Surveying lncRNA-lncRNA cooperations reveals dominant effect on tumor immunity cross cancers

[1]  Peng Wang,et al.  Identifying and characterizing lincRNA genomic clusters reveals its cooperative functions in human cancer , 2021, Journal of translational medicine.

[2]  U. Sack,et al.  Detection of Immune Checkpoint Receptors – A Current Challenge in Clinical Flow Cytometry , 2021, Frontiers in Immunology.

[3]  Xuan-Sheng Ding,et al.  Identification and validation of inferior prognostic genes associated with immune signatures and chemotherapy outcome in acute myeloid leukemia , 2021, Aging.

[4]  Xia Li,et al.  Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data , 2020, Nucleic Acids Res..

[5]  Hao Wu,et al.  Long Noncoding RNAs Control the Modulation of Immune Checkpoint Molecules in Cancer , 2020, Cancer Immunology Research.

[6]  Chuhsing Kate Hsiao,et al.  Network hub-node prioritization of gene regulation with intra-network association , 2020, BMC Bioinformatics.

[7]  Xin Yu,et al.  Long noncoding RNA LINC00324 exerts protumorigenic effects on liver cancer stem cells by upregulating fas ligand via PU box binding protein , 2020, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[8]  Xia Li,et al.  Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers , 2020, Nature Communications.

[9]  Uttiya Basu,et al.  Regulation of long non-coding RNAs and genome dynamics by the RNA surveillance machinery , 2020, Nature Reviews Molecular Cell Biology.

[10]  J. Galon,et al.  Tumor Immunology and Tumor Evolution: Intertwined Histories. , 2020, Immunity.

[11]  Xiuquan Xu,et al.  LncRNA MAGI2-AS3 Upregulates Cytokine Signaling 1 by Sponging miR-155 in Non-Small Cell Lung Cancer. , 2020, Cancer biotherapy & radiopharmaceuticals.

[12]  Jason I. Herschkowitz,et al.  Long noncoding RNA BHLHE40‐AS1 promotes early breast cancer progression through modulating IL‐6/STAT3 signaling , 2020, Journal of cellular biochemistry.

[13]  Zhi-Zhou Shi,et al.  Silencing of KCNK15-AS1 inhibits lung cancer cell proliferation via upregulation of miR-202 and miR-370 , 2019, Oncology letters.

[14]  A. Hakimi,et al.  Tumor Microenvironment Dynamics in Clear-Cell Renal Cell Carcinoma. , 2019, Cancer discovery.

[15]  N. Tang,et al.  MIR155HG is a prognostic biomarker and associated with immune infiltration and immune checkpoint molecules expression in multiple cancers , 2019, Cancer medicine.

[16]  Xia Li,et al.  Survey of miRNA-miRNA cooperative regulation principles across cancer types , 2019, Briefings Bioinform..

[17]  Dayu Wang,et al.  Epigenetic regulation of IncRNA KCNKI5-ASI in gastric cancer , 2019, Cancer management and research.

[18]  P. Lorigan,et al.  Anti-PD1 treatment of advanced melanoma: development of criteria for a safe stop. , 2019, Annals of oncology : official journal of the European Society for Medical Oncology.

[19]  Intertwined Histories , 2019 .

[20]  S. Perez,et al.  The role of immune infiltrates as prognostic biomarkers in patients with breast cancer , 2019, Cancer Immunology, Immunotherapy.

[21]  Chunlin Zhang,et al.  Analyzing the Interactions of mRNAs and ncRNAs to Predict Competing Endogenous RNA Networks in Osteosarcoma Chemo-Resistance. , 2019, Molecular therapy : the journal of the American Society of Gene Therapy.

[22]  I. Amit,et al.  Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma , 2019, Cell.

[23]  V. Costa,et al.  The Multifaceted Role of Annexin A1 in Viral Infections , 2023, Cells.

[24]  Kevin P. White,et al.  The DGCR5 long noncoding RNA may regulate expression of several schizophrenia-related genes , 2018, Science Translational Medicine.

[25]  Qifeng He,et al.  Long noncoding RNAs in cancer‐immunity cycle , 2018, Journal of cellular physiology.

[26]  J. Borst,et al.  CD4+ T cell help in cancer immunology and immunotherapy , 2018, Nature Reviews Immunology.

[27]  M. Xie,et al.  Long intergenic non-coding RNA 00324 promotes gastric cancer cell proliferation via binding with HuR and stabilizing FAM83B expression , 2018, Cell Death & Disease.

[28]  L. Pease,et al.  Integrative Genome-Wide Analysis of Long Noncoding RNAs in Diverse Immune Cell Types of Melanoma Patients. , 2018, Cancer research.

[29]  J. Gartner,et al.  Immune recognition of somatic mutations leading to complete durable regression in metastatic breast cancer , 2018, Nature Medicine.

[30]  Peter W. Laird,et al.  Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer , 2018, Cell.

[31]  Clement Adebamowo,et al.  Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context , 2018, Cell reports.

[32]  R. Weinberg,et al.  Understanding the tumor immune microenvironment (TIME) for effective therapy , 2018, Nature Medicine.

[33]  A. Moradi,et al.  The relationship between mitotic rate and depth of invasion in biopsies of malignant melanoma , 2018, Clinical, cosmetic and investigational dermatology.

[34]  E. Rozeman,et al.  Advanced Melanoma: Current Treatment Options, Biomarkers, and Future Perspectives , 2018, American Journal of Clinical Dermatology.

[35]  M. Ringnér,et al.  Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma , 2017, Nature Communications.

[36]  K. Hargadon Strategies to Improve the Efficacy of Dendritic Cell-Based Immunotherapy for Melanoma , 2017, Front. Immunol..

[37]  F. Grossi,et al.  Understanding the checkpoint blockade in lung cancer immunotherapy. , 2017, Drug discovery today.

[38]  Jeong Eon Lee,et al.  Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer , 2017, Nature Communications.

[39]  Hao Sun,et al.  LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells , 2017, Nucleic acids research.

[40]  W. Chan,et al.  Whole transcriptome analysis reveals dysregulated oncogenic lncRNAs in natural killer/T-cell lymphoma and establishes MIR155HG as a target of PRDM1 , 2017, Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine.

[41]  K. Pantel,et al.  Circulating and disseminated tumour cells — mechanisms of immune surveillance and escape , 2017, Nature Reviews Clinical Oncology.

[42]  Jun S. Liu,et al.  TIMER : AWeb Server for Comprehensive Analysis of Tumor-In fi ltrating Immune Cells , 2017 .

[43]  Natalia Castro,et al.  Human Pancreatic β Cell lncRNAs Control Cell-Specific Regulatory Networks , 2016, bioRxiv.

[44]  Shuai Jiang,et al.  T-cell immunometabolism against cancer. , 2016, Cancer letters.

[45]  Xiaonan Li,et al.  HULC cooperates with MALAT1 to aggravate liver cancer stem cells growth through telomere repeat-binding factor 2 , 2016, Scientific Reports.

[46]  Jay Shendure,et al.  Classification and characterization of microsatellite instability across 18 cancer types , 2016, Nature Medicine.

[47]  Dong Xu,et al.  Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia , 2016, Human Genomics.

[48]  Howard Y. Chang,et al.  Long Noncoding RNAs in Cancer Pathways. , 2016, Cancer cell.

[49]  Etienne Becht,et al.  Cancer immune contexture and immunotherapy. , 2016, Current opinion in immunology.

[50]  A. Ribas,et al.  Combination cancer immunotherapies tailored to the tumour microenvironment , 2016, Nature Reviews Clinical Oncology.

[51]  Wolfgang Krebs,et al.  The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin , 2016, Cell Research.

[52]  H. L. Wright,et al.  Differential changes in gene expression in human neutrophils following TNF‐α stimulation: Up‐regulation of anti‐apoptotic proteins and down‐regulation of proteins involved in death receptor signaling , 2015, Immunity, inflammation and disease.

[53]  Hanlee P. Ji,et al.  Pan-cancer analysis of the extent and consequences of intratumor heterogeneity , 2015, Nature Medicine.

[54]  O. Elemento,et al.  Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma , 2015, Genome Medicine.

[55]  Gene W. Yeo,et al.  The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression , 2015, Science.

[56]  Paul L. Roebuck,et al.  TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer. , 2015, Cancer research.

[57]  G. Freeman,et al.  Combination cancer immunotherapy and new immunomodulatory targets , 2015, Nature Reviews Drug Discovery.

[58]  Xia Li,et al.  Construction and analysis of lncRNA-lncRNA synergistic networks to reveal clinically relevant lncRNAs in cancer , 2015, Oncotarget.

[59]  L. Hui,et al.  High salt primes a specific activation state of macrophages, M(Na) , 2015, Cell Research.

[60]  M. Buck,et al.  Disease‐Associated Single‐Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells , 2015, Arthritis & rheumatology.

[61]  O. Elemento,et al.  Identification of Reprogrammed Myeloid Cell Transcriptomes in NSCLC , 2015, PloS one.

[62]  M. C. G. N. Van den Hout–van Vroonhoven,et al.  Allogeneic Mature Human Dendritic Cells Generate Superior Alloreactive Regulatory T Cells in the Presence of IL-15 , 2015, The Journal of Immunology.

[63]  Jamie B. Spangler,et al.  Interleukin-2 activity can be fine tuned with engineered receptor signaling clamps. , 2015, Immunity.

[64]  Ying Liu,et al.  Functional analysis and transcriptomic profiling of iPSC-derived macrophages and their application in modeling Mendelian disease. , 2015, Circulation research.

[65]  Miao Yu,et al.  Bacterial infection remodels the DNA methylation landscape of human dendritic cells , 2015, bioRxiv.

[66]  J. C. Love,et al.  Functional inflammatory profiles distinguish myelin-reactive T cells from patients with multiple sclerosis , 2015, Science Translational Medicine.

[67]  Yan Guo,et al.  A Cell-Based Systems Biology Assessment of Human Blood to Monitor Immune Responses after Influenza Vaccination , 2015, PloS one.

[68]  Traver Hart,et al.  Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation , 2015, The Journal of Immunology.

[69]  N. Hacohen,et al.  Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity , 2015, Cell.

[70]  Stephen C. J. Parker,et al.  Stretch-Enhancers Delineate Disease-Associated Regulatory Nodes in T Cells , 2014, Nature.

[71]  Mack Y Su,et al.  Global transcriptome analysis and enhancer landscape of human primary T follicular helper and T effector lymphocytes. , 2014, Blood.

[72]  Bjoern Peters,et al.  Transcriptional Profile of Tuberculosis Antigen–Specific T Cells Reveals Novel Multifunctional Features , 2014, The Journal of Immunology.

[73]  Bjoern Peters,et al.  Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility , 2014, Nature Immunology.

[74]  S. Kauschke,et al.  A GPBAR1 (TGR5) Small Molecule Agonist Shows Specific Inhibitory Effects on Myeloid Cell Activation In Vitro and Reduces Experimental Autoimmune Encephalitis (EAE) In Vivo , 2014, PloS one.

[75]  David S. Wishart,et al.  DrugBank 4.0: shedding new light on drug metabolism , 2013, Nucleic Acids Res..

[76]  Christofer L. Bäcklin,et al.  Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia , 2013, Genome Biology.

[77]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[78]  Xing Qiu,et al.  High-Resolution Temporal Response Patterns to Influenza Vaccine Reveal a Distinct Human Plasma Cell Gene Signature , 2013, Scientific Reports.

[79]  Lisa M. Chung,et al.  Identification of Genes Critical for Resistance to Infection by West Nile Virus Using RNA-Seq Analysis , 2013, Viruses.

[80]  O. Elemento,et al.  EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. , 2013, Cancer cell.

[81]  H. L. Wright,et al.  RNA-Seq Reveals Activation of Both Common and Cytokine-Specific Pathways following Neutrophil Priming , 2013, PloS one.

[82]  Olga M. Pena,et al.  Synthetic Cationic Peptide IDR-1018 Modulates Human Macrophage Differentiation , 2013, PloS one.

[83]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[84]  M. Mallmann,et al.  High-Resolution Transcriptome of Human Macrophages , 2012, PloS one.

[85]  R. Xavier,et al.  Candida albicans infection affords protection against reinfection via functional reprogramming of monocytes. , 2012, Cell host & microbe.

[86]  Min Pan,et al.  A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers , 2012, Genome research.

[87]  Charles Gawad,et al.  Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types , 2012, PloS one.

[88]  A. Syvänen,et al.  Digital gene expression profiling of primary acute lymphoblastic leukemia cells , 2011, Leukemia.

[89]  Peter Winter,et al.  SuperSAGE evidence for CD14++CD16+ monocytes as a third monocyte subset. , 2011, Blood.

[90]  Helga Thorvaldsdóttir,et al.  Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..

[91]  G. Getz,et al.  GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers , 2011, Genome Biology.

[92]  Yun Xiao,et al.  MiRNA–miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features , 2010, Nucleic acids research.

[93]  S. Hohmann UNICELLSYS - Understanding the cell's functional organization , 2010 .

[94]  Matthew D. Wilkerson,et al.  ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking , 2010, Bioinform..

[95]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[96]  B. Schönfisch,et al.  Analysis of risk factors determining prognosis of cutaneous squamous-cell carcinoma: a prospective study. , 2008, The Lancet. Oncology.

[97]  J. Manson,et al.  Prospective Study of , 2007 .

[98]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[99]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[100]  D. Graham Managing Malignant Melanoma , 1989, Plastic surgical nursing : official journal of the American Society of Plastic and Reconstructive Surgical Nurses.