TY - JOUR
T1 - Genetic and epigenetic analysis of non-small cell lung cancer with NotI-microarrays
AU - Dmitriev, Alexey A.
AU - Kashuba, Vladimir I.
AU - Haraldson, Klas
AU - Senchenko, Vera N.
AU - Pavlova, Tatiana V.
AU - Kudryavtseva, Anna V.
AU - Anedchenko, Ekaterina A.
AU - Krasnov, George S.
AU - Pronina, Irina V.
AU - Loginov, Vitalij I.
AU - Kondratieva, Tatiana T.
AU - Kazubskaya, Tatiana P.
AU - Braga, Eleonora A.
AU - Yenamandra, Surya P.
AU - Ignatjev, Ilya
AU - Ernberg, Ingemar
AU - Klein, George
AU - Lerman, Michael I.
AU - Zabarovsky, Eugene R.
N1 - Funding Information:
Statistical analysis. We used nonparametric statistical tests, We would like to thank Dr. Nina Oparina for helpful discussion because these tests can be used without assumption on Gauss-of our results. This work was supported by research grants from type data distribution, in contrast to parametric ones. If we use the Swedish Cancer Society, the Swedish Institute, the Swedish parametric test for non Gauss-distributed data, sensitivity of the Research Council and Karolinska Institute, State Contracts test decreases significantly. Using non-parametric methods gives 02.740.11.5227 and 16.552.11.7034 with the Russian Ministry us about 95% of parametric sensitivity, but we can be certain of Education and Science, grants 10-04-01213-a and 11-04-on accuracy of the obtained results. Nonparametric Wilcoxon 00269 from the Russian Foundation for Basic Research and by test was used to compare mRNA expression differences of tara UICC International Cancer Technology Transfer Fellowship get and reference genes in NSCLC samples. Kruskal-Wallis and to DAA. Mann-Whitney rank-sum tests, Fisher’s exact test and χ2 criteria were used for analysis of genomic DNA copy, methylation and SupplementalMaterial mRNA level changes in NSCLC groups with different histologi-Supplemental materials may be found here:
PY - 2012/5
Y1 - 2012/5
N2 - This study aimed to clarify genetic and epigenetic alterations that occur during lung carcinogenesis and to design perspective sets of newly identified biomarkers. The original method includes chromosome 3 specific NotI-microarrays containing 180 NotI clones associated with genes for hybridization with 40 paired normal/tumor DNA samples of primary lung tumors: 28 squamous cell carcinomas (SCC) and 12 adenocarcinomas (ADC). The NotI-microarray data were confirmed by qPC R and bisulfite sequencing analyses. Forty-four genes showed methylation and/or deletions in more than 15% of non-small cell lung cancer (NSC LC) samples. In general, SCC samples were more frequently methylated/ deleted than ADC. Moreover, the SCC alterations were observed already at stage I of tumor development, whereas in ADC many genes showed tumor progression specific methylation/deletions. Among genes frequently methylated/ deleted in NSC LC, only a few were already known tumor suppressor genes: RBSP3 (CTDSPL), VHL and THRB. The RPL32, LOC285205, FGD5 and other genes were previously not shown to be involved in lung carcinogenesis. Ten methylated genes, i.e., IQSEC1, RBSP3, ITGA9, FOXP1, LRRN1, GNAI2, VHL, FGD5, ALDH1L1 and BCL6 were tested for expression by qPC R and were found downregulated in the majority of cases. Three genes (RBSP3, FBLN2 and ITGA9) demonstrated strong cell growth inhibition activity. A comprehensive statistical analysis suggested the set of 19 gene markers, ANKRD28, BHLHE40, CGGBP1, RBSP3, EPHB1, FGD5, FOXP1, GORASP1/TTC21, IQSEC1, ITGA9, LOC285375, LRRC3B, LRRN1, MITF, NKIRAS1/RPL15, TRH, UBE2E2, VHL, WNT7A, to allow early detection, tumor progression, metastases and to discriminate between SCC and ADC with sensitivity and specificity of 80-100%.
AB - This study aimed to clarify genetic and epigenetic alterations that occur during lung carcinogenesis and to design perspective sets of newly identified biomarkers. The original method includes chromosome 3 specific NotI-microarrays containing 180 NotI clones associated with genes for hybridization with 40 paired normal/tumor DNA samples of primary lung tumors: 28 squamous cell carcinomas (SCC) and 12 adenocarcinomas (ADC). The NotI-microarray data were confirmed by qPC R and bisulfite sequencing analyses. Forty-four genes showed methylation and/or deletions in more than 15% of non-small cell lung cancer (NSC LC) samples. In general, SCC samples were more frequently methylated/ deleted than ADC. Moreover, the SCC alterations were observed already at stage I of tumor development, whereas in ADC many genes showed tumor progression specific methylation/deletions. Among genes frequently methylated/ deleted in NSC LC, only a few were already known tumor suppressor genes: RBSP3 (CTDSPL), VHL and THRB. The RPL32, LOC285205, FGD5 and other genes were previously not shown to be involved in lung carcinogenesis. Ten methylated genes, i.e., IQSEC1, RBSP3, ITGA9, FOXP1, LRRN1, GNAI2, VHL, FGD5, ALDH1L1 and BCL6 were tested for expression by qPC R and were found downregulated in the majority of cases. Three genes (RBSP3, FBLN2 and ITGA9) demonstrated strong cell growth inhibition activity. A comprehensive statistical analysis suggested the set of 19 gene markers, ANKRD28, BHLHE40, CGGBP1, RBSP3, EPHB1, FGD5, FOXP1, GORASP1/TTC21, IQSEC1, ITGA9, LOC285375, LRRC3B, LRRN1, MITF, NKIRAS1/RPL15, TRH, UBE2E2, VHL, WNT7A, to allow early detection, tumor progression, metastases and to discriminate between SCC and ADC with sensitivity and specificity of 80-100%.
KW - Biomarkers
KW - Epigenetics
KW - Lung cancer
KW - Methylation
KW - Methylation specific microarrays
KW - NotI-microarrays
KW - RT-qPCR
KW - Tumor-suppressor gene
UR - http://www.scopus.com/inward/record.url?scp=84860581254&partnerID=8YFLogxK
U2 - 10.4161/epi.19801
DO - 10.4161/epi.19801
M3 - Article
AN - SCOPUS:84860581254
SN - 1559-2294
VL - 7
SP - 502
EP - 513
JO - Epigenetics
JF - Epigenetics
IS - 5
ER -