Mutagen-specific mutation signature determines global microRNA binding

We are all individuals... bioinformatics in the personalized medicine era

The medical landscape is evolving at a rapid pace, creating the opportunity for more personalized patient treatment and shifting the way healthcare is approached and thought about. With the availability of (epi)genome-wide, transcriptomic and proteogenomic profiling techniques detailed characterization of a disease at the level of the individual is now possible, offering the opportunity for truly tailored approaches for treatment and patient care. While improvements are still expected, the techniques and the basic analytical tools have reached a state that these can be efficiently deployed in both routine research and clinical practice. Still, some major challenges remain. Notably, holistic approaches, integrating data from several sources, e.g. genomic and epigenomic, will increase the understanding of the underlying biological concepts and provide insight into the causes, effects and effective solutions. However, creating and validating such a knowledge base, potentially for different levels of expertise, and integrating several data points into meaningful information is not trivial.

MicroRNAs in skin response to UV radiation

Solar ultraviolet (UV) radiation, an ubiquitous environmental carcinogen, is classified depending on the wavelength, into three regions; short-wave UVC (200-280 nm), mid-wave UVB (280-320 nm), and long-wave UVA (320- 400 nm). The human skin, constantly exposed to UV radiation, particularly the UVB and UVA components, is vulnerable to its various deleterious effects such as erythema, photoaging, immunosuppression and cancer. To counteract these and for the maintenance of genomic integrity, cells have developed several protective mechanisms including DNA repair, cell cycle arrest and apoptosis. The network of damage sensors, signal transducers, mediators, and various effector proteins is regulated through changes in gene expression. MicroRNAs (miRNAs), a group of small non-coding RNAs, act as posttranscriptional regulators through binding to complementary sequences in the 3´-untranslated region of their target genes, resulting in either translational repression or target degradation. Recent studies show that miRNAs add an additional layer of complexity to the intricately controlled cellular responses to UV radiation. This review summarizes our current knowledge of the role of miRNAs in the regulation of the human skin response upon exposure to UV radiation.

New target genes of MITF-induced microRNA-211 contribute to melanoma cell invasion

The non-coding microRNAs (miRNA) have tissue- and disease-specific expression patterns. They down-regulate target mRNAs, which likely impacts on most fundamental cellular processes. Differential expression patterns of miRNAs are currently being exploited for identification of biomarkers for early disease diagnosis, prediction of progression for melanoma and other cancers and as promising drug targets, since they can easily be inhibited or replaced in a given cellular context. Before successfully manipulating miRNAs in clinical settings, their precise expression levels, endogenous functions and thus their target genes have to be determined. MiR-211, a melanocyte lineage-specific small non-coding miRNA, is located in an intron of TRPM1, a target gene of the microphtalmia-associated transcription factor (MITF). By transcriptionally up-regulating TRPM1, MITF, which is critical for both melanocyte differentiation and survival and for melanoma progression, indirectly drives the expression of miR-211. Expression of this miRNA is often reduced in melanoma samples. Here, we investigated functional roles of miR-211 by identifying and studying new target genes. We show that MITF-correlated miR-211 expression levels are mostly but not always reduced in a panel of 11 melanoma cell lines and in primary and metastatic melanoma compared to normal melanocytes and nevi, respectively. MiR-211 itself only marginally impacted on cell invasion and migration, while perturbation of some new miR-211 target genes, such as AP1S2, SOX11, IGFBP5, and SERINC3 significantly increased invasion. These results and the variable expression levels of miR-211 raise serious doubts on the value of miR-211 as a melanoma tumor-suppressing miRNA and/or as a biomarker for melanoma.

Integrative analysis of somatic mutations altering microRNA targeting in cancer genomes

Determining the functional impact of somatic mutations is crucial to understanding tumorigenesis and metastasis. Recent sequences of several cancers have provided comprehensive lists of somatic mutations across entire genomes, enabling investigation of the functional impact of somatic mutations in non-coding regions. Here, we study somatic mutations in 3'UTRs of genes that have been identified in four cancers and computationally predict how they may alter miRNA targeting, potentially resulting in dysregulation of the expression of the genes harboring these mutations. We find that somatic mutations create or disrupt putative miRNA target sites in the 3'UTRs of many genes, including several genes, such as MITF, EPHA3, TAL1, SCG3, and GSDMA, which have been previously associated with cancer. We also integrate the somatic mutations with germline mutations and results of association studies. Specifically, we identify putative miRNA target sites in the 3'UTRs of BMPR1B, KLK3, and SPRY4 that are disrupted by both somatic and germline mutations and, also, are in linkage disequilibrium blocks with high scoring markers from cancer association studies. The somatic mutation in BMPR1B is located in a target site of miR-125b; germline mutations in this target site have previously been both shown to disrupt regulation of BMPR1B by miR-125b and linked with cancer.

Reviewing the somatic genetics of melanoma: from current to future analytical approaches

Metastatic melanoma has traditionally been difficult to treat, and although molecularly based targeted therapies have shown promising results, they have yet to show consistent improvements in overall survival rates. Thus, identifying the key mutation events underlying the etiology of metastatic melanoma will no doubt lead to the improvement of existing therapeutic approaches and the development of new treatment strategies. Significant advances toward understanding the complexity of the melanoma genome have recently been achieved using next-generation sequencing (NGS) technologies. However, identifying those mutations driving tumorigenesis will continue to be a challenge for researchers, in part because of the high rates of mutation compared to other cancers. This article will review the catalog of mutations identified in melanoma through a variety of approaches, including the use of unbiased exome and whole-genome NGS platforms, as well discuss complementary strategies for identifying driver mutations. The promise of personalized medicine afforded by better understanding these mutation events should provide impetus for increased activity and rapid advances in this field.