Current Genomics (v.18, #3)

Centromeric Non-coding Transcription: Opening the Black Box of Chromosomal Instability? by Rodrigo Caceres-Gutierrez, Luis A. Herrera (227-235).
In eukaryotes, mitosis is tightly regulated to avoid the generation of numerical chromosome aberrations, or aneuploidies. The aneuploid phenotype is a consequence of chromosomal instability (CIN), i.e., an enhanced rate of chromosome segregation errors, which is frequently found in cancer cells and is associated with tumor aggressiveness and increased tumor cell survival potential. To avoid the generation of aneuploidies, cells rely on the spindle assembly checkpoint (SAC), a widely conserved mechanism that protects the genome against this type of error. This signaling pathway stops mitotic progression before anaphase until all chromosomes are correctly attached to spindle microtubules. However, impairment of the SAC cannot account for the establishment of CIN because cells bearing this phenotype have a functional SAC. Hence, in cells with CIN, anaphase is not triggered until all chromosomes are correctly attached to spindle microtubules and congressed at the metaphase plate. Thus, an interesting question arises: What mechanisms actually mediate CIN in cancer cells? Recent research has shown that some pathways involved in chromosome segregation are closely associated to centromere-encoded non-coding RNA (cencRNA) and that these RNAs are deregulated in abnormal conditions, such as cancer. These mechanisms may provide new explanations for chromosome segregation errors. The present review discusses some of these findings and proposes novel mechanisms for the establishment of CIN based on regulation by cencRNA.

Somatic Mutation Analyses in Studies of the Clonal Evolution and Diagnostic Targets of Prostate Cancer by Dmitry S. Mikhaylenko, Gennady D. Efremov, Vladimir V. Strelnikov, Dmitry V. Zaletaev, Boris Y. Alekseev (236-243).
Prostate cancer (PC) is the most common uro-oncological disease in the global population and still requires a more efficient laboratory diagnosis. Point mutations of oncogenes and tumor suppressor genes are the most frequent molecular genetic events in carcinogenesis. The mutations are responsible, to a great extent, for the clonal evolution of cancer and can be considered as primary candidate molecular markers of PC. Using next-generation sequencing to analyze the mutations in PC, the main molecular PC subtypes were identified, which depended on the presence of fusion genes and FOXA1, CHD1, and SPOP point mutations; other driver mutations responsible for the progression of PC subclones were also characterized. This review summarizes the data on early PC genetic markers (an mtDNA deletion, and TMPRSS2:ERG expression), as well as these somatic mutations at later stages of PC. Emphasis is placed on a switch in AR synthesis to a constitutively active variant and the point mutations that facilitate PC transition to a castration-refractory state that is resistant to new AR inhibitors. Based on the current whole-exome sequencing data, the frequencies and localizations of the somatic mutations that may provide new genetic diagnostic markers and drug targets are described.

The Genetics of Papillary Microcarcinomas of the Thyroid: Diagnostic and Prognostic Implications by Ana Cunha Rodrigues, Gustavo Penna, Elisabete Rodrigues, Patrícia Castro, Manuel Sobrinho-Simoes, Paula Soares (244-254).
Papillary microcarcinoma of the thyroid (mPTC) is defined by the WHO as a papillary thyroid cancer measuring 10mm or less in diameter and it is nowadays a topic of intense debate among the members of the medical community due to its apparent “epidemic” rise. Although these tumors follow almost always an indolent clinical course and carry an excellent prognosis, it is known that a small subset may display a potentially aggressive behavior. Nevertheless, we still lack an accurate way of predicting those which will cause significant disease. In an attempt to address this problem, a number of clinico-pathologic features have been studied as poor prognostic markers in mPTC, and their association with known genetic alterations in thyroid cancer has been evaluated. Herein we review the present knowledge concerning mPTC's genetic profile, namely the prevalence of BRAF (V600E), RAS and TERT promoter mutations and RET/PTC and PAX8-PPARG rearrangements and report the results of the evaluation in the putative prognostic value of these genetic alterations in mPTC.

Sequence alterations of the mitochondrial DNA (mtDNA) have been identified in many tumor types. Their nature is not entirely clear. Somatic mutation or shifts of heteroplasmic mtDNA variants may play a role. These sequence alterations exhibit a sufficient frequency in all tumor types investigated thus far to justify their use as a tumor marker. This statement is supported by the high copy number of mtDNA, which facilitates the detection of aberrant tumor-derived DNA in bodily fluids. This will be of special interest in tumors, which release a relatively high number of cells into bodily fluids, which are easily accessible, most strikingly in urinary bladder carcinoma. Due to the wide distribution of the observed base substitutions, deletions or insertions within the mitochondrial genome, high efforts for whole mtDNA sequencing (16.5 kb) from bodily fluids would be required, if the method would be intended for initial tumor screening. However, the usage of mtDNA for sensitive surveillance of known tumor diseases is a meaningful option, which may allow an improved noninvasive follow-up for the urinary bladder carcinoma, as compared to the currently existing cytological or molecular methods. Following a short general introduction into mtDNA, this review demonstrates that the scenario of a sensitive cancer follow-up by mtDNA-analysis deserves more attention. It would be most important to investigate precisely in the most relevant tumor types, if sequencing approaches in combination with simple PCR-assays for deletions/insertions in homopolymeric tracts has sufficient sensitivity to find most tumor-derived mtDNAs in bodily fluids.

Comparison of Alternative Splicing Junction Detection Tools Using RNASeq Data by Lizhong Ding, Ethan Rath, Yongsheng Bai (268-277).
Background: Alternative splicing (AS) is a posttranscriptional process that produces different transcripts from the same gene and is important to produce diverse protein products in response to environmental stimuli. AS occurs at specific sites on the mRNA sequence, some of which have been defined. Multiple bioinformatics tools have been developed to detect AS from experimental data.

Objectives: The goal of this review is to help researchers use specific tools to aid their research and to develop new AS detection tools based on these previously established tools.

Method: We selected 15 AS detection tools that were recently published; we classified and delineated them on several aspects. Also, a performance comparison of these tools with the same starting input was conducted.

Result: We reviewed the following categorized features of the tools: Publication information, working principles, generic and distinct workflows, running platform, input data requirement, sequencing depth dependency, reads mapped to multiple locations, isoform annotation basis, precise detected AS types, and performance benchmarks.

Conclusion: Through comparisons of these tools, we provide a panorama of the advantages and shortcomings of each tool and their scopes of application.

Helitrons and Retrotransposons Are Co-localized in Bos taurus Genomes by A. Babii, S. Kovalchuk, T. Glazko, G. Kosovsky, V. Glazko (278-286).
Background: DNA transposons helitrons are mobile genetic elements responsible for major movements of the genetic material within and across different genomes. This ability makes helitrons suitable candidate elements for the development of new approaches of multilocus genotyping of livestock animals, along with the well-known microsatellite loci.

Objective: We aimed to estimate the informativeness of helitron and microsatellite markers in assessing the consolidation and the "gene pool" standards of two commercial dairy cattle breeds (Ayrshire breed and holsteinized Black-and-White cattle) and one local breed of Kalmyk cattle, and to reveal any interbreed difference in the organization of genomic regions flanked by helitrons in the studied cattle breeds.

Method: We used the combination of two highly-polymorphic genomic elements - helitrons and trinucleotide microsatellites (AGC)6G and (GAG)6C, respectively - for genome scanning of the sampled groups of cattle. Also, we pyrosequenced the genomic regions flanked by the inverted repeats of 3'-end of Heligloria family of helitron fragments.

Results: Generally, the both combinations of markers generated polymorphic spectra, based on which certain interbreed differentiation could be observed. The analysis of the identified interspersed repeats suggests that in factory and local cattle the genomic regions flanked by helitron fragments are shaped differently and contain different superfamilies of transposable elements, especially retrotransposons.

Conclusion: Despite the well-known fact of retrotransposon-dependent microsatellite expansion, our data suggest that, in the cattle genome, the DNA transposons and microsatellites can also be found in close neighbourhood, and that helitrons and retrotransposons may form domains of increased variability - targets for factors of artificial selection.

Background: Relatively little cancer genome atlas data has been associated with clinically relevant stratifications of individual cancers.

Results: Mutations in two subsets of a cytoskeletal related and adhesion-related protein coding region set (CAPCRs) were determined to have strong associations with a negative outcome for melanoma, including a subset constituted by: DSCAM, FAT3, MUC17 and PCDHGC5 (p < 0.0001).

Conclusion: Roles for CAPCR mutations in cancer progression raise a question about the potential dominant negative impact of these mutations for multi-meric subcellular and extra-cellular protein structures.

Background: Type 2 diabetes (T2D) is a common multi-factorial disease that is primarily accounted to ineffective insulin action in lowering blood glucose level and later escalates to impaired insulin secretion by pancreatic ? cells. Deregulation in insulin signaling to its target organs is attributed to this disease phenotype. Various genome-wide microarray studies from multiple insulin responsive tissues have been conducted in past but due to inherent noise in microarray data and heterogeneity in disease etiology; reproduction of prioritized pathways/genes is very low across various studies.

Objective: In this study, we aim to identify consensus signaling and metabolic pathways through system level meta-analysis of multiple expression-sets to elucidate T2D pathobiology.

Method: We used 'R', an open source statistical environment, which is routinely used for Microarray data analysis particularly using special sets of packages available at Bioconductor. We primarily focused on gene-set analysis methods to elucidate various aspects of T2D.

Result: Literature-based evidences have shown the success of our approach in exploring various known aspects of diabetes pathophysiology.

Conclusion: Our study stressed the need to develop novel bioinformatics workflows to advance our understanding further in insulin signaling.