Project description:It has been postulated that noncoding RNAs (ncRNAs) are involved in the post-transcriptional control of gene expression, and may have contributed to the emergence of the complex attributes observed in mammalians. The complement of ncRNAs expressed from intronic regions of the human and mouse genomes comprises at least 78,147 and 39,660 transcriptional units, respectively. To identify conserved intronic sequences expressed in both humans and mice, we used custom-designed human cDNA microarrays to separately interrogate RNA from mouse and human liver, kidney and prostate tissues. An overlapping tissue expression signature was detected for both species, comprising 198 transcripts; among these, twenty two RNAs map to intronic regions with evidence of evolutionary conservation in humans and mice. Transcription of selected human-mouse intronic ncRNAs was confirmed using strand specific RT-PCR. Altogether, these results support an evolutionarily conserved role of intronic ncRNAs in human and mouse, which are likely to be involved in the fine tuning of gene expression regulation in different mammalian tissues. Keywords: tissue expression pattern 1. Experiment Design: 1.1. Type of experiment: The experiments described here aim to generate expression profiles from human and mouse prostate, kidney and liver tissue samples using a custom-designed cDNA microarray platform with 4,608 unique elements in replicate (9,216) enriched in gene fragments that map to intronic regions of known human genes. The platform consists of 3,355 probes of human cDNA fragments that map in the human genome sequence either to intronic regions of known genes (822), to unannotated regions of the human genome (241) or to known exons of RefSeq genes (2,292). We separately compared the expression profiles obtained from human and mouse samples to identify sequence conserved tissue-specific intronic transcripts. 1.2. Experimental factors: Tissues from liver, prostate and kidney from five adult male mice of the Balb/c strain were obtained and frozen in liquid nitrogen. Likewise, five non-tumor samples of human prostate, kidney or liver from our tumor bank were selected. All samples were obtained from patients who signed informed consent, and approval was received from the ethics committees of the hospitals. Total RNA was purified from tissues and treated with DNAse to reduce the levels of genomic DNA contaminant. Either human and or mouse samples from for each tissue from the five individuals were separately pooled using equal quantities of RNA. 1.3. The number of hybridizations performed in the experiment. RNA pools from each tissue sample was hybridized twice, performing a total of 18 hybridizations. 1.4. The type of reference used for the hybridizations, if any. All hybridizations included external mRNA spikes for quality control of the experiments (detailed below in section 2.5). Hybridizations were performed as single color experiments. 1.5. Hybridization design: Three aliquots of 15ug of the pool of total RNA from each tissue was labeled with Cy5-dUTP after reverse transcription (CyScribe first strand cDNA labeling kit, Amershan Biosciences) and hybridizations were carried out using all labeled-target in an Automate Slide Processor (Amershan Biosciences). Images were obtained using a Generation III Scanner (Amersham Biosciences). The human and mouse obtained expression data were independently analyzed using a highly stringent methodology, including different statistical approaches (see below for a detailed description). 1.6. Quality control steps taken: Integrity of total RNA was checked by electrophoresis using the Bio Sizing total RNA Nano assay in the 2100 Bioanalyzer (Agilent Technologies). Three replicates of each experiment were performed, as describe in the previous section.

Project description:Pancreatic ductal adenocarcinoma (PDAC) is known by its aggressiveness and lack of effective therapeutic options. Thus, improvement in current knowledge of molecular changes associated with pancreatic cancer is urgently needed to explore novel venues of diagnostics and treatment of this dismal disease. While there is mounting evidence that long noncoding RNAs (ncRNAs) transcribed from intronic and intergenic regions of the human genome may play different roles in the regulation of gene expression in normal and cancer cells, their expression pattern and biological relevance in pancreatic cancer is currently unknown. In the present work we investigated the relative abundance of a collection of ncRNAs in patients’ pancreatic tissue samples aiming at identifying gene expression profiles correlated to pancreatic cancer and metastasis. To investigate the relative abundance, we used a custom 3,355-element spotted cDNA microarray interrogating protein-coding genes and putative ncRNA were used to obtain expression profiles from 38 clinical samples of tumor and non-tumor pancreatic tissues. Bioinformatics analyses were performed to characterize structure and conservation of ncRNAs expressed in pancreatic tissues, as well as to identify expression signatures correlated to tissue histology. Strand-specific reverse transcription followed by PCR and qRT-PCR were employed to determine strandedness of ncRNAs and to validate microarray results, respectively. We found that long intronic/intergenic ncRNAs are ubiquitously expressed across tumor and non-tumor pancreatic tissue samples. Enrichment of promoter-H3K4me3 associated chromatin marks and over-representation of conserved DNA elements and stable secondary structure predictions suggest that these transcripts are generated from independent transcriptional units and that at least a fraction is under evolutionary selection, and thus potentially functional. Statistically significant expression signatures comprising protein-coding mRNAs and long ncRNAs that correlate to PDAC or to pancreatic cancer metastasis were identified. Interestingly, loci harboring intronic ncRNAs differentially expressed in PDAC metastases were enriched in genes associated to the MAPK pathway. Orientation-specific RT-PCR documented that intronic transcripts are expressed in sense, antisense or both orientations relative to protein-coding mRNAs. Differential expression of a subset of intronic ncRNAs (PPP3CB, MAP3K14 and DAPK1 loci) in metastatic samples was confirmed by Real-Time PCR. All this results reveal sets of long intronic ncRNAs expressed in pancreatic tissues whose abundance is correlated to PDAC or metastasis, thus pointing to the potential relevance of this class of transcripts in biological processes related to malignant transformation and metastasis in pancreatic cancer.

Project description:Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. Samples from 18 primary clear cell RCC tumors and 11 nontumor adjacent matched tissues were analyzed with 4k-probes microarrays. Oligoarrays with 44k-probes were used to interrogate 17 RCC samples (14 clear cell, 2 papillary, 1 chromophobe subtypes) split into four pools. Meta-analyses were performed by taking the genomic coordinates of the RCC-expressed lncRNAs, and cross-referencing them with microarray expression data from three additional human tissues (normal liver, prostate tumor and kidney nontumor samples), and with large-scale public data for epigenetic regulatory marks and for evolutionarily conserved sequences. A signature of 29 intronic lncRNAs differentially expressed between RCC and nontumor samples was obtained (false discovery rate (FDR) <5%). An additional signature of 26 intronic lncRNAs significantly correlated with the RCC five-year patient survival outcome was identified (FDR <5%, p-value M-bM-^IM-$0.01). We identified 4303 intronic antisense lncRNAs expressed in RCC, of which 25% were cis correlated (r >|0.6|) with the expression of the mRNA in the same locus across three human tissues. Gene Ontology (GO) analysis of those loci pointed to M-bM-^@M-^Xregulation of biological processesM-bM-^@M-^Y as the main enriched category. A module map analysis of all expressed protein-coding genes in RCC that had a significant (r M-bM-^IM-%|0.8|) trans correlation with the 20% most abundant lncRNAs identified 35 relevant (p <0.05) GO sets. In addition, we determined that 60% of these lncRNAs are evolutionarily conserved. At the genomic loci containing the intronic RCC-expressed lncRNAs, a strong association (p <0.001) was found between their transcription start sites and genomic marks such as CpG islands and histones methylation and acetylation. Intronic antisense lncRNAs are widely expressed in RCC tumors. Some of them are significantly altered in RCC in comparison with nontumor samples. The majority of these lncRNAs is evolutionarily conserved and possibly modulated by epigenetic modifications. Our data suggest that these RCC lncRNAs may contribute to the complex network of regulatory RNAs playing a role in renal cell malignant transformation. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

Project description:Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. Samples from 18 primary clear cell RCC tumors and 11 nontumor adjacent matched tissues were analyzed with 4k-probes microarrays. Oligoarrays with 44k-probes were used to interrogate 17 RCC samples (14 clear cell, 2 papillary, 1 chromophobe subtypes) split into four pools. Meta-analyses were performed by taking the genomic coordinates of the RCC-expressed lncRNAs, and cross-referencing them with microarray expression data from three additional human tissues (normal liver, prostate tumor and kidney nontumor samples), and with large-scale public data for epigenetic regulatory marks and for evolutionarily conserved sequences. A signature of 29 intronic lncRNAs differentially expressed between RCC and nontumor samples was obtained (false discovery rate (FDR) <5%). An additional signature of 26 intronic lncRNAs significantly correlated with the RCC five-year patient survival outcome was identified (FDR <5%, p-value M-bM-^IM-$0.01). We identified 4303 intronic antisense lncRNAs expressed in RCC, of which 25% were cis correlated (r >|0.6|) with the expression of the mRNA in the same locus across three human tissues. Gene Ontology (GO) analysis of those loci pointed to M-bM-^@M-^Xregulation of biological processesM-bM-^@M-^Y as the main enriched category. A module map analysis of all expressed protein-coding genes in RCC that had a significant (r M-bM-^IM-%|0.8|) trans correlation with the 20% most abundant lncRNAs identified 35 relevant (p <0.05) GO sets. In addition, we determined that 60% of these lncRNAs are evolutionarily conserved. At the genomic loci containing the intronic RCC-expressed lncRNAs, a strong association (p <0.001) was found between their transcription start sites and genomic marks such as CpG islands and histones methylation and acetylation. Intronic antisense lncRNAs are widely expressed in RCC tumors. Some of them are significantly altered in RCC in comparison with nontumor samples. The majority of these lncRNAs is evolutionarily conserved and possibly modulated by epigenetic modifications. Our data suggest that these RCC lncRNAs may contribute to the complex network of regulatory RNAs playing a role in renal cell malignant transformation. A total of 16 human renal tumors from clear cell renal cell carcinoma (RCC) patients were evaluated in this study. We compared the expression profiles of tumor samples obtained from patients with clear cell RCC who died as a consequence of the disease versus those alive without disease (5-years follow-up) to evaluate a possible correlation of the lncRNAs with patient survival. The set of clear cell RCC expression profiles was generated using a custom-designed cDNA microarray platform with 4,608 unique elements in replicate (9,216) enriched in gene fragments that map to intronic regions of known human genes (GPL3985).

Project description:Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. Samples from 18 primary clear cell RCC tumors and 11 nontumor adjacent matched tissues were analyzed with 4k-probes microarrays. Oligoarrays with 44k-probes were used to interrogate 17 RCC samples (14 clear cell, 2 papillary, 1 chromophobe subtypes) split into four pools. Meta-analyses were performed by taking the genomic coordinates of the RCC-expressed lncRNAs, and cross-referencing them with microarray expression data from three additional human tissues (normal liver, prostate tumor and kidney nontumor samples), and with large-scale public data for epigenetic regulatory marks and for evolutionarily conserved sequences. A signature of 29 intronic lncRNAs differentially expressed between RCC and nontumor samples was obtained (false discovery rate (FDR) <5%). An additional signature of 26 intronic lncRNAs significantly correlated with the RCC five-year patient survival outcome was identified (FDR <5%, p-value M-bM-^IM-$0.01). We identified 4303 intronic antisense lncRNAs expressed in RCC, of which 25% were cis correlated (r >|0.6|) with the expression of the mRNA in the same locus across three human tissues. Gene Ontology (GO) analysis of those loci pointed to M-bM-^@M-^Xregulation of biological processesM-bM-^@M-^Y as the main enriched category. A module map analysis of all expressed protein-coding genes in RCC that had a significant (r M-bM-^IM-%|0.8|) trans correlation with the 20% most abundant lncRNAs identified 35 relevant (p <0.05) GO sets. In addition, we determined that 60% of these lncRNAs are evolutionarily conserved. At the genomic loci containing the intronic RCC-expressed lncRNAs, a strong association (p <0.001) was found between their transcription start sites and genomic marks such as CpG islands and histones methylation and acetylation. Intronic antisense lncRNAs are widely expressed in RCC tumors. Some of them are significantly altered in RCC in comparison with nontumor samples. The majority of these lncRNAs is evolutionarily conserved and possibly modulated by epigenetic modifications. Our data suggest that these RCC lncRNAs may contribute to the complex network of regulatory RNAs playing a role in renal cell malignant transformation. A total of 22 human kidney tissue samples consisting of 11 primary renal tumors and 11 matched adjacent nontumor tissues from clear cell renal cell carcinmoa (RCC) patients were evaluated in this study. We compared the expression profiles of tumor and non-tumor samples obtained from patients with clear cell RCC to evaluate a possible correlation of the lncRNAs with renal malignancy. The set of clear cell RCC expression profiles was generated using a custom-designed cDNA microarray platform with 4,608 unique elements in replicate (9,216) enriched in gene fragments that map to intronic regions of known human genes (GPL3985).

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Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer

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