Use of Representational Difference Analysis and cDNA Arrays for Transcriptional Profiling of Tumor Tissue

Frohme, Marcus; Scharm, B; Delius, Hajo; Knecht, Rainald; Hoheisel, Jörg D.

doi:10.1111/j.1749-6632.2000.tb06703.x

Cited by 20 publications

(8 citation statements)

References 40 publications

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“…rs16901966 (region 2), rs11986220 (region 1) at 8q24 on chromosome 8 were verified to have consistent associations in various populations [ 18 , 27 , 33 , 34 , 35 ]. rs1983891 is located in FOXP4, which belongs to subfamily P of the forkhead box (FOX) transcription factor family, and is associated with kidney tumors, larynx carcinoma, and breast tumors [ 36 , 37 , 38 ]. At present, the potential role for FOXP4 in prostate tumorigenesis has not been determined.…”

Section: Discussionmentioning

confidence: 99%

The Cumulative Effect of Gene-Gene and Gene-Environment Interactions on the Risk of Prostate Cancer in Chinese Men

Liu

Shi

Yang

et al. 2016

IJERPH

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Prostate cancer (PCa) is a multifactorial disease involving complex genetic and environmental factors interactions. Gene-gene and gene-environment interactions associated with PCa in Chinese men are less studied. We explored the association between 36 SNPs and PCa in 574 subjects from northern China. Body mass index (BMI), smoking, and alcohol consumption were determined through self-administered questionnaires in 134 PCa patients. Then gene-gene and gene-environment interactions among the PCa-associated SNPs were analyzed using the generalized multifactor dimensionality reduction (GMDR) and logistic regression methods. Allelic and genotypic association analyses showed that six variants were associated with PCa and the cumulative effect suggested men who carried any combination of 1, 2, or ≥3 risk genotypes had a gradually increased PCa risk (odds ratios (ORs) = 1.79–4.41). GMDR analysis identified the best gene-gene interaction model with scores of 10 for both the cross-validation consistency and sign tests. For gene-environment interactions, rs6983561 CC and rs16901966 GG in individuals with a BMI ≥ 28 had ORs of 7.66 (p = 0.032) and 5.33 (p = 0.046), respectively. rs7679673 CC + CA and rs12653946 TT in individuals that smoked had ORs of 2.77 (p = 0.007) and 3.11 (p = 0.024), respectively. rs7679673 CC in individuals that consumed alcohol had an OR of 4.37 (p = 0.041). These results suggest that polymorphisms, either individually or by interacting with other genes or environmental factors, contribute to an increased risk of PCa.

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Section: Discussionmentioning

confidence: 99%

The Cumulative Effect of Gene-Gene and Gene-Environment Interactions on the Risk of Prostate Cancer in Chinese Men

Liu

Shi

Yang

et al. 2016

IJERPH

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“…Its advantages and limitations are well known [Hubank and Schatz, 1999;Chang, 2002]. Before DNA arrays were widely available, several labs used RDA to generate a library of clones that were subsequently arrayed onto nylon membranes and used for comparisons of normal and tumor tissues Welford et al, 1998;Frohme et al, 2000;Ismail et al, 2000]. For our purposes, RDA was attractive because target sequences are amplified by PCR with universal adapters annealed to every one of the digested fragments of DNA.…”

Section: Gene Expression and Discovery By Rdamentioning

confidence: 99%

New Chondrocyte Genes Discovered by Representational Difference Analysis of Chondroinduced Human Fibroblasts

Yates¹,

Forbes²,

Glowacki³

2004

Cells Tissues Organs

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This report includes a review of the potential for gene expression analyses to provide new information for solving problems in skeletal repair and regeneration. It focuses on two approaches: high-throughput gene array methods and representational difference analysis (RDA). The principles underlying these methods are presented with experimental tutorials and some applications. Second, this report includes a review of results from applying both approaches to an in vitro model of postnatal chondroinduction by demineralized bone powder (DBP). Human dermal fibroblasts (hDFs) cultured with DBP acquire a chondroblast phenotype and express cartilage-specific matrix proteins after 7 days. We used cDNA macroarrays and RDA to identify the genes that were altered prior to expression of the chondroblast phenotype, i.e., after only 3 days’ culture with DBP. Using a strategy of data management and reduction based upon biological functions, we reported several functional families of genes (cytoskeletal elements, protein synthesis/trafficking, and matrix molecules and their modifiers) that are upregulated during chondroinduction of hDFs. Together with histological and biochemical evidence of the chondroblast phenotype, the gene expression patterns indicate that there are specific stages of induced chondrocyte differentiation in this experimental system. Third, this report includes a new study, in which DBP-regulated genes were used as a data base to derive new information on the cell biology of chondrocytes. The objective was to determine whether a set of genes expressed during induction of chondrocyte differentiation is also expressed by mature articular chondrocytes. Our search of the literature for 59 of the DBP-regulated genes disclosed that expression of 20 of them (33%) had been documented in mature cartilage or chondrocytes. Of the 39 genes not previously documented in cartilage, 11 were tested by RT-PCR and all were found to be expressed in freshly isolated adult human chondrocytes. This review and these new data show how the strategy of high-throughput methods and functional data reduction can expand our knowledge of chondrocyte cell biology.

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“…Contrary to DDRT-PCR analysis, the cDNA-RDA method was infrequently used in plant functional genomics. Nevertheless, there are numerous positive reports from human genomics (Frohme et al, 2000;Yoon et al, 2001;Simkhovich et al, 2003) and rare examples from plants The increased tester-to-driver ratios are indicated. dp1, Homogeneous product of Karat/rhl1.a root transcriptome differentiation.…”

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confidence: 99%

Molecular Cloning and Characterization of β-Expansin Gene Related to Root Hair Formation in Barley

2006

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Root hairs are specialized epidermal cells that play a role in the uptake of water and nutrients from the rhizosphere and serve as a site of interaction with soil microorganisms. The process of root hair formation is well characterized in Arabidopsis (Arabidopsis thaliana); however, there is a very little information about the genetic and molecular basis of root hair development in monocots. Here, we report on isolation and cloning of the b-expansin (EXPB) gene HvEXPB1, tightly related to root hair initiation in barley (Hordeum vulgare). Using root transcriptome differentiation in the wild-type/root-hairless mutant system, a cDNA fragment present in roots of wild-type plants only was identified. After cloning of full-length cDNA and genomic sequences flanking the identified fragment, the subsequent bioinformatics analyses revealed homology of the protein coded by the identified gene to the EXPB family. Reverse transcription-PCR showed that expression of HvEXPB1 cosegregated with the root hair phenotype in F 2 progeny of the cross between the hairless mutant rhl1.a and the wild-type Karat parent variety. Expression of the HvEXPB1 gene was root specific; it was expressed in roots of wild-type forms, but not in coleoptiles, leaves, tillers, and spikes. The identified gene was active in roots of two other analyzed root hair mutants: rhp1.a developing root hair primordia only and rhs1.a with very short root hairs. Contrary to this, a complete lack of HvEXPB1 expression was observed in roots of the spontaneous root-hairless mutant bald root barley. All these observations suggest a role of the HvEXPB1 gene in the process of root hair formation in barley.

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Use of Representational Difference Analysis and cDNA Arrays for Transcriptional Profiling of Tumor Tissue

Cited by 20 publications

References 40 publications

The Cumulative Effect of Gene-Gene and Gene-Environment Interactions on the Risk of Prostate Cancer in Chinese Men

The Cumulative Effect of Gene-Gene and Gene-Environment Interactions on the Risk of Prostate Cancer in Chinese Men

New Chondrocyte Genes Discovered by Representational Difference Analysis of Chondroinduced Human Fibroblasts

Molecular Cloning and Characterization of β-Expansin Gene Related to Root Hair Formation in Barley

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