Gene co-expression and histone modification signatures are associated with melanoma progression, epithelial-to-mesenchymal transition, and metastasis

[1]  Francisco J. Sánchez-Rivera,et al.  Global regulation of the histone mark H3K36me2 underlies epithelial plasticity and metastatic progression. , 2020, Cancer discovery.

[2]  Keming Zhang,et al.  MTF2 Induces Epithelial-Mesenchymal Transition and Progression of Hepatocellular Carcinoma by Transcriptionally Activating Snail , 2019, OncoTargets and therapy.

[3]  Junhong Han,et al.  Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials , 2019, Signal Transduction and Targeted Therapy.

[4]  H. Cui,et al.  MYST1/KAT8 contributes to tumor progression by activating EGFR signaling in glioblastoma cells , 2019, Cancer medicine.

[5]  S. Oliverio,et al.  Modulation of autophagy by RTN-1C: role in autophagosome biogenesis , 2019, Cell Death & Disease.

[6]  Jason T. George,et al.  Histone deacetylases, Mbd3/NuRD, and Tet2 hydroxylase are crucial regulators of epithelial–mesenchymal plasticity and tumor metastasis , 2019, Oncogene.

[7]  Victor Tkachev,et al.  H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks , 2019, Cells.

[8]  C. Morrissey,et al.  COMMD3:BMI1 Fusion and COMMD3 Protein Regulate C-MYC Transcription: Novel Therapeutic Target for Metastatic Prostate Cancer , 2019, Molecular Cancer Therapeutics.

[9]  D. Moon,et al.  Upregulated TTYH2 expression is critical for the invasion and migration of U2OS human osteosarcoma cell lines. , 2019, Biochemical and biophysical research communications.

[10]  Joe-Marc Chauvin,et al.  IRF1 Inhibits Antitumor Immunity through the Upregulation of PD-L1 in the Tumor Cell , 2019, Cancer Immunology Research.

[11]  Zemin Zhang,et al.  GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis , 2019, Nucleic Acids Res..

[12]  A. Jaruga,et al.  H3K18Ac as a Marker of Cancer Progression and Potential Target of Anti-Cancer Therapy , 2019, Cells.

[13]  Jie Yao,et al.  The hyper-activation of transcriptional enhancers in breast cancer , 2019, Clinical Epigenetics.

[14]  Changying Guo,et al.  miR-29a contributes to breast cancer cells epithelial–mesenchymal transition, migration, and invasion via down-regulating histone H4K20 trimethylation through directly targeting SUV420H2 , 2019, Cell Death & Disease.

[15]  S. Kreis,et al.  Many ways to resistance: How melanoma cells evade targeted therapies. , 2019, Biochimica et biophysica acta. Reviews on cancer.

[16]  Jing Liu,et al.  Coexpression network analysis identified that plakophilin 1 is associated with the metastasis in human melanoma. , 2019, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

[17]  M. Millward,et al.  Prognostic Relevance of CCDC88C (Daple) Transcripts in the Peripheral Blood of Patients with Cutaneous Melanoma , 2018, Scientific Reports.

[18]  J. Utikal,et al.  Tackling malignant melanoma epigenetically: histone lysine methylation , 2018, Clinical Epigenetics.

[19]  G. Wagner,et al.  Cytidine monophosphate N-acetylneuraminic acid synthetase enhances invasion of human triple-negative breast cancer cells , 2018, OncoTargets and therapy.

[20]  Kiran K. Katta,et al.  The exostosin family of glycosyltransferases: mRNA expression profiles and heparan sulphate structure in human breast carcinoma cell lines , 2018, Bioscience reports.

[21]  Caixia Liu,et al.  CTNNAL1 inhibits ozone‐induced epithelial–mesenchymal transition in human bronchial epithelial cells , 2018, Experimental physiology.

[22]  Kwok-Kin Wong,et al.  EZH2-Mediated Primary Cilium Deconstruction Drives Metastatic Melanoma Formation. , 2018, Cancer cell.

[23]  N. Howlett,et al.  Understanding the Histone DNA Repair Code: H4K20me2 Makes Its Mark , 2018, Molecular Cancer Research.

[24]  Dylan M. Marchione,et al.  EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data. , 2018, Journal of proteome research.

[25]  D. Bishop,et al.  β-Catenin–mediated immune evasion pathway frequently operates in primary cutaneous melanomas , 2018, The Journal of clinical investigation.

[26]  Demetrios A. Spandidos,et al.  Cutaneous melanoma: From pathogenesis to therapy (Review) , 2018, International journal of oncology.

[27]  Yang Li,et al.  Network-based co-expression analysis for exploring the potential diagnostic biomarkers of metastatic melanoma , 2018, PloS one.

[28]  Z. Xuan,et al.  The protective role of DOT1L in UV-induced melanomagenesis , 2018, Nature Communications.

[29]  Anneliese O. Speak,et al.  Comparative genomics reveals that loss of lunatic fringe (LFNG) promotes melanoma metastasis , 2018, Molecular oncology.

[30]  N. Chandra,et al.  Identification of a gene signature for discriminating metastatic from primary melanoma using a molecular interaction network approach , 2017, Scientific Reports.

[31]  Lingyun Zhang,et al.  Pyridoxine 5′-phosphate oxidase is a novel therapeutic target and regulated by the TGF-β signalling pathway in epithelial ovarian cancer , 2017, Cell Death & Disease.

[32]  M. Hsiao,et al.  BICD1 expression, as a potential biomarker for prognosis and predicting response to therapy in patients with glioblastomas , 2017, Oncotarget.

[33]  Damian J. Matuszewski,et al.  A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family , 2017, Nature Communications.

[34]  D. Tremethick,et al.  The Histone Variant H2A.Z Is a Master Regulator of the Epithelial-Mesenchymal Transition. , 2017, Cell reports.

[35]  B. Price,et al.  The tale of a tail: histone H4 acetylation and the repair of DNA breaks , 2017, Philosophical Transactions of the Royal Society B: Biological Sciences.

[36]  Simon G. Coetzee,et al.  SIRT1 regulates Mxd1 during malignant melanoma progression , 2017, Oncotarget.

[37]  Austin E. Gillen,et al.  Alternative Polyadenylation of PRELID1 Regulates Mitochondrial ROS Signaling and Cancer Outcomes , 2017, Molecular Cancer Research.

[38]  Wenlin Huang,et al.  KMT2A promotes melanoma cell growth by targeting hTERT signaling pathway , 2017, Cell Death & Disease.

[39]  Chunying Li,et al.  Ubiquitination in melanoma pathogenesis and treatment , 2017, Cancer medicine.

[40]  I. Amit,et al.  Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. , 2017, Cell reports.

[41]  Kihyun Park,et al.  Writing, erasing and reading histone lysine methylations , 2017, Experimental &Molecular Medicine.

[42]  J. Casal,et al.  VE-cadherin RGD motifs promote metastasis and constitute a potential therapeutic target in melanoma and breast cancers , 2016, Oncotarget.

[43]  A. Weeraratna,et al.  Autophagy- An emerging target for melanoma therapy , 2016, F1000Research.

[44]  B. Garcia,et al.  Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis , 2016, Journal of visualized experiments : JoVE.

[45]  Andrew D. Rouillard,et al.  Enrichr: a comprehensive gene set enrichment analysis web server 2016 update , 2016, Nucleic Acids Res..

[46]  D. Bobbala,et al.  NLRC5 elicits antitumor immunity by enhancing processing and presentation of tumor antigens to CD8+ T lymphocytes , 2016, Oncoimmunology.

[47]  B. Garcia,et al.  Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications. , 2015, Analytical chemistry.

[48]  Karthik M. Kodigepalli,et al.  Regulation of deoxynucleotide metabolism in cancer: novel mechanisms and therapeutic implications , 2015, Molecular Cancer.

[49]  P. Hersey,et al.  Histone Modifications, Modifiers and Readers in Melanoma Resistance to Targeted and Immune Therapy , 2015, Cancers.

[50]  Amit Verma,et al.  Histone Variant H2A.Z.2 Mediates Proliferation and Drug Sensitivity of Malignant Melanoma. , 2015, Molecular cell.

[51]  Steven J. M. Jones,et al.  Genomic Classification of Cutaneous Melanoma , 2015, Cell.

[52]  Pietro Liò,et al.  The BioMart community portal: an innovative alternative to large, centralized data repositories , 2015, Nucleic Acids Res..

[53]  T. Kiyono,et al.  Suppressed rate of carcinogenesis and decreases in tumour volume and lung metastasis in CXCL14/BRAK transgenic mice , 2015, Scientific Reports.

[54]  Z. Szallasi,et al.  SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair , 2015, Oncogene.

[55]  D. Teti,et al.  Epigenetic regulation of p14ARF and p16INK4A expression in cutaneous and uveal melanoma. , 2015, Biochimica et biophysica acta.

[56]  M. Gaestel,et al.  The stress-responsive kinases MAPKAPK2/MAPKAPK3 activate starvation-induced autophagy through Beclin 1 phosphorylation , 2015, eLife.

[57]  Z. Kefalopoulou,et al.  Epigenetic Modifications in Cutaneous Malignant Melanoma: EZH2, H3K4me2, and H3K27me3 Immunohistochemical Expression is Enhanced at the Invasion Front of the Tumor , 2015, The American Journal of dermatopathology.

[58]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[59]  K. McManus,et al.  Mitotic Accumulation of Dimethylated Lysine 79 of Histone H3 Is Important for Maintaining Genome Integrity During Mitosis in Human Cells , 2014, Genetics.

[60]  A. Uzdensky,et al.  Expression of proteins involved in epigenetic regulation in human cutaneous melanoma and peritumoral skin , 2014, Tumor Biology.

[61]  H. Bi,et al.  The proliferation of malignant melanoma cells could be inhibited by ranibizumab via antagonizing VEGF through VEGFR1 , 2014, Molecular vision.

[62]  Sridhar Ramaswamy,et al.  Dynamic Chromatin Modification Sustains Epithelial-Mesenchymal Transition following Inducible Expression of Snail-1 , 2013, Cell reports.

[63]  C. Morrison,et al.  Facilitates chromatin transcription complex is an "accelerator" of tumor transformation and potential marker and target of aggressive cancers. , 2013, Cell reports.

[64]  Kazuhiro Takemoto,et al.  Modular organization of cancer signaling networks is associated with patient survivability , 2013, Biosyst..

[65]  B. de Strooper,et al.  BACE2 processes PMEL to form the melanosome amyloid matrix in pigment cells , 2013, Proceedings of the National Academy of Sciences.

[66]  Y. Miyagi,et al.  Global histone modification of H3K27 correlates with the outcomes in patients with metachronous liver metastasis of colorectal cancer. , 2013, European journal of surgical oncology : the journal of the European Society of Surgical Oncology and the British Association of Surgical Oncology.

[67]  W. Shi,et al.  The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote , 2013, Nucleic acids research.

[68]  S. Mai,et al.  Mining Gene Expression Signature for the Detection of Pre-Malignant Melanocytes and Early Melanomas with Risk for Metastasis , 2012, PloS one.

[69]  Huazhang Guo,et al.  Role of TRPM in melanocytes and melanoma , 2012, Experimental dermatology.

[70]  Christina Chan,et al.  Relevance of Network Hierarchy in Cancer Drug-Target Selection , 2012 .

[71]  G. Ge,et al.  Lysyl Oxidase, Extracellular Matrix Remodeling and Cancer Metastasis , 2012, Cancer Microenvironment.

[72]  A. Bosserhoff,et al.  Slit3 inhibits activator protein 1-mediated migration of malignant melanoma cells. , 2011, International journal of molecular medicine.

[73]  Bill B. Chen,et al.  FBXL2 is a ubiquitin E3 ligase subunit that triggers mitotic arrest , 2011, Cell cycle.

[74]  K. Peck,et al.  SCUBE3 is an endogenous TGF-β receptor ligand and regulates the epithelial-mesenchymal transition in lung cancer , 2011, Oncogene.

[75]  U. Certa,et al.  Interferon-alpha induces reversible DNA demethylation of the interferon-induced transmembrane protein-3 core promoter in human melanoma cells. , 2011, Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research.

[76]  Peter A. Jones,et al.  Epigenetic reprogramming as a key contributor to melanocyte malignant transformation , 2011, Epigenetics.

[77]  Raymond K. Auerbach,et al.  A User's Guide to the Encyclopedia of DNA Elements (ENCODE) , 2011, PLoS biology.

[78]  S. Galande,et al.  p300-mediated Acetylation of Histone H3 Lysine 56 Functions in DNA Damage Response in Mammals , 2010, The Journal of Biological Chemistry.

[79]  D. Rimm,et al.  Gab2-mediated signaling promotes melanoma metastasis. , 2009, The American journal of pathology.

[80]  L. Luzi,et al.  Melanoma: targeting signaling pathways and RaLP , 2009 .

[81]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[82]  R. Chammas,et al.  Melanocyte transformation associated with substrate adhesion impediment. , 2006, Neoplasia.

[83]  D. Bennett,et al.  A line of non‐tumorigenic mouse melanocytes, syngeneic with the B16 melanoma and requiring a tumour promoter for growth , 1987, International journal of cancer.

[84]  M. N. Epstein,et al.  A study of tumor progression: the precursor lesions of superficial spreading and nodular melanoma. , 1984, Human pathology.

[85]  S. Leachman,et al.  Identification of patients at risk of metastasis using a prognostic 31‐gene expression profile in subpopulations of melanoma patients with favorable outcomes by standard criteria , 2019, Journal of the American Academy of Dermatology.

[86]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

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