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Analysis of Differential Gene Expression and Core Canonical Pathways Involved in the Epithelial to Mesenchymal Transition of Triple Negative Breast Cancer Cells by Ingenuity Pathway Analysis

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Computational Molecular Bioscience 2023年第2期13卷 21-34页

作者： Elizabeth Cagle Brent Lake Anasua banerjee Jazmine Cuffee Narendra banerjee Darla Gilmartin Makaiyah Liverman Shennel Brown Erik Armstrong Santanu Bhattacharya Somiranjan Ghosh Tanmoy Mandal hirendra banerjee Department of Natural Health and Human Sciences Elizabeth City State University Campus of The University of North Carolina Elizabeth NC USA Department of Biochemistry and Molecular Biology Mayo College of Medicine and Science Jacksonville FL USA Department of Physiology and Biomedical Engineering Mayo College of Medicine and Science Jacksonville FL USA Departments of Pediatrics and Child Health College of Medicine Howard University Washington DC USA

Triple Negative Breast Cancer (TNBC) is a malignant form of cancer with very high mortality and morbidity. Epithelial to Mesenchymal Transition (EMT) is the most common pathophysiological change observed in cancer cells of epithelial origin that promotes metastasis, drug resistance and cancer stem cell formation. Since the information regarding differential gene expression in TNBC cells and cell signaling events leading to EMT is limited, this investigation was done by comparing transcriptomic data generated by RNA isolation and sequencing of a EMT model TNBC cell line in comparison to regular TNBC cells. RNA sequencing and Ingenuity Pathway Software Analysis (IPA) of the transcriptomic data revealed several upregulated and downregulated gene expressions along with novel core canonical pathways including Sirtuin signaling, Oxidative Phosphorylation and Mitochondrial dysfunction events involved in EMT changes of the TNBC cells.

关键词： Triple Negative Breast Cancer Epithelial to Mesenchymal Transition Core Canonical Pathways

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A Study of Differential Gene Expression and Core Canonical Pathways Involved in Rhenium Ligand Treated Epithelial Mesenchymal Transition (EMT) Induced A549 Lung Cancer Cell Lines by INGENUITY Software System

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Computational Molecular Bioscience 2022年第1期12卷 12-19页

作者： Christopher Krauss Chelsey Aurelus Kayla Johnston Joseph Hedley Satyendra banerjee Sarah Wisniewski Quentin Reaves Khadimou Dia Shenell Brown Victoria Bartlet Sheritta Gavin Jazmine Cuffee Narendra banerjee Kuldeep Rawat Santosh Mandal Zahidur Abedin Somiranjan Ghosh hirendra banerjee Department of Natural Sciences and Department of Health and Human Studies Elizabeth City State University University of NC Elizabeth City NC USA Department of Chemistry Morgan State University Baltimore MD USA PrimBio Research Institute LLC Exton PA USA Department of Pediatrics and Child Health Howard University Medical School Washington DC USA

Rhenium compounds have shown anti-cancer properties against many different types of cancer cell lines;however, the cellular signaling mechanisms involved in the cytotoxic properties of rhenium-based compounds were never deciphered or reported. In this manuscript, we report the results of an investigation done by RNA sequencing of rhenium treated A549 lung cancer cell lines along with an untreated vehicular control, analyzed by the Ingenuity Pathway Analysis (IPA) software system to decipher the core canonical pathways involved in rhenium induced cancer cell death. A549 EMT lung cancer cell lines were treated with rhenium ligand (Tricarbonylperrhenato(bathocuproine)rhenium(I), PR7) for seven days along with vehicular control. RNA was isolated from the treated and control cells and sequenced by a commercial company (PrimBio Corporation). The RNA sequencing data was analyzed by the INGNUITY software system and the core canonical pathways involved with differential gene expression were identified. Our report is showing that there are several cellular pathways involved in inducing cell death by rhenium-based compound PR7.

关键词： Rhenium Compounds Lung Cancer Epithelial

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Computational Molecular Bioscience 2020年第3期10卷 61-72页

作者： Dipendra C. Sengupta Matthew D. Hill Kevin R. Benton hirendra N. banerjee Department of Mathematics Computer Science & Engineering Technology Elizabeth City State University Elizabeth City North Carolina USA Department Natural Sciences Elizabeth City State University Elizabeth City North Carolina USA

The novel coronavirus (SARS-COV-2) is generally referred to as Covid-19 virus has spread to 213 countries with nearly 7 million confirmed cases and nearly 400,000 deaths. Such major outbreaks demand classification and origin of the virus genomic sequence, for planning, containment, and treatment. Motivated by the above need, we report two alignment-free methods combing with CGR to perform clustering analysis and create a phylogenetic tree based on it. To each DNA sequence we associate a matrix then define distance between two DNA sequences to be the distance between their associated matrix. These methods are being used for phylogenetic analysis of coronavirus sequences. Our approach provides a powerful tool for analyzing and annotating genomes and their phylogenetic relationships. We also compare our tool to ClustalX algorithm which is one of the most popular alignment methods. Our alignment-free methods are shown to be capable of finding closest genetic relatives of coronaviruses.

关键词： Covid-19 Chaos Game Representation Deoxyribonucleic Acid Phylogenetic Analysis Shannon Entropy

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Expression of Insulin-like Growth Factor-I in Uterusis Ovarian Steroid Dependent:An in situ Immunohistochemical Study in Rat

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Journal of Reproduction and Contraception 2012年第4期23卷 222-236页

作者： Daniel Mize Purba Jyoti Saikia hirendra N Sarma Department of Zoology (Center with potential for excellence in Biodiversity) Rajiv Gandhi University

Objective To study the immunohistochemical localization of insulin-like growth factor- I （IGF-I） in rats＇ uteri to determine if expression of the growth factor is ovarian steroid dependent. The study was carried out in presence and absence of ovary in situ of non pregnant females and during early gestation （day 1 to day 5.5）. Cyclic females were tested to observe the effect of native steroids on IGF-I expression. Adult females were ovariectomized （OVX） and injected （s.c） with estradiol-1713 in a dose of O.1 I^g/ml per day for three consecutive days at interval of 24 h prior to the collection of uterine horns. During the early pregnancy, studies were carried out on day 3.5 and day 5. 5 of geatation respectively to determine the Steroids＇ effects during pre- and post-implantation period Tamoxifen was administered （s.c） in a dose of 250 Ug/ml per day from day 1 to day 3 of gestation while, the prostaglandin F2a （PGF2a） was administered （s.c） from day 3 of gestation onward for three consecutive days at interval of 24 h in a dose of 150 μg/ml per day. Expression of lGF-I was immunohistochemically localised using IGF-1 antibody in paraffin embedded sections. Results IGF-I was expressed in rat uterus during estrus phase as well as during pre and post-implantation period The ovariectomized females＇ uteri lost the expression of IGF-1. Exogenous administration of tamoxifen and PGF2a reduce the expression of the growth factor. Conclusion Expression of lGF-1 in rat uterus during cyclic stage and early gestation depends upon the availability of circulating estrogen and progesterone. Uterine expression of lGF-I can be modulated by manipulating circulating ovarian steroid either during cyclic stage or during gestation.

关键词： IGF-I tamoxifen, PGF2a uterus implantation

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Chromatographic Fraction of Polygonum hydropiper Root Modulates the Expression of Transforming Growth Factor-βI (TGF-βI) in Rat Uterus during Days 2-6 of Gestation

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Journal of Reproduction and Contraception 2011年第3期22卷 153-167页

作者： Pranjiv Goswami Ajit Hazarika hirendra N Sarma Department of Zoology (Centre with Potential for Excellence in Biodiversity) Rajiv Gandhi University Department of Zoology Chaiduar College

Objective To examine the effect of the root extract on the growth factor during early pregnancy from day 2 to day 6 of gestation. Methods A purified form of root extract of Polygonum hydropiper was obtained by Thin Layer Chromatography （TLC）. Localization of transforming growth factor （TGF）- β1 was studied by immunohistochemistry and the expression of the mRNA of TGF- β1 was studied by Reverse transcriptase Polymerase Chain Reaction （RT-PCR） in uterine tissue from day 2 to day 6 of gestation. Results The TLC fraction treated in a dose of 5 mg/kg body weight per day showed decreased the number of implantation sites. The expression of TGF- β1 from day 2 to day 6 of gestation was altered by the TLCfraction and suppression of the mRNA transcript of the TGF- β1 on day 6 of gestation during implantation. Conclusion The root extract of Polygonum hydropiper in a dose of 5 mg/kg body weight per day decreased the expression of TGF- β1 in the implantation sites of rat uterus.

关键词： Polygonum hydropiper implantation sites TGF- β1 IHC RT-PCR Thin Layer Chromatography （TLC）

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Root Extract of Polygonum Hydropiper Alters the Expression of Rat Uterine Protein Profile in Presence and Absence of Ovary in-situ during Periimplantation Period:An Evidence on SDS-PAGE

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Journal of Reproduction and Contraception 2009年第4期20卷 223-236页

作者： Pranjiv Goswami Ajit Hazarika hirendra N Sarma Reproduction Research Laboratory Department of Zoology(Center with Potential for Excellence in Biodiversity)Rajiv Gandhi University Department of Zoology Chaiduar College

Objective To study its effects on reproductive performance in albino rats.Methods The chromatographic fraction （CF） of crude methanolic extract of the herb has been subcutaneously administered to female albino rats. Experiments were carried out in adult cyclic females and oavriectomised （OVX） females during early gestation period. Uterine horns were collected following the respective treatment regimen to stud）, the protein profile in 15% gel SDS-PAGE.Results The CF induced changes in the expression of protein in rat uterus. New proteins have been expressed in uterus of adult cyclic females having ovary in-situ. The OVX females treated with CF showed altered uterine protein profile compared with that of OVX control and OVX estradiol-17β （E2） treated rats. The CF exerted its effect on expression of uterine protein during early gestation period in rats. While uterine proteins of CF treated females were similar to that of controls during preimplantation period; many of the proteins on day 6 of gestation have been found either missing or expressed in lesser intensity.Conclusion The root of Polygonum hydropiper contains potential compound（s） which can alter the reproductive performance of female rats modulating uterine protein expression.

关键词： Polygonum hydropiper periimplantation uterine protein SDS-PAGE

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