title: Novel tumor suppressor candidates on chromosome 3 revealed by NotI-microarrays in cervical cancer.
abstract: Genetic and epigenetic alterations in cervical carcinomas were investigated using NotI-microarrays containing 180 cloned sequences flanking all NotI-sites associated with genes on chromosome 3. In total, 48 paired normal/tumor DNA samples, specifically enriched in NotI-sites, were hybridized to NotI-microarrays. Thirty genes, including tumor suppressors or candidates (for example, VHL, RBSP3/CTDSPL, ITGA9, LRRC3B, ALDH1L1, EPHB1) and genes previously unknown as cancer-associated (ABHD5, C3orf77, PRL32, LOC285375, FGD5 and others), showed methylation/deletion in 21-44% of tumors. The genes were more frequently altered in squamous cell carcinomas (SCC) than in adenocarcinomas (ADC, p<0.01). A set of seven potential markers (LRRN1, PRICKLE2, VHL, BHLHE40, RBSP3, CGGBP1 and SOX14) is promising for discrimination of ADC and SCC. Alterations of more than 20 genes simultaneously were revealed in 23% of SCC. Bisulfite sequencing analysis confirmed methylation as a frequent event in SCC. High down-regulation frequency was shown for RBSP3, ITGA9, VILL, APRG1/C3orf35 and RASSF1 (isoform A) genes (3p21.3 locus) in SCC. Both frequency and extent of RASSF1A and RBSP3 mRNA level decrease were more pronounced in tumors with lymph node metastases compared with non-metastatic ones (p ≤ 0.05). We confirmed by bisulfite sequencing that RASSF1 promoter methylation was a rare event in SCC and, for the first time, demonstrated RASSF1A down-regulation at both the mRNA and protein levels without promoter methylation in tumors of this histological type. Thus, our data revealed novel tumor suppressor candidates located on chromosome 3 and a frequent loss of epigenetic stability of 3p21.3 locus in combination with down-regulation of genes in cervical cancer.
authors.affiliation: Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia.
authors.forename: Vera N
authors.initials: VN
authors.lastname: Senchenko
authors.affiliation: N.N. Blokhin Russian Cancer Research Center; Russian Academy of Medical Sciences; Moscow, Russia.
authors.forename: Natalia P
authors.initials: NP
authors.lastname: Kisseljova
authors.affiliation: N.N. Blokhin Russian Cancer Research Center; Russian Academy of Medical Sciences; Moscow, Russia; Karolinska Institute; Department of Microbiology, Tumour and Cell Biology; Stockholm, Sweden.
authors.forename: Tatyana A
authors.initials: TA
authors.lastname: Ivanova
authors.affiliation: Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia.
authors.forename: Alexey A
authors.initials: AA
authors.lastname: Dmitriev
authors.affiliation: Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia; I.I.Mechnikov Scientific Research Institute of Vaccines and Sera; Russian Academy of Medical Sciences; Moscow, Russia.
authors.forename: George S
authors.initials: GS
authors.lastname: Krasnov
authors.affiliation: Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Kudryavtseva
authors.affiliation: Institute of Molecular Biology and Genetics; Ukrainian Academy of Sciences; Kiev, Ukraine.
authors.forename: Grigory V
authors.initials: GV
authors.lastname: Panasenko
authors.affiliation: Koltzov Institute of Developmental Biology; Russian Academy of Sciences; Moscow, Russia.
authors.forename: Evgeny B
authors.initials: EB
authors.lastname: Tsitrin
authors.affiliation: Affina Biotechnologies; Stamford, CT USA.
authors.forename: Michael I
authors.initials: MI
authors.lastname: Lerman
authors.affiliation: N.N. Blokhin Russian Cancer Research Center; Russian Academy of Medical Sciences; Moscow, Russia.
authors.forename: Fyodor L
authors.initials: FL
authors.lastname: Kisseljov
authors.affiliation: Institute of Molecular Biology and Genetics; Ukrainian Academy of Sciences; Kiev, Ukraine.
authors.forename: Vladimir I
authors.initials: VI
authors.lastname: Kashuba
authors.affiliation: Karolinska Institute; Department of Microbiology, Tumour and Cell Biology; Stockholm, Sweden.
authors.forename: Eugene R
authors.initials: ER
authors.lastname: Zabarovsky
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics*; D001483:Base Sequence; D014408:Biomarkers, Tumor / Q000235:genetics; D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D002893:Chromosomes, Human, Pair 3 / Q000235:genetics*; D019175:DNA Methylation; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry*; D015536:Down-Regulation; D044127:Epigenesis, Genetic; D005260:Female; D020869:Gene Expression Profiling; D016147:Genes, Tumor Suppressor; D006801:Humans; D059645:Mutation Rate; D020411:Oligonucleotide Array Sequence Analysis; D017384:Sequence Deletion; D025521:Tumor Suppressor Proteins / Q000378:metabolism; D002583:Uterine Cervical Neoplasms / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor; C411762:RASSF1 protein, human; D025521:Tumor Suppressor Proteins; D015252:Deoxyribonucleases, Type II Site-Specific; C038565:GCGGCCGC-specific type II deoxyribonucleases
keywords: DNA methylation; NotI-microarrays; cervical cancer; chromosome 3; deletions; expression; tumor-suppressors genes