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169 results on '"Varghese, Rency S."'

9. Data from Metabolomic Characterization of Hepatocellular Carcinoma in Patients with Liver Cirrhosis for Biomarker Discovery

Author

Di Poto, Cristina, primary, Ferrarini, Alessia, primary, Zhao, Yi, primary, Varghese, Rency S., primary, Tu, Chao, primary, Zuo, Yiming, primary, Wang, Minkun, primary, Nezami Ranjbar, Mohammad R., primary, Luo, Yue, primary, Zhang, Chi, primary, Desai, Chirag S., primary, Shetty, Kirti, primary, Tadesse, Mahlet G., primary, and Ressom, Habtom W., primary

Published
2023
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11. Supplementary Tables S1-S3 and Figure S1-S3. from Metabolomic Characterization of Hepatocellular Carcinoma in Patients with Liver Cirrhosis for Biomarker Discovery

Author

Di Poto, Cristina, primary, Ferrarini, Alessia, primary, Zhao, Yi, primary, Varghese, Rency S., primary, Tu, Chao, primary, Zuo, Yiming, primary, Wang, Minkun, primary, Nezami Ranjbar, Mohammad R., primary, Luo, Yue, primary, Zhang, Chi, primary, Desai, Chirag S., primary, Shetty, Kirti, primary, Tadesse, Mahlet G., primary, and Ressom, Habtom W., primary

Published
2023
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21. A Bayesian two-step integrative procedure incorporating prior knowledge for the identification of miRNA-mRNAs involved in hepatocellular carcinoma

Author

Denis, Marie, Varghese, Rency S., Barefoot, Megan E., Tadesse, Mahlet, Ressom, Habtom W., Denis, Marie, Varghese, Rency S., Barefoot, Megan E., Tadesse, Mahlet, and Ressom, Habtom W.

Abstract

Recent studies have confirmed the role of miRNA regulation of gene expression in oncogenesis for various cancers. In parallel, prior knowledge about relationships between miRNA and mRNA have been accumulated from biological experiments or statistical analyses. Improved identification of disease-associated miRNA-mRNA pairs may be achieved by incorporating prior knowledge into integrative genomic analyses. In this study we focus on 39 patients with hepatocellular carcinoma (HCC) and 25 patients with liver cirrhosis and use a flexible Bayesian two-step integrative method. We found 66 significant miRNA-mRNA pairs, several of which contain molecules that have previously been identified as potential biomarkers. These results demonstrate the utility of the proposed approach in providing a better understanding of relationships between different biological levels, thereby giving insights into the biological mechanisms underlying the diseases, while providing a better selection of biomarkers that may serve as diagnostic, prognostic, or therapeutic biomarker candidates.

Published
2022

23. MicroRNA-483-5p Inhibits Hepatocellular Carcinoma Cell Proliferation, Cell Steatosis, and Fibrosis by Targeting PPARα and TIMP2.

Author

Niture, Suryakant, Gadi, Sashi, Qi, Qi, Gyamfi, Maxwell Afari, Varghese, Rency S., Rios-Colon, Leslimar, Chimeh, Uchechukwu, Vandana, Ressom, Habtom W., and Kumar, Deepak

Subjects
PROTEINS, IN vitro studies, IN vivo studies, ANIMAL experimentation, MICRORNA, PEROXISOME proliferator-activated receptors, APOPTOSIS, CELLULAR signal transduction, GENE expression, CELL proliferation, RESEARCH funding, CELL lines, HEPATOCELLULAR carcinoma, MICE
Abstract

Simple Summary: Hepatocellular carcinoma (HCC) is the fifth leading and highly aggressive lethal liver cancer. The most common cause of HCC is liver cirrhosis because of multiple underlying etiologies, such as chronic hepatitis, nonalcoholic fatty liver disease (NAFLD), alcoholic fatty liver disease (AFLD), and hepatoxicity. In the current study, we characterize the role of microRNA-483-5p in NAFLD/AFLD and HCC progression and its potential use as a prognostic biomarker. MicroRNAs (miRNAs) are small non-coding RNA molecules that bind with the 3′ untranslated regions (UTRs) of genes to regulate expression. Downregulation of miR-483-5p (miR-483) is associated with the progression of hepatocellular carcinoma (HCC). However, the significant roles of miR-483 in nonalcoholic fatty liver disease (NAFLD), alcoholic fatty liver diseases (AFLD), and HCC remain elusive. In the current study, we investigated the biological significance of miR-483 in NAFLD, AFLD, and HCC in vitro and in vivo. The downregulation of miR-483 expression in HCC patients' tumor samples was associated with Notch 3 upregulation. Overexpression of miR-483 in a human bipotent progenitor liver cell line HepaRG and HCC cells dysregulated Notch signaling, inhibited cell proliferation/migration, induced apoptosis, and increased sensitivity towards antineoplastic agents sorafenib/regorafenib. Interestingly, the inactivation of miR-483 upregulated cell steatosis and fibrosis signaling by modulation of lipogenic and fibrosis gene expression. Mechanistically, miR-483 targets PPARα and TIMP2 gene expression, which leads to the suppression of cell steatosis and fibrosis. The downregulation of miR-483 was observed in mice liver fed with a high-fat diet (HFD) or a standard Lieber-Decarli liquid diet containing 5% alcohol, leading to increased hepatic steatosis/fibrosis. Our data suggest that miR-483 inhibits cell steatosis and fibrogenic signaling and functions as a tumor suppressor in HCC. Therefore, miR-483 may be a novel therapeutic target for NAFLD/AFLD/HCC management in patients with fatty liver diseases and HCC. [ABSTRACT FROM AUTHOR]

Published
2023
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24. Integrative Analysis of DNA Methylation and microRNA Expression Reveals Mechanisms of Racial Heterogeneity in Hepatocellular Carcinoma

Author

Varghese, Rency S., primary, Barefoot, Megan E., additional, Jain, Sidharth, additional, Chen, Yifan, additional, Zhang, Yunxi, additional, Alley, Amber, additional, Kroemer, Alexander H., additional, Tadesse, Mahlet G., additional, Kumar, Deepak, additional, Sherif, Zaki A., additional, and Ressom, Habtom W., additional

Published
2021
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29. Identification of miRNA-mRNA associations in hepatocellular carcinoma using hierarchical integrative model

Author

Varghese, Rency S., primary, Zhou, Yuan, additional, Barefoot, Megan, additional, Chen, Yifan, additional, Poto, Cristina Di, additional, Balla, Abdalla Kara, additional, Oliver, Everett, additional, Sherif, Zaki A., additional, Kumar, Deepak, additional, Kroemer, Alexander H., additional, Tadesse, Mahlet G., additional, and Ressom, Habtom, additional

Published
2020
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31. Analysis of mass spectral serum profiles for biomarker selection

Author

Ressom, Habtom W., Varghese, Rency S., Abdel-Hamid, Mohamed, Eissa, Sohair Abdel-Latif, Saha, Daniel, Goldman, Lenka, Petricoin, Emanuel F., Conrads, Thomas P., Veenstra, Timothy D., Loffredo, Christopher A., and Goldman, Radoslav

Published
2005

32. Using a spike-in experiment to evaluate analysis of LC-MS data

Author

Tuli Leepika, Tsai Tsung-Heng, Varghese Rency S, Xiao Jun Feng, Cheema Amrita, and Ressom Habtom W

Subjects
Difference detection, Label-free, Liquid chromatography-mass spectrometry (LC-MS), Spike-in peptide, Cytology, QH573-671
Abstract

Abstract Background Recent advances in liquid chromatography-mass spectrometry (LC-MS) technology have led to more effective approaches for measuring changes in peptide/protein abundances in biological samples. Label-free LC-MS methods have been used for extraction of quantitative information and for detection of differentially abundant peptides/proteins. However, difference detection by analysis of data derived from label-free LC-MS methods requires various preprocessing steps including filtering, baseline correction, peak detection, alignment, and normalization. Although several specialized tools have been developed to analyze LC-MS data, determining the most appropriate computational pipeline remains challenging partly due to lack of established gold standards. Results The work in this paper is an initial study to develop a simple model with "presence" or "absence" condition using spike-in experiments and to be able to identify these "true differences" using available software tools. In addition to the preprocessing pipelines, choosing appropriate statistical tests and determining critical values are important. We observe that individual statistical tests could lead to different results due to different assumptions and employed metrics. It is therefore preferable to incorporate several statistical tests for either exploration or confirmation purpose. Conclusions The LC-MS data from our spike-in experiment can be used for developing and optimizing LC-MS data preprocessing algorithms and to evaluate workflows implemented in existing software tools. Our current work is a stepping stone towards optimizing LC-MS data acquisition and testing the accuracy and validity of computational tools for difference detection in future studies that will be focused on spiking peptides of diverse physicochemical properties in different concentrations to better represent biomarker discovery of differentially abundant peptides/proteins.

Published
2012
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35. Discovery of potential urine-accessible metabolite biomarkers associated with muscle disease and corticosteroid response in the mdx mouse model for Duchenne

Author

Thangarajh, Mathula, primary, Zhang, Aiping, additional, Gill, Kirandeep, additional, Ressom, Habtom W., additional, Li, Zhenzhi, additional, Varghese, Rency S., additional, Hoffman, Eric P., additional, Nagaraju, Kanneboyina, additional, Hathout, Yetrib, additional, and Boca, Simina M., additional

Published
2019
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37. Metabolomic Analysis of Liver Tissues for Characterization of Hepatocellular Carcinoma

Author

Ferrarini, Alessia, primary, Di Poto, Cristina, additional, He, Shisi, additional, Tu, Chao, additional, Varghese, Rency S., additional, Kara Balla, Abdalla, additional, Jayatilake, Meth, additional, Li, Zhenzhi, additional, Ghaffari, Kian, additional, Fan, Ziling, additional, Sherif, Zaki A., additional, Kumar, Deepak, additional, Kroemer, Alexander, additional, Tadesse, Mahlet G., additional, and Ressom, Habtom W., additional

Published
2019
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39. Identification of race-associated metabolite biomarkers for hepatocellular carcinoma in patients with liver cirrhosis and hepatitis C virus infection

Author

Di Poto, Cristina, primary, He, Shisi, additional, Varghese, Rency S., additional, Zhao, Yi, additional, Ferrarini, Alessia, additional, Su, Shan, additional, Karabala, Abdullah, additional, Redi, Mesfin, additional, Mamo, Hassen, additional, Rangnekar, Amol S., additional, Fishbein, Thomas M., additional, Kroemer, Alexander H., additional, Tadesse, Mahlet G., additional, Roy, Rabindra, additional, Sherif, Zaki A., additional, Kumar, Deepak, additional, and Ressom, Habtom W., additional

Published
2018
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40. Metabolomic Characterization of Hepatocellular Carcinoma in Patients with Liver Cirrhosis for Biomarker Discovery

Author

Di Poto, Cristina, primary, Ferrarini, Alessia, additional, Zhao, Yi, additional, Varghese, Rency S., additional, Tu, Chao, additional, Zuo, Yiming, additional, Wang, Minkun, additional, Nezami Ranjbar, Mohammad R., additional, Luo, Yue, additional, Zhang, Chi, additional, Desai, Chirag S., additional, Shetty, Kirti, additional, Tadesse, Mahlet G., additional, and Ressom, Habtom W., additional

Published
2017
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41. Network-based analysis of reverse phase protein array data

Author

Varghese, Rency S, primary, Zuo, Yiming, additional, Zhao, Yi, additional, Zhang, Yong-Wei, additional, Jablonski, Sandra A, additional, Pierobon, Mariaelena, additional, Petricoin, Emanuel F, additional, Ressom, Habtom W, additional, and Weiner, Louis M, additional

Published
2016
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42. Metabolomic profiling of breast tumors using ductal fluid

Author

Do Canto, Luisa Matos, primary, Marian, Catalin, additional, Varghese, Rency S., additional, Ahn, Jaeil, additional, Da Cunha, Patricia A., additional, Willey, Shawna, additional, Sidawy, Mary, additional, Rone, Janice D., additional, Cheema, Amrita K., additional, Luta, George, additional, Nezami ranjbar, Mohammad R., additional, Ressom, Habtom W., additional, and Haddad, Bassem R., additional

Published
2016
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43. Multi-omic approaches for characterization of hepatocellular carcinoma

Author

Ressom, Habtom W., primary, Di Poto, Cristina, additional, Ferrarini, Alessia, additional, Hu, Yunli, additional, Nezami Ranjbar, Mohammad R., additional, Song, Ehwang, additional, Varghese, Rency S., additional, Wang, Minkun, additional, Zhou, Shiyue, additional, Zhu, Rui, additional, Zuo, Yiming, additional, Tadesse, Mahlet G., additional, and Mechref, Yehia, additional

Published
2016
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45. GC-MS Based Plasma Metabolomics for Identification of Candidate Biomarkers for Hepatocellular Carcinoma in Egyptian Cohort

Author

Nezami Ranjbar, Mohammad R., primary, Luo, Yue, additional, Di Poto, Cristina, additional, Varghese, Rency S., additional, Ferrarini, Alessia, additional, Zhang, Chi, additional, Sarhan, Naglaa I., additional, Soliman, Hanan, additional, Tadesse, Mahlet G., additional, Ziada, Dina H., additional, Roy, Rabindra, additional, and Ressom, Habtom W., additional

Published
2015
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46. LC-MS/MS-based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma

Author

Tsai, Tsung-Heng, primary, Song, Ehwang, additional, Zhu, Rui, additional, Di Poto, Cristina, additional, Wang, Minkun, additional, Luo, Yue, additional, Varghese, Rency S., additional, Tadesse, Mahlet G., additional, Ziada, Dina Hazem, additional, Desai, Chirag S., additional, Shetty, Kirti, additional, Mechref, Yehia, additional, and Ressom, Habtom W., additional

Published
2015
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48. LC–MS Profiling of N-Glycans Derived from Human Serum Samples for Biomarker Discovery in Hepatocellular Carcinoma

Author

Tsai, Tsung-Heng, primary, Wang, Minkun, additional, Di Poto, Cristina, additional, Hu, Yunli, additional, Zhou, Shiyue, additional, Zhao, Yi, additional, Varghese, Rency S., additional, Luo, Yue, additional, Tadesse, Mahlet G., additional, Ziada, Dina Hazem, additional, Desai, Chirag S., additional, Shetty, Kirti, additional, Mechref, Yehia, additional, and Ressom, Habtom W., additional

Published
2014
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50. LC–MS Based Serum Metabolomics for Identification of Hepatocellular Carcinoma Biomarkers in Egyptian Cohort

Author

Xiao, Jun Feng, primary, Varghese, Rency S., additional, Zhou, Bin, additional, Nezami Ranjbar, Mohammad R., additional, Zhao, Yi, additional, Tsai, Tsung-Heng, additional, Di Poto, Cristina, additional, Wang, Jinlian, additional, Goerlitz, David, additional, Luo, Yue, additional, Cheema, Amrita K., additional, Sarhan, Naglaa, additional, Soliman, Hanan, additional, Tadesse, Mahlet G., additional, Ziada, Dina Hazem, additional, and Ressom, Habtom W., additional

Published
2012
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