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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
The VLDL Receptor Regulates Membrane Progesterone Receptor
© 2018. Published by The Company of Biologists Ltd | Journal of Cell Science (2018) 131, jcs212522. doi:10.1242/jcs.212522 RESEARCH ARTICLE The VLDL receptor regulates membrane progesterone receptor trafficking and non-genomic signaling Nancy Nader, Maya Dib, Raphael Courjaret, Rawad Hodeify, Raya Machaca, Johannes Graumann and Khaled Machaca* ABSTRACT the plasma membrane and interact with the classical P4 receptor, is Progesterone mediates its physiological functions through activation of nonetheless effective at mediating non-genomic P4 signaling both transcription-coupled nuclear receptors and seven-pass- (Bandyopadhyay et al., 1998; Dressing et al., 2011; Peluso et al., transmembrane progesterone receptors (mPRs), which transduce 2002). These results argued for the presence of membrane P4 the rapid non-genomic actions of progesterone by coupling to various receptors that are distinct from the nuclear P4 receptors. In 2003, the signaling modules. However, the immediate mechanisms of action Thomas laboratory identified a family of membrane progesterone downstream of mPRs remain in question. Herein, we use an untargeted receptors (mPRs) from fish ovaries (Zhu et al., 2003a,b) that belong quantitative proteomics approach to identify mPR interactors to better to the progestin and adiponectin (AdipoQ) receptor family (also define progesterone non-genomic signaling. Surprisingly, we identify named PAQ receptors). However, the signal transduction cascade the very-low-density lipoprotein receptor (VLDLR) as an mPRβ downstream of mPRs that mediates the non-genomic actions of P4 (PAQR8) partner that is required for mPRβ plasma membrane remains unclear. localization. Knocking down VLDLR abolishes non-genomic The non-genomic action of mPR and the ensuing signaling progesterone signaling, which is rescued by overexpressing VLDLR. -
Progesterone Receptor Membrane Component 1 Promotes Survival of Human Breast Cancer Cells and the Growth of Xenograft Tumors
Cancer Biology & Therapy ISSN: 1538-4047 (Print) 1555-8576 (Online) Journal homepage: http://www.tandfonline.com/loi/kcbt20 Progesterone receptor membrane component 1 promotes survival of human breast cancer cells and the growth of xenograft tumors Nicole C. Clark, Anne M. Friel, Cindy A. Pru, Ling Zhang, Toshi Shioda, Bo R. Rueda, John J. Peluso & James K. Pru To cite this article: Nicole C. Clark, Anne M. Friel, Cindy A. Pru, Ling Zhang, Toshi Shioda, Bo R. Rueda, John J. Peluso & James K. Pru (2016) Progesterone receptor membrane component 1 promotes survival of human breast cancer cells and the growth of xenograft tumors, Cancer Biology & Therapy, 17:3, 262-271, DOI: 10.1080/15384047.2016.1139240 To link to this article: http://dx.doi.org/10.1080/15384047.2016.1139240 Accepted author version posted online: 19 Jan 2016. Published online: 19 Jan 2016. Submit your article to this journal Article views: 49 View related articles View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=kcbt20 Download by: [University of Connecticut] Date: 26 May 2016, At: 11:28 CANCER BIOLOGY & THERAPY 2016, VOL. 17, NO. 3, 262–271 http://dx.doi.org/10.1080/15384047.2016.1139240 RESEARCH PAPER Progesterone receptor membrane component 1 promotes survival of human breast cancer cells and the growth of xenograft tumors Nicole C. Clarka,*, Anne M. Frielb,*, Cindy A. Prua, Ling Zhangb, Toshi Shiodac, Bo R. Ruedab, John J. Pelusod, and James K. Prua aDepartment of Animal Sciences, -
The Roles of Histone Deacetylase 5 and the Histone Methyltransferase Adaptor WDR5 in Myc Oncogenesis
The Roles of Histone Deacetylase 5 and the Histone Methyltransferase Adaptor WDR5 in Myc oncogenesis By Yuting Sun This thesis is submitted in fulfilment of the requirements for the degree of Doctor of Philosophy at the University of New South Wales Children’s Cancer Institute Australia for Medical Research School of Women’s and Children’s Health, Faculty of Medicine University of New South Wales Australia August 2014 PLEASE TYPE THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: Sun First name: Yuting Other name/s: Abbreviation for degree as given in the University calendar: PhD School : School of·Women's and Children's Health Faculty: Faculty of Medicine Title: The Roles of Histone Deacetylase 5 and the Histone Methyltransferase Adaptor WDR5 in Myc oncogenesis. Abstract 350 words maximum: (PLEASE TYPE) N-Myc Induces neuroblastoma by regulating the expression of target genes and proteins, and N-Myc protein is degraded by Fbxw7 and NEDD4 and stabilized by Aurora A. The class lla histone deacetylase HDAC5 suppresses gene transcription, and blocks myoblast and leukaemia cell differentiation. While histone H3 lysine 4 (H3K4) trimethylation at target gene promoters is a pre-requisite for Myc· induced transcriptional activation, WDRS, as a histone H3K4 methyltransferase presenter, is required for H3K4 methylation and transcriptional activation mediated by a histone H3K4 methyltransferase complex. Here, I investigated the roles of HDAC5 and WDR5 in N-Myc overexpressing neuroblastoma. I have found that N-Myc upregulates HDAC5 protein expression, and that HDAC5 represses NEDD4 gene expression, increases Aurora A gene expression and consequently upregulates N-Myc protein expression in neuroblastoma cells. -
Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. -
Progesterone – Friend Or Foe?
Frontiers in Neuroendocrinology 59 (2020) 100856 Contents lists available at ScienceDirect Frontiers in Neuroendocrinology journal homepage: www.elsevier.com/locate/yfrne Progesterone – Friend or foe? T ⁎ Inger Sundström-Poromaaa, , Erika Comascob, Rachael Sumnerc, Eileen Ludersd,e a Department of Women’s and Children’s Health, Uppsala University, Sweden b Department of Neuroscience, Science for Life Laboratory, Uppsala University, Uppsala, Sweden c School of Pharmacy, University of Auckland, New Zealand d School of Psychology, University of Auckland, New Zealand e Laboratory of Neuro Imaging, School of Medicine, University of Southern California, Los Angeles, USA ARTICLE INFO ABSTRACT Keywords: Estradiol is the “prototypic” sex hormone of women. Yet, women have another sex hormone, which is often Allopregnanolone disregarded: Progesterone. The goal of this article is to provide a comprehensive review on progesterone, and its Emotion metabolite allopregnanolone, emphasizing three key areas: biological properties, main functions, and effects on Hormonal contraceptives mood in women. Recent years of intensive research on progesterone and allopregnanolone have paved the way Postpartum depression for new treatment of postpartum depression. However, treatment for premenstrual syndrome and premenstrual Premenstrual dysphoric disorder dysphoric disorder as well as contraception that women can use without risking mental health problems are still Progesterone needed. As far as progesterone is concerned, we might be dealing with a two-edged sword: while its metabolite allopregnanolone has been proven useful for treatment of PPD, it may trigger negative symptoms in women with PMS and PMDD. Overall, our current knowledge on the beneficial and harmful effects of progesterone is limited and further research is imperative. Introduction 1. -
VITA Peter M. Govey
The Pennsylvania State University The Graduate School Department of Bioengineering MULTISCALE ANABOLIC BONE RESPONSES TO FLUID FLOW AND POST-IRRADITION LOADING A Dissertation in Bioengineering by Peter M. Govey © 2015 Peter M. Govey Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 The dissertation of Peter M. Govey was reviewed and approved* by the following: Henry J. Donahue Michael and Myrtle Baker Professor of Orthopaedics and Rehabilitation, Cellular and Molecular Physiology, and Bioengineering Dissertation Advisor Chair of Committee Justin Brown Assistant Professor of Bioengineering Gregory Lewis Assistant Professor of Orthopaedics and Rehabilitation Christopher Niyibizi Associate Professor of Orthopaedics and Rehabilitation Christopher Siedlecki Professor of Surgery and Bioengineering Cheng Dong Distinguished Professor of Bioengineering Head of the Department of Bioengineering *Signatures are on file in the Graduate School. ii ABSTRACT Bone responds to its mechanical environment, strengthening in response to daily use and wasting during disuse. Examples of disuse include bed rest, immobility, and microgravity experienced in space. Bone resorption may be exacerbated by aging, radiation exposure, sex hormone reduction, and various other pathologies, leading to osteoporosis. Resulting insufficiency fractures represent a tremendous toll on our population’s health, and current treatments such as anti-resorptive bisphosphonates are stop-gap measures with accompanying complications. Improved -
Supplementary Data
Supplementary Fig. 1 A B Responder_Xenograft_ Responder_Xenograft_ NON- NON- Lu7336, Vehicle vs Lu7466, Vehicle vs Responder_Xenograft_ Responder_Xenograft_ Sagopilone, Welch- Sagopilone, Welch- Lu7187, Vehicle vs Lu7406, Vehicle vs Test: 638 Test: 600 Sagopilone, Welch- Sagopilone, Welch- Test: 468 Test: 482 Responder_Xenograft_ NON- Lu7860, Vehicle vs Responder_Xenograft_ Sagopilone, Welch - Lu7558, Vehicle vs Test: 605 Sagopilone, Welch- Test: 333 Supplementary Fig. 2 Supplementary Fig. 3 Supplementary Figure S1. Venn diagrams comparing probe sets regulated by Sagopilone treatment (10mg/kg for 24h) between individual models (Welsh Test ellipse p-value<0.001 or 5-fold change). A Sagopilone responder models, B Sagopilone non-responder models. Supplementary Figure S2. Pathway analysis of genes regulated by Sagopilone treatment in responder xenograft models 24h after Sagopilone treatment by GeneGo Metacore; the most significant pathway map representing cell cycle/spindle assembly and chromosome separation is shown, genes upregulated by Sagopilone treatment are marked with red thermometers. Supplementary Figure S3. GeneGo Metacore pathway analysis of genes differentially expressed between Sagopilone Responder and Non-Responder models displaying –log(p-Values) of most significant pathway maps. Supplementary Tables Supplementary Table 1. Response and activity in 22 non-small-cell lung cancer (NSCLC) xenograft models after treatment with Sagopilone and other cytotoxic agents commonly used in the management of NSCLC Tumor Model Response type -
G Protein-Coupled Receptors Function As Cell Membrane Receptors for the Steroid Hormone 20-Hydroxyecdysone Xiao-Fan Zhao
Zhao Cell Communication and Signaling (2020) 18:146 https://doi.org/10.1186/s12964-020-00620-y REVIEW Open Access G protein-coupled receptors function as cell membrane receptors for the steroid hormone 20-hydroxyecdysone Xiao-Fan Zhao Abstract G protein-coupled receptors (GPCRs) are cell membrane receptors for various ligands. Recent studies have suggested that GPCRs transmit animal steroid hormone signals. Certain GPCRs have been shown to bind steroid hormones, for example, G protein-coupled estrogen receptor 1 (GPER1) binds estrogen in humans, and Drosophila dopamine/ecdysteroid receptor (DopEcR) binds the molting hormone 20-hydroxyecdysone (20E) in insects. This review summarizes the research progress on GPCRs as animal steroid hormone cell membrane receptors, including the nuclear and cell membrane receptors of steroid hormones in mammals and insects, the 20E signaling cascade via GPCRs, termination of 20E signaling, and the relationship between genomic action and the nongenomic action of 20E. Studies indicate that 20E induces a signal via GPCRs to regulate rapid cellular responses, including rapid Ca2+ release from the endoplasmic reticulum and influx from the extracellular medium, as well as rapid protein phosphorylation and subcellular translocation. 20E via the GPCR/Ca2+/PKC/signaling axis and the GPCR/cAMP/PKA- signaling axis regulates gene transcription by adjusting transcription complex formation and DNA binding activity. GPCRs can bind 20E in the cell membrane and after being isolated, suggesting GPCRs as cell membrane receptors of 20E. This review deepens our understanding of GPCRs as steroid hormone cell membrane receptors and the GPCR-mediated signaling pathway of 20E (20E-GPCR pathway), which will promote further study of steroid hormone signaling via GPCRs, and presents GPCRs as targets to explore new pharmaceutical materials to treat steroid hormone-related diseases or control pest insects. -
Supplementary Materials and Tables a and B
SUPPLEMENTARY MATERIAL 1 Table A. Main characteristics of the subset of 23 AML patients studied by high-density arrays (subset A) WBC BM blasts MYST3- MLL Age/Gender WHO / FAB subtype Karyotype FLT3-ITD NPM status (x109/L) (%) CREBBP status 1 51 / F M4 NA 21 78 + - G A 2 28 / M M4 t(8;16)(p11;p13) 8 92 + - G G 3 53 / F M4 t(8;16)(p11;p13) 27 96 + NA G NA 4 24 / M PML-RARα / M3 t(15;17) 5 90 - - G G 5 52 / M PML-RARα / M3 t(15;17) 1.5 75 - - G G 6 31 / F PML-RARα / M3 t(15;17) 3.2 89 - - G G 7 23 / M RUNX1-RUNX1T1 / M2 t(8;21) 38 34 - + ND G 8 52 / M RUNX1-RUNX1T1 / M2 t(8;21) 8 68 - - ND G 9 40 / M RUNX1-RUNX1T1 / M2 t(8;21) 5.1 54 - - ND G 10 63 / M CBFβ-MYH11 / M4 inv(16) 297 80 - - ND G 11 63 / M CBFβ-MYH11 / M4 inv(16) 7 74 - - ND G 12 59 / M CBFβ-MYH11 / M0 t(16;16) 108 94 - - ND G 13 41 / F MLLT3-MLL / M5 t(9;11) 51 90 - + G R 14 38 / F M5 46, XX 36 79 - + G G 15 76 / M M4 46 XY, der(10) 21 90 - - G NA 16 59 / M M4 NA 29 59 - - M G 17 26 / M M5 46, XY 295 92 - + G G 18 62 / F M5 NA 67 88 - + M A 19 47 / F M5 del(11q23) 17 78 - + M G 20 50 / F M5 46, XX 61 59 - + M G 21 28 / F M5 46, XX 132 90 - + G G 22 30 / F AML-MD / M5 46, XX 6 79 - + M G 23 64 / M AML-MD / M1 46, XY 17 83 - + M G WBC: white blood cell. -
Supplementary Table 1
Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7 -
Open Sadiesteffens Dissertation Final.Pdf
The Pennsylvania State University The Graduate School College of Medicine MECHANISM OF DRUG ACTION OF THE SPECIFIC CK2 INHIBITOR CX-4945 IN ACUTE MYELOID LEUKEMIA A Dissertation in Biomedical Sciences by Sadie Lynne Steffens 2015 Sadie Lynne Steffens Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2015 The dissertation of Sadie Lynne Steffens was reviewed and approved* by the following: Sinisa Dovat Physician, Associate Professor of Pediatrics, Pharmacology, & Biochemistry Director, Translational Research – Four Diamonds Pediatric Cancer Research Center Dissertation Advisor Chair of Committee Barbara A. Miller Physician, Professor of Pediatrics Chief, Division of Pediatric Hematology/Oncology Sergei A. Grigoryev Professor of Biochemistry and Molecular Biology Jong K. Yun Associate Professor of Pharmacology Ralph L. Keil Associate Professor of Biochemistry and Molecular Biology Chair, Biomedical Sciences Graduate Program *Signatures are on file in the Graduate School ii ABSTRACT Acute myeloid leukemia (AML) is a malignant disease of the myeloid line of blood cells and is characterized by the rapid growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells. Cytarabine and other currently available treatments for acute myeloid leukemia are highly toxic and insufficient, as more than half of all AML patients develop resistance to chemotherapeutic agents. Since AML often affects older people who are less tolerant of chemotherapy, there is need for novel, targeted, less toxic drugs in order to improve survival for this disease. Casein Kinase II (CK2) is a pro-oncogenic serine/threonine kinase that is essential for cellular proliferation.