Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function

Cabanski, Christopher R.; White, Nicole M.; Dang, Ha X.; Silva-Fisher, Jessica; Rauck, Corinne E; Cicka, Danielle; Maher, Christopher A.

doi:10.1080/15476286.2015.1038012

Cited by 86 publications

(93 citation statements)

References 78 publications

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“…We report 271 pan-cancer lncRNAs, including famous cancerassociated lncRNAs such as PVT1 and many novel cases. Public datasets confirmed the upregulation of 25 and downregulation of three of these lncRNAs in at least two primary tumor types (23,24) and we further validated upregulation of two novel lncRNAs by qRTPCR in a cDNA panel covering eight tumor types. We also identify 90 enhancer RNA-producing regions that are recurrently activated in cancer cell lines.…”

Section: Discussionsupporting

confidence: 59%

“…We also looked for the overlap with the lists of pan-cancer lncRNAs to the 229 "onco-lncRNAs" identified by Cabanski and colleagues (24), which allowed us to confirm three additional upregulated lncRNAs (Supplementary Table S10B and S10D). Our analysis of preprocessed TCGA RNA-seq data also allowed us to confirm deregulation of four lncRNAs, two already confirmed by miTranscriptome and Cabanski (MEG3 and DGCR5) and two that were missed by other reports; downregulation of the MT1L pseudogene and most notably the up-regulation of PVT1, which is a well-known lncRNA oncogene (25).…”

Section: Pan-cancer Long-noncoding Rnasmentioning

confidence: 99%

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Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

Kaczkowski¹,

Tanaka

Kawaji

et al. 2016

Cancer Research

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Genes that are commonly deregulated in cancer are clinically attractive as candidate pan-diagnostic markers and therapeutic targets. To globally identify such targets, we compared Cap Analysis of Gene Expression profiles from 225 different cancer cell lines and 339 corresponding primary cell samples to identify transcripts that are deregulated recurrently in a broad range of cancer types. Comparing RNA-seq data from 4,055 tumors and 563 normal tissues profiled in the The Cancer Genome Atlas and FANTOM5 datasets, we identified a core transcript set with theranostic potential. Our analyses also revealed enhancer RNAs, which are upregulated in cancer, defining promoters that overlap with repetitive elements (especially SINE/Alu and LTR/ERV1 elements) that are often upregulated in cancer. Lastly, we documented for the first time upregulation of multiple copies of the REP522 interspersed repeat in cancer. Overall, our genomewide expression profiling approach identified a comprehensive set of candidate biomarkers with pan-cancer potential, and extended the perspective and pathogenic significance of repetitive elements that are frequently activated during cancer progression.Cancer Res; 76(2); 216-26. Ó2015 AACR.

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Section: Discussionsupporting

confidence: 59%

Section: Pan-cancer Long-noncoding Rnasmentioning

confidence: 99%

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

Kaczkowski¹,

Tanaka

Kawaji

et al. 2016

Cancer Research

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“…Recent studies reveal that specific lncRNA expression is associated with disease state (27,49), strongly supporting the utility of lncRNAs in clinical diagnosis and prognosis. Loss of LKB1 function in NSCLC cells caused differential responses to therapeutic agents in vitro and in animal studies.…”

Section: Discussionmentioning

confidence: 90%

“…The human genome encodes more than 10,000 lncRNAs, and currently only a handful of lncRNAs have been characterized (24)(25)(26). lncRNA expression is frequently deregulated in cancer and shows cell-or tissue-type specificity (27)(28)(29), suggesting significant roles for lncRNAs in human cancers. Though lncRNAs remain an understudied class of genes, they have been shown to participate in cancer cell proliferation, survival, migration, and invasion, likely through exertion of multiple regulatory functions at the transcriptional, posttranscriptional, and epigenetic levels (23,30).…”

Section: Introductionmentioning

confidence: 99%

cAMP/CREB-regulated LINC00473 marks LKB1-inactivated lung cancer and mediates tumor growth

Chen¹,

Li²,

Lin³

et al. 2016

Journal of Clinical Investigation

175

194

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“…LINC00346 deletion (1%), amplification (2-5%) breast cancer [41], bladder cancer [42], hepatocellular carcinoma [43] LINC00511 amplification (4-25%) cMYC, GATA3, ZNF217 PTEN breast cancer [44], non--small cell lung cancer [ …”

Section: Smg7-as1 Amplification (3-21%) Tp53 Fgfr Erbb2mentioning

confidence: 99%

A Combined Bioinformatics and Literature Based Approach for Identification of Long Non-coding RNAs That Modulate Vitamin D Receptor Signaling in Breast Cancer

Oskooei¹,

Ghafouri‐Fard²,

Mir³

2018

Klin Onkol

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Kombinovaný bio informatický a literární přístup k identifikaci dlouhých nekódujících molekul RNA, které modulují signalizaci přes receptor vitaminu D u karcinomu prsu Kholghi Oskooei V., Ghafouri-Fard S., Omrani MD Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran SummaryBackground: Long non-cod ing RNAs (lncRNAs) as an important fraction of human transcriptome have been shown to exert fundamental role in regulation of signal ing pathways implicated in carcinogenesis. Among them is vitamin D receptor (VDR) signal ing whose participation in various cancers includ ing breast cancer (BC) is evident. In spite of the presence of several evidences for participation of lncRNAs as well as VDR signal ing in BC pathogenesis, no comprehensive study has evaluated the link between lncRNA dysregulation and VDR signal ing in BC. Aim: To introduce a bio informatics approach for identification of lncRNAs that modulate VDR signal ing in BC. This approach includes co-expression analysis, in silico identification of lncRNAs that target VDR and literature search. Conclusions: Tens of lncRNAs are predicted to affect VDR signaling. Among them are some lncRNAs such as MALAT1 which has prominent role in BC pathogenesis. Identification of the lncRNAs that influence VDR gene expression is possible through in silico analysis. Consider ing the prominent role of VDR in BC pathogenesis as well as availability of VDR modulat ing agents, evaluation of VDR signal ing pathway and related networks are of practical significance and bio informatics tools are expected to facilitate such action.

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Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function

Cited by 86 publications

References 78 publications

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

cAMP/CREB-regulated LINC00473 marks LKB1-inactivated lung cancer and mediates tumor growth

A Combined Bioinformatics and Literature Based Approach for Identification of Long Non-coding RNAs That Modulate Vitamin D Receptor Signaling in Breast Cancer

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