Array-based approaches for the identification of epigenetic silenced tumor suppressor genes.

Abstract:

:Carcinogenesis involves the inactivation or inhibition of genes that function as tumor suppressors. Deletions, mutations, or epigenetic silencing of tumor suppressor genes can lead to altered growth, differentiation, and apoptosis. DNA methylation and histone modifications are important epigenetic mechanisms of gene regulation and play essential roles both independently and cooperatively in tumor initiation and progression. Realization that many tumor suppressor genes are silenced by epigenetic mechanisms has stimulated discovery of novel tumor suppressor genes. One of the most useful of these approaches is an epigenetic reactivation screening strategy that combines treatment of cancer cells in vitro with DNA methyltransferase and/or histone deacetylase (HDAC) inhibitors, followed by global gene expression analysis using microarrays, to identify upregulated genes. This approach is most effective when complemented by microarray analyses to identify genes repressed in primary tumors. Recently, using cancer cell lines treated with a DNA methylation inhibitor and/or a HDAC inhibitor in conjunction with cDNA microarray analysis, candidate tumor suppressor genes, which are subject to epigenetic silencing, have been identified in endometrial, colorectal, esophageal, and pancreatic cancers. An increasing number of studies have utilized epigenetic reactivation screening to discover novel tumor suppressor genes in cancer. The results of some of the most recent studies are highlighted in this review.

journal_name

Curr Genomics

journal_title

Current genomics

authors

Takai N,Narahara H

doi

10.2174/138920208783884892

subject

Has Abstract

pub_date

2008-03-01 00:00:00

pages

22-4

issue

1

eissn

1389-2029

issn

1875-5488

journal_volume

9

pub_type

杂志文章
  • Alström syndrome: genetics and clinical overview.

    abstract::Alström syndrome is a rare autosomal recessive genetic disorder characterized by cone-rod dystrophy, hearing loss, childhood truncal obesity, insulin resistance and hyperinsulinemia, type 2 diabetes, hypertriglyceridemia, short stature in adulthood, cardiomyopathy, and progressive pulmonary, hepatic, and renal dysfunc...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920211795677912

    authors: Marshall JD,Maffei P,Collin GB,Naggert JK

    更新日期:2011-05-01 00:00:00

  • Crosstalk Between DNA and Histones: Tet's New Role in Embryonic Stem Cells.

    abstract::Embryonic stem (ES) cells are characterized by the expression of an extensive and interconnected network of pluripotency factors which are downregulated in specialized cells. Epigenetic mechanisms, including DNA methylation and histone modifications, are also important in maintaining this pluripotency program in ES ce...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920212803759730

    authors: Sui X,Price C,Li Z,Chen J

    更新日期:2012-12-01 00:00:00

  • Genetic variants in diseases of the extrapyramidal system.

    abstract::Knowledge on the genetics of movement disorders has advanced significantly in recent years. It is now recognized that disorders of the basal ganglia have genetic basis and it is suggested that molecular genetic data will provide clues to the pathophysiology of normal and abnormal motor control. Progress in molecular g...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202914666131210213327

    authors: Oczkowska A,Kozubski W,Lianeri M,Dorszewska J

    更新日期:2014-02-01 00:00:00

  • Vegetable Oil: Nutritional and Industrial Perspective.

    abstract::Oils of plant origin have been predominantly used for food-based applications. Plant oils not only represent a non-polluting renewable resource but also provide a wide diversity in fatty acids (FAs) composition with diverse applications. Besides being edible, they are now increasingly being used in industrial applicat...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202917666160202220107

    authors: Kumar A,Sharma A,Upadhyaya KC

    更新日期:2016-06-01 00:00:00

  • Antigenic Differences Between Normal and Malignant Cells as a Basis for Treatment of Intracerebral Neoplasms Using a DNA-Based Vaccine.

    abstract::Antigenic differences between normal and malignant cells of the cancer patient form the rationale for clinical immunotherapeutic strategies. Because the antigenic phenotype of neoplastic cells varies widely among different cells within the same malignant cell-population, immunization with a vaccine that stimulates imm...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920206778426951

    authors: Lichtor T,Glick RP,O-Sullivan I,Cohen EP

    更新日期:2006-06-01 00:00:00

  • Metabolic Modeling of Microbial Community Interactions for Health, Environmental and Biotechnological Applications.

    abstract::In nature, microbes do not exist in isolation but co-exist in a variety of ecological and biological environments and on various host organisms. Due to their close proximity, these microbes interact among themselves, and also with the hosts in both positive and negative manners. Moreover, these interactions may modula...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202919666180911144055

    authors: Ang KS,Lakshmanan M,Lee NR,Lee DY

    更新日期:2018-12-01 00:00:00

  • A graphical weighted power improving multiplicity correction approach for SNP selections.

    abstract::Controlling for the multiplicity effect is an essential part of determining statistical significance in large-scale single-locus association genome scans on Single Nucleotide Polymorphisms (SNPs). Bonferroni adjustment is a commonly used approach due to its simplicity, but is conservative and has low power for large-s...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920291505141106103959

    authors: Saunders G,Fu G,Stevens JR

    更新日期:2014-10-01 00:00:00

  • Analytical Models For Genetics of Human Traits Influenced By Sex.

    abstract::Analytical models usually assume an additive sex effect by treating it as a covariate to identify genetic associations with sex-influenced traits. Their underlying assumptions are violated by ignoring interactions of sex with genetic factors and heterogeneous genetic effects by sex. Methods to deal with the problems a...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202917666160420142601

    authors: Lee C

    更新日期:2015-10-01 00:00:00

  • WITMSG: Large-scale Prediction of Human Intronic m6A RNA Methylation Sites from Sequence and Genomic Features.

    abstract:Introduction:N6-methyladenosine (m6A) is one of the most widely studied epigenetic modifications. It plays important roles in various biological processes, such as splicing, RNA localization and degradation, many of which are related to the functions of introns. Although a number of computational approaches have been p...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202921666200211104140

    authors: Liu L,Lei X,Meng J,Wei Z

    更新日期:2020-01-01 00:00:00

  • NeuroArray, A Custom CGH Microarray to Decipher Copy Number Variants in Alzheimer's Disease.

    abstract:Background:Copy Number Variants (CNVs) represent a prevailing type of structural variation (deletions or duplications) in the human genome. In the last few years, several studies have demonstrated that CNVs represent significant mutations in Alzheimer's Disease (AD) hereditability. Currently, innovative high-throughput...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202919666180122141425

    authors: Cuccaro D,Guarnaccia M,Iemmolo R,D'Agata V,Cavallaro S

    更新日期:2018-09-01 00:00:00

  • A Systematic In-silico Analysis of Helicobacter pylori Pathogenic Islands for Identification of Novel Drug Target Candidates.

    abstract:BACKGROUND:Helicobacter pylori is associated with inflammation of different areas, such as the duodenum and stomach, causing gastritis and gastric ulcers leading to lymphoma and cancer. Pathogenic islands are a type of clustered mobile elements ranging from 10-200 Kb contributing to the virulence of the respective path...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202918666170705160615

    authors: Nammi D,Yarla NS,Chubarev VN,Tarasov VV,Barreto GE,Pasupulati AMC,Aliev G,Neelapu NRR

    更新日期:2017-10-01 00:00:00

  • DNA instability at chromosomal fragile sites in cancer.

    abstract::Human chromosomal fragile sites are specific genomic regions which exhibit gaps or breaks on metaphase chromosomes following conditions of partial replication stress. Fragile sites often coincide with genes that are frequently rearranged or deleted in human cancers, with over half of cancer-specific translocations con...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920210791616699

    authors: Dillon LW,Burrow AA,Wang YH

    更新日期:2010-08-01 00:00:00

  • MicroRNAs in Lung Cancer Oncogenesis and Tumor Suppression: How it Can Improve the Clinical Practice?

    abstract:Background:Lung cancer (LC) development is a process that depends on genetic mutations. The DNA methylation, an important epigenetic modification, is associated with the expression of non-coding RNAs, such as microRNAs. MicroRNAs are particularly essential for cell physiology, since they play a critical role in tumor s...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202921999200630144712

    authors: Pozza DH,De Mello RA,Araujo RLC,Velcheti V

    更新日期:2020-08-01 00:00:00

  • Clinical and Rehabilitative Management of Retinitis Pigmentosa: Up-to-Date.

    abstract::The term retinitis pigmentosa (RP) indicates a heterogeneous group of genetic rare ocular diseases in which either rods or cones are prevalently damaged. RP represents the most common hereditary cause of blindness in people from 20 to 60 years old. In general, the different RP forms consist of progressive photo-recept...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920211795860125

    authors: Parmeggiani F,Sato G,De Nadai K,Romano MR,Binotto A,Costagliola C

    更新日期:2011-06-01 00:00:00

  • Single-cell RNA Sequencing: In-depth Decoding of Heart Biology and Cardiovascular Diseases.

    abstract:Background:The cardiac system is a combination of a complex structure, various cells, and versatile specified functions and sophisticated regulatory mechanisms. Moreover, cardiac diseases that encompass a wide range of endogenous conditions, remain a serious health burden worldwide. Recent genome-wide profiling techniq...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202921999200604123914

    authors: Chen Z,Wei L,Duru F,Chen L

    更新日期:2020-12-01 00:00:00

  • Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling.

    abstract::RNA-Seq is a recently developed sequencing technology, that through the analysis of cDNA allows for unique insights into the transcriptome of a cell. The data generated by RNA-Seq provides information on gene expression, alternative splicing events and the presence of non-coding RNAs. It has been realised non-coding R...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202911314030003

    authors: Mills JD,Kawahara Y,Janitz M

    更新日期:2013-05-01 00:00:00

  • EGFR Intron Recombination in Human Gliomas: Inappropriate Diversion of V(D)J Recombination?

    abstract::The epidermal growth factor receptor (EGFR) is a membrane-bound, 170 kDa, protein tyrosine kinase that plays an important role in tumorigenesis. The EGFR gene, which is composed of over 168 kb of sequence, including a 123-kb first intron, is frequently amplified and rearranged in malignant gliomas leading to the expre...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920207780833838

    authors: Fenstermaker RA,Ciesielski MJ

    更新日期:2007-05-01 00:00:00

  • Compounds From Celastraceae Targeting Cancer Pathways and Their Potential Application in Head and Neck Squamous Cell Carcinoma: A Review.

    abstract::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 dev...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202917666160803160934

    authors: Hernandes C,Pereira AMS,Severino P

    更新日期:2017-02-01 00:00:00

  • A general quantitative genetic model for haplotyping a complex trait in humans.

    abstract::Uncertainty about linkage phases of multiple single nucleotide polymorphisms (SNPs) in heterozygous diploids challenges the identification of specific DNA sequence variants that encode a complex trait. A statistical technique implemented with the EM algorithm has been developed to infer the effects of SNP haplotypes f...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920207782446179

    authors: Wu S,Yang J,Wang C,Wu R

    更新日期:2007-08-01 00:00:00

  • Mechano-regulation of alternative splicing.

    abstract::Alternative splicing contributes to the complexity of proteome by producing multiple mRNAs from a single gene. Affymetrix exon arrays and experiments in vivo or in vitro demonstrated that alternative splicing was regulated by mechanical stress. Expression of mechano-growth factor (MGF) which is the splicing isoform of...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920213804999156

    authors: Liu H,Tang L

    更新日期:2013-03-01 00:00:00

  • Prostate Cancer Gene Regulatory Network Inferred from RNA-Seq Data.

    abstract:Background:Cancer is a complex disease with a lucid etiology and in understanding the causation, we need to appreciate this complexity. Objective:Here we are aiming to gain insights into the genetic associations of prostate cancer through a network-based systems approach using the BC3Net algorithm. Methods:Specifical...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202919666181107122005

    authors: Moore D,Simoes RM,Dehmer M,Emmert-Streib F

    更新日期:2019-01-01 00:00:00

  • MicroRNA and Cancer: Tiny Molecules with Major Implications.

    abstract::Cancer is currently a major public health problem and, as such, emerging research is making significant progress in identifying major players in its biology. One recent topic of interest involves microRNAs (miRNAs) which are small, non-coding RNA molecules that inhibit gene expression post-transcriptionally. They acco...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920208784139555

    authors: Vandenboom Ii TG,Li Y,Philip PA,Sarkar FH

    更新日期:2008-04-01 00:00:00

  • Do mtDNA Mutations Participate in the Pathogenesis of Sporadic Parkinson's Disease?

    abstract::The pathogenesis of sporadic Parkinson's disease (PD) remains enigmatic. Mitochondrial complex-I defects are known to occur in the substantia nigra (SN) of PD patients and are also debated in some extracerebral tissues. Early sequencing efforts of the mitochondrial DNA (mtDNA) did not reveal specific mutations, but a ...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920209789503879

    authors: Kirches E

    更新日期:2009-12-01 00:00:00

  • Overview of Genomic Tools for Circular Visualization in the Next-generation Genomic Sequencing Era.

    abstract::After human genome sequencing and rapid changes in genome sequencing methods, we have entered into the era of rapidly accumulating genome-sequencing data. This has derived the development of several types of methods for representing results of genome sequencing data. Circular genome visual-ization tools are also criti...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202920666190314092044

    authors: Parveen A,Khurana S,Kumar A

    更新日期:2019-02-01 00:00:00

  • Integrated analysis of transcriptomic and proteomic data.

    abstract::Until recently, understanding the regulatory behavior of cells has been pursued through independent analysis of the transcriptome or the proteome. Based on the central dogma, it was generally assumed that there exist a direct correspondence between mRNA transcripts and generated protein expressions. However, recent st...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202911314020003

    authors: Haider S,Pal R

    更新日期:2013-04-01 00:00:00

  • miR-15b and miR-21 as Circulating Biomarkers for Diagnosis of Glioma.

    abstract::Malignant gliomas are lethal primary intracranial tumors. To date, little information on the role of deregulated genes in gliomas have been identified. As the involvement of miRNAs in the carcinogenesis is well known, we carried out a pilot study to identify, as potential biomarkers, differentially expressed microRNAs...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202916666150707155610

    authors: Ivo D'Urso P,Fernando D'Urso O,Damiano Gianfreda C,Mezzolla V,Storelli C,Marsigliante S

    更新日期:2015-10-01 00:00:00

  • The Relation Between Promoter Chromatin Status, Xyr1 and Cellulase Ex-pression in Trichoderma reesei.

    abstract::The ascomycete Trichoderma reesei is used for the production of plant cell wall-degrading enzymes in industrial scale. The interplay of the transactivator Xyr1 and the repressor Cre1 mainly regulates the expression of these enzymes. During induc-ing conditions, such as in the presence of sophorose, the transcription o...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202917666151116211812

    authors: Mello-de-Sousa TM,Rassinger A,Derntl C,Poças-Fonseca MJ,Mach RL,Mach-Aigner AR

    更新日期:2016-04-01 00:00:00

  • Molecular Population Genetics and Evolution of the Chagas' Disease Vector Triatoma infestans (Hemiptera: Reduviidae).

    abstract::Triatoma infestans (Klug) is the main vector of Chagas' disease in the Southern Cone of Latin America between the latitudes 10° S and 46° S. The long-term effectiveness of the control campaigns is greatly dependent upon the vector population structure. Mitochondrial DNA (mtDNA) genes have been used in a number of T. i...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/13892029113149990006

    authors: García BA,de Rosas AR,Blariza MJ,Grosso CG,Fernández CJ,Stroppa MM

    更新日期:2013-08-01 00:00:00

  • A Comprehensive Review of Dysregulated miRNAs Involved in Cervical Cancer.

    abstract::MicroRNAs(miRNAs) have become the center of interest in oncology. In recent years, various studies have demonstrated that miRNAs regulate gene expression by influencing important regulatory genes and thus are responsible for causing cervical cancer. Cervical cancer being the third most diagnosed cancer among the femal...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202915666140528003249

    authors: Sharma G,Dua P,Agarwal SM

    更新日期:2014-08-01 00:00:00

  • The Genetics of Papillary Microcarcinomas of the Thyroid: Diagnostic and Prognostic Implications.

    abstract::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 clin...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202918666170105094459

    authors: Rodrigues AC,Penna G,Rodrigues E,Castro P,Sobrinho-Simões M,Soares P

    更新日期:2017-06-01 00:00:00