57 research outputs found
Preparation of haloplex cardiogenetic panel for targeted sequencing of heart rhythm disorders
Evaluation of long noncoding RNA MALAT1 as a candidate blood-based biomarker for the diagnosis of non-small cell lung cancer
Non-protein coding RNA biomarkers and differential expression in cancers: a review
<p>Abstract</p> <p>Background</p> <p>In these years a huge number of human transcripts has been found that do not code for proteins, named non-protein coding RNAs. In most cases, small (miRNAs, snoRNAs) and long RNAs (antisense RNA, dsRNA, and long RNA species) have many roles, functioning as regulators of other mRNAs, at transcriptional and post-transcriptional level, and controlling protein ubiquitination and degradation. Various species of npcRNAs have been found differentially expressed in different types of cancer. This review discusses the published data and new results on the expression of a subset of npcRNAs.</p> <p>Conclusion</p> <p>These results underscore the complexity of the RNA world and provide further evidence on the involvement of functional RNAs in cancer cell growth control.</p
Long non-coding RNAs and cancer: a new frontier of translational research?
Author manuscriptTiling array and novel sequencing technologies have made available the transcription profile of the entire human genome. However, the extent of transcription and the function of genetic elements that occur outside of protein-coding genes, particularly those involved in disease, are still a matter of debate. In this review, we focus on long non-coding RNAs (lncRNAs) that are involved in cancer. We define lncRNAs and present a cancer-oriented list of lncRNAs, list some tools (for example, public databases) that classify lncRNAs or that scan genome spans of interest to find whether known lncRNAs reside there, and describe some of the functions of lncRNAs and the possible genetic mechanisms that underlie lncRNA expression changes in cancer, as well as current and potential future applications of lncRNA research in the treatment of cancer.RS is supported as a fellow of the TALENTS Programme (7th R&D Framework Programme, Specific Programme: PEOPLE—Marie Curie Actions—COFUND). MIA is supported as a PhD fellow of the FCT (Fundação para a Ciência e Tecnologia), Portugal. GAC is supported as a fellow by The University of Texas MD Anderson Cancer Center Research Trust, as a research scholar by The University of Texas System Regents, and by the Chronic Lymphocytic Leukemia Global Research Foundation. Work in GAC’s laboratory is supported in part by the NIH/ NCI (CA135444); a Department of Defense Breast Cancer Idea Award; Developmental Research Awards from the Breast Cancer, Ovarian Cancer, Brain Cancer, Multiple Myeloma and Leukemia Specialized Programs of Research Excellence (SPORE) grants from the National Institutes of Health; a 2009 Seena Magowitz–Pancreatic Cancer Action Network AACR Pilot Grant; the Laura and John Arnold Foundation and the RGK Foundation
Long non-coding RNA ANRIL is upregulated in hepatocellular carcinoma and regulates cell proliferation by epigenetic silencing of KLF2
Preparation of haloplex cardiogenetic panel for targeted sequencing of heart rhythm disorders
Long Non Coding RNAs (lncRNAs) are dysregulated in Malignant Pleural Mesothelioma (MPM)
Malignant Pleural Mesothelioma (MPM) is an aggressive cancer that is often diagnosed at an advanced stage and is characterized by a long latency period (20-40 years between initial exposure and diagnosis) and prior exposure to asbestos. Currently accurate diagnosis of MPM is difficult due to the lack of sensitive biomarkers and despite minor improvements in treatment, median survival rates do not exceed 12 months. Accumulating evidence suggests that aberrant expression of long non-coding RNAs (lncRNAs) play an important functional role in cancer biology. LncRNAs are a class of recently discovered non-protein coding RNAs >200 nucleotides in length with a role in regulating transcription. Here we used NCode long noncoding microarrays to identify differentially expressed lncRNAs potentially involved in MPM pathogenesis. High priority candidate lncRNAs were selected on the basis of statistical (P3-fold difference). Expression levels of 9 candidate lncRNAs were technically validated using RT-qPCR, and biologically validated in three independent test sets: (1) 57 archived MPM tissues obtained from extrapleural pneumonectomy patients, (2) 15 cryopreserved MPM and 3 benign pleura, and (3) an extended panel of 10 MPM cell lines. RT-qPCR analysis demonstrated consistent up-regulation of these lncRNAs in independent datasets. ROC curve analysis showed that two candidates were able to separate benign pleura and MPM with high sensitivity and specificity, and were associated with nodal metastases and survival following induction chemotherapy. These results suggest that lncRNAs have potential to serve as biomarkers in MPM
Metabolomic Profiling Identifies Biochemical Pathways Associated with Castration-Resistant Prostate Cancer
Despite
recent developments in treatment strategies, castration-resistant
prostate cancer (CRPC) is still the second leading cause of cancer-associated
mortality among American men, the biological underpinnings of which
are not well understood. To this end, we measured levels of 150 metabolites
and examined the rate of utilization of 184 metabolites in metastatic
androgen-dependent prostate cancer (AD) and CRPC cell lines using
a combination of targeted mass spectrometry and metabolic phenotyping.
Metabolic data were used to derive biochemical pathways that were
enriched in CRPC, using Oncomine concept maps (OCM). The enriched
pathways were then examined in-silico for their association with treatment
failure (i.e., prostate specific antigen (PSA) recurrence or biochemical
recurrence) using published clinically annotated gene expression data
sets. Our results indicate that a total of 19 metabolites were altered
in CRPC compared to AD cell lines. These altered metabolites mapped
to a highly interconnected network of biochemical pathways that describe
UDP glucuronosyltransferase (UGT) activity. We observed an association
with time to treatment failure in an analysis employing genes restricted
to this pathway in three independent gene expression data sets. In
summary, our studies highlight the value of employing metabolomic
strategies in cell lines to derive potentially clinically useful predictive
tools
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