Identification of novel long non-coding RNAs in prostate cancers
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE59745 | GEO | 2015/03/02
SECONDARY ACCESSION(S): PRJNA256097
REPOSITORIES: GEO
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Project description:Long non-coding RNAs show highly tissue and disease specific expression profiles. We analyzed prostate cancer and normal adjacent prostate samples to identify cancer-specific transcripts and found 334 candidates, of which 15 were validated by RT-PCR. 8 Prostate cancer samples from radical prostatectomies, 12 samples from normal adjacent prostate, 12 samples from lymph node metastasis and 10 samples from transurethral resection of the prostrate were included in this study. These samples contained more than 70% cancer and less than 30% stromal tissue.
2015-03-02 | E-GEOD-59745 | biostudies-arrayexpress
Project description:The clear cell subtype of renal cell carcinoma (RCC) is the most lethal and prevalent cancer of the urinary system. To investigate the molecular changes associated with malignant transformation in clear cell RCC, the gene expression profiles of matched samples of tumor and adjacent non-neoplastic tissue were obtained from 6 patients. A custom-built cDNA microarray platform was used, comprising 2,292 probes that map to exons of genes and 822 probes for noncoding RNAs mapping to intronic regions. Intronic transcription was detected in all normal and neoplastic renal tissues. A subset of 55 transcripts was significantly down-regulated in clear cell RCC relative to the matched non-tumor tissue as determined by a combination of two statistical tests and leave-one-out patient cross-validation. Among the down-regulated transcripts, 49 mapped to untranslated or coding exons and 6 were intronic relative to known exons of protein-coding genes. Lower levels of expression of SIN3B, TRIP3, SYNJ2BP and NDE1 (p < 0.02), and of intronic transcripts derived from SND1 and ACTN4 loci (p < 0.05), were confirmed in clear cell RCC by Real-time RT-PCR. A subset of 25 transcripts was deregulated in additional 6 non-clear cell RCC samples, pointing to common transcriptional alterations in RCC irrespective of the histological subtype or differentiation state of the tumor. Our results indicate a novel set of tumor suppressor gene candidates, including noncoding intronic RNAs, which may play a significant role in malignant transformations of normal renal cells. Fluorescently labeled cDNA targets derived from tumor and non-tumor tissue from each patient were combined and hybridized to spotted cDNA microarrays. For each patient, a replicate hybridization with dye-swap of labeled targets was performed. For each tissue (tumor and adjacent non-tumor tissue), there are 4 replicate mesurements for each probe.
2010-06-25 | E-GEOD-7367 | biostudies-arrayexpress
Project description:The emergence of cancers involves numerous coding and non-coding genes. Understanding the contribution of non-coding RNAs (ncRNAs) to the cancer neighborhood is crucial for interpreting the interaction between molecular markers of cancer. However, there is a lack of systematic studies on the involvement of ncRNAs in the cancer neighborhood. In this paper, we construct an interaction network which encompasses multiple genes. We focus on the fundamental topological indicator, namely connectivity, and evaluate its performance when applied to cancer-affected genes using statistical indices. Our findings reveal that ncRNAs significantly enhance the connectivity of affected genes and mediate the inclusion of more genes in the cancer module. To further explore the role of ncRNAs in the network, we propose a connectivity-based method which leverages the bridging function of ncRNAs across cancer-affected genes and reveals the non-coding RNAs extended omnigenic module (NeOModule). Topologically, this module promotes the formation of cancer patterns involving ncRNAs. Biologically, it is enriched with cancer pathways and treatment targets, providing valuable insights into disease relationships.
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Project description:Prostate cancer is one of the major cancers that seriously affect men's health. The low specificity of prostate-specific antigen (PSA) for prostate cancer has resulted in the overdiagnosis and subsequent overtreatment of clinically indolent tumors. There is an urgent need for noninvasive and easy diagnostic assays to help evaluate whether a prostate biopsy is warranted. Many non-coding RNAs (eg, microRNAs, long non-coding RNAs, circular RNAs) have been reported to play key roles in prostate cancer progression, showing great potential to impact cancer diagnostics and therapies. Remarkably, exosomes secreted by cells into body fluids contain molecules that reflect the disease information, and urinary exosomes could be used to detect prostate cancer as a new type of liquid biopsies. Non-coding RNAs are enriched and stable in exosomes. We performed high-throughput sequencing on urine-derived exosomes of 11 patients with high-grade (Gleason score 7 or greater) prostate cancer and 11 patients with benign prostatic hyperplasia to screen differentially expressed non-coding RNAs.
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Project description:The majority of studies on human cancers published to date focus on coding genes. More recently, however, non-coding RNAs (ncRNAs) are gaining growing recognition as important regulatory components. Here we characterise the ncRNA landscape in 442 head and neck squamous cell carcinomas (HNSCs) from the cancer genome atlas (TCGA). HNSCs represent an intriguing case to study the potential role of ncRNA as a function of viral presence, especially as HPV is potentially oncogenic. Thus, we identify HPV16-positive (HPV16+) and HPV-negative (HPV-) tumours and study the expression of ncRNAs on both groups. Overall, the ncRNAs comprise 36% of all differentially expressed genes, with antisense RNAs being the most represented ncRNA type (12.6%). Protein-coding genes appear to be more frequently downregulated in tumours compared with controls, whereas ncRNAs show significant upregulation in tumours, especially in HPV16+ tumours. Overall, expression of pseudogenes, antisense and short RNAs is elevated in HPV16+ tumours, while the remaining long non-coding RNA types are more active in all HNSC tumours independent of HPV status. In addition, we identify putative regulatory targets of differentially expressed ncRNAs. Among these 'targets' we find several well-established oncogenes, tumour suppressors, cytokines, growth factors and cell differentiation genes, which indicates the potential involvement of ncRNA in the control of these key regulators as a direct consequence of HPV oncogenic activity. In conclusion, our findings establish the ncRNAs as crucial transcriptional components in HNSCs. Our results display the great potential for the study of ncRNAs and the role they have in human cancers.
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Project description:PTEN is one of the most altered tumor suppressor genes in human prostate cancer. Prostate specific-Pten-deficient mouse models develop prostate cancer eventually progressing to CRPC, also due to alterations of the tumor immune infiltrate.
2024-08-21 | GSE272965 | GEO
Project description:Gynecologic cancer is a significant cause of death in women worldwide, with cervical cancer, ovarian cancer, and endometrial cancer being among the most well-known types. The initiation and progression of gynecologic cancers involve a variety of biological functions, including angiogenesis and metastasis-given that death mostly occurs from metastatic tumors that have invaded the surrounding tissues. Therefore, understanding the molecular pathways underlying gynecologic cancer metastasis is critical for enhancing patient survival and outcomes. Recent research has revealed the contribution of numerous non-coding RNAs (ncRNAs) to metastasis and invasion of gynecologic cancer by affecting specific cellular pathways. This review focuses on three types of gynecologic cancer (ovarian, endometrial, and cervical) and three kinds of ncRNAs (long non-coding RNAs, microRNAs, and circular RNAs). We summarize the detailed role of non-coding RNAs in the different pathways and molecular interactions involved in the invasion and metastasis of these cancers.
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Project description:Through digital rectal examinations and routine prostate-specific antigen (PSA) screening, early treatment of prostate cancer has become possible. However, prostate cancer is a complex and heterogeneous disease. In many patients, cancer cells can invade adjacent tissues and metastasize to other tissues, resulting in difficultly to cure. For the treatment of primary and metastatic prostate cancer, a significant problem is how to improve its survival time. Here, we collect 7 untreated primary and metastatic prostate cancer and 6 benign prostate hyperplasia samples under ultrasound guidance by experienced radiologists using the 18-G needle. Through mass spectrometry, we have completely depicted the protein atlas of primary and metastatic prostate cancer and benign prostate hyperplasia. Through bioinformatics analysis, experimental verification, and combined clinical data, we discover that the ribosome signaling pathway promotes the progression of prostate cancer and is associated with a poor prognosis. Among them, Mrpl1, Mrpl4, and Mrpl16 may be biomolecular markers for diagnosis and prognosis.
2021-09-05 | PXD028211 |
Project description:The clear cell subtype of renal cell carcinoma (RCC) is the most lethal and prevalent cancer of the urinary system. To investigate the molecular changes associated with malignant transformation in clear cell RCC, the gene expression profiles of matched samples of tumor and adjacent non-neoplastic tissue were obtained from 6 patients. A custom-built cDNA microarray platform was used, comprising 2,292 probes that map to exons of genes and 822 probes for noncoding RNAs mapping to intronic regions. Intronic transcription was detected in all normal and neoplastic renal tissues. A subset of 55 transcripts was significantly down-regulated in clear cell RCC relative to the matched non-tumor tissue as determined by a combination of two statistical tests and leave-one-out patient cross-validation. Among the down-regulated transcripts, 49 mapped to untranslated or coding exons and 6 were intronic relative to known exons of protein-coding genes. Lower levels of expression of SIN3B, TRIP3, SYNJ2BP and NDE1 (p < 0.02), and of intronic transcripts derived from SND1 and ACTN4 loci (p < 0.05), were confirmed in clear cell RCC by Real-time RT-PCR. A subset of 25 transcripts was deregulated in additional 6 non-clear cell RCC samples, pointing to common transcriptional alterations in RCC irrespective of the histological subtype or differentiation state of the tumor. Our results indicate a novel set of tumor suppressor gene candidates, including noncoding intronic RNAs, which may play a significant role in malignant transformations of normal renal cells. Keywords: Disease state analysis
2008-03-25 | GSE7367 | GEO
Project description:The discovery of long non-coding RNA (lncRNA) has dramatically altered our understanding of cancer. Here, we describe a comprehensive analysis of lncRNA alterations at transcriptional, genomic, and epigenetic levels in 5,037 human tumor specimens across 13 cancer types from The Cancer Genome Atlas. Our results suggest that the expression and dysregulation of lncRNAs are highly cancer type specific compared with protein-coding genes. Using the integrative data generated by this analysis, we present a clinically guided small interfering RNA screening strategy and a co-expression analysis approach to identify cancer driver lncRNAs and predict their functions. This provides a resource for investigating lncRNAs in cancer and lays the groundwork for the development of new diagnostics and treatments.
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