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Current Genomics

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https://www.readbyqxmd.com/read/28659725/system-level-meta-analysis-of-microarray-datasets-for-elucidation-of-diabetes-mellitus-pathobiology
#1
Aditya Saxena, Kumar Sachin, Ashok Kumar Bhatia
BACKGROUND: Type 2 diabetes (T2D) is a common multi-factorial disease that is primarily ac-counted to ineffective insulin action in lowering blood glucose level and later escalates to impaired insu-lin secretion by pancreatic β cells. Deregulation in insulin signaling to its target organs is attributed to this disease phenotype. Various genome-wide microarray studies from multiple insulin responsive tis-sues have been conducted in past but due to inherent noise in microarray data and heterogeneity in dis-ease etiology; reproduction of prioritized pathways/genes is very low across various studies...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28659724/identification-of-sets-of-cytoskeletal-related-and-adhesion-related-coding-region-mutations-in-the-tcga-melanoma-dataset-that-correlate-with-a-negative-outcome
#2
John M Yavorski, Rebecca J Stoll, Mohammad D Samy, James A Mauro, George Blanck
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, in-cluding 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 struc-tures...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28659723/helitrons-and-retrotransposons-are-co-localized-in-bos-taurus-genomes
#3
A Babii, S Kovalchuk, T Glazko, G Kosovsky, V Glazko
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 live-stock 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 inter-breed difference in the organization of genomic regions flanked by helitrons in the studied cattle breeds...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28659722/comparison-of-alternative-splicing-junction-detection-tools-using-rna-seq-data
#4
REVIEW
Lizhong Ding, Ethan Rath, Yongsheng Bai
BACKGROUND: Alternative splicing (AS) is a posttranscriptional process that produces differ-ent 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 de-fined. 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...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28659721/mtdna-as-a-cancer-marker-a-finally-closed-chapter
#5
REVIEW
Elmar Kirches
Sequence alterations of the mitochondrial DNA (mtDNA) have been identified in many tu-mor types. Their nature is not entirely clear. Somatic mutation or shifts of heteroplasmic mtDNA vari-ants may play a role. These sequence alterations exhibit a sufficient frequency in all tumor types investi-gated thus far to justify their use as a tumor marker. This statement is supported by the high copy num-ber 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...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28659720/the-genetics-of-papillary-microcarcinomas-of-the-thyroid-diagnostic-and-prognostic-implications
#6
REVIEW
Ana Cunha Rodrigues, Gustavo Penna, Elisabete Rodrigues, Patrícia Castro, Manuel Sobrinho-Simões, Paula Soares
Papillary microcarcinoma of the thyroid (mPTC) is defined by the WHO as a papillary thy-roid 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 sub-set may display a potentially aggressive behavior. Nevertheless, we still lack an accurate way of predict-ing those which will cause significant disease...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28659719/somatic-mutation-analyses-in-studies-of-the-clonal-evolution-and-diagnostic-targets-of-prostate-cancer
#7
REVIEW
Dmitry S Mikhaylenko, Gennady D Efremov, Vladimir V Strelnikov, Dmitry V Zaletaev, Boris Y Alekseev
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 sup-pressor genes are the most frequent molecular genetic events in carcinogenesis. The mutations are re-sponsible, to a great extent, for the clonal evolution of cancer and can be considered as primary candi-date 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...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28603453/centromeric-non-coding-transcription-opening-the-black-box-of-chromosomal-instability
#8
REVIEW
Rodrigo Cáceres-Gutiérrez, Luis A Herrera
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...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28367077/protein-and-genetic-composition-of-four-chromatin-types-in-drosophila-melanogaster-cell-lines
#9
Lidiya V Boldyreva, Fyodor P Goncharov, Olga V Demakova, Tatyana Yu Zykova, Victor G Levitsky, Nikolay N Kolesnikov, Alexey V Pindyurin, Valeriy F Semeshin, Igor F Zhimulev
BACKGROUND: Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) and identified a set of 12 proteins enriched in the regions corresponding to interbands of salivary gland polytene chromosomes. Using these data, we developed a bioinformatic pipeline that partitioned the Drosophila genome into four chromatin types that we hereby refer to as aquamarine, lazurite, malachite and ruby. RESULTS: Here, we describe the properties of these chromatin types across different cell lines...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367076/genetic-imbalance-in-patients-with-cervical-artery-dissection
#10
Caspar Grond-Ginsbach, Bowang Chen, Michael Krawczak, Rastislav Pjontek, Philip Ginsbach, Yanxiang Jiang, Shérine Abboud, Marie-Luise Arnold, Anna Bersano, Tobias Brandt, Valeria Caso, Stéphanie Debette, Martin Dichgans, Andreas Geschwendtner, Giacomo Giacalone, Juan-José Martin, Antti J Metso, Tiina M Metso, Armin J Grau, Manja Kloss, Christoph Lichy, Alessandro Pezzini, Christopher Traenka, Stefan Schreiber, Vincent Thijs, Emmanuel Touzé, Elisabetta Del Zotto, Turgut Tatlisumak, Didier Leys, Philippe A Lyrer, Stefan T Engelter
BACKGROUND: Genetic and environmental risk factors are assumed to contribute to the susceptibility to cervical artery dissection (CeAD). To explore the role of genetic imbalance in the etiology of CeAD, copy number variants (CNVs) were identified in high-density microarrays samples from the multicenter CADISP (Cervical Artery Dissection and Ischemic Stroke Patients) study and from control subjects from the CADISP study and the German PopGen biobank. Microarray data from 833 CeAD patients and 2040 control subjects (565 subjects with ischemic stroke due to causes different from CeAD and 1475 disease-free individuals) were analyzed...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367075/anticancer-natural-compounds-as-epigenetic-modulators-of-gene-expression
#11
REVIEW
Edward A Ratovitski
Accumulating evidence shows that hallmarks of cancer include: "genetic and epigenetic alterations leading to inactivation of cancer suppressors, overexpression of oncogenes, deregulation of intracellular signaling cascades, alterations of cancer cell metabolism, failure to undergo cancer cell death, induction of epithelial to mesenchymal transition, invasiveness, metastasis, deregulation of immune response and changes in cancer microenvironment, which underpin cancer development". Natural compounds as bioactive ingredients isolated from natural sources (plants, fungi, marine life forms) have revolutionized the field of anticancer therapeutics and rapid developments in preclinical studies are encouraging...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367074/anti-cancer-phytometabolites-targeting-cancer-stem-cells
#12
REVIEW
Heron F V Torquato, Márcia I Goettert, Giselle Z Justo, Edgar J Paredes-Gamero
Medicinal plants are a plentiful source of bioactive molecules with much structural diversity. In cancer treatment, molecules obtained from plants represent an attractive alternative to other treatments because several plant-derived compounds have exhibited lower toxicity and higher selectivity against cancer cells. In this review, we focus on the possible application of bioactive molecules obtained from plants against more primitive cell populations in cancers, cancer stem cells. Cancer stem cells are present in several kinds of tumors and are responsible for recurrences and metastases...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367073/natural-compounds-as-modulators-of-non-apoptotic-cell-death-in-cancer-cells
#13
Luis Miguel Guamán-Ortiz, Maria Isabel Ramirez Orellana, Edward A Ratovitski
Cell death is an innate capability of cells to be removed from microenvironment, if and when they are damaged by multiple stresses. Cell death is often regulated by multiple molecular pathways and mechanism, including apoptosis, autophagy, and necroptosis. The molecular network underlying these processes is often intertwined and one pathway can dynamically shift to another one acquiring certain protein components, in particular upon treatment with various drugs. The strategy to treat human cancer ultimately relies on the ability of anticancer therapeutics to induce tumor-specific cell death, while leaving normal adjacent cells undamaged...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367072/natural-compounds-as-modulators-of-cell-cycle-arrest-application-for-anticancer-chemotherapies
#14
REVIEW
Natalia Bailon-Moscoso, Gabriela Cevallos-Solorzano, Juan Carlos Romero-Benavides, Maria Isabel Ramirez Orellana
Natural compounds from various plants, microorganisms and marine species play an important role in the discovery novel components that can be successfully used in numerous biomedical applications, including anticancer therapeutics. Since uncontrolled and rapid cell division is a hallmark of cancer, unraveling the molecular mechanisms underlying mitosis is key to understanding how various natural compounds might function as inhibitors of cell cycle progression. A number of natural compounds that inhibit the cell cycle arrest have proven effective for killing cancer cells in vitro, in vivo and in clinical settings...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367071/anticancer-natural-compounds-molecular-mechanisms-and-functions-%C3%A2-part-ii
#15
Edward A Ratovitski
No abstract text is available yet for this article.
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28503092/management-of-gene-variants-of-unknown-significance-analysis-method-and-risk-assessment-of-the-vhl-mutation-p-p81s-c-241c-t
#16
REVIEW
Daniela Alosi, Marie Luise Bisgaard, Sophie Nowak Hemmingsen, Lotte Nylandsted Krogh, Hanne Birte Mikkelsen, Marie Louise Mølgaard Binderup
BACKGROUND: Evaluation of the pathogenicity of a gene variant of unknown significance (VUS) is crucial for molecular diagnosis and genetic counseling, but can be challenging. This is especially so in phenotypically variable diseases, such as von Hippel-Lindau disease (vHL). vHL is caused by germline mutations in the VHL gene, which predispose to the development of multiple tumors such as central nervous system hemangioblastomas and renal cell carcinoma (RCC). OBJECTIVE: We propose a method for the evaluation of VUS pathogenicity through our experience with the VHL missense mutation c...
February 2017: Current Genomics
https://www.readbyqxmd.com/read/28503091/natural-compounds-as-anticancer-agents-targeting-dna-topoisomerases
#17
REVIEW
Chetan Kumar Jain, Hemanta Kumar Majumder, Susanta Roychoudhury
DNA topoisomerases are important cellular enzymes found in almost all types of living cells (eukaryotic and prokaryotic). These enzymes are essential for various DNA metabolic processes e.g. replication, transcription, recombination, chromosomal decatenation etc. These enzymes are important molecular drug targets and inhibitors of these enzymes are widely used as effective anticancer and antibacterial drugs. However, topoisomerase inhibitors have some therapeutic limitations and they exert serious side effects during cancer chemotherapy...
February 2017: Current Genomics
https://www.readbyqxmd.com/read/28503090/compounds-from-celastraceae-targeting-cancer-pathways-and-their-potential-application-in-head-and-neck-squamous-cell-carcinoma-a-review
#18
REVIEW
Camila Hernandes, Ana Maria Soares Pereira, Patricia Severino
Squamous cell carcinoma of the head and neck is one of the most common cancer types worldwide. It initiates on the epithelial lining of the upper aerodigestive tract, at most instances as a consequence of tobacco and alcohol consumption. Treatment options based on conventional therapies or targeted therapies under development have limited efficacy due to multiple genetic alterations typically found in this cancer type. Natural products derived from plants often possess biological activities that may be valuable in the development of new therapeutic agents for cancer treatment...
February 2017: Current Genomics
https://www.readbyqxmd.com/read/28503089/anticancer-chemodiversity-of-ranunculaceae-medicinal-plants-molecular-mechanisms-and-functions
#19
REVIEW
Da-Cheng Hao, Chun-Nian He, Jie Shen, Pei-Gen Xiao
The buttercup family, Ranunculaceae, comprising more than 2,200 species in at least 62 genera, mostly herbs, has long been used in folk medicine and worldwide ethnomedicine since the beginning of human civilization. Various medicinal phytometabolites have been found in Ranunculaceae plants, many of which, such as alkaloids, terpenoids, saponins, and polysaccharides, have shown anti-cancer activities in vitro and in vivo. Most concerns have been raised for two epiphany molecules, the monoterpene thymoquinone and the isoquinoline alkaloid berberine...
February 2017: Current Genomics
https://www.readbyqxmd.com/read/28503088/restoring-trail-induced-apoptosis-using-naturopathy-hercules-joins-hand-with-nature-to-triumph-over-lernaean-hydra
#20
REVIEW
Ammad Ahmad Farooqi, Cosmo Damiano Gadaleta, Girolamo Ranieri, Sundas Fayyaz, Ilaria Marech
Cancer is a multifaceted disease. Our deepened knowledge about genetic and biological mechanisms of cancer cells presents an opportunity to explore the inter-individual differences in the body's ability to metabolize and respond to different nutrients. It is becoming progressively more understandable that the deregulation of several signaling pathways and the alterations in apoptotic response are some of the major determinants that underpin carcinogenesis. Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL)-mediated signaling has gained a remarkable appreciation because of its ability to selectively induce apoptosis in cancer cells leaving normal cells intact...
February 2017: Current Genomics
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