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Genomics, Proteomics & Bioinformatics

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https://www.readbyqxmd.com/read/28813639/exploitation-of-gene-expression-and-cancer-biomarkers-in-paving-the-path-to-era-of-personalized-medicine
#1
REVIEW
Hala Fawzy Mohamed Kamel, Hiba Saeed A Bagader Al-Amodi
Cancer therapy agents have been used extensively as cytotoxic drugs against tissue or organ of a specific type of cancer. With the better understanding of molecular mechanisms underlying carcinogenesis and cellular events during cancer progression and metastasis, it is now possible to use targeted therapy for these molecular events. Targeted therapy is able to identify cancer patients with dissimilar genetic defects at cellular level for the same cancer type and consequently requires individualized approach for treatment...
August 13, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28811232/cyp2a6-polymorphisms-associate-with-outcomes-of-s-1-plus-oxaliplatin-chemotherapy-in-chinese-gastric-cancer-patients
#2
LETTER
Lin Yang, Shanshan Zou, Chang Shu, Yan Song, Yong-Kun Sun, Wen Zhang, Aiping Zhou, Xinghua Yuan, Yi Yang, Songnian Hu
Gastric carcinomaisaheterogeneous malignant disease involving genetic factors. To identify predictive markers for gastric cancer treatment in Chinese patients, we evaluated the association between polymorphisms of the gene encoding cytochrome P450 2A6 (CYP2A6) and outcomes of S-1 plus oxaliplatin (SOX) chemotherapy treatment. Clinical data on 60 consecutive gastric cancer patients receiving SOX regimen were collected prospectively. We sequenced all exons of CYP2A6 and a total of 22 different polymorphisms were detected in the present study...
August 12, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28811231/a-step-forward-in-precision-medicine-on-one-belt-one-road
#3
EDITORIAL
Jun Yu
No abstract text is available yet for this article.
August 12, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28797870/future-strategies-on-glioma-research-from-big-data-to-the-clinic
#4
Hang Cao, Feiyifan Wang, Xue-Jun Li
No abstract text is available yet for this article.
August 7, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28642113/paralog-divergent-features-may-help-reduce-off-target-effects-of-drugs-hints-from-glucagon-subfamily-analysis
#5
Zhining Sa, Jingqi Zhou, Yangyun Zou, Zhixi Su, Xun Gu
Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures and drug-binding pockets. To identify targetable differences between paralogs, we analyzed two types (type-I and type-II) of functional divergence between two paralogs in the known target protein receptor family G-protein coupled receptors (GPCRs) at the amino acid level. Paralogous protein receptors in glucagon-like subfamily, glucagon receptor (GCGR) and glucagon-like peptide-1 receptor (GLP-1R), exhibit divergence in ligands and are clinically validated drug targets for type 2 diabetes...
June 19, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28602845/silencing-of-transposable-elements-by-pirnas-in-drosophila-an-evolutionary-perspective
#6
REVIEW
Shiqi Luo, Jian Lu
Transposable elements (TEs) are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated biological processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level...
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28602844/primate-specific-long-non-coding-rnas-and-micrornas
#7
REVIEW
Hassaan Mehboob Awan, Abdullah Shah, Farooq Rashid, Ge Shan
Non-coding RNAs (ncRNAs) are critical regulators of gene expression in essentially all life forms. Long ncRNAs (lncRNAs) and microRNAs (miRNAs) are two important RNA classes possessing regulatory functions. Up to date, many primate-specific ncRNAs have been identified and investigated. Their expression specificity to primate lineage suggests primate-specific roles. It is thus critical to elucidate the biological significance of primate or even human-specific ncRNAs, and to develop potential ncRNA-based therapeutics...
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28602785/downregulation-of-mir-503-promotes-escc-cell-proliferation-migration-and-invasion-by-targeting-cyclin-d1
#8
Lanfang Jiang, Zitong Zhao, Leilei Zheng, Liyan Xue, Qimin Zhan, Yongmei Song
Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive cancers in China, but the underlying molecular mechanism of ESCC is still unclear. Involvement of microRNAs has been demonstrated in cancer initiation and progression. Despite the reported function of miR-503 in several human cancers, its detailed anti-oncogenic role and clinical significance in ESCC remain undefined. In this study, we examined miR-503 expression by qPCR and found the downregulation of miR-503 expression in ESCC tissue relative to adjacent normal tissues...
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28599852/non-coding-transcripts-from-enhancers-new-insights-into-enhancer-activity-and-gene-expression-regulation
#9
REVIEW
Hongjun Chen, Guangshi Du, Xu Song, Ling Li
Long non-coding RNAs (lncRNAs) have gained widespread interest in the past decade owing to their enormous amount and surprising functions implicated in a variety of biological processes. Some lncRNAs exert function as enhancers, i.e., activating gene transcription by serving as the cis-regulatory molecules. Furthermore, recent studies have demonstrated that many enhancer elements can be transcribed and produce RNA molecules, which are termed as enhancer RNAs (eRNAs). The eRNAs are not merely the by-product of the enhancer transcription...
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28533025/enhancer-derived-rna-a-primer
#10
REVIEW
Feng Liu
Enhancer-derived RNAs (eRNAs) are a group of RNAs transcribed by RNA polymerase II from the domain of transcription enhancers, a major type of cis-regulatory elements in the genome. The correlation between eRNA production and enhancer activity has stimulated studies on the potential role of eRNAs in transcriptional regulation. Additionally, eRNA has also served as a marker for global identification of enhancers. Here I review the brief history and fascinating properties of eRNAs.
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28533024/epitranscriptomics-toward-a-better-understanding-of-rna-modifications
#11
Xushen Xiong, Chengqi Yi, Jinying Peng
No abstract text is available yet for this article.
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28533023/the-rna-modification-n-6-methyladenosine-and-its-implications-in-human-disease
#12
REVIEW
Pedro J Batista
Impaired gene regulation lies at the heart of many disorders, including developmental diseases and cancer. Furthermore, the molecular pathways that control gene expression are often the target of cellular parasites, such as viruses. Gene expression is controlled through multiple mechanisms that are coordinated to ensure the proper and timely expression of each gene. Many of these mechanisms target the life cycle of the RNA molecule, from transcription to translation. Recently, another layer of regulation at the RNA level involving RNA modifications has gained renewed interest of the scientific community...
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28529100/transcriptional-and-post-transcriptional-gene-regulation-by-long-non-coding-rna
#13
REVIEW
Iain M Dykes, Costanza Emanueli
Advances in genomics technology over recent years have led to the surprising discovery that the genome is far more pervasively transcribed than was previously appreciated. Much of the newly-discovered transcriptome appears to represent long non-coding RNA (lncRNA), a heterogeneous group of largely uncharacterised transcripts. Understanding the biological function of these molecules represents a major challenge and in this review we discuss some of the progress made to date. One major theme of lncRNA biology seems to be the existence of a network of interactions with microRNA (miRNA) pathways...
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28549934/in-vitro-metabolomic-approaches-to-investigating-the-potential-biological-effects-of-phenolic-compounds-an-update
#14
REVIEW
Úrsula Catalán, Laura Barrubés, Rosa Maria Valls, Rosa Solà, Laura Rubió
Dietary phenolic compounds (PCs) have been receiving interest for their presumed roles in disease prevention. However, there is a lack of studies on the underlying molecular mechanisms. In this regard, in vitro metabolomic approaches are suitable for the investigation of the molecular changes in response to PC exposure. Up to date, the biological effects of PCs have only been examined for PCs from rosemary (Rosmarinus officinalis), olive oil, and resveratrol using cell-based metabolomic approach, although transcriptomic and/or proteomic studies have also been conducted in the same in vitro cell experiment in some cases...
May 23, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28392481/protein-array-based-approaches-for-biomarker-discovery-in-cancer
#15
REVIEW
Yi Huang, Heng Zhu
Biomarkers are deemed to be potential tools in early diagnosis, therapeutic monitoring, and prognosis evaluation for cancer, with simplicity as well as economic advantages compared with computed tomography and biopsy. However, most of the current cancer biomarkers present insufficient sensitivity as well as specificity. Therefore, there is urgent requirement for the discovery of biomarkers for cancer. As one of the most exciting emerging technologies, protein array provides a versatile and robust platform in cancer proteomics research because it shows tremendous advantages of miniaturized features, high throughput, and sensitive detections in last decades...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28392480/network-analysis-reveals-a-signaling-regulatory-loop-in-the-pik3ca-mutated-breast-cancer-predicting-survival-outcome
#16
Shauna R McGee, Chabane Tibiche, Mark Trifiro, Edwin Wang
Mutated genes are rarely common even in the same pathological type between cancer patients and as such, it has been very challenging to interpret genome sequencing data and difficult to predict clinical outcomes. PIK3CA is one of a few genes whose mutations are relatively popular in tumors. For example, more than 46.6% of luminal-A breast cancer samples have PIK3CA mutated, whereas only 35.5% of all breast cancer samples contain PIK3CA mutations. To understand the function of PIK3CA mutations in luminal A breast cancer, we applied our recently-proposed Cancer Hallmark Network Framework to investigate the network motifs in the PIK3CA-mutated luminal A tumors...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28392479/circulating-tumor-dna-as-biomarkers-for-cancer-detection
#17
REVIEW
Xiao Han, Junyun Wang, Yingli Sun
Detection of circulating tumor DNAs (ctDNAs) in cancer patients is an important component of cancer precision medicine ctDNAs. Compared to the traditional physical and biochemical methods, blood-based ctDNA detection offers a non-invasive and easily accessible way for cancer diagnosis, prognostic determination, and guidance for treatment. While studies on this topic are currently underway, clinical translation of ctDNA detection in various types of cancers has been attracting much attention, due to the great potential of ctDNA as blood-based biomarkers for early diagnosis and treatment of cancers...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28392478/disease-biomarkers-for-precision-medicine-challenges-and-future-opportunities
#18
EDITORIAL
Edwin Wang, William C S Cho, S C Cesar Wong, Siqi Liu
No abstract text is available yet for this article.
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28392477/lirex-a-package-for-identification-of-long-inverted-repeats-in-genomes
#19
Yong Wang, Jiao-Mei Huang
Long inverted repeats (LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is highly complicated when mismatches and indels between the repeats are permitted. Long inverted repeat explorer (Lirex) was developed and introduced in this report. Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28391009/the-promise-of-pharmacogenomics-in-reducing-toxicity-during-acute-lymphoblastic-leukemia-maintenance-treatment
#20
REVIEW
Shoshana Rudin, Marcus Marable, R Stephanie Huang
Pediatric acute lymphoblastic leukemia (ALL) affects a substantial number of children every year and requires a long and rigorous course of chemotherapy treatments in three stages, with the longest phase, the maintenance phase, lasting 2-3years. While the primary drugs used in the maintenance phase, 6-mercaptopurine (6-MP) and methotrexate (MTX), are necessary for decreasing risk of relapse, they also have potentially serious toxicities, including myelosuppression, which may be life-threatening, and gastrointestinal toxicity...
April 2017: Genomics, Proteomics & Bioinformatics
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