EXCLI J EXCLI Journal 1611-2156 Leibniz Research Centre for Working Environment and Human Factors 2017-1043 10.17179/excli2017-1043 Doc1326 Editorial material Highlight report: The relationship of DNA copy number alterations and mRNA levels in cancer Hammad Seddik * 1 Department of Forensic Medicine and Veterinary Toxicology, Faculty of Veterinary Medicine, South Valley University, 83523-Qena, Egypt *To whom correspondence should be addressed: Seddik Hammad, Department of Forensic Medicine and Veterinary Toxicology, Faculty of Veterinary Medicine, South Valley University, 83523-Qena, Egypt, E-mail: seddik.hammad@vet.svu.edu.eg 21 12 2017 2017 16 1326 1327 06 12 2017 20 12 2017 Copyright © 2017 Hammad 2017

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licence (http://creativecommons.org/licenses/by/4.0/) You are free to copy, distribute and transmit the work, provided the original author and source are credited.

This article is available from http://www.excli.de/vol16/Hammad_Editorial_21122017_proof.pdf


Recently, a genome-wide study about gene copy number gains and corresponding expression levels has been analyzed in a cohort of 190 non-small cell lung cancer (NSCLC) patients (Jabs et al., 2017[5]). The authors report that approximately half of the analyzed gene copy number-gene expression pairs correlated significantly. However, only 1.6 % (corresponding to 301 genes) of the analyzed pairs (gene copy number- mRNA) showed very strong correlations with a correlation coefficient higher than 0.7 (Jabs et al., 2017[5]). The authors studied the location of these 301 genes and observed that they are found predominantly in 10 chromosomal `hotspot regions´ with a width of approximately 15 Mbp. The most probable explanation of these `hotspots´ is that these genes show higher mean expression levels; moreover, copy number variations are more likely in these regions. Both, mRNA expression level and the frequency of copy number gain in the patient cohort were significantly associated with the correlation coefficient of copy number-gene expression pairs. An interesting result is that some of the genes with high correlation between copy number and mRNA levels are significantly associated with survival. Indeed, prognostic genes were overrepresented among the subset of highly correlating copy number-gene expression pairs (Jabs et al., 2017[5]).

Since decades, much effort has been invested to better understand the relationship between gene expression and prognosis of tumors (Hellwig et al., 2016[4]; Stock et al., 2015[13]; Sicking et al., 2014[12][11]; Ghallab et al., 2015[2]; Malik et al., 2015[9]; Lohr et al., 2015[8]; Shakeri et al., 2016[10]). However, it has also become clear that it is challenging to achieve a relevant improvement of prognostication by gene expression signatures compared to the use of clinicopathological parameters alone (Grinberg et al., 2017[3]; Sicking et al., 2014[12][11]). A further research focus is the identification of improved anti-cancer agents and the identification of subsets of patients who profit from a specific chemotherapy (Uzor, 2016[15]; Jigyasu et al., 2016[6]; Kwak et al., 2016[7]; Benarba, 2015[1]; Tatokoro et al., 2015[14]). It is often easier to isolate DNA from archived tumor material than obtaining the easily degradable mRNA. The systematic study of Jabs et al. identified a subset of genes with a very strong correlation of DNA copy number and mRNA levels. Therefore, further analysis of prognostic or predictive relevance of these genes can be performed based on DNA which may facilitate progress in this field of research.

Benarba B Use of medicinal plants by breast cancer patients in Algeria EXCLI J 2015 14 1164 1166 Ghallab A Highlight report: Role of the circadian clock system in breast cancer EXCLI J 2015 14 540 541 Grinberg M Djureinovic D Brunnström HR Mattsson JS Edlund K Hengstler JG Reaching the limits of prognostication in non-small cell lung cancer: an optimized biomarker panel fails to outperform clinical parameters Mod Pathol 2017 30 964 977 Hellwig B Madjar K Edlund K Marchan R Cadenas C Heimes AS Epsin family member 3 and ribosome-related genes are associated with late metastasis in estrogen receptor-positive breast cancer and long-term survival in non-small cell lung cancer using a genome-wide identification and validation strategy PLoS One 2016 11 12 e0167585 Jabs V Edlund K König H Grinberg M Madjar K Rahnenführer J Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer PLoS One 2017 12 11 e0187246 Jigyasu AK Siddiqui S Lohani M Khan IA Arshad M Chemically synthesized CdSe quantum dots inhibit growth of human lung carcinoma cells via ROS generation EXCLI J 2016 15 54 63 Kwak Y Lee J Ju J Anti-cancer activities of Brassica juncea leaves in vitro EXCLI J 2016 15 699 710 Lohr M Hellwig B Edlund K Mattsson JS Botling J Schmidt M Identification of sample annotation errors in gene expression datasets Arch Toxicol 2015 89 2265 2272 Malik SS Masood N Yasmin A Prostate cancer and glutathione S-transferase deletions EXCLI J 2015 14 1049 1054 Shakeri H Gharesouran J Fakhrjou A Esfahani A Mohaddes Ardebili SM DNA methylation assessment as a prognostic factor in invasive breast cancer using methylation-specific multiplex ligation dependent probe amplification EXCLI J 2016 15 11 20 Sicking I Edlund K Wesbuer E Weyer V Battista MJ Lebrecht A Prognostic influence of pre-operative C-reactive protein in node-negative breast cancer patients PLoS One 2014 9 10 e111306 Sicking I Rommens K Battista MJ Böhm D Gebhard S Lebrecht A Prognostic influence of cyclooxygenase-2 protein and mRNA expression in node-negative breast cancer patients BMC Cancer 2014 14 952 Stock AM Klee F Edlund K Grinberg M Hammad S Marchan R Gelsolin Is Associated with Longer Metastasis-free Survival and Reduced Cell Migration in Estrogen Receptor-positive Breast Cancer Anticancer Res 2015 35 5277 5285 Tatokoro M Koga F Yoshida S Kihara K Heat shock protein 90 targeting therapy: state of the art and future perspective EXCLI J 2015 14 48 58 Uzor PF Recent developments on potential new applications of emetine as anti-cancer agent EXCLI J 2016 15 323 328