title: Genetic and epigenetic analysis of non-small cell lung cancer with NotI-microarrays.
abstract: 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 qPCR and bisulfite sequencing analyses. Forty-four genes showed methylation and/or deletions in more than 15% of non-small cell lung cancer (NSCLC) 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 NSCLC, 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, ITGA 9, FOXP1, LRRN1, GNAI2, VHL, FGD5, ALDH1L1 and BCL6 were tested for expression by qPCR 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%.
authors.affiliation: Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.
authors.forename: Alexey A
authors.initials: AA
authors.lastname: Dmitriev
authors.forename: Vladimir I
authors.initials: VI
authors.lastname: Kashuba
authors.forename: Klas
authors.initials: K
authors.lastname: Haraldson
authors.forename: Vera N
authors.initials: VN
authors.lastname: Senchenko
authors.forename: Tatiana V
authors.initials: TV
authors.lastname: Pavlova
authors.forename: Anna V
authors.initials: AV
authors.lastname: Kudryavtseva
authors.forename: Ekaterina A
authors.initials: EA
authors.lastname: Anedchenko
authors.forename: George S
authors.initials: GS
authors.lastname: Krasnov
authors.forename: Irina V
authors.initials: IV
authors.lastname: Pronina
authors.forename: Vitalij I
authors.initials: VI
authors.lastname: Loginov
authors.forename: Tatiana T
authors.initials: TT
authors.lastname: Kondratieva
authors.forename: Tatiana P
authors.initials: TP
authors.lastname: Kazubskaya
authors.forename: Eleonora A
authors.initials: EA
authors.lastname: Braga
authors.forename: Surya P
authors.initials: SP
authors.lastname: Yenamandra
authors.forename: Ilya
authors.initials: I
authors.lastname: Ignatjev
authors.forename: Ingemar
authors.initials: I
authors.lastname: Ernberg
authors.forename: George
authors.initials: G
authors.lastname: Klein
authors.forename: Michael I
authors.initials: MI
authors.lastname: Lerman
authors.forename: Eugene R
authors.initials: ER
authors.lastname: Zabarovsky
mesh_terms: D000230:Adenocarcinoma / Q000175:diagnosis / Q000235:genetics; D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D002289:Carcinoma, Non-Small-Cell Lung / Q000175:diagnosis / Q000235:genetics*; D002294:Carcinoma, Squamous Cell / Q000175:diagnosis / Q000235:genetics; D016022:Case-Control Studies; D045744:Cell Line, Tumor; D002893:Chromosomes, Human, Pair 3 / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D018450:Disease Progression; D044127:Epigenesis, Genetic; D005260:Female; D017353:Gene Deletion; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D005820:Genetic Testing / Q000379:methods*; D020662:Guanine Nucleotide Exchange Factors; D006801:Humans; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012680:Sensitivity and Specificity; D014162:Transfection; D025521:Tumor Suppressor Proteins; D051794:Von Hippel-Lindau Tumor Suppressor Protein
chemical_list: D014408:Biomarkers, Tumor; C486483:CTDSPL protein, human; C572072:FGD5 protein, human; D020662:Guanine Nucleotide Exchange Factors; D025521:Tumor Suppressor Proteins; D051794:Von Hippel-Lindau Tumor Suppressor Protein; C497446:VHL protein, human