RNA regulation in mammals

A nine-long non-coding RNA signature for prognosis prediction of patients with lung squamous cell carcinoma

BACKGROUND

Lung squamous cell carcinoma (LUSC) is malignant disease with poor therapeutic response and unfavourable prognosis.

OBJECTIVE

This study aims to develop a long non-coding RNA (lncRNA) signature for survival prediction in patients with LUSC.

METHODS

We obtained lncRNA expression profiles of 493 LUSC cases from The Cancer Genome Atlas, and randomly divided the samples into a training set (n= 296) and a testing set (n= 197). Univariate Cox regression and random survival forest algorithm were performed to select optimum survival-related lncRNAs.

RESULTS

A lncRNA-focused risk score model was then constructed for prognosis prediction in the training set and further validated in the testing set and the entire set. Finally, bioinformatics analysis was carried out to explore the potential signaling pathways associated with the prognostic lncRNAs. A set of 9 lncRNAs were found to be strongly correlated with overall survival of LUSC patients. These 9 lncRNAs were integrated into a prognostic signature, which could separate patients into high- and low-risk groups with significantly different survival times in the training set (median: 30.5 vs. 80.5 months, log-rank P< 0.001). This signature was also confirmed in the testing set and the entire set. Besides, the prognostic value of the 9-lncRNA signature was independent of clinical features and maintained stable in stratified analyses. Functional enrichment study suggested that the 9 lncRNAs may be mainly involved in metabolism-related pathways, phosphatidylinositol signaling system, p53 signaling pathway, and notch signaling pathway.

CONCLUSIONS

Our study demonstrated the potential clinical implication of the 9-lncRNA signature for survival prediction of LUSC patients.

Distinct hepatitis B virus integration patterns in hepatocellular carcinoma and adjacent normal liver tissue

Infection by the hepatitis B virus (HBV) is one of the main etiologies of hepatocellular carcinoma (HCC). During chronic infection, HBV DNA can integrate into the human genome, and this has been postulated as a possible mechanism of HBV-induced HCC. In this study we used 2199 HBV integration sites from Dr.VIS v2.0 and mapped them to the human genome (hg19) to obtain viral integration sites (VIS) related to protein-coding and non-protein-coding genes. In total, we found 1,377 and 767 VIS within close proximity to protein coding genes and noncoding genes, respectively. Genes affected more than two times included 23.1% of protein-coding genes and 24.7% of long noncoding RNAs (lncRNA). Only 4.8% of VIS were shared between HCC and non-tumor tissues. HBV integrations were more common in chromosomes 5, 8, 10, and 19 in HCC tissue and chromosomes 1 and 2 in non-tumorous tissue. The number of integration sites on each chromosome correlated with the number of fragile sites in non-tumorous tissue but not in HCC tissue. Functional enrichment analysis of the protein-coding genes containing or in close proximity to HBV integration sites in HCC tissue showed an enrichment of cancer related gene ontology terms. Additionally, the most frequently associated lncRNA genes were related to telomere maintenance, protein modification processes, and chromosome localization. Thus, HBV may have preferred integration sites in the human genome that serve a critical role in HCC development. These results show that HCC treatment may benefit from the development of next generation anti-viral therapies.

Functional roles of long non-coding RNA in human breast cancer

The discovery of long noncoding RNA (LncRNA) changes our view of transcriptional and posttranscriptional regulation of gene expression. With application of new research techniques such as high-throughput sequencing, the biological functions of LncRNAs are gradually becoming to be understood. Multiple studies have shown that LncRNAs serve as carcinogenic factors or tumor suppressors in breast cancer with abnormal expression, prompts the question of whether they have potential value in predicting the stages and survival rate of breast cancer patients, and also as therapeutic targets. Focusing on the latest research data, this review mainly summarizes the tumorigenic mechanisms of certain LncRNAs in breast cancer, in order to provide a theoretical basis for finding safer, more effective treatment of breast cancer at the LncRNA molecular level.

MicroRNA target and gene validation in viruses and bacteria

Noncoding RNAs (ncRNAs) constitute an evolutionary conserved system involved in the regulation of biological functions at posttranscriptional level. The capability to rapidly adapt their metabolism is essential for the survival of organisms. NcRNAs are a valuable means used by cells to rapidly transfer and internalize an external signal. NcRNAs are capable not only to influence the translational phase but also to affect epigenetic processes. They have been identified in almost all kingdoms of life (from archaea to human and plants). In this chapter we outline the currently available resources that could be used for the screening of viral and bacterial ncRNAs.

Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity

Canonical duplex RNA assumes only the A-form conformation at the secondary structure level while, in contrast, a wide range of noncanonical, tertiary conformations of RNA occur. Here, we show how the 2'-hydroxyl controls RNA conformational properties. Quantum mechanical calculations reveal that the orientation of the 2'-hydroxyl significantly alters the intrinsic flexibility of the phosphodiester backbone, favoring the A-form in duplex RNA when it is in the base orientation and facilitating sampling of a wide range of noncanonical, tertiary structures when it is in the O3' orientation. Influencing the orientation of the 2'-hydroxyl are interactions with the environment, as evidenced by crystallographic survey data, indicating the 2'-hydroxyl to sample more of the O3' orientation in noncanonical RNA structures. These results indicate that the 2'-hydroxyl acts as a "switch", both limiting the conformation of RNA to the A-form at the secondary structure level and allowing RNA to sample a wide range of noncanonical tertiary conformations.

The RNA interference-virus interplay: tools of nature for gene modulation, morphogenesis, evolution and a possible mean for aflatoxin control

This article points out, that viruses, in an interplay with RNA interference and as vehicles for intergenic and interspecies gene transfer, may work as agents for intracellular gene modulation, for steering of individual morphogenesis and as a driving force of evolution in the toolbox of nature. This is illustrated in particular in the light of a fungal double-stranded RNA virus that may be employed as a suitable agent for a biological control of aflatoxins, the most carcinogenic natural substances occurring in food and feedstuff.

Progress & prospects: gene therapy in aging

Studies performed on various experimental model systems indicate that genetic interventions can increase longevity, even if in a highly protected laboratory condition. Generally, such interventions required partial or complete switching off of the gene and inhibiting the activity of its gene products, which normally have other well-defined roles in metabolic processes. Overexpression of some genes, such as stress response and antioxidant genes, in some model systems also extends their longevity. Such genetic interventions may not be easily applicable to humans without knowing their effects on human growth, development, maturation, reproduction and other characteristics. Studies on the association of single nucleotide polymorphisms and multiple polymorphisms (haplotype) in genes with human longevity have identified several genes whose frequencies increase or decrease with age. Whether genetic redesigning can be achieved in the wake of numerous and complex epigenetic factors that effectively determine the life course and the life span of an individual still appears to be a 'mission impossible'.

Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

We undertook a genome-wide search for novel noncoding RNAs (ncRNA) in the malaria parasite Plasmodium falciparum. We used the RNAz program to predict structures in the noncoding regions of the P. falciparum 3D7 genome that were conserved with at least one of seven other Plasmodium spp. genome sequences. By using Northern blot analysis for 76 high-scoring predictions and microarray analysis for the majority of candidates, we have verified the expression of 33 novel ncRNA transcripts including four members of a ncRNA family in the asexual blood stage. These transcripts represent novel structured ncRNAs in P. falciparum and are not represented in any RNA databases. We provide supporting evidence for purifying selection acting on the experimentally verified ncRNAs by comparing the nucleotide substitutions in the predicted ncRNA candidate structures in P. falciparum with the closely related chimp malaria parasite P. reichenowi. The high confirmation rate within a single parasite life cycle stage suggests that many more of the predictions may be expressed in other stages of the organism's life cycle.

Detection of spliced and unspliced forms of germline TCR-Vbeta transcripts in extrathymic lymphoid sites

Germline TCR-Vbeta transcription is commonly considered an event coupled with rearrangement of TCR genes in T cells. The extent of germline Vbeta transcription is studied here in a range of cell types and in several mouse strains. A sensitive semi-quantitative RT-PCR method was developed to specifically detect germline and not rearranged transcripts. Germline transcription of a range of different Vbeta genes was detected along with rearranged transcripts in bone marrow, thymus, mesenteric lymph node and spleen. Some transcripts were also detected in low level in non-lymphoid tissues including heart, liver and brain. Expression was also studied in the C57BL/6J-beta2microglobulin-/- (C57BL/6J-beta2M-/-) mouse model that lacks NK1.1 T cells and predominantly utilises Vbeta8.2 in the formation of a TCR. beta2M-/- mice, which lack both CD1-dependent NK1.1 T cells and CD8+ T cells, showed germline TCR-Vbeta8 transcription in most tissues indicating that germline transcription is not specifically related to CD1-dependent NK1.1 T cells. In many tissues, multiple transcripts were amplified representing both spliced and unspliced forms of germline Vbeta. For most Vbeta genes, the expression of spliced and unspliced forms was equivalent. Given an abundance of unspliced transcripts, the presence of alternative ORFs encoding a novel protein was investigated within the TCR-Vbeta genes. Sequence analysis of ORFs showed only genes with a high level of similarity to TCR-beta. All data reflect the prevalence of germline transcripts in vivo and raise questions about their functional role.

Site-specific cleavage of CD59 mRNA by endoplasmic reticulum-localized ribonuclease, IRE1

IRE1, an ER-localized transmembrane-RNase, plays a central role in ER stress response. Upon ER stress, IRE1 induces various adaptive genes through the processing of mRNA encoding the transcription factor XBP1. Moreover, it was recently reported that in fly IRE1 attenuates the expression of several genes by cleaving mRNAs, but it has been unclear whether such a mechanism also exists in mammal. In this study, we searched for IRE1alpha-cleaved mRNAs in mammalian cells and identified human CD59 (complement defense 59) mRNA as a novel cleavage target. In addition, the expression of CD59 was significantly attenuated by overexpression of IRE1alpha or ER stress. These results suggest that IRE1alpha-mediated mRNA cleavage functions even in mammals as a common system to regulate gene expression.

Recent computational approaches to understand gene regulation: mining gene regulation in silico

This paper reviews recent computational approaches to the understanding of gene regulation in eukaryotes. Cis-regulation of gene expression by the binding of transcription factors is a critical component of cellular physiology. In eukaryotes, a number of transcription factors often work together in a combinatorial fashion to enable cells to respond to a wide spectrum of environmental and developmental signals. Integration of genome sequences and/or Chromatin Immunoprecipitation on chip data with gene-expression data has facilitated in silico discovery of how the combinatorics and positioning of transcription factors binding sites underlie gene activation in a variety of cellular processes.The process of gene regulation is extremely complex and intriguing, therefore all possible points of view and related links should be carefully considered. Here we attempt to collect an inventory, not claiming it to be comprehensive and complete, of related computational biological topics covering gene regulation, which may en-lighten the process, and briefly review what is currently occurring in these areas.We will consider the following computational areas:o gene regulatory network construction;o evolution of regulatory DNA;o studies of its structural and statistical informational properties;o and finally, regulatory RNA.

Characterization of frequently deleted 6q locus in prostate cancer

The long arm of chromosome 6 is frequently deleted in diverse human neoplasms. Our previous study showed a minimum deletion region between markers D6S1056 and D6S300 on chromosome 6q in primary prostate cancer (CaP). In this study, we further refined a 200-kb minimal region of deletion (6qTSG1) centered around D6S1013 marker. The 6qTSG1 transcripts contained complex multiple splicing variants with low or absent expression in CaP cells. None of the transcripts identified contained open reading frames that code for a protein in the NCBI database. The expression of 6qTSG transcripts revealed interesting hormonal regulation relevant to CaP biology. Expression of 6q TSG transcript was induced in LNCaP cells that were cultured in charcoal-stripped serum medium suggesting an upregulation of 6qTSG transcript by androgen ablation and cell growth inhibition/apoptosis. Induction of 6qTSG1 expression in response to androgen ablation was abrogated in androgen-independent derivatives of LNCaP cells. In summary, we have defined a candidate CaP suppressor locus on chromosome 6q16.1, and deletions of this locus are frequently associated with prostate tumorigenesis. In the light of emerging role of noncoding RNAs in cancer biology including CaP, future investigations of 6qTSG11 locus is warranted.