Biology subjects

Kotulkar, M.

Publications and source records attributed to Kotulkar, M..

7 recordsLinked to original sources

bioRxiv2024

Multi-Omics after O-GlcNAc Alteration Identifies Cellular Processes Working Synergistically to Promote Aneuploidy

Pharmacologic or genetic manipulation of O-GlcNAcylation, an intracellular, single sugar post-translational modification, are difficult to interpret due to the pleotropic nature of O-GlcNAc and the vast signaling pathways it regulates. To address this issue, we employed either OGT (O-GlcNAc transferase), OGA (O-GlcNAcase) liver knockouts, or pharmacological inhibition of OGA coupled with multi-Omics analysis and bioinformatics. We identified numerous genes, proteins, phospho-proteins, or metabolites that were either inversely or equivalently changed between conditions. Moreover, we identified pathways in OGT knockout samples associated with increased aneuploidy. To test and validate these pathways, we induced liver growth in OGT knockouts by partial hepatectomy. OGT knockout livers showed a robust aneuploidy phenotype with disruptions in mitosis, nutrient sensing, protein metabolism/amino acid metabolism, stress response, and HIPPO signaling demonstrating how OGT is essential in controlling aneuploidy pathways. Moreover, these data show how a multi-Omics platform can discern how OGT can synergistically fine-tune multiple cellular pathways.

cell biology↗

bioRxiv2023

Role of HNF4alpha-cMyc Interaction in CDE-diet Induced Liver Injury and Regeneration

BackgroundHepatocyte nuclear factor 4 alpha (HNF4) is a nuclear factor essential for liver function and regeneration. HNF4 negatively regulates the expression of cMyc, which plays an important role in proliferation and differentiation during liver regeneration. This study investigated the role of HNF4-cMyc interaction in regulating liver injury and regeneration using the choline-deficient and ethionine-supplemented (0.15%) (CDE) diet feeding model, which exhibits characteristics of chronic liver diseases including liver injury, inflammation, early fibrotic changes along with hepatocyte and biliary epithelial cell regeneration, and activation of hepatic progenitor cells (HPC). MethodsWild-type (WT), hepatocyte-specific knockout of HNF4 (HNF4-KO), cMyc (cMyc-KO), and HNF4-cMyc double knockout (DKO) mice were fed a CDE diet for one week to induce subacute liver injury. To study regeneration and recovery, mice were fed a one-week CDE diet followed by a one-week recovery period on a normal chow diet. ResultsWT mice showed significant liver injury and decreased HNF4 mRNA and protein expression after one week of a CDE diet. WT mice also showed an increase in markers of proliferation and HPC activation, but no major change in markers of inflammation or fibrosis. The HNF4-KO mice exhibited baseline hepatomegaly, which significantly declined during the recovery period. HNF4 deletion resulted in significantly higher injury compared to WT mice after one week of CDE diet feeding but similar recovery. Markers of inflammation, fibrosis, proliferation, and HPC activation were significantly higher in HNF4-KO mice during the injury period but declined during the recovery period. The cMyc-KO mice showed increased injury after one week of the CDE diet, but it was substantially lower than the WT and HNF4-KO mice. Deletion of cMyc resulted in a significant activation of inflammatory genes higher than in the WT and HNF4-KO mice. Whereas fibrosis and proliferation markers increased in cMyc-KO mice, they were substantially lower than in HNF4-KO mice and similar to WT mice. cMyc-KO also showed an increase in HPC markers following one week of CDE-induced injury. Deletion of both HNF4 and cMyc in DKO mice resulted in significant liver injury comparable to the HNF4-KO mice after one week of CDE diet feeding, but led to complete recovery. Markers of inflammation, fibrosis, and proliferation increased after CDE diet feeding, were higher than WT mice, and comparable to HNF4-KO mice. Interestingly, DKO mice showed a significant increase in HPC markers both following one week of CDE-induced injury and after one week of recovery. ConclusionsThese data indicate that deletion of HNF4 increases and deletion of cMyc decreases subacute liver injury induced by a one week CDE diet feeding. Deletion of HNF4 results in increased inflammation, fibrosis, proliferation, and HPC activation, all of which except inflammation are reduced following cMyc deletion. Simultaneous deletion of HNF4 and cMyc results in a phenotype similar to HNF4 deletion but with higher HPC activation. Taken together, these data show that HNF4 protects against inflammatory and fibrotic change following CDE diet-induced injury, which is driven by cMyc.

pathology↗

bioRxiv2023

Regulation of Hepatic Xenosensor Function by HNF4alpha

Nuclear receptors including Aryl hydrocarbon Receptor (AhR), Constitutive Androstane Receptor (CAR), Pregnane X Receptor (PXR), and Peroxisome Proliferator-Activated Receptor-alpha (PPAR) function as xenobiotic sensors. Hepatocyte nuclear factor 4alpha (HNF4) is a highly conserved orphan nuclear receptor essential for liver function. We tested the hypothesis that HNF4 is essential for function of these four major xenosensors. Wild-type (WT) and hepatocyte-specific HNF4 knockout (HNF4-KO) mice were treated with the mouse-specific activators of AhR (TCDD, 30 {micro}g/kg), CAR (TCPOBOP, 2.5 {micro}g/g), PXR, (PCN, 100 {micro}g/g), and PPAR (WY-14643, 1 mg/kg). Blood and liver tissue samples were collected to study nuclear receptor activation. TCDD (AhR agonist) treatment did not affect the liver-to-body weight ratio (LW/BW) in either WT or HNF4-KO mice. Further, TCDD activated AhR in both WT and HNF4-KO mice, confirmed by increase in expression of its target genes. TCPOBOP (CAR agonist) significantly increased the LW/BW ratio and CAR target gene expression in WT mice, but not in HNF4-KO mice. PCN (a mouse PXR agonist) significantly increased LW/BW ratio in both WT and HNF4-KO mice however, it failed to induce PXR target genes in HNF4 KO mice. The treatment of WY-14643 (PPAR agonist) increased LW/BW ratio and PPAR target gene expression in WT mice but not in HNF4-KO mice. Together, these data indicate that the function of CAR, PXR, and PPAR but not of AhR was disrupted in HNF4-KO mice. These results demonstrate that HNF4 function is critical for the activation of hepatic xenosensors, which are critical for toxicological responses.

pharmacology and toxicology↗

bioRxiv2023

HNF4a regulates acyl chain remodeling and ether lipid accumulation in hepatic steatosis

Hepatocyte nuclear factor 4 (HNF4) is an established transcriptional master regulator of differentiation, maintenance, and metabolism. Polymorphisms in HNF4 are linked to several diseases in humans including diabetes and nonalcoholic fatty liver disease (NAFLD). Identifying novel regulation of lipid metabolism by HNF4 would inform on NAFLD development and progression. We directly assessed HNF4 activity through chromatin immunoprecipitation (ChIP)-sequencing and integration of untargeted lipidomics. Direct regulation by HNF4 can be difficult to assess due to the role of HNF4 in liver homeostasis; to rapidly disrupt activity, mice were exposed to cold stress which induces hepatic steatosis in several hours. Cold exposure shifted HNF4 activity with differential genome occupancy of more than 50% of HNF4 binding sites. Focusing on HNF4 binding to promoter with active transcription determined that HNF4 directly regulates fatty acid desaturation, ether lipid synthesis, and peroxisomal biogenesis in response to cold exposure. Integration of lipidomics found that cold exposure increases the very long chain polyunsaturated fatty acid composition of the hepatic lipid pool, including ether lipids, in an HNF4 dependent manner. Because portions of ether lipid synthesis are in the peroxisome and peroxisomal biogenesis is directly HNF4 regulated, we analyzed peroxisomal abundance and found increases with cold exposure that are ablated with loss of HNF4. This peroxisomal regulation was independent of PPAR-- a known regulator of peroxisomes and lipid metabolism--since loss of HNF4 was not rescued by PPAR overexpression. These data determined that regulation of hepatic steatosis by HNF4 is more complex than triglyceride accumulation and includes acyl chain modifications, ether lipid synthesis, and peroxisomal oxidation.

molecular biology↗

bioRxiv2023

The Essential Role of O-GlcNAcylation in Hepatic Differentiation

Background & AimsO-GlcNAcylation is a post-translational modification catalyzed by the enzyme O-GlcNAc transferase (OGT), which transfers a single N-acetylglucosamine sugar from UDP-GlcNAc to the protein on serine and threonine residues on proteins. Another enzyme, O-GlcNAcase (OGA), removes this modification. O-GlcNAcylation plays an important role in pathophysiology. Here, we report that O-GlcNAcylation is essential for hepatocyte differentiation, and chronic loss results in fibrosis and hepatocellular carcinoma. MethodsSingle-cell RNA-sequencing was used to investigate hepatocyte differentiation in hepatocyte-specific OGT-KO mice with increased hepatic O-GlcNAcylation and in OGA-KO mice with decreased O-GlcNAcylation in hepatocytes. HCC patient samples and the DEN-induced hepatocellular carcinoma (HCC) model were used to investigate the effect of modulation of O-GlcNAcylation on the development of liver cancer. ResultsLoss of hepatic O-GlcNAcylation resulted in disruption of liver zonation. Periportal hepatocytes were the most affected by loss of differentiation characterized by dysregulation of glycogen storage and glucose production. OGT-KO mice exacerbated DEN-induced HCC development with increased inflammation, fibrosis, and YAP signaling. Consistently, OGA-KO mice with increased hepatic O-GlcNAcylation inhibited DEN-induced HCC. A progressive loss of O-GlcNAcylation was observed in HCC patients. ConclusionsOur study shows that O-GlcNAcylation is a critical regulator of hepatic differentiation, and loss of O-GlcNAcylation promotes hepatocarcinogenesis. These data highlight increasing O-GlcNAcylation as a potential therapy in chronic liver diseases, including HCC. Lay SummaryProteins in cells are modified by the addition of a single glucosamine sugar molecule called O-GlcNAcylation. Loss of O-GlcNAcylation in hepatocytes, the most common type of cells in the liver, causes the liver to lose its function and can result in increased liver diseases such as fibrosis and cancer. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/528884v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@aed343org.highwire.dtl.DTLVardef@1b00966org.highwire.dtl.DTLVardef@391ef9org.highwire.dtl.DTLVardef@206d8c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISingle-Cell RNA-sequencing reveals loss of metabolic liver zonation in O-GlcNAcylation deficient livers. C_LIO_LILoss of O-GlcNAcylation promoted DEN-Induced HCC. C_LIO_LIIncrease of hepatic O-GlcNAcylation prevented HCC progression. C_LI

pathology↗

bioRxiv2023

Identifying Human Specific Adverse Outcome Pathways of Per- and Polyfluoroalkyl Substances Using Liver-Chimeric Humanized Mice

BackgroundPer- and polyfluoroalkyl substances (PFAS) are persistent organic pollutants with myriad adverse effects. While perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS) are the most common contaminants, levels of replacement PFAS, such as perfluoro-2-methyl-3-oxahexanoic acid (GenX), are increasing. In rodents, PFOA, PFOS, and GenX have several adverse effects on the liver, including nonalcoholic fatty liver disease. ObjectiveWe aimed to determine human-relevant mechanisms of PFAS induced adverse hepatic effects using FRG liver-chimeric humanized mice with livers repopulated with functional human hepatocytes. MethodsMale humanized mice were treated with 0.067 mg/L of PFOA, 0.145 mg/L of PFOS, or 1 mg/L of GenX in drinking water for 28 days. Liver and serum were collected for pathology and clinical chemistry, respectively. RNA-sequencing coupled with pathway analysis was used to determine molecular mechanisms. ResultsPFOS caused a significant decrease in total serum cholesterol and LDL/VLDL, whereas GenX caused a significant elevation in LDL/VLDL with no change in total cholesterol and HDL. PFOA had no significant changes in serum LDL/VLDL and total cholesterol. All three PFAS induced significant hepatocyte proliferation. RNA-sequencing with alignment to the human genome showed a total of 240, 162, and 619 differentially expressed genes after PFOA, PFOS, and GenX exposure, respectively. Upstream regulator analysis revealed inhibition of NR1D1, a transcriptional repressor important in circadian rhythm, as the major common molecular change in all PFAS treatments. PFAS treated mice had significant nuclear localization of NR1D1. In silico modeling showed PFOA, PFOS, and GenX potentially interact with the DNA-binding domain of NR1D1. DiscussionThese data implicate PFAS in circadian rhythm disruption via inhibition of NR1D1. These studies show that FRG humanized mice are a useful tool for studying the adverse outcome pathways of environmental pollutants on human hepatocytes in situ.

pharmacology and toxicology↗

bioRxiv2021

Regulation of Liver Regeneration by hepatocyte O-GlcNAcylation in mice

The liver has a unique capacity to regenerate after injury in a highly orchestrated and regulated manner. Here we report that O-GlcNAcylation, an intracellular post-translational modification (PTM) regulated by two enzymes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), is a critical termination signal for liver regeneration (LR) following partial hepatectomy (PHX). We studied liver regeneration after PHX on hepatocyte specific OGT and OGA knockout mice (OGT-KO and OGA-KO), which caused a significant decrease (OGT-KO) and increase (OGA-KO) in hepatic O-GlcNAcylation, respectively. OGA-KO mice had normal regeneration, but the OGT-KO mice exhibited substantial defects in termination of liver regeneration with increased liver injury, sustained cell proliferation resulting in significant hepatomegaly, hepatic dysplasia and appearance of small nodules at 28 days after PHX. This was accompanied by a sustained increase in expression of cyclins along with significant induction in pro-inflammatory and pro-fibrotic gene expression in the OGT-KO livers. RNA-Seq studies revealed inactivation of hepatocyte nuclear 4 alpha (HNF4), the master regulator of hepatic differentiation and a known termination signal, in OGT-KO mice at 28 days after PHX, which was confirmed by both Western blot and IHC analysis. Furthermore, a significant decrease in HNF target genes was observed in OGT-KO mice, indicating a lack of hepatocyte differentiation following decreased hepatic O-GlcNAcylation. Immunoprecipitation experiments revealed HNF4 is O-GlcNAcylated in normal differentiated hepatocytes. These studies show that O-GlcNAcylation plays a critical role in the termination of LR via regulation of HNF4 in hepatocytes. Layman summaryO-GlcNAcylation is a protein modification that plays a critical role in various biological processes including cell proliferation, differentiation, and disease progression. These studies show that O-GlcNAcylation in hepatocytes is essential for proper liver regeneration. Without O-GlcNAcylation, hepatocytes keep on proliferating eventually forming liver tumors.

pathology↗