Identification of genes differentially over-expressed in lung squamous cell carcinoma using combination of cDNA subtraction and microarray analysis

Wang, Tongtong; Hopkins, Deborah A.; Schmidt, Cecilia; Silva, Sandra; Houghton, Raymond L.; Takita, Hiroshi; Repasky, Elizabeth; Reed, Steven G.

doi:10.1038/sj.onc.1203457

Cited by 93 publications

(64 citation statements)

References 27 publications

(21 reference statements)

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“…In this context, there are numerous studies of the use of disease profiles in tumours of clinically relevant subgroups, including the brain (Sallinen et al, 2000), oesophagus (Lu et al, 2001), lung (Wang et al, 2000), . We recently developed an in-house cDNA microarray derived from our oligocapped human cDNA library prepared from noncancerous and cancerous tongue tissues, and oral cancer cell lines (Moriya et al, 2003).…”

Section: Discussionmentioning

confidence: 99%

Aberrant expression of RAB1A in human tongue cancer

et al. 2005

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This study was designed to identify specific gene expression changes in tongue squamous cell carcinomas (TSCCs) compared with normal tissues using in-house cDNA microarray that comprised of 2304 full-length cDNAs from a cDNA library prepared from normal oral tissues, primary oral cancers, and oral cancer cell lines. The genes identified by our microarray system were further analysed at the mRNA or protein expression level in a series of clinical samples by real-time quantitative reverse transcriptasepolymerase chain reaction (qRT -PCR) analysis and imuunohositochemistry. The microarray analysis identified a total of 16 genes that were significantly upregulated in common among four TSCC specimens. Consistent with the results of the microarray, increased mRNA levels of selected genes with known molecular functions were found in the four TSCCs. Among genes identified, Rab1a, a member of the Ras oncogene family, was further analysed for its protein expression in 54 TSCCs and 13 premalignant lesions. We found a high prevalence of Rab1A-overexpression not only in TSCCs (98%) but also in premalignant lesions (93%). Thus, our results suggest that rapid characterisation of the target gene(s) for TSCCs can be accomplished using our in-house cDNA microarray analysis combined with the qRT -PCR and immunohistochemistry, and that the Rab1A is a potential biomarker of tongue carcinogenesis.

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Section: Discussionmentioning

confidence: 99%

Aberrant expression of RAB1A in human tongue cancer

et al. 2005

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“…5,6 By using cDNA library subtraction and large-scale DNA screening techniques, the IMP3 gene has been found to be expressed in pancreatic and lung carcinomas. 7,8 The IMP3 protein consists of 580 amino-acid residues and is encoded by a 4350-nucleotide mRNA transcript. The IMP3 gene is located on chromosome 7p11.5.…”

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confidence: 99%

IMP3 is a novel biomarker for adenocarcinoma in situ of the uterine cervix: an immunohistochemical study in comparison with p16INK4a expression

et al. 2007

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Adenocarcinoma in situ of the uterine cervix remains a diagnostic challenge in a small proportion of cases. This suggests a need for biomarker that may be of help in establishing the diagnosis. The aim of this study was to evaluate the potential of insulin-like growth factor-II mRNA-binding protein 3 and cyclin-dependent kinase inhibitor p16 INK4a as biomarkers for adenocarcinoma in situ. Forty-four samples of adenocarcinoma in situ from 40 patients and 23 control cases of benign uterine cervix were included in this study. In addition to benign endocervical epithelium, 19 of these 23 control cases also showed focal tubal metaplasia. Cytoplasmic immunoreactivity for insulin-like growth factor-II mRNA-binding protein 3 was identified in 41 (93%) adenocarcinoma in situ samples, among which, 29 (71%), 10 (24%), and 2 (5%) samples showed insulin-like growth factor-II mRNA-binding protein 3 positive staining in 50% or more, 45 to o50 and o5% of adenocarcinoma in situ lesional cells, respectively. Immunohistochemical reaction intensity for insulin-like growth factor-II mRNA-binding protein 3 was found to be strong in 34 adenocarcinoma in situ samples, intermediate in five, and weak in two. All 23 control cases were negative for insulin-like growth factor-II mRNAbinding protein 3. p16 INK4a expression was identified in all of the adenocarcinoma in situ samples with intermediate staining intensity seen in seven samples and strong in the remainder. Fourteen of 19 (74%) tubal metaplasia cases showed p16 INK4a immunoreactivity in 450% of the tubal metaplastic epithelium with staining intensity ranging from weak to strong. Our findings demonstrate significant expression of insulin-like growth factor-II mRNA-binding protein 3 and p16 INK4a in adenocarcinoma in situ as compared to benign endocervical glands, suggesting that expression of these biomarkers may be helpful in the distinction of adenocarcinoma in situ from benign endocervical glands, particularly in difficult borderline cases.

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“…This library clone capacity was much lesser than those of serial subtraction [5,13] or standard PCR-based cDNA subtraction protocols, which often generate libraries of capacities ranging from a few thousands to more than 10,000 clones [4,8,11,12]. Totally, 46 clones from plating assays were randomly selected for 5'-end single-pass DNA sequencing.…”

Section: Resultsmentioning

confidence: 99%

“…This limits rapid and more efficient detections of uniquely expressed target gene(s) within a defined biological material or process [5,7]. Such challenge coupled generally with the larger clone capacity of the first subtraction library had inspired current subtraction protocol modifications [4,12], among which some have involved a few to extended serial subtractions [5,8,13], whereas the others had combined both subtraction and microarray hybridization [4,7,9] for determining target specific genes. However, this usually is tedious and entails technical complexity and increased reagent and labor costs while also extending the experimental period.…”

Section: Introductionmentioning

confidence: 99%

A Novel mRNA Level Subtraction Method for Quick Identification of Target-Orientated Uniquely Expressed Genes Between Peanut Immature Pod and Leaf

Matand

Williams

2009

Biol Proced Online

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Subtraction technique has been broadly applied for target gene discovery. However, most current protocols apply relative differential subtraction and result in great amount clone mixtures of unique and differentially expressed genes. This makes it more difficult to identify unique or target-orientated expressed genes. In this study, we developed a novel method for subtraction at mRNA level by integrating magnetic particle technology into driver preparation and tester–driver hybridization to facilitate uniquely expressed gene discovery between peanut immature pod and leaf through a single round subtraction. The resulting target clones were further validated through polymerase chain reaction screening using peanut immature pod and leaf cDNA libraries as templates. This study has resulted in identifying several genes expressed uniquely in immature peanut pod. These target genes can be used for future peanut functional genome and genetic engineering research.

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Identification of genes differentially over-expressed in lung squamous cell carcinoma using combination of cDNA subtraction and microarray analysis

Cited by 93 publications

References 27 publications

Aberrant expression of RAB1A in human tongue cancer

Aberrant expression of RAB1A in human tongue cancer

IMP3 is a novel biomarker for adenocarcinoma in situ of the uterine cervix: an immunohistochemical study in comparison with p16INK4a expression

A Novel mRNA Level Subtraction Method for Quick Identification of Target-Orientated Uniquely Expressed Genes Between Peanut Immature Pod and Leaf

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