Pan-cancer analysis of genomic and transcriptomic data reveals the prognostic relevance of human proteasome genes in different cancer types

[1]  B. Győrffy,et al.  MultipleTesting.com: A tool for life science researchers for multiple hypothesis testing correction , 2021, bioRxiv.

[2]  E. Ruppin,et al.  Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma , 2020, Nature Communications.

[3]  Toshima Z. Parris,et al.  Pan-cancer analyses of human nuclear receptors reveal transcriptome diversity and prognostic value across cancer types , 2020, Scientific Reports.

[4]  E. Lander,et al.  Identification of cancer driver genes based on nucleotide context , 2019, Nature Genetics.

[5]  Yukun Hu,et al.  Feature article: Silencing PSME3 induces colorectal cancer radiosensitivity by downregulating the expression of cyclin B1 and CKD1 , 2019, Experimental biology and medicine.

[6]  V. Karpov,et al.  Proteasomes and Several Aspects of Their Heterogeneity Relevant to Cancer , 2019, Front. Oncol..

[7]  H. Overkleeft,et al.  Structure-Based Design of Inhibitors Selective for Human Proteasome β2c or β2i Subunits , 2019, Journal of medicinal chemistry.

[8]  V. Karpov,et al.  Biological consequences of structural and functional proteasome diversity , 2018, Heliyon.

[9]  J. E. Park,et al.  Next‐generation proteasome inhibitors for cancer therapy , 2018, Translational research : the journal of laboratory and clinical medicine.

[10]  G. Ren,et al.  PSMD2 regulates breast cancer cell proliferation and cell cycle progression by modulating p21 and p27 proteasomal degradation. , 2018, Cancer letters.

[11]  A. Bertolotti,et al.  Regulation of proteasome assembly and activity in health and disease , 2018, Nature Reviews Molecular Cell Biology.

[12]  Hua Wang,et al.  PSMB4 overexpression enhances the cell growth and viability of breast cancer cells leading to a poor prognosis. , 2018, Oncology reports.

[13]  A. Rosenwald,et al.  Spectrum and functional validation of PSMB5 mutations in multiple myeloma , 2018, Leukemia.

[14]  Andreas Martin,et al.  Structure and Function of the 26S Proteasome. , 2018, Annual review of biochemistry.

[15]  Toshima Z. Parris,et al.  Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma , 2018, Oncotarget.

[16]  J. Azzi,et al.  The immunoproteasome: An old player with a novel and emerging role in alloimmunity , 2017, American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.

[17]  C. Annunziata,et al.  Proteasome inhibitors: structure and function. , 2017, Seminars in oncology.

[18]  M. Hochstrasser,et al.  Proteasome Structure and Assembly. , 2017, Journal of molecular biology.

[19]  Q. Dou,et al.  Targeting the ubiquitin-proteasome system for cancer treatment: discovering novel inhibitors from nature and drug repurposing , 2017, Cancer and Metastasis Reviews.

[20]  D. Slamon,et al.  Proteasome ubiquitin receptor PSMD4 is an amplification target in breast cancer and may predict sensitivity to PARPi , 2017, Genes, chromosomes & cancer.

[21]  A. Goldberg,et al.  Inhibition of the Proteasome β2 Site Sensitizes Triple-Negative Breast Cancer Cells to β5 Inhibitors and Suppresses Nrf1 Activation. , 2017, Cell chemical biology.

[22]  R. Orlowski,et al.  Proteasome inhibitors in cancer therapy , 2017, Nature Reviews Clinical Oncology.

[23]  G. Ren,et al.  The transcription levels and prognostic values of seven proteasome alpha subunits in human cancers , 2016, Oncotarget.

[24]  S. Batra,et al.  Emerging role of immunoproteasomes in pathophysiology , 2016, Immunology and cell biology.

[25]  Sébastien Lemieux,et al.  Expression of immunoproteasome genes is regulated by cell-intrinsic and –extrinsic factors in human cancers , 2016, Scientific Reports.

[26]  L. Vermeulen,et al.  Cancer stem cells don't waste their time cleaning-low proteasome activity, a marker for cancer stem cell function. , 2016, Annals of translational medicine.

[27]  Y. Doki,et al.  Cancer Stem-like Properties in Colorectal Cancer Cells with Low Proteasome Activity , 2016, Clinical Cancer Research.

[28]  T. Lumley,et al.  Advanced Forest Plot Using 'grid' Graphics , 2016 .

[29]  Laura Smith,et al.  The role of PSMD9 in human disease: future clinical and therapeutic implications , 2015 .

[30]  Hiroaki Kimura,et al.  New Insights into the Function of the Immunoproteasome in Immune and Nonimmune Cells , 2015, Journal of immunology research.

[31]  Marc L. Mendillo,et al.  Compromising the 19S proteasome complex protects cells from reduced flux through the proteasome , 2015, eLife.

[32]  S. Murata,et al.  Redundant Roles of Rpn10 and Rpn13 in Recognition of Ubiquitinated Proteins and Cellular Homeostasis , 2015, PLoS genetics.

[33]  R. Vierstra,et al.  Autophagic Degradation of the 26S Proteasome Is Mediated by the Dual ATG8/Ubiquitin Receptor RPN10 in Arabidopsis. , 2015, Molecular cell.

[34]  A. Dillin,et al.  The role of protein clearance mechanisms in organismal ageing and age-related diseases , 2014, Nature Communications.

[35]  Beatriz Carvalho,et al.  Focal chromosomal copy number aberrations in cancer-Needles in a genome haystack. , 2014, Biochimica et biophysica acta.

[36]  M. Sharon,et al.  Regulating the 20S Proteasome Ubiquitin-Independent Degradation Pathway , 2014, Biomolecules.

[37]  A. Goldberg,et al.  Proteasome-Mediated Processing of Nrf1 Is Essential for Coordinate Induction of All Proteasome Subunits and p97 , 2014, Current Biology.

[38]  N. Chondrogianni,et al.  Proteasome activation delays aging in vitro and in vivo. , 2014, Free radical biology & medicine.

[39]  B. Monsarrat,et al.  Label-free quantitative proteomics reveals the dynamics of proteasome complexes composition and stoichiometry in a wide range of human cell lines. , 2014, Journal of proteome research.

[40]  V. Speirs,et al.  PSMD9 expression predicts radiotherapy response in breast cancer , 2014, Molecular Cancer.

[41]  D. Vilchez,et al.  The Mechanistic Links Between Proteasome Activity, Aging and Age-related Diseases , 2014, Current genomics.

[42]  A. Gomes.  Genetics of Proteasome Diseases , 2013, Scientifica.

[43]  S. Arii,et al.  Visualization of stem cell features in human hepatocellular carcinoma reveals in vivo significance of tumor‐host interaction and clinical course , 2013, Hepatology.

[44]  Hans Clevers,et al.  The cancer stem cell: premises, promises and challenges , 2011, Nature Medicine.

[45]  D. Wolf,et al.  Faculty Opinions recommendation of Transcription factor Nrf1 mediates the proteasome recovery pathway after proteasome inhibition in mammalian cells. , 2010 .

[46]  Per Karlsson,et al.  Clinical Implications of Gene Dosage and Gene Expression Patterns in Diploid Breast Carcinoma , 2010, Clinical Cancer Research.

[47]  N. Chondrogianni,et al.  Nuclear Erythroid Factor 2-mediated Proteasome Activation Delays Senescence in Human Fibroblasts* , 2010, The Journal of Biological Chemistry.

[48]  D. Finley,et al.  Recognition and processing of ubiquitin-protein conjugates by the proteasome. , 2009, Annual review of biochemistry.

[49]  S. Gygi,et al.  Isolation of mammalian 26S proteasomes and p97/VCP complexes using the ubiquitin-like domain from HHR23B reveals novel proteasome-associated proteins. , 2009, Biochemistry.

[50]  Keiji Tanaka,et al.  Molecular mechanisms of proteasome assembly , 2009, Nature Reviews Molecular Cell Biology.

[51]  D. Albertson,et al.  DNA profiling of primary serous ovarian and Fallopian tube carcinomas with array comparative genomic hybridization and multiplex ligation‐dependent probe amplification , 2007, The Journal of pathology.

[52]  Keiji Tanaka,et al.  Rpn10-Mediated Degradation of Ubiquitinated Proteins Is Essential for Mouse Development , 2007, Molecular and Cellular Biology.

[53]  Keiji Tanaka,et al.  Regulation of CD8+ T Cell Development by Thymus-Specific Proteasomes , 2007, Science.

[54]  Michal Sharon,et al.  Structural Organization of the 19S Proteasome Lid: Insights from MS of Intact Complexes , 2006, PLoS biology.

[55]  D. Albertson,et al.  Gene amplification in cancer. , 2006, Trends in genetics : TIG.

[56]  A. Wilkinson,et al.  Gankyrin: a new oncoprotein and regulator of pRb and p53. , 2006, Trends in cell biology.

[57]  Tomoko Masuda,et al.  The oncoprotein gankyrin binds to MDM2/HDM2, enhancing ubiquitylation and degradation of p53. , 2005, Cancer cell.

[58]  Li Chen,et al.  Increased proteasome activity, ubiquitin-conjugating enzymes, and eEF1A translation factor detected in breast cancer tissue. , 2005, Cancer research.

[59]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[60]  M. Kwak,et al.  Antioxidants Enhance Mammalian Proteasome Expression through the Keap1-Nrf2 Signaling Pathway , 2003, Molecular and Cellular Biology.

[61]  M. Polymeropoulos,et al.  Gene expression profiling detects gene amplification and differentiates tumor types in breast cancer. , 2003, Cancer research.

[62]  M. Sogin,et al.  Phylogenomic Analysis of the α Proteasome Gene Family from Early-Diverging Eukaryotes , 2000, Journal of Molecular Evolution.

[63]  R. Huber,et al.  Structure of 20S proteasome from yeast at 2.4Å resolution , 1997, Nature.

[64]  H. Nothwang,et al.  Phylogenic relationships of the amino acid sequences of prosome (proteasome, MCP) subunits , 1994, Molecular and General Genetics MGG.

[65]  K. Duff,et al.  Targeting the 26S Proteasome To Protect Against Proteotoxic Diseases. , 2018, Trends in molecular medicine.

[66]  M. Lai,et al.  PSMB5 plays a dual role in cancer development and immunosuppression. , 2017, American journal of cancer research.

[67]  D. Ferrington,et al.  Immunoproteasomes: structure, function, and antigen presentation. , 2012, Progress in molecular biology and translational science.

[68]  C. Hill,et al.  Proteasome activators. , 2011, Molecular cell.

[69]  M. Stratton,et al.  A census of amplified and overexpressed human cancer genes , 2010, Nature Reviews Cancer.

[70]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[71]  M. Kwak,et al.  Modulation of Gene Expression by Cancer Chemopreventive Dithiolethiones through the Keap1-Nrf2 Pathway IDENTIFICATION OF NOVEL GENE CLUSTERS FOR CELL SURVIVAL* , 2003 .

[72]  M. Sogin,et al.  Phylogenomic analysis of the alpha proteasome gene family from early-diverging eukaryotes. , 2000, Journal of molecular evolution.

[73]  K Tanaka,et al.  Structure and functions of the 20S and 26S proteasomes. , 1996, Annual review of biochemistry.