A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events

We address here the issue of prioritizing non-coding mutations in the tumoral genome. To this aim, we created two independent computational models. The first (germline) model estimates purifying selection based on population SNP data. The second (somatic) model estimates tumor mutation density based on whole genome tumor sequencing. We show that each model reflects a different set of constraints acting either on the normal or tumor genome, and we identify the specific genome features that most contribute to these constraints. Importantly, we show that the somatic mutation model carries independent functional information that can be used to narrow down the non-coding regions that may be relevant to cancer progression. On this basis, we identify positions in non-coding RNAs and the non-coding parts of mRNAs that are both under purifying selection in the germline and protected from mutation in tumors, thus introducing a new strategy for future detection of cancer driver elements in the expressed non-coding genome.     

3D genome and its disorganization in diseases

The chromosomes in eukaryotic cells are highly folded and organized to form dynamic three-dimensional (3D) structures. In recent years, many technologies including chromosome conformation capture (3C) and 3C-based technologies (Hi-C, ChIA-PET) have been developed to investigate the 3D structure of chromosomes. These technologies are enabling research on how gene regulatory events are affected by the 3D genome structure, which is increasingly implicated in the regulation of gene expression and cellular functions. Importantly, many diseases are associated with genetic variations, most of which are located in non-coding regions. However, it is difficult to determine the mechanisms by which these variations lead to diseases. With 3D genome technologies, we can now better determine the consequences of non-coding genome alterations via their impact on chromatin interactions and structures in cancer and other diseases. In this review, we introduce the various 3D genome technologies, with a focus on their application to cancer and disease research, as well as future developments to extend their utility.     

Crosstalk between lncRNAs in the apoptotic pathway and therapeutic targets in cancer

The assertion that a significant portion of the mammalian genome has not been translated and that non-coding RNA accounts for over half of polyadenylate RNA have received much attention. In recent years, increasing evidence proposes non-coding RNAs (ncRNAs) as new regulators of various cellular processes, including cancer progression and nerve damage. Apoptosis is a type of programmed cell death critical for homeostasis and tissue development. Cancer cells often have inhibited apoptotic pathways. It has recently been demonstrated that up/down-regulation of various lncRNAs in certain types of tumors shapes cancer cells' response to apoptotic stimuli. This review discusses the most recent studies on lncRNAs and apoptosis in healthy and cancer cells. In addition, the role of lncRNAs as novel targets for cancer therapy is reviewed here. Finally, since it has been shown that lncRNA expression is associated with specific types of cancer, the potential for using lncRNAs as biomarkers is also discussed.     

The non-coding genome: a universe in expansion for fine-tuning the coding world

A report on the EMBO/EMBL Symposium on The Non-Coding Genome, held in Heidelberg, Germany, 9-12 October, 2013.We share 98% coding genome similarity with mouse and have about the same number of protein coding genes as worms, yet the differences in complexity are obvious. Where is this complexity encoded? A huge change in our understanding of genome evolution and regulation of gene expression arrived with the development of high-throughput sequencing technologies. It turns out that most of our genome is transcribed, but only a small percentage has coding information imbedded. The rest of the genome, the non-coding genome, mistakenly labeled as ‘junk DNA’, is where evolutionary complexity resides. In The Non-Coding Genome meeting, several research studies delved deeper into the importance of the non-coding genome, identifying novel classes of non-coding RNAs (ncRNAs) and novel regulatory functions, and expanding our knowledge about this new world, opening more exciting questions to study and answer.     

MicroRNA在肿瘤发生发展和诊断中作用的研究进展

microRNA是一类由内源基因编码的长度约为18-25个核苷酸的非编码单链RNA分子,可以与靶基因mRNA的3'非编码区结合,通过降解靶m RNA或(和)抑制靶m RNA转录后翻译调节靶蛋白的生成,从而发挥其生物学作用。目前,在人体基因组内发现的microRNA已经超过2500多个,可能调节着人类1/3的基因,在维持正常干细胞功能、调控细胞增殖分化及恶性肿瘤发生过程中均起重要作用。既往的研究表明microRNA与基因之间相互调控的失衡导致肿瘤的发生。从分子水平上研究microRNA与肿瘤发生的关系,检测microRNA与肿瘤相关基因表达情况的改变,分析肿瘤组织和血清中microRNA表达量与肿瘤分型的关系,将有利于肿瘤的病因学研究,早期发现和肿瘤治疗及预后判断。本文主要就microRNA在肿瘤发生发展和诊断中作用的研究进展进行了综述。     

Non-coding RNAs in human disease

The relevance of the non-coding genome to human disease has mainly been studied in the context of the widespread disruption of microRNA (miRNA) expression and function that is seen in human cancer. However, we are only beginning to understand the nature and extent of the involvement of non-coding RNAs (ncRNAs) in disease. Other ncRNAs, such as PIWI-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), transcribed ultraconserved regions (T-UCRs) and large intergenic non-coding RNAs (lincRNAs) are emerging as key elements of cellular homeostasis. Along with microRNAs, dysregulation of these ncRNAs is being found to have relevance not only to tumorigenesis, but also to neurological, cardiovascular, developmental and other diseases. There is great interest in therapeutic strategies to counteract these perturbations of ncRNAs.     

LncRNA的结构、功能及其与疾病的关系

70%的人类基因组能够被转录,而其中仅有1%～2%的转录本能够编码蛋白,余下98%均为非编码RNA（non-coding RNA,ncRNA）.在ncRNA中,长度大于200核苷酸称为长链非编码RNA（long non-coding RNA,LncRNA）,占全部ncRNA的80%～90%．LncRNA除了数量庞大以外,还具有表达量较低、物种间保守性较差及细胞表达特异性等特点,使LncRNA结构及作用机制等研究充满挑战．目前关于LncRNA的研究主要集中于功能方面．LncRNA能够广泛参与生物体的各种生理及病理过程,如表观遗传学调控、癌症、神经系统功能等．LncRNA作用机制众多,能够以分子诱饵、分子向导、分子支架及信号通路的调节剂等多种角色参与调节机体各种生物学过程．解析LncRNA的分子结构、深入研究其在生物体生理及病理过程中所发挥的作用,并揭示其作用机制,不仅能够加深对生物体生理及病理过程的认识,同时也能给某些疾病的诊断、防治提供新的思路及解决途径．本文综述了近年来有关LncRNA结构、功能及作用机制相关研究进展,以期为后续LncRNA相关研究提供参考.     

A molecular clock based on the expansion of gene families.

There is evidence to suggest that eukaryotic genomes are subject to frequent insertions and deletions of non-coding DNA. This may lead to a gradual increase or decrease in genome size, or to a dynamic equilibrium in which the overall size remains constant. We argue, however, that there is a bias favouring an accumulation of non-coding DNA in the proximity of genes. Such bias causes a progressive change in genome structure regardless of whether the overall genome size increases, decreases or remains constant. We show that this change may serve as a 'molecular clock', supplementing that provided by nucleotide substitution rates.     

Factors contributing to the outcome of oxidative damage to nucleic acids

Oxidative damage to DNA appears to be a factor in cancer, yet explanations for why highly elevated levels of such lesions do not always result in cancer remain elusive. Much of the genome is non-coding and lesions in these regions might be expected to have little biological effect, an inference supported by observations that there is preferential repair of coding sequences. RNA has an important coding function in protein synthesis, and yet the consequences of RNA oxidation are largely unknown. Some non-coding nucleic acid is functional, e.g. promoters, and damage to these sequences may well have biological consequences. Similarly, oxidative damage to DNA may promote microsatellite instability, inhibit methylation and accelerate telomere shortening. DNA repair appears pivotal to the maintenance of genome integrity, and genetic alterations in repair capacity, due to single nucleotide polymorphisms or mutation, may account for inter-individual differences in cancer susceptibility. This review will survey these aspects of oxidative damage to nucleic acids and their implication for disease.     

Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes

Much emphasis has been placed on the identification, functional characterization, and therapeutic potential of somatic variants in tumor genomes. However, the majority of somatic variants lie outside coding regions and their role in cancer progression remains to be determined. In order to establish a system to test the functional importance of non-coding somatic variants in cancer, we created a low-passage cell culture of a metastatic melanoma tumor sample. As a foundation for interpreting functional assays, we performed whole-genome sequencing and analysis of this cell culture, the metastatic tumor from which it was derived, and the patient-matched normal genomes. When comparing somatic mutations identified in the cell culture and tissue genomes, we observe concordance at the majority of single nucleotide variants, whereas copy number changes are more variable. To understand the functional impact of non-coding somatic variation, we leveraged functional data generated by the ENCODE Project Consortium. We analyzed regulatory regions derived from multiple different cell types and found that melanocyte-specific regions are among the most depleted for somatic mutation accumulation. Significant depletion in other cell types suggests the metastatic melanoma cells de-differentiated to a more basal regulatory state. Experimental identification of genome-wide regulatory sites in two different melanoma samples supports this observation. Together, these results show that mutation accumulation in metastatic melanoma is nonrandom across the genome and that a de-differentiated regulatory architecture is common among different samples. Our findings enable identification of the underlying genetic components of melanoma and define the differences between a tissue-derived tumor sample and the cell culture created from it. Such information helps establish a broader mechanistic understanding of the linkage between non-coding genomic variations and the cellular evolution of cancer.     

MicroRNAs as oncogenes

MicroRNAs (miRNAs) are a class of non-coding RNAs that function as endogenous triggers of the RNA interference pathway. Originally discovered in Caenorhabditis elegans, this group of tiny RNAs has moved to the forefront of biology. With over 300 miRNA genes identified in the human genome, and a plethora of predicted mRNA targets, it is believed that these small RNAs have a central role in diverse cellular and developmental processes. Concordant with this, aberrant expression of miRNA genes could lead to human disease, including cancer. Although the connection of miRNAs with cancer has been suspected for several years, four recent studies have confirmed the suspicion that miRNAs regulate cell proliferation and apoptosis, and play a role in cancer.     

Pericentromeric Satellite III transcripts induce etoposide resistance

Non-coding RNA from pericentromeric satellite repeats are involved in stress-dependent splicing processes, maintenance of heterochromatin, and are required to protect genome stability. Here we show that the long non-coding satellite III RNA (SatIII) generates resistance against the topoisomerase IIa (TOP2A) inhibitor etoposide in lung cancer. Because heat shock conditions (HS) protect cells against the toxicity of etoposide, and SatIII is significantly induced under HS, we hypothesized that the protective effect could be traced back to SatIII. Using genome methylation profiles of patient-derived xenograft mouse models we show that the epigenetic modification of the SatIII DNA locus and the resulting SatIII expression predict chemotherapy resistance. In response to stress, SatIII recruits TOP2A to nuclear stress bodies, which protects TOP2A from a complex formation with etoposide and results in decreased DNA damage after treatment. We show that BRD4 inhibitors reduce the expression of SatIII, restoring etoposide sensitivity.Subject terms: Cancer therapeutic resistance, Epigenetics, Long non-coding RNAs