👤 Anirban Chatterjee

We previously used a myoblast model of fusion-positive rhabdomyosarcoma (FP-RMS) to show that FGF8, a PAX3-FOXO1 (P3F) transcriptional target, is required for P3F-driven tumorigenicity and, when aberrantly expressed, can maintain tumorigenicity in P3F-independent recurrent tumors. We report in this study that FGF8, FGFR1, and FGFR4 are often highly expressed in FP-RMS tumors. High FGF8 expression in FP-RMS cells is associated with high sensitivity to an FGFR4 inhibitor and a pan-FGFR inhibitor. Although downregulating FGF8 resulted in loss of sensitivity to these inhibitors, FGF8 upregulation in myoblasts decreased FGFR4 expression and sensitized the cells to an FGFR1 inhibitor and a pan-FGFR inhibitor. FGF8 downregulation of FGFR4 expression was reverted by inhibitors of FGFR1, MEK, or ERK, thus defining a signaling pathway by which FGF8 mediates this regulatory effect. Finally, high FGF8 expression in P3F-independent recurrent tumors was attributable to a rearrangement of viral long terminal repeat (LTR) sequences into the FGF8 3' untranslated region, resulting in increased FGF8 mRNA stability. These findings indicate that FGF8 exerts oncogenic effects in FP-RMS via FGFR4 and may exert oncogenic effects in P3F-independent relapses via FGFR1. Our study reveals the functional significance of FGF8 in FP-RMS and provides a rationale for preclinical studies of FGFR inhibitors in FP-RMS. Show less

Epithelial-mesenchymal transition (EMT) and cell migration are two essential cellular processes involved in normal biological events such as embryogenesis, organ development, and wound healing, and are also associated with pathological conditions like cancer metastasis. Recent studies have indicated that the microtubule cytoskeleton and its associated proteins play significant roles in these processes. In this study, we investigated how fidgetin, a microtubule-severing and depolymerizing enzyme, affects EMT and cell migration by depleting it in MDA-MB-231 breast cancer cells. Our data show that depletion of endogenous fidgetin reduces the cell migration rate in both wound-healing and single-cell motility assays. During EMT, transcription factors such as Snail, Slug (Snail2), Twist, and Zeb play pivotal roles by regulating the expression of EMT-related genes. In this study, we found that fidgetin depletion reduces the expression of Slug and Zeb1 in MDA-MB-231 breast cancer cells under both basal and EMT-induced conditions. Consistent with these findings, we observed that fidgetin depletion downregulates N-cadherin and vimentin expression in EMT-induced MDA-MB-231 cells, thereby influencing cell motility. Further investigations revealed that fidgetin also affects microtubule plus-end tracking proteins (+TIPs). Specifically, we detected reduced expression of CLIP-170 in fidgetin-depleted cells. Immunofluorescence analysis showed that EB1 comets occupied a smaller area at microtubule plus ends upon fidgetin depletion. Additionally, the size of focal adhesions was significantly increased, although no changes were observed in the expression levels of focal adhesion kinase (FAK). Our findings indicate that microtubule regulation by fidgetin influences cancer cell motility by altering the expression of EMT-promoting transcription factors and modulating the accumulation of focal adhesion and EB1 proteins. These results suggest that fidgetin could be a promising therapeutic target in cancer. Show less

Disruption of photoreceptor-retinal pigment epithelium (RPE) interface with loss of photoreceptor outer segments (POSs) in the retina is a pathological hallmark of several neurodegenerative and retinal diseases including lysosomal storage disorder's like CLN3 disease. However, the retina is a functional composite Acid ceramidase deficiency and consequently altered sphingolipid signaling promotes disease phenotype(s) in a lysosomal storage disorder, CLN3 disease. Show less

The development of FGFR1-driven stem cell leukemia and lymphoma syndrome (SCLL) in mouse models is accompanied by an increase in highly heterogenous myeloid derived suppressor cells (MDSCs), which promote immune evasion. To dissect this heterogeneity, we used a combination of CyTOF and scRNA-Seq to define the phenotypes and genotypes of these MDSCs. CyTOF demonstrated increased levels of circulating macrophages in the peripheral blood of leukemic mice, and flow cytometry demonstrated that these macrophages were derived from Ly6C Show less

Background Metabolic syndrome (MetS) is a major public-health concern that substantially increases the risk of cardiovascular disease and type 2 diabetes. Traditional lipid profiles may not fully capture the atherogenic burden in MetS, prompting investigation of novel lipid biomarkers, such as lipoprotein(a) (Lp(a)), apolipoproteins, and the Comprehensive Lipid Tetrad Index (CLTI). This study evaluated the association of these biomarkers with MetS in an Indian outpatient population. Methods In a cross-sectional study of 707 adults aged 25-75 years at a tertiary care hospital in Jamnagar, Gujarat, MetS was diagnosed using NCEP-ATP III criteria. Serum Lp(a), apolipoprotein A-I (Apo A-I), apolipoprotein B (Apo B), and CLTI were measured using standard methods. Associations were tested using Chi-square analyses and logistic regression, and diagnostic performance was assessed by receiver operating characteristic (ROC) curve analysis. Results MetS was present in 397/707 (56.15%) participants, occurring in 197/332 (59.34%) of females and 200/375 (53.33%) of males. Elevated Lp(a), elevated Apo B, elevated CLTI, and reduced Apo A-I were all significantly associated with MetS (p < 0.001 for each). ROC analysis demonstrated the highest diagnostic accuracy for CLTI (area under the curve, or AUC = 0.835, 95% CI 0.806-0.862), followed by Lp(a) (AUC = 0.760, 95% CI 0.730-0.794), Apo B (AUC = 0.700, 95% CI 0.665-0.734), and Apo A-I (AUC = 0.620, 95% CI 0.584-0.657). Multivariable logistic regression identified elevated blood pressure, low high-density lipoprotein cholesterol, and elevated triglycerides as significant predictors of abnormal biomarker levels. Conclusion In this Indian outpatient cohort, CLTI and Lp(a) showed strong predictive value for MetS, and outperformed Apo A-I and Apo B when used alone. Incorporating CLTI and Lp(a) into clinical assessment may improve early detection and risk stratification in individuals at risk of MetS. Show less

NGS (next-generation sequencing) has become a rapid advance in discovering the variants in the genomic data for disease diagnosis, prognosis, and therapeutic decision. However, the scope of detecting single nucleotide polymorphisms (SNPs) becomes limited by the availability of reliable high-throughput data. OUD (opioid use disorder) is a chronic condition marked by prolonged opioid misuse, leading to cycles of relapse and remission. The discovery of genetic variants associated with OUD is constrained by limited genomic data, making it crucial to identify these variants and their genetic factors. The identification of variants from RNA-seq (RNA-sequencing) data can become the representative of the SNP analysis that is generally preferred from the whole genome or exome sequencing data. This study aimed to identify variants from gene expression data downloaded from NCBI GEO with accession PRJNA492904 in postmortem ventral midbrain specimens of chronic opioid users. We hypothesized that the NRXN3 gene would exhibit the highest number of variants due to its significant role in neuronal synapse function and its association with opioid addiction and impulsivity. We utilized RNA-Seq data from OUD patients (PRJNA492904, NCBI SRA) to detect variants in expressed RNA, which can indicate functional protein changes. Eight genes were analyzed: BDNF, DRD2, DRD3, NRXN3, OPRD1, OPRM1, and NGFB, with a primary focus on NRXN3. Our findings revealed the highest number of variants in NRXN3 compared to the other genes, highlighting its potential importance in OUD and the robustness of RNA-Seq in variant detection. Show less

Introduction The signal transducer and activator of transcription-1 (STAT-1) are tightly controlled signaling pathways, with induced genes acting as positive and negative regulators. Persistent activation of the signal transducer and activator of transcription (STATs), particularly signal transducer and activator of transcription-3 (STAT-3) and signal transducer and activator of transcription-5 (STAT-5), is common in human tumors and cell lines. STAT molecules act as transcription factors, regulated by ligands like interferon-α (IFN-α), interferon-γ (IFN-γ), epidermal growth factor (EGF), platelet-derived growth factor (PDGF), interleukin-6 (IL-6) and interleukin-27 (IL-27). STAT-1 mutations can cause infections like periodontitis, a chronic inflammatory disease affecting gum tissue and bone. STAT-1 drug-gene interactions are being studied for therapeutic applications. Our study aims to predict drug-gene interactions of STAT-1 receptors in periodontal inflammation using graph attention networks (GATs). Methodology The study used a dataset of 215 drug-gene interactions to train and test a GAT model. The data was cleaned and normalized before being subjected to GATs using the Python library. Cytoscape and cytoHubba were used to visualize and analyze biological networks, including drug-gene interactome networks. The GAT model consisted of two graph attention layers, with the first layer producing eight features and the second layer aggregating outputs for binary classification. The model was trained using the Adam optimizer and CrossEntropyLoss function. Results The drug-gene interactome network, analyzed using Cytoscape, had 657 nodes, 1591 edges, and 4.755 neighbors. The predictive GAT model had low accuracy due to data availability and complexity. Conclusion The GAT model for drug-gene interactions in periodontal inflammation had low accuracy due to data limitations, complexity, and inability to capture all relevant features. Show less

Blood lipids during pregnancy are associated with cardiovascular diseases and adverse pregnancy outcomes. Genome-wide association studies (GWAS) in predominantly male European ancestry populations have identified genetic loci associated with blood lipid levels. However, the genetic architecture of blood lipids in pregnant women remains poorly understood. Our goal was to identify genetic loci associated with blood lipid levels among pregnant women from diverse ancestry groups and to evaluate whether previously known lipid loci in predominantly European adults are transferable to pregnant women. The trans-ancestry GWAS were conducted on serum levels of total cholesterol, high-density lipoprotein cholesterol (HDL), low-density lipoprotein cholesterol (LDL) and triglycerides during first trimester among pregnant women from four population groups (608 European-, 623 African-, 552 Hispanic- and 235 East Asian-Americans) recruited in the NICHD Fetal Growth Studies cohort. The four GWAS summary statistics were combined using trans-ancestry meta-analysis approaches that account for genetic heterogeneity among populations. Loci in CELSR2 and APOE were genome-wide significantly associated (p-value < 5×10 This trans-ancestry GWAS meta-analysis in pregnant women identified associations that concur with four known adult lipid loci. Limited replication of known lipid-loci from predominantly European study populations to pregnant women underlines the need for genomic studies of lipids in ancestrally diverse pregnant women. ClinicalTrials.gov, NCT00912132. Show less

Ashwagandha extracts play a significant role in traditional Indian medicine to help treat a wide range of disorders from amnesia, erectile dysfunction, neurodegenerative and cardiovascular diseases, cancer, stress, anxiety, and many more. Ashwagandha root is enriched with bioactive plant metabolites of which withanolides are the most important ones. The concentration and constitution of withanolides primarily determine ashwagandha's potency and pharmacology. Various factors modulate the withanolide constitution in the plant-derived extracts, rendering inconsistent therapeutic efficacy. Standardisation of the extraction protocol and a better understanding of the pharmacology mechanism of different extracts with varied withanolide constitutions is therefore critical for developing reliable, repeatable, and effective ashwagandha-based treatment. Here, we work toward defining indication mechanisms for two varieties of ashwagandha extract-ASHWITH (ASH-Ext1) and Regenolide (ASH-Ext2)-with different proprietary withanolide proportions. ASH-Ext1 was studied for antioxidant signaling modulation using HEK293, HeLa, and A549 cells, and ASH-Ext2 was studied for subcellular drug targets associated with the reactivation and longevity of human hair follicles, using primary human hair follicle dermal papilla cells (HFDPCs). Study findings support the antioxidant activity and Nrf2 signaling modulation by ASH-Ext1 in various cell models. Of note, ASH-Ext2 was found to increase The results of drug target modulation show us that the withanolide constitution associated with different extraction protocols influences the pharmacological potential of the extract significantly and points to the value of standardisation not only of total withanolide content but also of internal withanolide proportions. Show less

Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (P Show less

Metabolomics genome wide association study (GWAS) help outline the genetic contribution to human metabolism. However, studies to date have focused on relatively healthy, population-based samples of White individuals. Here, we conducted a GWAS of 537 blood metabolites measured in the Chronic Renal Insufficiency Cohort (CRIC) Study, with separate analyses in 822 White and 687 Black study participants. Trans-ethnic meta-analysis was then applied to improve fine-mapping of potential causal variants. Mean estimated glomerular filtration rate was 44.4 and 41.5 mL/min/1.73m Show less

To compare the level of pro and anti-inflammatory cytokines, and angiogenic mediators between Rheumatoid arthritis (RA) patients with and without subclinical synovitis (SS) in remission state, to find the correlation of these mediators with Greyscale synovitis (GSS) and power Doppler (PD) scores, and to find the probable predictor/s of SS. 52 RA patients in remission state were recruited and subdivided into with and without SS group by Ultrasonography (USG) of 14 joints. Total GSS and PD scoring was done. The serum levels of the pro/anti-inflammatory cytokines and angiogenic mediators were compared between groups, and correlation and regression analysis were done with GSS and PD scores. 63.46% patients had USG evidence of SS. Patients with SS had significantly higher levels of pro-inflammatory and angiogenic mediators [matrix-metalloproteinase -3 (p = 0.0001), Tumour necrosis factor-α (p = 0.0001), Interleukin (IL)-6 (p = 0.001), IL-1b (p = 0.0001), IL-17 (p = 0.0005), IL-33 (p = 0.0003), Tie-2 (p = 0.0001), vascular endothelial growth factor (VEGF (p = 0.03)], and lower anti-inflammatory cytokines [IL-27 (p = 0.0003), IL-10(p = 0.0001)]. A strong positive correlation of GSS score was noted with IL-17(r = 0.7), IL-6 (r = 0.7), IL-1b (r = 0.7), and IL-33 (r = 0.6). Multiple linear regression model identified IL-17 and IL-6 as predictors of GSS score, and TNF-α and VEGF as predictors of PD score. IL-17 level > 249 picogram/millilitre (pg/ml) could predict the SS with high specificity (89.5%). Patients with SS in the remission state of RA showed altered expression of some of the pro/anti-inflammatory/angiogenic markers compared to those not having SS. IL-17, IL-6, VEGF, and TNF-α could be the predictors of USG synovial scores. Show less

Rare pathogenic variants in cardiomyopathy (CM) genes can predispose to cardiac remodeling or fibrosis. We studied the carrier status for such variants in adults without clinical cardiovascular disease (CVD) in whom cardiac MRI (CMR)-derived measures of myocardial fibrosis were obtained in the Multi-Ethnic Study of Atherosclerosis (MESA). To identify CM-associated pathogenic variants and assess their relative prevalence in participants with extensive myocardial fibrosis by CMR. MESA whole-genome sequencing data was evaluated to capture variants in CM-associated genes ( A total of 1,135 MESA participants had available genetic data and phenotypic measures and were free of clinical CVD at the time of CMR. We identified 6,349 rare variants in CM-associated genes in the overall MESA population, of which six pathogenic/likely pathogenic (P/LP) variants were present in the phenotyped subpopulation. The genes harboring P/LP variants in the case group were We observed a higher prevalence of rare potentially pathogenic CM associated genetic variants in participants with significant myocardial fibrosis quantified in CMR as compared to controls without significant fibrosis. No cardiac structural or functional differences were found between participants with or without P/LP variants. Show less

The epithelial to mesenchymal transition (EMT) is crucial for cancer progression and chemoresistance. EMT is a dynamic process with multiple phases that change cell migration and invasion activity. We used pan-cancer expression data to find 14-LncRNAs that had a high correlation with the EMT markers VIM, CDH1, FN1, SNAI1, and SNAI2. The expression of 14 EMT-associated LncRNA, which also showed high cancer specificity, was used to calculate the pan-cancer EMT score. The EMT score was then applied to the 32 cancer types to classify them as epithelial, epithelial-mesenchymal, mesenchymal-epithelial, or mesenchymal tumors. We discovered that the EMT score is a poor prognostic predictor and that as tumor mesenchymal nature increased, patient survival decreased. We also showed that the cell of origin did not influence the EMT nature of tumors. Pathway analysis employing protein expression data revealed that the PI3K pathway is the most crucial in determining the EMTness of tumors. Further, we divided CCLE-cell lines into EMT classes and discovered that mesenchymal cells, which exhibited higher PI3K pathway activation, were more sensitive to PI3K inhibitors than epithelial cells. We identified Linc01615 as a mesenchymal LncRNA whose expression significantly correlated with survival in several cancer types. We showed that Linc01615 is regulated by the TGFβ-STAT3 pathway in a feedback loop. Knockdown of Linc01615 inhibited cell proliferation and migration by regulating the PI3K pathway and mesenchymal markers. We also identified RP4-568C11.4 as an epithelial cancer marker. We showed that knocking down RP4-568C11.4 decreased cell growth but not migration. In addition, we discovered that ESR1 regulates RP4-5681C11.4 in breast cancer. Taken together, we have developed a pan-cancer EMT signature. Also, we found two new LncRNAs that have different effects on cancer development and EMT. Show less

Recurrent and metastatic pheochromocytoma (PCC) are rare advanced endocrine neoplasms with limited treatment options. Insight into the pathogenic molecular alterations in patients with advanced PCC can provide therapeutic options for precisely targeting dysregulated pathways. We report the discovery and characterization of a novel BRAF-containing fusion transcript and its downstream molecular alterations in a patient with recurrent PCC with peritoneal seeding (pheochromocytomatosis). We reviewed the medical record of a patient with pheochromocytomatosis. A comprehensive pan-cancer molecular profiling using next-generation sequencing (NGS) as well as confirmatory real-time-quantitative PCR were performed on surgical specimens. BRAF rearrangement and downstream molecular changes were assayed using fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC), respectively. Western blot was used to assess the in vitro activation of the mitogen-activated protein kinase (MAPK) signaling pathway and the EMT markers in transfected HEK-293 cells. The NGS analysis of a specimen from a 72-year-old female patient with pheochromocytomatosis showed an in-frame fusion of exon 3 of Glucocorticoid Induced 1 (GLCCI1) to exon 9 of BRAF. The upstream auto-inhibitory domain of BRAF was excluded from the GLCCI1-BRAF fusion; however, the downstream BRAF kinase domain was intact. A BRAF rearrangement was confirmed via a BRAF-specific break-apart FISH assay. Four separate tumor foci harbored GLCCI1-BRAF fusion. IHC demonstrated increased phosphorylated MEK. HEK-293 cells transfected with the GLCCI1-BRAF fusion demonstrated increased phosphorylated MEK as well as higher expression of EMT markers SNAI1 and ZEB1 in vitro. We demonstrate a novel pathogenic gene fusion of GLCCI1 with the oncogenic kinase domain of BRAF, resulting in an activation of the MAPK signaling pathway and EMT markers. Thus, this patient may benefit from clinically available MEK and/or BRAF inhibitors when systemic therapy is indicated. This report is the first of GLCCI1 fused to BRAF in a human neoplasm and only the second BRAF-containing fusion transcript in PCC. Detailed molecular characterization of PCC can be a valuable tool in managing patients with recurrent PCC and pheochromocytomatosis that represents a significant clinical challenge. Show less

Non-alcoholic fatty liver disease (NAFLD) is a global epidemic that often progresses to liver cirrhosis and hepatocellular carcinoma. In contrast to most world populations where NAFLD is mostly prevalent among obese, NAFLD among Indians and generally among South and South-East Asians is unique and highly prevalent among individuals who are lean. Genetics of NAFLD in Indian populations is understudied. In this study, we have used an exome-wide approach to identify genetic determinants of hepatic fat content (HFC) in India. HFC was measured in 244 participants using Proton magnetic resonance spectroscopy (H1-MRS). Quantitative trait loci (QTL) mapping was done exome-wide, to identify SNPs associated with HFC. The effects of the interaction between adiposity and QTLs on HFC were studied using a regression model. Association of the significant loci with disease severity was studied in 146 NAFLD patients among 244 participants, who underwent liver biopsy. Our study identified 4 significantly associated SNPs (rs738409 and rs2281135 (PNPLA3), rs3761472 (SAMM50), rs17513722 (FAM161A) and rs4788084), with HFC after adjusting for the effects of covariates (p-value < 0.0005). rs738409, rs2281135 (PNPLA3), and rs3761472 (SAMM50) were associated with hepatocyte ballooning, lobular and portal inflammation and non-alcoholic steatohepatitis (NASH) (p-value < 0.05). rs4788048 is an eQTL for IL27 and SULT1A2 genes, both of which are highly expressed in healthy livers and are likely to be involved in NAFLD pathogenesis. Our study identified the novel association of rs4788084 with HFC, which regulates the expression of IL-27, an immune regulatory gene. We further showed that adiposity affected the HFC, irrespective of the genetic predisposition. Show less

There is increasing evidence that pleiotropy, the association of multiple traits with the same genetic variants/loci, is a very common phenomenon. Cross-phenotype association tests are often used to jointly analyze multiple traits from a genome-wide association study (GWAS). The underlying methods, however, are often designed to test the global null hypothesis that there is no association of a genetic variant with any of the traits, the rejection of which does not implicate pleiotropy. In this article, we propose a new statistical approach, PLACO, for specifically detecting pleiotropic loci between two traits by considering an underlying composite null hypothesis that a variant is associated with none or only one of the traits. We propose testing the null hypothesis based on the product of the Z-statistics of the genetic variants across two studies and derive a null distribution of the test statistic in the form of a mixture distribution that allows for fractions of variants to be associated with none or only one of the traits. We borrow approaches from the statistical literature on mediation analysis that allow asymptotic approximation of the null distribution avoiding estimation of nuisance parameters related to mixture proportions and variance components. Simulation studies demonstrate that the proposed method can maintain type I error and can achieve major power gain over alternative simpler methods that are typically used for testing pleiotropy. PLACO allows correlation in summary statistics between studies that may arise due to sharing of controls between disease traits. Application of PLACO to publicly available summary data from two large case-control GWAS of Type 2 Diabetes and of Prostate Cancer implicated a number of novel shared genetic regions: 3q23 (ZBTB38), 6q25.3 (RGS17), 9p22.1 (HAUS6), 9p13.3 (UBAP2), 11p11.2 (RAPSN), 14q12 (AKAP6), 15q15 (KNL1) and 18q23 (ZNF236). Show less

SULT2B1b (SULT2B) is a prostate-expressed hydroxysteroid sulfotransferase, which may regulate intracrine androgen homeostasis by mediating 3β-sulfation of dehydroepiandrosterone (DHEA), the precursor for 5α-dihydrotestosterone (DHT) biosynthesis. The aldo-keto reductase (AKR)1C3 regulates androgen receptor (AR) activity in castration-resistant prostate cancer (CRPC) by promoting tumor tissue androgen biosynthesis from adrenal DHEA and also by functioning as an AR-selective coactivator. Herein we report that SULT2B-depleted CRPC cells, arising from stable RNA interference or gene knockout (KO), are markedly upregulated for AKR1C3, activated for ERK1/2 survival signal, and induced for epithelial-to-mesenchymal (EMT)-like changes. EMT was evident from increased mesenchymal proteins and elevated EMT-inducing transcription factors SNAI1 and TWIST1 in immunoblot and single-cell mass cytometry analyses. SULT2B KO cells showed greater motility and invasion in vitro; growth escalation in xenograft study; and enhanced metastatic potential predicted on the basis of decreased cell stiffness and adhesion revealed from atomic force microscopy analysis. While AR and androgen levels were unchanged, AR activity was elevated, since PSA and FKBP5 mRNA induction by DHT-activated AR was several-fold higher in SULT2B-silenced cells. AKR1C3 silencing prevented ERK1/2 activation and SNAI1 induction in SULT2B-depleted cells. SULT2B was undetectable in nearly all CRPC metastases from 50 autopsy cases. Primary tumors showed variable and Gleason score (GS)-independent SULT2B levels. CRPC metastases lacking SULT2B expressed AKR1C3. Since AKR1C3 is frequently elevated in advanced prostate cancer, the inhibitory influence of SULT2B on AKR1C3 upregulation, ERK1/2 activation, EMT-like induction, and on cell motility and invasiveness may be clinically significant. Pathways regulating the inhibitory SULT2B-AKR1C3 axis may inform new avenue(s) for targeting SULT2B-deficient prostate cancer. Show less

Deregulated epithelial-to-mesenchymal transition constitutes one of the major aspects of cancer progression. In this study, to identify key molecular principles of EMT pathway in prostate carcinogenesis, an elaborate gene expression profiling was conducted by qRT-PCR and Western blot analyses. A preponderance of mesenchymal trait was observed in the pathological samples of prostate cancer. To simulate an appropriate in vitro model, PC3 cell line was subjected to hypoxic stress, which resulted in elevated expression of vimentin along with EMT-mediating transcription factors Zeb1 and Slug. To conciliate this mesenchymal behavior of PC3 cells, hsa-miR-200c was deliberately overexpressed which led to a marked reduction of cell motility and expression of vimentin, N-cadherin, Zeb1 and Slug with concurrent increase in level of β-catenin. hsa-miR-200c was demonstrated to appease hypoxia-aggravated changes in cellular morphology by coordinated repression of vimentin, Zeb1 and Slug. Mode of action for hsa-miR-200c was mediated through transcriptional repression of Zeb1 and Slug interacting with E-box sequences in the vimentin promoter as documented by promoter assay. This ability of hsa-miR-200c to reclaim epithelial traits leads to the anticipation that molecular reprogramming of Zeb1-Slug/vimentin axis may relieve aggressiveness of prostate cancer. Show less

In rare variant association studies, aggregating rare and/or low frequency variants, may increase statistical power for detection of the underlying susceptibility gene or region. However, it is unclear which variants, or class of them, in a gene contribute most to the association. We proposed a subregion-based burden test (REBET) to simultaneously select susceptibility genes and identify important underlying subregions. The subregions are predefined by shared common biologic characteristics, such as the protein domain or functional impact. Based on a subset-based approach considering local correlations between combinations of test statistics of subregions, REBET is able to properly control the type I error rate while adjusting for multiple comparisons in a computationally efficient manner. Simulation studies show that REBET can achieve power competitive to alternative methods when rare variants cluster within subregions. In two case studies, REBET is able to identify known disease susceptibility genes, and more importantly pinpoint the unreported most susceptible subregions, which represent protein domains essential for gene function. R package REBET is available at https://dceg.cancer.gov/tools/analysis/rebet. Show less

A functional crosstalk between epigenetic regulators and metabolic control could provide a mechanism to adapt cellular responses to environmental cues. We report that the well-known nuclear MYST family acetyl transferase MOF and a subset of its non-specific lethal complex partners reside in mitochondria. MOF regulates oxidative phosphorylation by controlling expression of respiratory genes from both nuclear and mtDNA in aerobically respiring cells. MOF binds mtDNA, and this binding is dependent on KANSL3. The mitochondrial pool of MOF, but not a catalytically deficient mutant, rescues respiratory and mtDNA transcriptional defects triggered by the absence of MOF. Mof conditional knockout has catastrophic consequences for tissues with high-energy consumption, triggering hypertrophic cardiomyopathy and cardiac failure in murine hearts; cardiomyocytes show severe mitochondrial degeneration and deregulation of mitochondrial nutrient metabolism and oxidative phosphorylation pathways. Thus, MOF is a dual-transcriptional regulator of nuclear and mitochondrial genomes connecting epigenetics and metabolism. Show less

Metabolic syndrome (MetS) refers to the clustering of cardiometabolic risk factors, including dyslipidemia, central adiposity, hypertension, and hyperglycemia, in individuals. Identification of pleiotropic genetic factors associated with MetS traits may shed light on key pathways or mediators underlying MetS. Using the Metabochip array in 15 148 African Americans from the Population Architecture using Genomics and Epidemiology (PAGE) study, we identify susceptibility loci and investigate pleiotropy among genetic variants using a subset-based meta-analysis method, ASsociation-analysis-based-on-subSETs (ASSET). Unlike conventional models that lack power when associations for MetS components are null or have opposite effects, Association-analysis-based-on-subsets uses 1-sided tests to detect positive and negative associations for components separately and combines tests accounting for correlations among components. With Association-analysis-based-on-subsets, we identify 27 single nucleotide polymorphisms in 1 glucose and 4 lipids loci (TCF7L2, LPL, APOA5, CETP, and APOC1/APOE/TOMM40) significantly associated with MetS components overall, all P<2.5e-7, the Bonferroni adjusted P value. Three loci replicate in a Hispanic population, n=5172. A novel African American-specific variant, rs12721054/APOC1, and rs10096633/LPL are associated with ≥3 MetS components. We find additional evidence of pleiotropy for APOE, TOMM40, TCF7L2, and CETP variants, many with opposing effects (eg, the same rs7901695/TCF7L2 allele is associated with increased odds of high glucose and decreased odds of central adiposity). We highlight a method to increase power in large-scale genomic association analyses and report a novel variant associated with all MetS components in African Americans. We also identify pleiotropic associations that may be clinically useful in patient risk profiling and for informing translational research of potential gene targets and medications. Show less

Inadequate magnesium (Mg) intake is a widespread problem, with over 50% of women of reproductive age consuming less than the Recommended Dietary Allowance (RDA). Because pregnancy increases the requirement for Mg and the beneficial effects of magnesium sulfate for preeclampsia/eclampsia and fetal neuroprotection are well described, we examined the outcomes of Mg deficiency during pregnancy. Briefly, pregnant Swiss Webster mice were fed either control or Mg-deficient diets starting on gestational day (GD) 6 through euthanasia on GD17. Mg-deficient dams had significantly reduced weight gain and higher plasma adipokines, in the absence of inflammation. Livers of Mg-deficient dams had significantly higher saturated fatty acids (SFAs) and monounsaturated fatty acids (MUFAs) and lower polyunsaturated fatty acids (PUFAs), including docosahexaenoic acid (DHA) (P < 0.0001) and arachidonic acid (AA) (P < 0.0001). Mechanistically, Mg deficiency was accompanied by enhanced desaturase and elongase mRNA expression in maternal livers along with higher circulating insulin and glucose concentrations (P < 0.05) and increased mRNA expression of Srebf1 and Chrebp, regulators of fatty acid synthesis (P < 0.05). Fetal pups exposed to Mg deficiency were growth-restricted and exhibited reduced survival. Mg-deficient fetal livers showed lower MUFAs and higher PUFAs, with lower desaturase and elongase mRNA expression than controls. In addition, DHA concentrations were lower in Mg-deficient fetal brains (P < 0.05). These results indicate that Mg deficiency during pregnancy influences both maternal and fetal fatty acid metabolism, fetal growth and fetal survival, and support better understanding maternal Mg status before and during pregnancy. Show less

The tumor suppressor, PTEN is key to the regulation of diverse cellular processes, making it a prime candidate to be tightly regulated. The PTEN level is controlled in a major way by E3 ligase-mediated degradation through the Ubiquitin-Proteasome System (UPS). Nedd 4-1, XIAP, and WWP2 have been shown to maintain PTEN turnover. Here, we report that CHIP, the chaperone-associated E3 ligase, induces ubiquitination and regulates the proteasomal turnover of PTEN. It was apparent from our findings that PTEN transiently associates with the molecular chaperones and thereby gets diverted to the degradation pathway through its interaction with CHIP. The TPR domain of CHIP and parts of the N-terminal domain of PTEN are required for their interaction. Overexpression of CHIP leads to elevated ubiquitination and a shortened half-life of endogenous PTEN. On the other hand, depletion of endogenous CHIP stabilizes PTEN. CHIP is also shown to regulate PTEN-dependent transcription presumably through its down-regulation. PTEN shared an inverse correlation with CHIP in human prostate cancer patient samples, thereby triggering the prospects of a more complex mode of PTEN regulation in cancer. Show less

Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and ∼ 2.8 million SNPs in up to 123,865 individuals with targeted follow up of 42 SNPs in up to 125,931 additional individuals. We confirmed 14 known obesity susceptibility loci and identified 18 new loci associated with body mass index (P < 5 × 10⁻⁸), one of which includes a copy number variant near GPRC5B. Some loci (at MC4R, POMC, SH2B1 and BDNF) map near key hypothalamic regulators of energy balance, and one of these loci is near GIPR, an incretin receptor. Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation. Show less

Huntington's disease is caused by expansion of a polyglutamine tract found in the amino-terminal of the ubiquitously expressed protein huntingtin. Well studied in its mutant form, huntingtin has a wide variety of normal functions, loss of which may also contribute to disease progression. Widespread transcriptional dysfunction occurs in brains of Huntington's disease patients and in transgenic mouse and cell models of Huntington's disease. To identify new transcriptional pathways altered by the normal and/or abnormal function of huntingtin, we probed several nuclear receptors, normally expressed in the brain, for binding to huntingtin in its mutant and wild-type forms. Wild-type huntingtin could bind to a number of nuclear receptors; LXRalpha, PPARgamma, VDR and TRalpha1. Over-expression of huntingtin activated, while knockout of huntingtin decreased, LXR mediated transcription of a reporter gene. Loss of huntingtin also decreased expression of the LXR target gene, ABCA1. In vivo, huntingtin deficient zebrafish had a severe phenotype and reduced expression of LXR regulated genes. An LXR agonist was able to partially rescue the phenotype and the expression of LXR target genes in huntingtin deficient zebrafish during early development. Our data suggest a novel function for wild-type huntingtin as a co-factor of LXR. However, this activity is lost by mutant huntingtin that only interacts weakly with LXR. Show less