Biology subjects

Singh, M. K.

Publications and source records attributed to Singh, M. K..

At least 19 recordsLinked to original sources

bioRxiv2025

AI-Assisted Cryo-ET Workflow for 3D Visualization of Chromatin during Cellular Differentiation

Understanding how chromatin architecture changes during cellular differentiation requires structural methods that can resolve native genomic organization at high resolution. Here, we present an AI-assisted cryo-electron tomography (cryo-ET) and segmentation workflow to quantify chromatin compaction across various stages of motor neuron differentiation from induced pluripotent stem cells (iPSC). By directly imaging extracted and vitrified chromatin, we preserve native structure and avoid artifacts from heavy metal staining and resin embedding. Using three-dimensional (3D) density analysis, we measure chromatin density and capture the progressive increase in chromatin compaction with lineage commitment. This is then correlated with population-averaged Hi-C experiments, observing consistency between the microscale higher order structure of chromatin and global contact patterns. Our approach enables direct visualization of chromatin organization under near-physiological conditions, bridging the gap between structural imaging and genome-wide contact mapping. This platform therefore establishes an AI-assisted experimental framework for linking chromatin architecture to regulatory mechanisms during differentiation.

genomics↗

bioRxiv2025

YAP/TAZ activation in fibroblasts coordinates fibrotic remodeling, fibroinflammation, and epithelial dysfunction in pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease marked by progressive scarring with unknown causes and limited treatments. Myofibroblasts drive fibrosis by depositing excess matrix, however the mechanisms driving fibroblast-to-myofibroblast transformation and how myofibroblast-secreted factors disrupt the alveolar niche, undermining lung repair and regeneration remain poorly understood. Here we show that YAP and TAZ are activated in lung fibroblasts from pulmonary fibrosis patients and bleomycin-treated mice. Targeted deletion of Yap/Taz in fibroblasts significantly dampened the fibroinflammatory response, decreased myofibroblast activation, and ultimately resulted in attenuated fibrosis and enhanced regeneration of alveolar epithelial cells after bleomycin-induced injury. Conversely, fibroblast-specific overexpression of constitutively active YAP (YAP5SA) aggravated fibrosis by amplifying fibroinflammatory responses and simultaneously suppressing alveolar epithelial regeneration. Pharmacological inhibition of YAP/TAZ using verteporfin halted the development of bleomycin-induced fibrosis and even reversed established fibrosis in mice. Verteporfin effectively prevented fibroblast-to-myofibroblast transition and promoted collagen I degradation by lowering TIMP levels and enhancing activation of MMP1 and MMP9, demonstrating the significance of the YAP-TIMP-MMP1/9 axis in facilitating ECM breakdown. Furthermore, YAP activation in fibroblasts disrupted alveolar type II (AT2) cell homeostasis by inducing senescence through IGF1-IGF1R-mediated paracrine signaling. Blocking IGF1 signaling with a neutralizing antibody reduced the number of senescent AT2 cells, demonstrating the significance of the YAP-IGF1-IGF1R axis in maintaining alveolar epithelial cell homeostasis. Targeting YAP/TAZ may offer therapeutic strategies to mitigate pulmonary fibrosis by simultaneously mitigating pathological fibroblast activation, fibroinflammatory response, reducing AT2 cell senescence, and promoting alveolar epithelial regeneration.

cell biology↗

bioRxiv2025

Evolutionary origin and functional diversification of plant GBF1-type ARF guanine-nucleotide exchange factors

Large ARF GTPase-activating guanine-nucleotide exchange factors (ARF-GEFs) are essential regulators of membrane trafficking across the eukaryotes. Although conserved, the GBF1-type ARF-GEFs underwent plant-specific evolution. Of the 3 paralogs in Arabidopsis thaliana, AtGNOM-LIKE1 (AtGNL1) performs the GBF1 task of retrograde Golgi-ER traffic whereas AtGNOM mediates polar recycling from endosomes to the basal plasma membrane. AtGNL2 is specific to pollen and is functionally equivalent to AtGNOM. To clarify their evolutionary origin and functional diversification in the plant lineage, we established a phylogenetic tree and ortho-synteny groups (OSGs), which enabled identification of AtGNOM and AtGNL1 orthologs. In addition, somatic paralogs from several species were functionally analysed in transgenic Arabidopsis plants and tested for GNOM-specific DCB-DCB domain interaction in yeast two-hybrid assays. Our results support the following scenario. The ancient plant-specific GBF1-type ARF-GEF was functionally equivalent to AtGNOM and mediated both polar recycling and secretory trafficking. GNL2 only arose in the early flowering plants and then evolved independently. Genome duplication in the basal eudicots - but neither in monocots nor in magnoliids - gave rise to the AtGNL1 ortholog, distinguished by its unique OSG. The AtGNL1 ortholog lost the ability of DCB-DCB interaction and was free to evolve independently, eventually acquiring AtGNL1 function in the rosid clade of core eudicots. In eudicot evolution, the AtGNOM ortholog underwent repeated transposition to different OSGs whereas the AtGNL1 ortholog was recurrently lost but eventually positively selected. This evolutionary process uncoupled polar recycling required for gravitropic response or lateral root initiation from secretory trafficking required for growth.

plant biology↗

bioRxiv2025

FLIM Imaging of mCherryTYG Deciphers pH Dynamics and Lifestyles of Salmonella Typhimurium

Intracellular pH regulation is fundamental to bacterial adaptation, virulence, and survival in diverse environments. Salmonella Typhimurium, a key human pathogen, exploits host and environmental pH cues to transition between planktonic, biofilm, and virulence-associated states. However, precise tools to monitor bacterial pH dynamics at subcellular resolution have been limited. Herein, we report the development and application of mCherryTYG, a genetically encoded pH-sensitive fluorophore optimized for fluorescence lifetime imaging (FLIM), enabling robust and high-resolution pH measurements across diverse conditions. mCherryTYG demonstrated exceptional sensitivity across a broad pH range (5.5-8.5) with consistent lifetime responses, and was unaffected by temperature, buffer composition, or ionic strength. Using FLIM, we characterized the pH dynamics of Salmonella across in vitro, host, and biofilm contexts. Under acidic stress in vitro, Salmonella maintained a uniform intracellular pH ([~]6.04), providing clarity on previously debated heterogeneity. In infections of HeLa cells, Salmonella existed in distinct pH environments: acidic vacuolar pH ([~]5.89) and neutral cytoplasmic pH ([~]7.10). During the late infection stage, [~]17% of the bacterial population retained an acidic pH. Biofilm studies revealed stratified pH profiles, with acidic pH near the bottom and neutral pH at the surface, mirroring patterns observed in other pathogens. In heterologous host models, pH gradients shaped bacterial adaptation strategies. In C. elegans, Salmonella experienced a progressive pH gradient from neutral pH ([~]7.10) in the anterior lumen to acidic pH ([~]6.45) in the posterior. Similarly, in zebrafish, Salmonella encountered acidic lysosome-rich enterocytes ([~]5.84) and neutral regions ([~]7.33) in the anterior gut. This study establishes mCherryTYG-FLIM as a transformative tool for studying bacterial pH regulation, revealing pH as a critical modulator of Salmonella lifestyle transitions: virulence, and persistence. Our findings provide new insights into host-microbe interactions and present pH as a promising target for therapeutic interventions against bacterial infections.

microbiology↗

bioRxiv2024

A constricted mitochondrial morphology optimizes respiration.

Mitochondria assemble in a dynamic tubular network with a morphology governed by mitochondrial fusion and fission, which regulate all mitochondrial functions including oxidative phosphorylation 1-4. Yet, the link between mitochondrial morphology and respiration remains unclear 5-9. Here, we discover a previously unknown mitochondrial morphology dedicated to respiratory growth of Saccharomyces cerevisiae, which we refer to as "Ringo". The Ringo morphology is characterized by stable constrictions of mitochondrial tubules. Ringo constrictions are mediated by the yeast dynamin Dnm1 and, unlike mitochondrial fission 10-12, occur in the absence of contacts with the endoplasmic reticulum. Our data show that the Ringo morphology regulates mitochondrial DNA homeostasis during respiration to ensure stoichiometric assembly of OXPHOS complexes, demonstrating that the shape of mitochondria actively contributes to optimal respiration. One-Sentence Summary: We report a new mitochondrial morphology that actively contributes to optimal respiration in yeast.

cell biology↗

bioRxiv2024

Plxnd1-mediated mechanosensing of blood flow controls the caliber of the Dorsal Aorta via the transcription factor Klf2

The cardiovascular system generates and responds to mechanical forces. The heartbeat pumps blood through a network of vascular tubes, which adjust their caliber in response to the hemodynamic environment. However, how endothelial cells in the developing vascular system integrate inputs from circulatory forces into signaling pathways to define vessel caliber is poorly understood. Using vertebrate embryos and in vitro-assembled microvascular networks of human endothelial cells as models, flow and genetic manipulations, and custom software, we reveal that Plexin-D1, an endothelial Semaphorin receptor critical for angiogenic guidance, employs its mechanosensing activity to serve as a crucial positive regulator of the Dorsal Aortas (DA) caliber. We also uncover that the flow-responsive transcription factor KLF2 acts as a paramount mechanosensitive effector of Plexin-D1 that enlarges endothelial cells to widen the vessel. These findings illuminate the molecular and cellular mechanisms orchestrating the interplay between cardiovascular development and hemodynamic forces. HighlightsO_LIPlexin-D1 mechanosensing of blood flow tunes the caliber of the Dorsal Aorta (DA) C_LIO_LIThe DA widens without raising endothelial cell numbers, which can change separate from the caliber C_LIO_LIThe Kruppel-like transcription factor 2 (KLF2) is a key Plexin-D1 mechano-effector during development C_LIO_LIKLF2 increases endothelial cell size to expand the DA caliber C_LI

developmental biology↗

bioRxiv2023

Plasmodium falciparum MORC protein modulates gene expression through interaction with heterochromatin

Dynamic control of gene expression is critical for blood stage development of malaria parasites. Here, we used multi-omic analyses to investigate transcriptional regulation by the chromatin-associated microrchidia protein, MORC, during asexual blood stage development of the human malaria parasite Plasmodium falciparum. We show that PfMORC (PF3D7_1468100) interacts with a suite of nuclear proteins, including APETALA2 (AP2) transcription factors (PfAP2-G5, PfAP2-O5, PfAP2-I, PF3D7_0420300, PF3D7_0613800, PF3D7_1107800, and PF3D7_1239200), a DNA helicase DS60 (PF3D7_1227100), and other chromatin remodelers (PfCHD1 and PfEELM2). Transcriptomic analysis of PfMORCHA-glmS knockdown parasites revealed 163 differentially expressed genes belonging to hypervariable multigene families, along with upregulation of genes mostly involved in host cell invasion. In vivo genome-wide chromatin occupancy analysis during both trophozoite and schizont stages of development demonstrates that PfMORC is recruited to repressed, multigene families, including the var genes in subtelomeric chromosomal regions. Collectively, we find that PfMORC is found in chromatin complexes that play a role in the epigenetic control of asexual blood stage transcriptional regulation and chromatin organization.

microbiology↗

bioRxiv2023

A Non-Coding Variant in SLC15A4 Drives Lysosomal Deacidification and Lupus Susceptibility

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near the SLC15A4 gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer of SLC15A4. Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters of SLC15A4, GLTLD1, and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.

genetics↗

bioRxiv2023

YAP/TAZ are Crucial Regulator of Macrophage-mediated Pulmonary Inflammation and Fibrosis after Bleomycin-induced Injury

Pulmonary fibrosis (PF) is the most common form of end stage interstitial devastating lung disease characterized by the scarring of lung due to excessive production of extracellular matrix (ECM). Recent studies have revealed the impact of macrophages in inflammation-induced fibrosis and distinct subsets of macrophages differentially contributes to the development of PF. However, the regulatory mechanisms and proinflammatory/profibrotc behaviour of heterogeneous population of lung macrophages during fibrogenesis remain incompletely understood. Here, we demonstrate the macrophage-specific role of Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) in the development of bleomycin-induced inflammation and PF in mice. Both YAP/TAZ are activated in lung macrophages of fibrotic patients and of mice after bleomycin-induced injury. Myeloid-specific genetic deletion of Yap/Taz resulted in reduced recruitment of monocyte-derived alveolar macrophages (Mo-AMs), leading to an impaired inflammatory response, reduced PF and improved regeneration of alveolar epithelial cells in bleomycin-injured lung. However, overexpression of Yap in macrophages augmented the Mo-AMs recruitment in lung leading to increased proinflammatory response, exacerbated fibrotic response and decreased regeneration of alveolar epithelial cells in bleomycin-injured lung. We demonstrate that YAP/TAZ regulate PF through the activation of macrophage recruitment driver C-C motif chemokine ligand 2 (CCL2) and blocking of CCL2 with neutralizing antibody prevented YAP-induced inflammatory and fibrotic response. We also demonstrate that YAP/TAZ regulate macrophage polarization as well as macrophage-fibroblasts crosstalk by regulating expression of Methyl-CpG-binding domain 2 (MBD2) during bleomycin-induced PF. Taken together, we show that YAP/TAZ are potent regulators of macrophage polarization, infiltration and macrophage-mediated proinflammatory/profibrotic response during PF.

molecular biology↗

bioRxiv2022

A diet-independent zebrafish model for NAFLD recapitulates patient lipid profiles and offers a system for small molecule screening

Non-alcoholic Fatty Liver Disease (NAFLD) or pathological hepatic lipid overload, is considered to affect obese individuals. However, NAFLD in lean individuals is prevalent, especially in South Asian population. The pathophysiology of lean NAFLD is not well understood and most animal models of NAFLD use the high-fat diet paradigm. To bridge this gap, we have developed a diet-independent model of NAFLD in zebrafish. We have previously showed that chronic systemic inflammation causes metabolic changes in the liver leading to hepatic fat accumulation in an IL6 overexpressing (IL6-OE) zebrafish model. In the present study, we compared the hepatic lipid composition of adult IL6-OE zebrafish to the controls and found an accumulation of saturated triacylglycerols and a reduction in the unsaturated triacylglycerol species reminiscent of NAFLD patients. Zebrafish is an ideal system for chemical genetic screens. We tested whether the hepatic lipid accumulation in the IL6-OE is responsive to chemical treatment. We found that PPAR-gamma agonist Rosiglitazone, known to reduce lipid overload in the high fat diet models of NAFLD, could ameliorate the fatty liver phenotype of the IL6-OE fish. Rosiglitazone treatment reduced the accumulation of saturated lipids and showed a concomitant increase in unsaturated TAG species in our inflammation-induced NAFLD model. Our observations suggest that the IL6-OE model can be effective for small molecule screening to identify compounds that can reverse hepatic lipid accumulation, especially relevant to lean NAFLD.

pharmacology and toxicology↗

bioRxiv2022

Semaphorin3F reduces vascular endothelial and smooth muscle cell PI3K activation and decreases neointimal plaque formation

We previously conducted genetic analyses, and identified semaphorin signaling as associating with coronary artery disease. Of the semaphorins, human vascular expression profiling suggested SEMA3F as potentially linked to atherogenesis. In hyperlipidemic mice, SEMA3F reduced aortic lesion area, and increased fibrous cap endothelial content, leading to plaque stability. In a disturbed-flow-mediated endothelial dysfunction-driven lesion model, the absence of Sema3f increased plaques, further implicating SEMA3F in endothelial function. Monocyte adhesion to Sema3f-/- vascular endothelial cells (VECs) was elevated, driven by increased PI3K activity, leading to increased NF-{kappa}B-mediated elevation in VCAM1 and ICAM1 expression, suggesting that SEMA3F reduces VEC PI3K activity. Increased permeability led to increased monocyte transmigration through Sema3f-/- VECs, and mTOR phosphorylation was decreased, suppressing VE-cadherin expression and cell-cell adherens junction stability. Actomyosin fiber formation was decreased in Sema3f-/- VECs, which was reversed by PI3K inhibition, further implicating SEMA3F in adherens junction stability. In Sema3f-/- vascular smooth muscle cells (VSMCs), active PI3K was also increased. PI3K facilitates VSMC proliferation, migration, and pro-atherogenic phenotype switching, which were reduced by SEMA3F. In agreement, in a model of VSMC proliferation and migration-induced neointima formation, SEMA3F reduced plaques. Semaphorin3F is causally atheroprotective. SEMA3Fs suppression of VEC and VSMC PI3K activation may contribute to its atheroprotection.

physiology↗

bioRxiv2021

Heterodimers of functionally divergent ARF-GEF paralogues prevented by self-interacting dimerisation domain

Functionally divergent paralogs of homomeric proteins do not form potentially deleterious heteromers, which requires distinction between self and non-self (Hochberg et al., 2018; Marchant et al, 2019; Marsh and Teichmann, 2015). In Arabidopsis, two ARF guanine-nucleotide exchange factors (ARF-GEFs) related to mammalian GBF1, named GNOM and GNL1, can mediate coatomer complex (COPI)-coated vesicle formation in retrograde Golgi-endoplasmic reticulum (ER) traffic (Geldner et al., 2003; Richter et al., 2007; Teh and Moore, 2007). Unlike GNL1, however, GNOM is also required for polar recycling of endocytosed auxin efflux regulator PIN1 from endosomes to the plasma membrane. Here we show that these paralogues form homodimers constitutively but no heterodimers. We also address why and how GNOM and GNL1 might be kept separate. These paralogues share a common domain organisation and each N-terminal dimerisation (DCB) domain can interact with the complementary fragment ({Delta}DCB) of its own and the other protein. However, unlike self-interacting DCBGNOM (Grebe et al., 2000; Anders et al., 2008), DCBGNL1 did not interact with itself nor DCBGNOM. DCBGNOM removal or replacement with DCBGNL1, but not disruption of cysteine bridges that stabilise DCB-DCB interaction, resulted in GNOM-GNL1 heterodimers which impaired developmental processes such as lateral root formation. We propose precocious self-interaction of the DCBGNOM domain as a mechanism to preclude formation of fitness-reducing GNOM-GNL1 heterodimers.

plant biology↗

bioRxiv2021

ShareLoc - an open platform for sharing localization microscopy data

Novel insights and more powerful analytical tools can emerge from the reanalysis of existing data sets, especially via machine learning methods. Despite the widespread use of single molecule localization microscopy (SMLM) for super-resolution bioimaging, the underlying data are often not publicly accessible. We developed ShareLoc (https://shareloc.xyz), an open platform designed to enable sharing, easy visualization and reanalysis of SMLM data. We discuss its features and show how data sharing can improve the performance and robustness of SMLM image reconstruction by deep learning.

bioinformatics↗

bioRxiv2020

PRAK-03202: A triple antigen VLP vaccine candidate against SARS CoV-2

The rapid development of safe and effective vaccines against SARS CoV-2 is the need of the hour for the coronavirus outbreak. Here, we have developed PRAK-03202, the worlds first triple antigen VLP vaccine candidate in a highly characterized S. cerevisiae-based D-CryptTM platform, which induced SARS CoV-2 specific neutralizing antibodies in BALB/c mice. Immunizations using three different doses of PRAK-03202 induces antigen specific (Spike, envelope and membrane proteins) humoral response and neutralizing potential. PBMCs from convalescent patients, when exposed to PRAK-03202, showed lymphocyte proliferation and elevated IFN-{gamma} levels suggestive of conservation of epitopes and induction of T helper 1 (Th1)-biased cellular immune responses. These data support the clinical development and testing of PRAK-03202 for use in humans.

immunology↗

bioRxiv2020

Applying Machine Learning to Increase Efficiency and Accuracy of Meta-Analytic Review

The rapidly burgeoning quantity and complexity of publications makes curating and synthesizing information for meta-analyses ever more challenging. Meta-analyses require manual review of abstracts for study inclusion, which is time consuming, and variation among reviewer interpretation of inclusion/exclusion criteria for selecting a paper to be included in a review can impact a studys outcome. To address these challenges in efficiency and accuracy, we propose and evaluate a machine learning approach to capture the definition of inclusion/exclusion criteria using a machine learning model to automate the selection process. We trained machine learning models on a manually reviewed dataset from a meta-analysis of resilience factors influencing psychopathology development. Then, the trained models were applied to an oncology dataset and evaluated for efficiency and accuracy against trained human reviewers. The results suggest that machine learning models can be used to automate the paper selection process and reduce the abstract review time while maintaining accuracy comparable to trained human reviewers. We propose a novel approach which uses model confidence to propose a subset of abstracts for manual review, thereby increasing the accuracy of the automated review while reducing the total number of abstracts requiring manual review. Furthermore, we delineate how leveraging these models more broadly may facilitate the sharing and synthesis of research expertise across disciplines.

neuroscience↗

bioRxiv2020

Default Mode and Salience Network Alterations in Suicidal and Non-Suicidal Self-Injurious Thoughts and Behaviors in Adolescents with Depression

Suicidal ideation (SI) and non-suicidal self-injury (NSSI) are two distinct yet often co-occurring risk factors for suicide in adolescents. Elucidating the neurobiological patterns that specifically characterize SI and NSSI in adolescents is needed to inform the use of these markers in intervention studies and to develop brain-based treatment targets. Here, we clinically assessed 70 adolescents--49 adolescents with depression and 21 healthy controls--to determine SI and NSSI history. Twenty-eight of the depressed adolescents had a history of SI and 29 had a history of NSSI (20 overlapping). All participants underwent a resting-state fMRI scan. We compared groups in network coherence of subdivisions of the central executive network (CEN), default mode network (DMN), and salience network (SN). We also examined group differences in between-network connectivity and explored brain-behavior correlations. Depressed adolescents with SI and with NSSI had lower coherence in the ventral DMN compared to those without SI or NSSI, respectively, and healthy controls (all ps<0.043). Depressed adolescents with NSSI had lower coherence in the anterior DMN and in insula-SN (all ps<0.030), and higher CEN-DMN connectivity compared to those without NSSI and healthy controls (all ps<0.030). Lower network coherence in all DMN subnetworks and insula-SN were associated with higher SI and NSSI (all ps<0.001). Thus, SI and NSSI are related to brain networks associated with difficulties in self-referential processing and future planning, while NSSI specifically is related to brain networks associated with disruptions in interoceptive awareness. Intrinsic network patterns may be reliable biomarkers of SI and NSSI in adolescents.

neuroscience↗

bioRxiv2020

INTS13 Mutations Causing a Developmental Ciliopathy Disrupt Integrator Complex Assembly

Oral-facial-digital syndromes (OFD) are a heterogeneous group of congenital disorders characterized by malformations of the face and oral cavity, and digit anomalies. To date, mutations in 12 ciliary-related genes have been identified that cause several types of OFD, suggesting that OFDs constitute a subgroup of developmental ciliopathies. Through homozygosity mapping and exome sequencing of two families with variable OFD type 2, we identified distinct germline mutations in INTS13, a subunit of the Integrator complex. This 14-component complex associates with RNAPII and can cleave nascent RNA to modulate gene expression. We determined that INTS13 utilizes a discrete domain within its C-terminus to bind the Integrator cleavage module, which is disrupted by the identified germline INTS13 mutations. Depletion of INTS13 disrupts ciliogenesis in human cultured cells and causes dysregulation of a broad collection of ciliary genes. Accordingly, its knockdown in Xenopus embryos lead to motile cilia anomalies. Altogether, we show that mutations in INTS13 cause an autosomal recessive ciliopathy, which reveals key interactions within Integrator components.

biochemistry↗

bioRxiv2020

Chronic exposure to IL6 leads to deregulation of glycolysis and fat accumulation in the zebrafish liver

BACKGROUND AND AIMS Inflammation is a constant in Non-Alcoholic Fatty Liver Disease (NAFLD) and is usually considered a consequence. We propose that inflammation can be a cause for NAFLD. Obesity is strongly associated with (NAFLD), but not always. NAFLD in lean individuals is more common in certain populations, especially Asian-Indians. Lean healthy Indians also have a higher basal circulating IL6 suggesting a link with inflammation. We propose that inflammation-induced fatty liver could be relevant for studying obesity-independent NAFLD. Commonly used high-fat diet-induced NAFLD animal models are not ideal for testing this hypothesis.APPROACH AND RESULTS In this study we used a transgenic zebrafish with chronic systemic overexpression of human IL6 (IL6-OE) and found accumulation of triglyceride in the liver. We performed comparative transcriptomics and proteomics on the IL6-OE liver and found an expression signature distinct from the diet-based NAFLD models. We discovered a deregulation of glycolysis/gluconeogenesis pathway, especially a robust down regulation of the glycolytic enzyme aldolase b in the IL6-OE liver. Metabolomics of the IL6-OE liver showed accumulation of hexose monophosphates and their derivatives, which can act as precursors for triglyceride synthesis. Patients with the genetic disease Hereditary Fructose Intolerance (HFI) caused by ALDOLASE B deficiency also have a higher propensity to develop fatty liver disease.CONCLUSIONS Our study demonstrates a causative role for inflammation in intrahepatic lipid accumulation. Further, our results suggest that IL6-driven repression of glycolysis/gluconeogenesis, specifically aldolase b, may be a novel mechanism for development of fatty liver, especially in obesity-independent NAFLD.Competing Interest StatementThe authors have declared no competing interest.List of AbbreviationsNAFLDNon-Alcoholic Fatty Liver DiseaseIL6Interleukin 6OEOverexpressionHFIHigh Fructose IntoleranceNASHNon-Alcoholic SteatohepatitisSLESystemic Lupus ErythematosusIBDInflammatory Bowel DiseaseRARheumatoid ArthritisHFDHigh Fat dietqRT-PCRQuantitative Real-Time Polymerase Chain ReactionPPARPeroxisome Proliferator-Activated ReceptorDHAPDihydroxyacetone PhosphateView Full Text

molecular biology↗