bear, leopard and tiger. Overall, human footprint had a high negative impact on geneflow in tigers, followed by leopards, sloth bears and the least on jungle cats. Individual landscape variables- land-use, human population density, density of linear features and roads- impacted the study species differently. Although land-use was found to be an important variable explaining genetic connectivity for all four species, the amount of variation explained, the optimum spatial resolution and the resistance offered by different land-use classes varied.\n\nMain conclusionsAs expected from theory, but rarely demonstrated using empirical data, the pattern of spatial autocorrelation of genetic variation scaled with dispersal ability and density of the study species. Landscape genetic analyses revealed species-specific impact of landscape features and provided insights into interactions between species biology and landscape structure. Our results emphasize the need for incorporating functional connectivity data from multiple species for landscape-level conservation planning.

ecology↗