Erscheint 4 Ausgaben pro Jahr
ISSN Druckformat: 0731-8898
ISSN Online: 2162-6537
IF:
2.4
5-Year IF:
2.8
Immediacy Index:
0.5
Eigenfactor:
0.00049
JCI:
0.59
SJR:
0.429
SNIP:
0.507
CiteScore™::
3.9
H-Index:
49
Indexed in
MET, HGF, EGFR, and PXN Gene Copy Number in Lung Cancer Using DNA Extracts from FFPE Archival Samples and Prognostic Significance
Get access
ABSTRAKT
Gene copy number analysis for some of the important molecules in lung tumorogenesis, such as MET, hepatocyte growth factor [(HGF), ligand for MET), epidermal growth factor receptor (EGFR), and paxillin (PXN), is likely to determine both the type of treatment and prognosis. Formalin-fixed paraffin-embedded (FFPE) archival tumor tissue samples are an excellent source for determining key molecular changes in the OncoGenome; however, existing extraction procedures yield relatively poor quality genomic DNA fragments. Although FISH is the method of choice for determining amplification of a gene, a more rapid quantitative poly-merase chain reaction (qPCR) technique to determine gene copy number can be used when reasonably good quality genomic DNA is available. We report here a relatively rapid method based on microwave/chelex-100 treatment that gives rise to genomic DNA fragments ranging from 1 to 12 Kb and beyond, thereby attesting to its superior quality. Genomic PCR for β-globin gene gave reliable and reproducible results. The number of steps for extracting the DNA was kept to a minimum, and instead of precipitating the DNA, we preserved the genomic DNA extracts so as to prevent a loss in DNA yield. We found the extracts to be stable and amenable to qPCR and mutational analysis. Using lung adenocarcinoma FFPE samples and cell lines derived from lung adenocarcinomas, we demonstrated that the gene copy number for MET in lung adenocarcinoma tissue samples was preferentially increased over EGFR, HGF, and PXN and that it positively correlated with a better prognosis. In contrast, the genomic DNA extracted from 25 NSCLC cell lines gave a relatively higher gene copy number for all four genes evaluated. Our results indicate that the microwave/chelex-100-based method yields good-quality genomic DNA extracts that can be used for complex DNA analysis, such as determination of gene copy number. In addition, our data demonstrated that the adenocarcinoma cell lines potentially evolved under ex vivo conditions, and therefore, in genetic studies it is imperative to use primary tumors for generalized conclusions about lung tumors.
-
Serracino Hilary S., Franklin Wilbur A., Aisner Dara L., Molecular Pathology of Non–Small Cell Lung Cancer, Surgical Pathology Clinics, 5, 4, 2012. Crossref
-
Gopalan Vinod, Yasuda Koichi, Pillai Suja, Tiang Thomas, Leung Melissa, Lu Cu-Tai, Tang Johnny Chuek-on, Smith Robert A, Lam Alfred King-Yin, Gene amplified in oesophageal cancer 1 (GAEC1)amplification in colorectal cancers and its impact on patient's survival, Journal of Clinical Pathology, 66, 8, 2013. Crossref
-
Scagliotti Giorgio V., Novello Silvia, von Pawel Joachim, The emerging role of MET/HGF inhibitors in oncology, Cancer Treatment Reviews, 39, 7, 2013. Crossref
-
Li Detao, Li Fengzeng, Wu Yanfeng, Zhou Dandan, Chen Hui, Quantification of serum MET in non-small-cell lung cancer and its clinical significance, Clinical Biochemistry, 48, 3, 2015. Crossref
-
Catenacci Daniel V.T., Cervantes Gustavo, Yala Soheil, Nelson Erik A., El-Hashani Essam, Kanteti Rajani, El Dinali Mohamed, Hasina Rifat, Brägelmann Johannes, Seiwert Tanguy, Sanicola Michele, Henderson Les, Grushko Tatyana A., Olopade Olufunmilayo, Karrison Theodore, Bang Yung-Jue, Kim Woo Ho, Tretiakova Maria, Vokes Everett, Frank David A., Kindler Hedy L., Huet Heather, Salgia Ravi, RON(MST1R)is a novel prognostic marker and therapeutic target for gastroesophageal adenocarcinoma, Cancer Biology & Therapy, 12, 1, 2011. Crossref
-
Lund Bendik, Najmi Laeya A., Wesolowska-Andersen Agata, Landsem Veslemøy M., Rasmussen Kirsten K., Borst Louise, Gupta Ramneek, Schmiegelow Kjeld, Klungland Helge, Archival Bone Marrow Samples, Applied Immunohistochemistry & Molecular Morphology, 23, 1, 2015. Crossref
-
Kowalczuk Oksana, Kozlowski Miroslaw, Niklinska Wiesława, Kisluk Joanna, Niklinska Barbara Joanna, Niklinski Jacek, Increased MET Gene Copy Number but Not mRNA Level Predicts Postoperative Recurrence in Patients with Non–Small Cell Lung Cancer, Translational Oncology, 7, 5, 2014. Crossref
-
Feng Yan, Minca Eugen C., Lanigan Christopher, Liu Angen, Zhang Wei, Yin Lihong, Pennell Nathan A., Farver Carol, Tubbs Raymond, Ma Patrick C., High MET Receptor Expression But Not Gene Amplification in ALK 2p23 Rearrangement Positive Non–Small-Cell Lung Cancer, Journal of Thoracic Oncology, 9, 5, 2014. Crossref
-
Lawrence Ryan E., Salgia Ravi, MET molecular mechanisms and therapies in lung cancer, Cell Adhesion & Migration, 4, 1, 2010. Crossref
-
Sakashita Shingo, Li Dongping, Nashima Naohumi, Minami Yuko, Furuya Shuuichiro, Morishita Yukio, Tachibana Keisei, Sato Yukio, Noguchi Masayuki, Overexpression of immunoglobulin (CD79a) binding protein1 (IGBP-1) in small lung adenocarcinomas and its clinicopathological significance, Pathology International, 61, 3, 2011. Crossref
-
Arriola E, Cañadas I, Arumí-Uría M, Dómine M, Lopez-Vilariño J A, Arpí O, Salido M, Menéndez S, Grande E, Hirsch F R, Serrano S, Bellosillo B, Rojo F, Rovira A, Albanell J, MET phosphorylation predicts poor outcome in small cell lung carcinoma and its inhibition blocks HGF-induced effects in MET mutant cell lines, British Journal of Cancer, 105, 6, 2011. Crossref
-
Kanteti Rajani, Krishnaswamy Soundararajan, Catenacci Daniel, Tan Yi-Hung Carol, EL-Hashani Essam, Cervantes Gustavo, Husain Aliya N., Tretiakova Maria, Vokes Everett E., Huet Heather, Salgia Ravi, Differential expression of RON in small and non-small cell lung cancers, Genes, Chromosomes and Cancer, 51, 9, 2012. Crossref
-
Lohmann Sabine, Bahle Beatrix, Herold Andrea, Schuster Julian, Formalin-Fixed Paraffin-Embedded Tissue (FFPET) Sections for Nucleic Acid-Based Analysis in Biomarker Discovery and Early Drug Development, in General Methods in Biomarker Research and their Applications, 2015. Crossref
-
West Lisandra, Vidwans Smruti J., Campbell Nicholas P., Shrager Jeff, Simon George R., Bueno Raphael, Dennis Phillip A., Otterson Gregory A., Salgia Ravi, Batra Surinder K., A Novel Classification of Lung Cancer into Molecular Subtypes, PLoS ONE, 7, 2, 2012. Crossref
-
Feng Yan, Thiagarajan Praveena S., Ma Patrick C., MET Signaling: Novel Targeted Inhibition and Its Clinical Development in Lung Cancer, Journal of Thoracic Oncology, 7, 2, 2012. Crossref
-
Dziadziuszko Rafal, Wynes Murry W., Singh Shalini, Asuncion Bernadette Reyna, Ranger-Moore James, Konopa Krzysztof, Rzyman Witold, Szostakiewicz Barbara, Jassem Jacek, Hirsch Fred R., Correlation between MET Gene Copy Number by Silver In Situ Hybridization and Protein Expression by Immunohistochemistry in Non-small Cell Lung Cancer, Journal of Thoracic Oncology, 7, 2, 2012. Crossref
-
Mendes Rita, Carreira Bárbara, Baptista Pedro V., Fernandes Alexandra R., Non-small cell lung cancer biomarkers and targeted therapy - two faces of the same coin fostered by nanotechnology, Expert Review of Precision Medicine and Drug Development, 1, 2, 2016. Crossref
-
Yuan Xiguo, Zhang Junying, Zhang Shengli, Yu Guoqiang, Wang Yue, Shomron Noam, Comparative Analysis of Methods for Identifying Recurrent Copy Number Alterations in Cancer, PLoS ONE, 7, 12, 2012. Crossref
-
Dimou Anastasios, Non Lemuel, Chae Young Kwang, Tester William J., Syrigos Konstantinos N., Chellappan Srikumar P., MET Gene Copy Number Predicts Worse Overall Survival in Patients with Non-Small Cell Lung Cancer (NSCLC); A Systematic Review and Meta-Analysis, PLoS ONE, 9, 9, 2014. Crossref
-
Deakin Nicholas O., Turner Christopher E., Adams Josephine C., Distinct roles for paxillin and Hic-5 in regulating breast cancer cell morphology, invasion, and metastasis, Molecular Biology of the Cell, 22, 3, 2011. Crossref
-
Lohmann Sabine, Bahle Beatrix, Herold Andrea, Schuster Julian, Formalin-Fixed Paraffin-Embedded Tissue (FFPET) Sections for Nucleic Acid-Based Analysis in Biomarker Discovery and Early Drug Development, in General Methods in Biomarker Research and their Applications, 2014. Crossref
-
Patil Vikas, Mahalingam Kulandaivelu, A four-protein expression prognostic signature predicts clinical outcome of lower-grade glioma, Gene, 679, 2018. Crossref
-
Malik Raeva, Mambetsariev Isa, Fricke Jeremy, Chawla Neal, Nam Arin, Pharaon Rebecca, Salgia Ravi, MET receptor in oncology: From biomarker to therapeutic target, in Receptor Tyrosine Kinases, 147, 2020. Crossref
-
Liu Xianchen, Xu Dong, Xu Xiaodong, Xue Qiang, Gao Xuesong, Tang Chong, MiR-216b regulates the tumorigenesis of gastric cancer by targeting PXN, Pathology - Research and Practice, 218, 2021. Crossref
-
Xu Weiyi, Alpha Kyle M., Zehrbach Nicholas M., Turner Christopher E., Yap Alpha, Paxillin promotes breast tumor collective cell invasion through maintenance of adherens junction integrity, Molecular Biology of the Cell, 33, 2, 2022. Crossref
-
Rolle Cleo E., Kanteti Rajani, Surati Mosmi, Nandi Suvobroto, Dhanasingh Immanuel, Yala Soheil, Tretiakova Maria, Arif Qudsia, Hembrough Todd, Brand Toni M., Wheeler Deric L., Husain Aliya N., Vokes Everett E., Bharti Ajit, Salgia Ravi, Combined MET Inhibition and Topoisomerase I Inhibition Block Cell Growth of Small Cell Lung Cancer, Molecular Cancer Therapeutics, 13, 3, 2014. Crossref
-
Hasina Rifat, Mollberg Nathan, Kawada Ichiro, Mutreja Karun, Kanade Geetanjali, Yala Soheil, Surati Mosmi, Liu Ren, Li Xiuqing, Zhou Yue, Ferguson Benjamin D., Nallasura Vidya, Cohen Kenneth S., Hyjek Elizabeth, Mueller Jeffery, Kanteti Rajani, El Hashani Essam, Kane Dorothy, Shimada Yutaka, Lingen Mark W., Husain Aliya N., Posner Mitchell C., Waxman Irving, Villaflor Victoria M., Ferguson Mark K., Varticovski Lyuba, Vokes Everett E., Gill Parkash, Salgia Ravi, Critical Role for the Receptor Tyrosine Kinase EPHB4 in Esophageal Cancers, Cancer Research, 73, 1, 2013. Crossref