Systematic identification of lincRNA‐based prognostic biomarkers by integrating lincRNA expression and copy number variation in lung adenocarcinoma

Copy number alterations (CNAs) of lincRNAs act as one of important mechanisms in disrupting lincRNA expression which may play critical roles during tumorigenesis in lung adenocarcinoma (LUAD). The copy number alterations of lincRNAs can mark the spectrum of cancer progression and may serve as biomarkers for prognosis in LUAD, however it is rarely studied. We analyzed RNASeq data for 488 LUAD patients from TCGA portal and 58 healthy subjects to identify prognostic lincRNAs predictive of patient survival. Computational analysis entailing integration of expression and copy number alteration data revealed five prognostic lincRNAs: RBPMS‐AS1, TDRKH‐AS1, LINC00578, RP11‐470 M17.2 and LINC00941. The copy number alterations in the LINC00578 and RP11‐470 M17.2 genes were positively associated with the longer overall survival of LUAD patients. The CNA in LINC00941 was negatively associated with the longer overall survival. Copy number amplification significantly correlated with increased expression of TDRKH‐AS1, which regulates telomere organization and EZH2‐mediated epigenetic silencing of CDKN1A, CDKN1B and IL24. Decreased survival of LUAD patients was associated with high LINC00941 expression. The LINC00941 regulates the PI3K‐AKT signaling pathway, focal adhesion by influencing potential targets, such as KRAS proto‐oncogene GTPase and VEGFC. These lincRNA‐based prognostic biomarkers may destroy important cancer‐related biological processes contributing to LUAD prognosis. In summary, we demonstrate the prognostic potential of four differentially expressed lincRNAs with copy number alterations (RBPMS‐AS1, TDRKH‐AS1, LINC00578 and RP11‐470 M17.2) that are positively associated with longer overall survival of LUAD patients. One differentially expressed lincRNA LINC00941 with copy number alterations was negatively associated with longer overall survival of LUAD patients.

[1]  Xing Chen,et al.  LncRNADisease: a database for long-non-coding RNA-associated diseases , 2012, Nucleic Acids Res..

[2]  Jie He,et al.  The incidences and mortalities of major cancers in China, 2009 , 2013, Chinese journal of cancer.

[3]  S. Rho,et al.  Programmed cell death 6 (PDCD6) inhibits angiogenesis through PI3K/mTOR/p70S6K pathway by interacting of VEGFR-2. , 2012, Cellular signalling.

[4]  Howard Y. Chang,et al.  Long Noncoding RNAs: Cellular Address Codes in Development and Disease , 2013, Cell.

[5]  Stefano Monti,et al.  Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[6]  Lingzhi Wang,et al.  Gene microarray analysis of lncRNA and mRNA expression profiles in patients with high-grade ovarian serous cancer , 2018, International journal of molecular medicine.

[7]  Jie Chen,et al.  Long Noncoding RNA Expression Profiles of Lung Adenocarcinoma Ascertained by Microarray Analysis , 2014, PloS one.

[8]  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.

[9]  E. Zhang,et al.  A novel lncRNA, LUADT1, promotes lung adenocarcinoma proliferation via the epigenetic suppression of p27 , 2015, Cell Death and Disease.

[10]  H. Du,et al.  Myeloid-Specific Expression of Api6/AIM/Spα Induces Systemic Inflammation and Adenocarcinoma in the Lung1 , 2009, The Journal of Immunology.

[11]  A. Jemal,et al.  Global cancer statistics , 2011, CA: a cancer journal for clinicians.

[12]  David G. Knowles,et al.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.

[13]  A. Jemal,et al.  Cancer statistics, 2018 , 2018, CA: a cancer journal for clinicians.

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

[15]  Yusuke Nakamura,et al.  A genome-wide association study identifies two new susceptibility loci for lung adenocarcinoma in the Japanese population , 2012, Nature Genetics.

[16]  Igor Jurisica,et al.  Gene expression–based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study , 2008, Nature Medicine.

[17]  H. Du,et al.  Myeloid-specific expression of Api6/AIM/Sp alpha induces systemic inflammation and adenocarcinoma in the lung. , 2009, Journal of immunology.

[18]  Xia Li,et al.  Chromatin states modify network motifs contributing to cell-specific functions , 2015, Scientific Reports.

[19]  N. Grishin,et al.  Genetic defects in surfactant protein A2 are associated with pulmonary fibrosis and lung cancer. , 2009, American journal of human genetics.

[20]  W. Guo,et al.  Dysregulated MiR-3150a-3p Promotes Lumbar Intervertebral Disc Degeneration by Targeting Aggrecan , 2018, Cellular Physiology and Biochemistry.

[21]  Zhen Su,et al.  Integrative genomic analyses reveal clinically relevant long non-coding RNA in human cancer , 2013 .

[22]  Xia Li,et al.  'Traffic light rules': Chromatin states direct miRNA-mediated network motifs running by integrating epigenome and regulatome. , 2016, Biochimica et biophysica acta.

[23]  Zhaoxia Wang,et al.  Long intergenic non-coding RNA 00152 promotes lung adenocarcinoma proliferation via interacting with EZH2 and repressing IL24 expression , 2017, Molecular Cancer.

[24]  F. Piva,et al.  LncRNA co-expression network analysis reveals novel biomarkers for pancreatic cancer , 2018, Carcinogenesis.

[25]  M. Barbosa,et al.  Recurrent copy number variations as risk factors for neurodevelopmental disorders: critical overview and analysis of clinical implications , 2015, Journal of Medical Genetics.

[26]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[27]  Shuli Kang,et al.  Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network , 2011, Nucleic acids research.

[28]  M. Loda,et al.  Lung adenocarcinoma with EGFR amplification has distinct clinicopathologic and molecular features in never-smokers. , 2009, Cancer research.

[29]  Cole Trapnell,et al.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.

[30]  Ming Sun,et al.  Long non-coding RNA LINC01133 represses KLF2, P21 and E-cadherin transcription through binding with EZH2, LSD1 in non small cell lung cancer , 2016, Oncotarget.

[31]  Runsheng Chen,et al.  Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA-MUF Interaction with ANXA2 and miR-34a. , 2017, Cancer research.

[32]  Wei Zhang,et al.  The incidences and mortalities of major cancers in China, 2010 , 2014, Chinese journal of cancer.

[33]  E. Wherry.  Faculty Opinions recommendation of Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. , 2009 .

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

[35]  Nadav S. Bar,et al.  Landscape of transcription in human cells , 2012, Nature.

[36]  Wira Eka Putra,et al.  Chemotherapy-Induced IL34 Enhances Immunosuppression by Tumor-Associated Macrophages and Mediates Survival of Chemoresistant Lung Cancer Cells. , 2016, Cancer research.

[37]  Jing Liu,et al.  The Long Noncoding RNA MEG3 Contributes to Cisplatin Resistance of Human Lung Adenocarcinoma , 2015, PloS one.

[38]  R. Xu,et al.  LncRNAs and miRNAs: potential biomarkers and therapeutic targets for prostate cancer. , 2016, American journal of translational research.

[39]  A. Jemal,et al.  Global cancer statistics, 2012 , 2015, CA: a cancer journal for clinicians.

[40]  Jing Liu,et al.  The Long Noncoding RNA HOTAIR Contributes to Cisplatin Resistance of Human Lung Adenocarcinoma Cells via downregualtion of p21WAF1/CIP1 Expression , 2013, PloS one.

[41]  Xuedan Chen,et al.  Up-regulation of lncRNA CASC9 promotes esophageal squamous cell carcinoma growth by negatively regulating PDCD4 expression through EZH2 , 2017, Molecular Cancer.

[42]  David Madigan,et al.  High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis. , 2014, Biostatistics.

[43]  A. Shlien,et al.  Copy number variations and cancer , 2009, Genome Medicine.

[44]  Zhaoli Chen,et al.  Integrated bioinformatics analysis of chromatin regulator EZH2 in regulating mRNA and lncRNA expression by ChIP sequencing and RNA sequencing , 2016, Oncotarget.

[45]  N. Kosaka,et al.  The Clinical Relevance of the miR-197/CKS1B/STAT3-mediated PD-L1 Network in Chemoresistant Non-small-cell Lung Cancer , 2015, Molecular therapy : the journal of the American Society of Gene Therapy.

[46]  H. J. Kim,et al.  Clinicopathologic and prognostic significance of c-MYC copy number gain in lung adenocarcinomas , 2014, British Journal of Cancer.

[47]  Armin Koch,et al.  Personalized medicine using DNA biomarkers: a review , 2012, Human Genetics.

[48]  Yixue Li,et al.  Global Prioritizing Disease Candidate lncRNAs via a Multi-level Composite Network , 2017, Scientific Reports.

[49]  Peng Wang,et al.  Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers , 2015, Nucleic Acids Res..

[50]  Hongyan Xu,et al.  A general method for accurate estimation of false discovery rates in identification of differentially expressed genes , 2014, Bioinform..

[51]  F. Collins,et al.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.

[52]  Wei-min Li,et al.  Genetic variation in PDCD6 and susceptibility to lung cancer. , 2012, Asian Pacific journal of cancer prevention : APJCP.

[53]  Yunyan Gu,et al.  Differential expression analysis at the individual level reveals a lncRNA prognostic signature for lung adenocarcinoma , 2017, Molecular Cancer.

[54]  Edward S. Kim,et al.  Prognostic and predictive biomarkers post curative intent therapy. , 2017, Annals of translational medicine.

[55]  D. Damian,et al.  Statistical concerns about the GSEA procedure , 2004, Nature Genetics.

[56]  B. Tang,et al.  Long noncoding RNA LINC00675 enhances phosphorylation of vimentin on Ser83 to suppress gastric cancer progression. , 2018, Cancer letters.

[57]  Mark D Robinson,et al.  edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. , 2014, Methods in molecular biology.

[58]  Nicky J Welton,et al.  Enhanced secondary analysis of survival data: reconstructing the data from published Kaplan-Meier survival curves , 2012, BMC Medical Research Methodology.

[59]  Muhammad Nawaz,et al.  Vesiculated Long Non-Coding RNAs: Offshore Packages Deciphering Trans-Regulation between Cells, Cancer Progression and Resistance to Therapies , 2017, Non-coding RNA.

[60]  Bradley P. Coe,et al.  Genomic markers for malignant progression in pulmonary adenocarcinoma with bronchioloalveolar features , 2008, Proceedings of the National Academy of Sciences.

[61]  S. Gabriel,et al.  Pan-cancer patterns of somatic copy-number alteration , 2013, Nature Genetics.

[62]  H. Du,et al.  Api6/AIM/Spα/CD5L overexpression in alveolar type II epithelial cells induces spontaneous lung adenocarcinoma. , 2011, Cancer research.

[63]  E. Felip,et al.  Erlotinib versus standard chemotherapy as first-line treatment for European patients with advanced EGFR mutation-positive non-small-cell lung cancer (EURTAC): a multicentre, open-label, randomised phase 3 trial. , 2012, The Lancet. Oncology.

[64]  Steven J. M. Jones,et al.  Comprehensive molecular profiling of lung adenocarcinoma , 2014, Nature.

[65]  Matthew D. Wilkerson,et al.  Differential Pathogenesis of Lung Adenocarcinoma Subtypes Involving Sequence Mutations, Copy Number, Chromosomal Instability, and Methylation , 2012, PloS one.

[66]  N. An,et al.  Long non-coding RNA Linc00675 suppresses cell proliferation and metastasis in colorectal cancer via acting on miR-942 and Wnt/β-catenin signaling. , 2018, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

[67]  J. Rinn,et al.  Modular regulatory principles of large non-coding RNAs , 2012, Nature.

[68]  Angela N. Brooks,et al.  Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing , 2012, Cell.

[69]  A. Schetter,et al.  Combination of protein coding and noncoding gene expression as a robust prognostic classifier in stage I lung adenocarcinoma. , 2013, Cancer research.