Substrate Specificity and Regulation of Nedd4 Proteins
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PLEKHO1 Knockdown Inhibits RCC Cell Viability in Vitro and in Vivo, Potentially by the Hippo and MAPK/JNK Pathways
INTERNATIONAL JOURNAL OF ONCOLOGY 55: 81-92, 2019 PLEKHO1 knockdown inhibits RCC cell viability in vitro and in vivo, potentially by the Hippo and MAPK/JNK pathways ZI YU1,2*, QIANG LI3*, GEJUN ZHANG2, CHENGCHENG LV1, QINGZHUO DONG2, CHENG FU1, CHUIZE KONG2 and YU ZENG1 1Department of Urology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042; 2Department of Urology, The First Hospital of China Medical University, Shenyang, Liaoning 110001; 3Department of Pathology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China Received November 17, 2018; Accepted May 17, 2019 DOI: 10.3892/ijo.2019.4819 Abstract. Renal cell carcinoma (RCC) is the most common involved in the serine/threonine-protein kinase hippo and JNK type of kidney cancer. By analysing The Cancer Genome signalling pathways. Together, the results of the present study Atlas (TCGA) database, 16 genes were identified to be suggest that PLEKHO1 may contribute to the development consistently highly expressed in RCC tissues compared with of RCC, and therefore, further study is needed to explore its the matched para-tumour tissues. Using a high-throughput cell potential as a therapeutic target. viability screening method, it was found that downregulation of only two genes significantly inhibited the viability of Introduction 786-O cells. Among the two genes, pleckstrin homology domain containing O1 (PLEKHO1) has never been studied in In 2018, kidney cancer is estimated to be diagnosed in RCC, to the best of our knowledge, and its expression level nearly 403,200 people worldwide and to lead to almost was shown to be associated with the prognosis of patients with 175,000 cancer-related deaths according to the latest data RCC in TCGA dataset. -
Podocyte Specific Knockdown of Klf15 in Podocin-Cre Klf15flox/Flox Mice Was Confirmed
SUPPLEMENTARY FIGURE LEGENDS Supplementary Figure 1: Podocyte specific knockdown of Klf15 in Podocin-Cre Klf15flox/flox mice was confirmed. (A) Primary glomerular epithelial cells (PGECs) were isolated from 12-week old Podocin-Cre Klf15flox/flox and Podocin-Cre Klf15+/+ mice and cultured at 37°C for 1 week. Real-time PCR was performed for Nephrin, Podocin, Synaptopodin, and Wt1 mRNA expression (n=6, ***p<0.001, Mann-Whitney test). (B) Real- time PCR was performed for Klf15 mRNA expression (n=6, *p<0.05, Mann-Whitney test). (C) Protein was also extracted and western blot analysis for Klf15 was performed. The representative blot of three independent experiments is shown in the top panel. The bottom panel shows the quantification of Klf15 by densitometry (n=3, *p<0.05, Mann-Whitney test). (D) Immunofluorescence staining for Klf15 and Wt1 was performed in 12-week old Podocin-Cre Klf15flox/flox and Podocin-Cre Klf15+/+ mice. Representative images from four mice in each group are shown in the left panel (X 20). Arrows show colocalization of Klf15 and Wt1. Arrowheads show a lack of colocalization. Asterisk demonstrates nonspecific Wt1 staining. “R” represents autofluorescence from RBCs. In the right panel, a total of 30 glomeruli were selected in each mouse and quantification of Klf15 staining in the podocytes was determined by the ratio of Klf15+ and Wt1+ cells to Wt1+ cells (n=6 mice, **p<0.01, unpaired t test). Supplementary Figure 2: LPS treated Podocin-Cre Klf15flox/flox mice exhibit a lack of recovery in proteinaceous casts and tubular dilatation after DEX administration. -
Transcriptome Analyses of Rhesus Monkey Pre-Implantation Embryos Reveal A
Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Transcriptome analyses of rhesus monkey pre-implantation embryos reveal a reduced capacity for DNA double strand break (DSB) repair in primate oocytes and early embryos Xinyi Wang 1,3,4,5*, Denghui Liu 2,4*, Dajian He 1,3,4,5, Shengbao Suo 2,4, Xian Xia 2,4, Xiechao He1,3,6, Jing-Dong J. Han2#, Ping Zheng1,3,6# Running title: reduced DNA DSB repair in monkey early embryos Affiliations: 1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 2 Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China 3 Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 4 University of Chinese Academy of Sciences, Beijing, China 5 Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China 6 Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China * Xinyi Wang and Denghui Liu contributed equally to this work 1 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press # Correspondence: Jing-Dong J. Han, Email: [email protected]; Ping Zheng, Email: [email protected] Key words: rhesus monkey, pre-implantation embryo, DNA damage 2 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT Pre-implantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA) and cell fate commitment. -
Nedd4 and Nedd4-2: Closely Related Ubiquitin-Protein Ligases with Distinct Physiological Functions
Cell Death and Differentiation (2010) 17, 68–77 & 2010 Macmillan Publishers Limited All rights reserved 1350-9047/10 $32.00 www.nature.com/cdd Review Nedd4 and Nedd4-2: closely related ubiquitin-protein ligases with distinct physiological functions B Yang*,1 and S Kumar*,2 The Nedd4 (neural precursor cell-expressed developmentally downregulated gene 4) family of ubiquitin ligases (E3s) is characterized by a distinct modular domain architecture, with each member consisting of a C2 domain, 2–4 WW domains, and a HECT-type ligase domain. Of the nine mammalian members of this family, Nedd4 and its close relative, Nedd4-2, represent the ancestral ligases with strong similarity to the yeast, Rsp5. In Saccharomyces cerevisiae Rsp5 has a key role in regulating the trafficking, sorting, and degradation of a large number of proteins in multiple cellular compartments. However, in mammals the Nedd4 family members, including Nedd4 and Nedd4-2, appear to have distinct functions, thereby suggesting that these E3s target specific proteins for ubiquitylation. In this article we focus on the biology and emerging functions of Nedd4 and Nedd4-2, and review recent in vivo studies on these E3s. Cell Death and Differentiation (2010) 17, 68–77; doi:10.1038/cdd.2009.84; published online 26 June 2009 Ubiquitylation controls biological signaling in many different ubiquitin-protein ligase (E3). A protein can be monoubiquity- ways.1,2 For example, the ubiquitylation of a misfolded or lated, multi-monoubiquitylated, or polyubiquitylated, and the damaged protein leads to its degradation by the 26S type of ubiquitylation determines the fate of the protein.1,2 proteasome before it can get to its subcellular site where it Ubiquitin itself contains seven lysine residues, all of which can normally functions. -
Supplemental Information
Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig. -
E3 Ubiquitin Ligases: Key Regulators of Tgfβ Signaling in Cancer Progression
International Journal of Molecular Sciences Review E3 Ubiquitin Ligases: Key Regulators of TGFβ Signaling in Cancer Progression Abhishek Sinha , Prasanna Vasudevan Iyengar and Peter ten Dijke * Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; [email protected] (A.S.); [email protected] (P.V.I.) * Correspondence: [email protected]; Tel.: +31-71-526-9271 Abstract: Transforming growth factor β (TGFβ) is a secreted growth and differentiation factor that influences vital cellular processes like proliferation, adhesion, motility, and apoptosis. Regulation of the TGFβ signaling pathway is of key importance to maintain tissue homeostasis. Perturbation of this signaling pathway has been implicated in a plethora of diseases, including cancer. The effect of TGFβ is dependent on cellular context, and TGFβ can perform both anti- and pro-oncogenic roles. TGFβ acts by binding to specific cell surface TGFβ type I and type II transmembrane receptors that are endowed with serine/threonine kinase activity. Upon ligand-induced receptor phosphorylation, SMAD proteins and other intracellular effectors become activated and mediate biological responses. The levels, localization, and function of TGFβ signaling mediators, regulators, and effectors are highly dynamic and regulated by a myriad of post-translational modifications. One such crucial modification is ubiquitination. The ubiquitin modification is also a mechanism by which crosstalk with other signaling pathways is achieved. Crucial effector components of the ubiquitination cascade include the very diverse family of E3 ubiquitin ligases. This review summarizes the diverse roles of E3 ligases that act on TGFβ receptor and intracellular signaling components. -
Smurf2-Mediated Stabilization of DNA Topoisomerase Iiα Controls Genomic Integrity
Published OnlineFirst June 13, 2017; DOI: 10.1158/0008-5472.CAN-16-2828 Cancer Molecular and Cellular Pathobiology Research Smurf2-Mediated Stabilization of DNA Topoisomerase IIa Controls Genomic Integrity Andrea Emanuelli1, Aurora P. Borroni1, Liat Apel-Sarid2, Pooja A. Shah1, Dhanoop Manikoth Ayyathan1, Praveen Koganti1, Gal Levy-Cohen1, and Michael Blank1 Abstract DNA topoisomerase IIa (Topo IIa) ensures genomic integ- pathological chromatin bridges formed during mitosis, a trait rity and unaltered chromosome inheritance and serves as a of Topo IIa–deficient cells and a hallmark of chromosome major target of several anticancer drugs. Topo IIa function is instability. Introducing Topo IIa into Smurf2-depleted cells well understood, but how its expression is regulated remains rescued this phenomenon. Smurf2 was a determinant of Topo unclear. Here, we identify the E3 ubiquitin ligase Smurf2 as a IIa protein levels in normal and cancer cells and tissues, and its physiologic regulator of Topo IIa levels. Smurf2 physically levels affected cell sensitivity to the Topo II–targeting drug interacted with Topo IIa and modified its ubiquitination status etoposide. Our results identified Smurf2 as an essential regu- to protect Topo IIa from the proteasomal degradation in dose- lator of Topo IIa, providing novel insights into its control and catalytically dependent manners. Smurf2-depleted cells and into the suggested tumor-suppressor functions of Smurf2. exhibited a reduced ability to resolve DNA catenanes and Cancer Res; 77(16); 1–11. Ó2017 AACR. Introduction mice knockout for Smurf2 develop a wide spectrum of tumors in different organs and tissues. These and other studies estab- DNA topoisomerase IIa (Topo IIa) is the major form of the lished Smurf2 as an important regulator of genomic integrity, Topo II enzyme in cycling vertebrate cells that acts to untangle whose inactivation results in carcinogenesis (7). -
The UBE2L3 Ubiquitin Conjugating Enzyme: Interplay with Inflammasome Signalling and Bacterial Ubiquitin Ligases
The UBE2L3 ubiquitin conjugating enzyme: interplay with inflammasome signalling and bacterial ubiquitin ligases Matthew James George Eldridge 2018 Imperial College London Department of Medicine Submitted to Imperial College London for the degree of Doctor of Philosophy 1 Abstract Inflammasome-controlled immune responses such as IL-1β release and pyroptosis play key roles in antimicrobial immunity and are heavily implicated in multiple hereditary autoimmune diseases. Despite extensive knowledge of the mechanisms regulating inflammasome activation, many downstream responses remain poorly understood or uncharacterised. The cysteine protease caspase-1 is the executor of inflammasome responses, therefore identifying and characterising its substrates is vital for better understanding of inflammasome-mediated effector mechanisms. Using unbiased proteomics, the Shenoy grouped identified the ubiquitin conjugating enzyme UBE2L3 as a target of caspase-1. In this work, I have confirmed UBE2L3 as an indirect target of caspase-1 and characterised its role in inflammasomes-mediated immune responses. I show that UBE2L3 functions in the negative regulation of cellular pro-IL-1 via the ubiquitin- proteasome system. Following inflammatory stimuli, UBE2L3 assists in the ubiquitylation and degradation of newly produced pro-IL-1. However, in response to caspase-1 activation, UBE2L3 is itself targeted for degradation by the proteasome in a caspase-1-dependent manner, thereby liberating an additional pool of IL-1 which may be processed and released. UBE2L3 therefore acts a molecular rheostat, conferring caspase-1 an additional level of control over this potent cytokine, ensuring that it is efficiently secreted only in appropriate circumstances. These findings on UBE2L3 have implications for IL-1- driven pathology in hereditary fever syndromes, and autoinflammatory conditions associated with UBE2L3 polymorphisms. -
Identification of Candidate Genes and Pathways Associated with Obesity
animals Article Identification of Candidate Genes and Pathways Associated with Obesity-Related Traits in Canines via Gene-Set Enrichment and Pathway-Based GWAS Analysis Sunirmal Sheet y, Srikanth Krishnamoorthy y , Jihye Cha, Soyoung Choi and Bong-Hwan Choi * Animal Genome & Bioinformatics, National Institute of Animal Science, RDA, Wanju 55365, Korea; [email protected] (S.S.); [email protected] (S.K.); [email protected] (J.C.); [email protected] (S.C.) * Correspondence: [email protected]; Tel.: +82-10-8143-5164 These authors contributed equally. y Received: 10 October 2020; Accepted: 6 November 2020; Published: 9 November 2020 Simple Summary: Obesity is a serious health issue and is increasing at an alarming rate in several dog breeds, but there is limited information on the genetic mechanism underlying it. Moreover, there have been very few reports on genetic markers associated with canine obesity. These studies were limited to the use of a single breed in the association study. In this study, we have performed a GWAS and supplemented it with gene-set enrichment and pathway-based analyses to identify causative loci and genes associated with canine obesity in 18 different dog breeds. From the GWAS, the significant markers associated with obesity-related traits including body weight (CACNA1B, C22orf39, U6, MYH14, PTPN2, SEH1L) and blood sugar (PRSS55, GRIK2), were identified. Furthermore, the gene-set enrichment and pathway-based analysis (GESA) highlighted five enriched pathways (Wnt signaling pathway, adherens junction, pathways in cancer, axon guidance, and insulin secretion) and seven GO terms (fat cell differentiation, calcium ion binding, cytoplasm, nucleus, phospholipid transport, central nervous system development, and cell surface) which were found to be shared among all the traits. -
Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A. -
SMURF1 As a Novel Regulator of PGC-1A Stuart A
St. Cloud State University theRepository at St. Cloud State Culminating Projects in Biology Department of Biology 5-2016 SMURF1 as a Novel Regulator of PGC-1a Stuart A. Fogarty Saint Cloud State University, [email protected] Follow this and additional works at: https://repository.stcloudstate.edu/biol_etds Recommended Citation Fogarty, Stuart A., "SMURF1 as a Novel Regulator of PGC-1a" (2016). Culminating Projects in Biology. 9. https://repository.stcloudstate.edu/biol_etds/9 This Thesis is brought to you for free and open access by the Department of Biology at theRepository at St. Cloud State. It has been accepted for inclusion in Culminating Projects in Biology by an authorized administrator of theRepository at St. Cloud State. For more information, please contact [email protected]. SMURF1 as a Novel Regulator of PGC-1α By Stuart Alexander Fogarty A Thesis Submitted to the Graduate Faculty of St. Cloud State University in Partial Fulfillment of the Requirements for the Degree of Master of Science in Biology May, 2016 Thesis Committee: Dr. Brian Olson, Chairperson Dr. Timothy Schuh Dr. Latha Ramakrishnan 2 Abstract Parkinson’s disease is a neurodegenerative disorder caused by the impairment and/or death of the dopaminergic neurons in the area of the brain that controls movement, and is diagnosed in roughly 60,000 Americans each year. Low levels of the protein PGC-1α have been linked to this disease, but efforts to find a chemical that causes higher production of PGC-1α. Therefore, the focus must change to determining whether or not it is possible to reduce the degradation of PGC- 1α without impacting the production rate of PGC-1α, thereby increasing PGC-1α levels. -
Partial Least Squares Based Gene Expression Analysis in Renal Failure Shuang Ding, Yinhai Xu, Tingting Hao and Ping Ma*
Ding et al. Diagnostic Pathology 2014, 9:137 http://www.diagnosticpathology.org/content/9/1/137 RESEARCH Open Access Partial least squares based gene expression analysis in renal failure Shuang Ding, Yinhai Xu, Tingting Hao and Ping Ma* Abstract Background: Preventive and therapeutic options for renal failure are still limited. Gene expression profile analysis is powerful in the identification of biological differences between end stage renal failure patients and healthy controls. Previous studies mainly used variance/regression analysis without considering various biological, environmental factors. The purpose of this study is to investigate the gene expression difference between end stage renal failure patients and healthy controls with partial least squares (PLS) based analysis. Methods: With gene expression data from the Gene Expression Omnibus database, we performed PLS analysis to identify differentially expressed genes. Enrichment and network analyses were also carried out to capture the molecular signatures of renal failure. Results: We acquired 573 differentially expressed genes. Pathway and Gene Ontology items enrichment analysis revealed over-representation of dysregulated genes in various biological processes. Network analysis identified seven hub genes with degrees higher than 10, including CAND1, CDK2, TP53, SMURF1, YWHAE, SRSF1,andRELA.Proteins encoded by CDK2, TP53,andRELA have been associated with the progression of renal failure in previous studies. Conclusions: Our findings shed light on expression character of renal failure patients with the hope to offer potential targets for future therapeutic studies. Virtual Slides: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/ 1450799302127207 Keywords: Renal failure, Partial least squares, Gene expression, Network Background detect dysregulated genes.