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Wan D, He L, Guo C, Zhong Z, Yan X, Cao J, Xu Q, Zhang H, Duan B. m6A-related lncRNAs predict prognosis and indicate cell cycle in gastric cancer. Front Genet 2023; 14:1140218. [PMID: 37408779 PMCID: PMC10319253 DOI: 10.3389/fgene.2023.1140218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/11/2023] [Indexed: 07/07/2023] Open
Abstract
Background: N6-methyladenosine (m6A) modification is a common epigenetic methylation modification of RNA, which plays an important role in gastric carcinogenesis and progression by regulating long non-coding RNA (lncRNA). This study is aimed to investigate the potential prognostic signatures of m6A -related lncRNAs in STAD. Methods: The m6A-related lncRNAs with the most significant impact on gastric cancer prognosis in the TCGA database were identified by bioinformatics and machine learning methods. The m6A-related lncRNA prognostic model (m6A-LPS) and nomogram was constructed by Cox regression analysis with the minimum absolute contraction and selection operator (LASSO) algorithm. The functional enrichment analysis of m6A-related lncRNAs was also investigated. The miRTarBase, miRDB and TargetScan databases were utilized to establish a prognosis-related network of competing endogenous RNA (ceRNA) by bioinformatics methods. The correlation of AL391152.1 expressions and cell cycle were experimentally testified by qRT-PCR and flow cytometry. Results: In total, 697 lncRNAs that were identified as m6A-related lncRNAs in GC samples. The survival analysis showed that 18 lncRNAs demonstrated prognostic values. A risk model with 11 lncRNAs was established by Lasso Cox regression, and can predict the prognosis of GC patients. Cox regression analysis and ROC curve indicated that this lncRNA prediction model was an independent risk factor for survival rates. Functional enrichment analysis and ceRNA network revealed that the nomogram was notably associated with cell cycle. qRT-PCR and flow cytometry revealed that downregulation of GC m6A-related lncRNA AL391152.1 could decrease cyclins expression in SGC7901 cells. Conclusion: A m6A-related lncRNAs prognostic model was established in this study, which can be applied to predict prognosis and cell cycle in gastric cancer.
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Affiliation(s)
- Dong Wan
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lingnan He
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Cheng Guo
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zishao Zhong
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiaohan Yan
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jia Cao
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qinwei Xu
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Haibin Zhang
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bensong Duan
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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Koh J, Hogue JA, Roman SA, Scheri RP, Fradin H, Corcoran DL, Sosa JA. Transcriptional profiling reveals distinct classes of parathyroid tumors in PHPT. Endocr Relat Cancer 2018; 25:407-420. [PMID: 29475894 PMCID: PMC5826637 DOI: 10.1530/erc-17-0470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 02/01/2018] [Indexed: 12/20/2022]
Abstract
The clinical presentation of primary hyperparathyroidism (PHPT) varies widely, although the underlying mechanistic reasons for this disparity remain unknown. We recently reported that parathyroid tumors can be functionally segregated into two distinct groups on the basis of their relative responsiveness to ambient calcium, and that patients in these groups differ significantly in their likelihood of manifesting bone disability. To examine the molecular basis for this phenotypic variation in PHPT, we compared the global gene expression profiles of calcium-sensitive and calcium-resistant parathyroid tumors. RNAseq and proteomic analysis identified a candidate set of differentially expressed genes highly correlated with calcium-sensing capacity. Subsequent quantitative assessment of the expression levels of these genes in an independent cohort of parathyroid tumors confirmed that calcium-sensitive tumors cluster in a discrete transcriptional profile group. These data indicate that PHPT is not an etiologically monolithic disorder and suggest that divergent molecular mechanisms could drive the observed phenotypic differences in PHPT disease course, provenance, and outcome.
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Affiliation(s)
- James Koh
- Dept. of Surgery, Duke University Medical Center, Durham, NC
- Duke Clinical Research Institute, Duke University Medical Center
- To whom reprint requests should be addressed: James Koh, Ph.D., Department of Surgery, Duke University Medical Center, Durham, NC 27710, Phone: 919-684-0892, FAX: 919-681-6622,
| | - Joyce A. Hogue
- Dept. of Surgery, Duke University Medical Center, Durham, NC
| | | | | | | | | | - Julie A. Sosa
- Dept. of Surgery, Duke University Medical Center, Durham, NC
- Dept. of Medicine, Duke University
- Duke Cancer Institute, Duke University Medical Center
- Duke Clinical Research Institute, Duke University Medical Center
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3
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Kwon MJ, Kim RN, Song K, Jeon S, Jeong HM, Kim JS, Han J, Hong S, Oh E, Choi JS, An J, Pollack JR, Choi YL, Park CK, Shin YK. Genes co-amplified with ERBB2 or MET as novel potential cancer-promoting genes in gastric cancer. Oncotarget 2017; 8:92209-92226. [PMID: 29190909 PMCID: PMC5696175 DOI: 10.18632/oncotarget.21150] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/27/2017] [Indexed: 12/18/2022] Open
Abstract
Gastric cancer (GC), one of the most common cancers worldwide, has a high mortality rate due to limited treatment options. Identifying novel and promising molecular targets is a major challenge that must be overcome if treatment of advanced GC is to be successful. Here, we used comparative genomic hybridization and gene expression microarrays to examine genome-wide DNA copy number alterations (CNAs) and global gene expression in 38 GC samples from old and young patients. We identified frequent CNAs, which included copy number gains on chromosomes 3q, 7p, 8q, 20p, and 20q and copy number losses on chromosomes 19p and 21p. The most frequently gained region was 7p21.1 (55%), whereas the most frequently deleted region was 21p11.1 (50%). Recurrent highly amplified regions 17q12 and 7q31.1-7q31.31 harbored two well-known oncogenes: ERBB2 and MET. Correlation analysis of CNAs and gene expression levels identified CAPZA2 (co-amplified with MET) and genes GRB7, MIEN1, PGAP3, and STARD3 (co-amplified with ERBB2) as potential candidate cancer-promoting genes (CPGs). Public dataset analysis confirmed co-amplification of these genes with MET or ERBB2 in GC tissue samples, and revealed that high expression (except for PGAP3) was significantly associated with shorter overall survival. Knockdown of these genes using small interfering RNA led to significant suppression of GC cell proliferation and migration. Reduced GC cell proliferation mediated by CAPZA2 knockdown was attributable to attenuated cell cycle progression and increased apoptosis. This study identified novel candidate CPGs co-amplified with MET or ERBB2, and suggests that they play a functional role in GC.
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Affiliation(s)
- Mi Jeong Kwon
- College of Pharmacy, Kyungpook National University, Daegu, Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu, Korea
| | - Ryong Nam Kim
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Korea
| | - Kyoung Song
- R&D center, ABION Inc., Guro-gu, Seoul, Korea
| | - Sinyoung Jeon
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Hae Min Jeong
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Joo Seok Kim
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Jinil Han
- Gencurix, Inc., Guro-gu, Seoul, Korea
| | - Sungyoul Hong
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Ensel Oh
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Sun Choi
- The Center for Anti-cancer Companion Diagnostics, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Korea
| | - Jungsuk An
- Department of Pathology, Gachon University Gil Medical Center, Incheon, Korea
| | - Jonathan R Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Yoon-La Choi
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Cheol-Keun Park
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Kee Shin
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Korea.,The Center for Anti-cancer Companion Diagnostics, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
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Clinical Implications of Rabphillin-3A-Like Gene Alterations in Breast Cancer. PLoS One 2015; 10:e0129216. [PMID: 26070152 PMCID: PMC4466565 DOI: 10.1371/journal.pone.0129216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/06/2015] [Indexed: 11/29/2022] Open
Abstract
For the rabphillin-3A-like (RPH3AL) gene, a putative tumor suppressor, the clinical significance of genetic alterations in breast cancers was evaluated. DNA and RNA were extracted from formalin-fixed, paraffin-embedded (FFPE) cancers and matching normal tissues. DNA samples were assessed for loss of heterozygosity (LOH) at the 17p13.3 locus of RPH3AL and the 17p13.1 locus of the tumor suppressor, TP53. RPH3AL was sequenced, and single nucleotide polymorphisms (SNPs) were genotyped. RNA samples were evaluated for expression of RPH3AL, and FFPE tissues were profiled for its phenotypic expression. Alterations in RPH3AL were correlated with clinicopathological features, LOH of TP53, and patient survival. Of 121 cancers, 80 had LOH at one of the RPH3AL locus. LOH of RHP3AL was associated with nodal metastasis, advanced stage, large tumor size, and poor survival. Although ~50% were positive for LOH at the RPH3AL and TP53 loci, 19 of 105 exhibited LOH only at the RPH3AL locus. Of these, 12 were non-Hispanic Caucasians (Whites), 15 had large tumors, and 12 were older (>50 years). Patients exhibiting LOH at both loci had shorter survival than those without LOH at these loci (log-rank, P = 0.014). LOH at the TP53 locus alone was not associated with survival. Analyses of RPH3AL identified missense point mutations in 19 of 125 cases, a SNP (C>A) in the 5’untranslated region at -25 (5’UTR-25) in 26 of 104, and a SNP (G>T) in the intronic region at 43 bp downstream to exon-6 (intron-6-43) in 79 of 118. Genotype C/A or A/A of the SNP at 5’UTR-25 and genotype T/T of a SNP at intron-6-43 were predominantly in Whites. Low levels of RNA and protein expression of RPH3AL were present in cancers relative to normal tissues. Thus, genetic alterations in RPH3AL are associated with aggressive behavior of breast cancers and with short survival of patients.
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Abstract
In terms of its molecular biology and molecular genetics, medulloblastoma is the most thoroughly studied of the pediatric brain tumors. Alterations in chromosome 17, usually an isochromosome 17q, are the most common cytogenetic abnormalities. Similarly, deletion of the short arm of one 17 chromosome, the result of formation of an iso17q, is the most common molecular biological abnormality found. The gene or genes important in the development of medulloblastoma found on chromsome 17 have not yet been identified. Both a tumor suppressor gene and an oncogene have been identified that may play a role in the development of this tumor type. The Patched (PTC) tumor suppressor gene is inactivated in approximately 15% of medulloblatomas; this alteration may be specific to the desmoplastic variant. Oncogenic mutations in the beta-catenin gene are found in a small subset of medulloblastomas. Both of these genes play central roles in developmental pathways. Prognosis in this tumor type has been related to the level of expression of the neurotrophin receptor trkC. In this review, these and other molecular biological and genetic findings are discussed with respect to the development of medulloblastoma.
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Affiliation(s)
- C Raffel
- Department of Pediatric Neurosurgery, Mayo Eugenio Litta Children's Hospital, Mayo Clinic, Rochester, Minnesota
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6
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Letouzé E, Rosati R, Komechen H, Doghman M, Marisa L, Flück C, de Krijger RR, van Noesel MM, Mas JC, Pianovski MAD, Zambetti GP, Figueiredo BC, Lalli E. SNP array profiling of childhood adrenocortical tumors reveals distinct pathways of tumorigenesis and highlights candidate driver genes. J Clin Endocrinol Metab 2012; 97:E1284-93. [PMID: 22539591 DOI: 10.1210/jc.2012-1184] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT Childhood adrenocortical tumors (ACT) are rare malignancies, except in southern Brazil, where a higher incidence rate is associated to a high frequency of the founder R337H TP53 mutation. To date, copy number alterations in these tumors have only been analyzed by low-resolution comparative genomic hybridization. OBJECTIVE We analyzed an international series of 25 childhood ACT using high-resolution single nucleotide polymorphism arrays to: 1) detect focal copy number alterations highlighting candidate driver genes; and 2) compare genetic alterations between Brazilian patients carrying the R337H TP53 mutation and non-Brazilian patients. RESULTS We identified 16 significantly recurrent chromosomal alterations (q-value < 0.05), the most frequent being -4q34, +9q33-q34, +19p, loss of heterozygosity (LOH) of chromosome 17 and 11p15. Focal amplifications and homozygous deletions comprising well-known oncogenes (MYC, MDM2, PDGFRA, KIT, MCL1, BCL2L1) and tumor suppressors (TP53, RB1, RPH3AL) were identified. In addition, eight focal deletions were detected at 4q34, defining a sharp peak region around the noncoding RNA LINC00290 gene. Although non-Brazilian tumors with a mutated TP53 were similar to Brazilian tumors, those with a wild-type TP53 displayed distinct genomic profiles, with significantly fewer rearrangements (P = 0.019). In particular, three alterations (LOH of chromosome 17, +9q33-q34, and -4q34) were significantly more frequent in TP53-mutated samples. Finally, two of four TP53 wild-type tumors displayed as sole rearrangement a copy-neutral LOH of the imprinted region at 11p15, supporting a major role for this region in ACT development. CONCLUSIONS Our findings highlight potential driver genes and cellular pathways implicated in childhood ACT and demonstrate the existence of different oncogenic routes in this pathology.
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Affiliation(s)
- Eric Letouzé
- Program Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, 14 rue Corvisart, 75013 Paris, France.
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7
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Gutiérrez ML, Muñoz-Bellvis L, Abad MDM, Bengoechea O, González-González M, Orfao A, Sayagués JM. Association between genetic subgroups of pancreatic ductal adenocarcinoma defined by high density 500 K SNP-arrays and tumor histopathology. PLoS One 2011; 6:e22315. [PMID: 21811587 PMCID: PMC3141022 DOI: 10.1371/journal.pone.0022315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 06/19/2011] [Indexed: 11/28/2022] Open
Abstract
The specific genes and genetic pathways associated with pancreatic ductal adenocarcinoma are still largely unknown partially due to the low resolution of the techniques applied so far to their study. Here we used high-density 500 K single nucleotide polymorphism (SNP)-arrays to define those chromosomal regions which most commonly harbour copy number (CN) alterations and loss of heterozygozity (LOH) in a series of 20 PDAC tumors and we correlated the corresponding genetic profiles with the most relevant clinical and histopathological features of the disease. Overall our results showed that primary PDAC frequently display (>70%) extensive gains of chromosomes 1q, 7q, 8q and 20q, together with losses of chromosomes 1p, 9p, 12q, 17p and 18q, such chromosomal regions harboring multiple cancer- and PDAC-associated genes. Interestingly, these alterations clustered into two distinct genetic profiles characterized by gains of the 2q14.2, 3q22.1, 5q32, 10q26.13, 10q26.3, 11q13.1, 11q13.3, 11q13.4, 16q24.1, 16q24.3, 22q13.1, 22q13.31 and 22q13.32 chromosomal regions (group 1; n = 9) versus gains at 1q21.1 and losses of the 1p36.11, 6q25.2, 9p22.1, 9p24.3, 17p13.3 and Xp22.33 chromosomal regions (group 2; n = 11). From the clinical and histopathological point of view, group 1 cases were associated with smaller and well/moderately-differentiated grade I/II PDAC tumors, whereas and group 2 PDAC displayed a larger size and they mainly consisted of poorly-differentiated grade III carcinomas. These findings confirm the cytogenetic complexity and heterogenity of PDAC and provide evidence for the association between tumor cytogenetics and its histopathological features. In addition, we also show that the altered regions identified harbor multiple cancer associate genes that deserve further investigation to determine their relevance in the pathogenesis of PDAC.
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Affiliation(s)
- María Laura Gutiérrez
- Servicio General de Citometría, Departamento de Medicina and Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
| | - Luís Muñoz-Bellvis
- Unidad de Cirugía Hepatobiliopancreática y Trasplante de Páncreas, Departamento de Cirugía, Hospital Universitario de Salamanca, Salamanca, Spain
| | - María del Mar Abad
- Departamento de Patología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Oscar Bengoechea
- Departamento de Patología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - María González-González
- Servicio General de Citometría, Departamento de Medicina and Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Servicio General de Citometría, Departamento de Medicina and Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
- * E-mail:
| | - José María Sayagués
- Servicio General de Citometría, Departamento de Medicina and Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
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Ambatipudi S, Gerstung M, Gowda R, Pai P, Borges AM, Schäffer AA, Beerenwinkel N, Mahimkar MB. Genomic profiling of advanced-stage oral cancers reveals chromosome 11q alterations as markers of poor clinical outcome. PLoS One 2011; 6:e17250. [PMID: 21386901 PMCID: PMC3046132 DOI: 10.1371/journal.pone.0017250] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 01/22/2011] [Indexed: 11/19/2022] Open
Abstract
Identifying oral cancer lesions associated with high risk of relapse and predicting clinical outcome remain challenging questions in clinical practice. Genomic alterations may add prognostic information and indicate biological aggressiveness thereby emphasizing the need for genome-wide profiling of oral cancers. High-resolution array comparative genomic hybridization was performed to delineate the genomic alterations in clinically annotated primary gingivo-buccal complex and tongue cancers (n = 60). The specific genomic alterations so identified were evaluated for their potential clinical relevance. Copy-number changes were observed on chromosomal arms with most frequent gains on 3q (60%), 5p (50%), 7p (50%), 8q (73%), 11q13 (47%), 14q11.2 (47%), and 19p13.3 (58%) and losses on 3p14.2 (55%) and 8p (83%). Univariate statistical analysis with correction for multiple testing revealed chromosomal gain of region 11q22.1–q22.2 and losses of 17p13.3 and 11q23–q25 to be associated with loco-regional recurrence (P = 0.004, P = 0.003, and P = 0.0003) and shorter survival (P = 0.009, P = 0.003, and P 0.0001) respectively. The gain of 11q22 and loss of 11q23-q25 were validated by interphase fluorescent in situ hybridization (I-FISH). This study identifies a tractable number of genomic alterations with few underlying genes that may potentially be utilized as biological markers for prognosis and treatment decisions in oral cancers.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Carcinoma, Squamous Cell/diagnosis
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Cells, Cultured
- Chromosome Aberrations
- Chromosomes, Human, Pair 11/genetics
- Comparative Genomic Hybridization
- Disease Progression
- Female
- Gene Expression Profiling
- Genome, Human
- HeLa Cells
- Humans
- In Situ Hybridization, Fluorescence
- Male
- Middle Aged
- Mouth Neoplasms/diagnosis
- Mouth Neoplasms/genetics
- Mouth Neoplasms/pathology
- Neoplasm Staging
- Prognosis
- Validation Studies as Topic
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Affiliation(s)
- Srikant Ambatipudi
- Tata Memorial Centre (TMC), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Cancer Research Institute (CRI), Navi Mumbai, India
| | - Moritz Gerstung
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Ravindra Gowda
- Tata Memorial Centre (TMC), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Cancer Research Institute (CRI), Navi Mumbai, India
| | - Prathamesh Pai
- Head and Neck Unit, Tata Memorial Hospital, Tata Memorial Centre (TMC), Mumbai, India
| | - Anita M. Borges
- Department of Pathology and Laboratory Medicine, S. L. Raheja Hospital, Mumbai, India
| | - Alejandro A. Schäffer
- Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, United States of America
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Manoj B. Mahimkar
- Tata Memorial Centre (TMC), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Cancer Research Institute (CRI), Navi Mumbai, India
- * E-mail:
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McCabe MG, Ichimura K, Pearson DM, Liu L, Clifford SC, Ellison DW, Collins VP. Novel mechanisms of gene disruption at the medulloblastoma isodicentric 17p11 breakpoint. Genes Chromosomes Cancer 2009; 48:121-31. [DOI: 10.1002/gcc.20625] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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10
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Katkoori VR, Jia X, Chatla C, Kumar S, Ponnazhagan S, Callens T, Messiaen L, Grizzle WE, Manne U. Clinical significance of a novel single nucleotide polymorphism in the 5' untranslated region of the Rabphillin-3A-Like gene in colorectal adenocarcinoma. FRONT BIOSCI-LANDMRK 2008; 13:1050-61. [PMID: 17981610 DOI: 10.2741/2742] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The recently identified human ortholog of the Rabphillin-3A-Like (RPH3AL) gene, located at the 17p13.3 locus, has been assessed for its mutational status and clinical significance in colorectal adenocarcinoma (CRC). Prospectively collected 95 frozen CRCs and their matching benign colonic epithelial tissues were evaluated for mutations and mRNA expression. Since, we observed a higher incidence of a single nucleotide polymorphism (SNP) at the -25 position in the 5'untranslated region (5'UTR-25) of RPH3AL, we performed the genotyping analysis of this SNP in a retrospective CRC cohort (n=134) to assess their clinical importance. Univariate and multivariate outcome analyses were performed. The cDNA analysis has detected point mutations in 6 CRCs, coding region SNPs in 14 CRCs, and non-coding region SNPs in 38 CRCs. Combined analyses of both cohorts has demonstrated that the incidence of SNP at 5'UTR-25 was 41% (95 of 229), and its A/A genotype (9%, 20 of 229) was observed exclusively in non-Hispanic Caucasians, and 19 of these cases were diagnosed with nodal metastasis. Patients who exhibited homozygous for A or C alleles had a significantly decreased levels of mRNA expression, increased risk of CRC recurrence and mortality. Therefore, these findings have significant clinical implications in assessing the aggressiveness of CRC.
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Affiliation(s)
- Venkat R Katkoori
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294-7331, USA
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Hui ABY, Takano H, Lo KW, Kuo WL, Lam CNY, Tong CYK, Chang Q, Gray JW, Ng HK. Identification of a novel homozygous deletion region at 6q23.1 in medulloblastomas using high-resolution array comparative genomic hybridization analysis. Clin Cancer Res 2005; 11:4707-16. [PMID: 16000565 DOI: 10.1158/1078-0432.ccr-05-0128] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The aim of this study is to comprehensively characterize genome copy number aberrations in medulloblastomas using high-resolution array comparative genomic hybridization. EXPERIMENTAL DESIGN High-density genomic arrays containing 1,803 BAC clones were used to define recurrent chromosomal regions of gains or losses throughout the whole genome of medulloblastoma. A series of 3 medulloblastoma cell lines and 16 primary tumors were investigated. RESULTS The detected consistent chromosomal aberrations included gains of 1q21.3-q23.1 (36.8%), 1q32.1 (47.4%), 2p23.1-p25.3 (52.6%), 7 (57.9%), 9q34.13-q34.3 (47.4%), 17p11.2-q25.3 (89.5%), and 20q13.31-q13.33 (42.1%), as well as losses of 3q26.1 (57.9%), 4q31.23-q32.3 (42.1%), 6q23.1-25.3 (57.9%), 8p22-23.3 (79%), 10q24.32-26.2 (57.9%), and 16q23.2-q24.3 (63.2%). One of the most notable aberrations was a homozygous deletion on chromosome 6q23 in the cell line DAOY, and single copy loss on 30.3% primary tumors. Further analyses defined a 0.887 Mbp minimal region of homozygous deletion at 6q23.1 flanked by markers SHGC-14149 (6q22.33) and SHGC-110551 (6q23.1). Quantitative reverse transcription-PCR analysis showed complete loss of expression of two genes located at 6q23.1, AK091351 (hypothetical protein FLJ34032) and KIAA1913, in the cell line DAOY. mRNA levels of these genes was reduced in cell lines D283 and D384, and in 50% and 70% of primary tumors, respectively. CONCLUSION Current array comparative genomic hybridization analysis generates a comprehensive pattern of chromosomal aberrations in medulloblastomas. This information will lead to a better understanding of medulloblastoma tumorigenesis. The delineated regions of gains or losses will indicate locations of medulloblastoma-associated genes. A 0.887 Mbp homozygous deletion region was newly identified at 6q23.1. Frequent detection of reduced expression of AK091351 and KIAA1913 genes implicates them as suppressors of medulloblastoma tumorigenesis.
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Affiliation(s)
- Angela B Y Hui
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Hong Kong SAR, PR China
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12
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Abstract
Central nervous system (CNS) neoplasms can be diagnostically challenging, due to remarkably wide ranges in histologic appearance, biologic behavior, and therapeutic approach. Nevertheless, accurate diagnosis is the critical first step in providing optimal patient care. As with other oncology-based specialties, there is a rapidly expanding interest and enthusiasm for identifying and utilizing new biomarkers to enhance the day-to-day practice of surgical neuropathology. In this regard, the field is primed by recent advances in basic research, elucidating the molecular mechanisms of tumorigenesis and progression in the most common adult and pediatric brain tumors. Thus far, few have made the transition into routine clinical practice, the most notable example being 1p and 19q testing in oligodendroglial tumors. However, the field is rapidly evolving and many other biomarkers are likely to emerge as useful ancillary diagnostic, prognostic, or therapeutic aids. The goal of this article is to highlight the most common genetic alterations currently implicated in CNS tumors, focusing most on those that are either already in common use in ancillary molecular diagnostics testing or are likely to become so in the near future.
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Affiliation(s)
- Christine E Fuller
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, and Division of Neuropathology, Washington University School of Medicine, St. Louis, MO, USA.
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Manabe S, Nishimura N, Yamamoto Y, Kitamura H, Morimoto S, Imai M, Nagahiro S, Seino S, Sasaki T. Identification and characterization of Noc2 as a potential Rab3B effector protein in epithelial cells. Biochem Biophys Res Commun 2004; 316:218-25. [PMID: 15003533 DOI: 10.1016/j.bbrc.2004.02.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2004] [Indexed: 11/16/2022]
Abstract
The Rab3 family small G proteins (Rab3A-D) are involved in the regulated secretory pathway of brain and secretory tissues. Among Rab3-interacting proteins, Rabphilin-3, Rim, and Noc2, all of which contain a conserved Rab3-binding domain (RBD3), are generally recognized Rab3 effector proteins in neurons and secretory cells. Although Rab3B was also detected in epithelial cells, its function remained unknown. We isolated cDNA sequences from human epithelial Caco2-cell mRNA by degenerate RT-PCR based on the conserved amino acid sequence of RBD3. Multiple cDNA clones were identified as encoding Noc2. Northern blot analysis revealed that Noc2 mRNA was expressed not only in secretory tissues but also in epithelial tissues and cell lines. A pull-down assay demonstrated that Noc2 bound to Rab3B in a GTP-dependent manner. When Noc2 was co-expressed with the GTP-bound form of Rab3B, it was recruited from the cytosol to perinuclear membranes. Furthermore, overexpression of Noc2 inhibited the cell-surface transport of basolateral vesicular stomatitis virus glycoprotein. These results suggest that Noc2 functions as a potential Rab3B effector protein in epithelial cells.
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Affiliation(s)
- Shinji Manabe
- Department of Biochemistry, The University of Tokushima, Graduate School of Medicine, Tokushima 770-8503, Japan
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Risio M, Casorzo L, Chiecchio L, De Rosa G, Rossini FP. Deletions of 17p are associated with transition from early to advanced colorectal cancer. ACTA ACUST UNITED AC 2003; 147:44-9. [PMID: 14580770 DOI: 10.1016/s0165-4608(03)00188-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Several chromosome defects parallel morphologic evolution in colorectal tumor progression. Allelic losses in the short arm of chromosome 17, the majority encompassing the 17p13.3 band, have been found in advanced cancer in the absence of TP53 mutations, suggesting that loss of genes in this chromosome region is relevant for tumorigenesis. The aim of this study was to investigate 17p13.3 deletions throughout the colorectal tumor progression using two-color fluorescence in situ hybridization. Histologic sections from 20 colorectal adenomas containing early invasive carcinoma were analyzed by interphase fluorescence in situ hybridization using a centromeric probe for chromosome 17 simultaneously with a subtelomeric probe mapping to the 17p13.3 band. Separate evaluation was made for sectors corresponding to adenoma tissue with low-grade dysplasia, high-grade dysplasia, and early cancer. The same technique was also used in 20 cases of advanced adenocarcinoma of the large bowel. Loss of one centromeric signal was observed in 20, 40, 50, and 10% of low-grade dysplasia, high-grade dysplasia, early cancer, and advanced cancer, respectively (P<0.02 early vs. advanced cancer). Subtelomeric 17p deletions were seen in 60% of advanced cancer and in 15% of early cancer (P<0.01). These findings indicate that loss of genes from the 17p13.3 chromosome region may play an important role in sustaining the transition from early to advanced cancer in colorectal tumor progression.
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Affiliation(s)
- Mauro Risio
- Unit of Pathology, Institute for Cancer Research and Treatment, Strada Provinciale 142, Km. 3.95, 10060, Candiolo, Torino, Italy.
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Yingling J, Toyo-Oka K, Wynshaw-Boris A. Miller-Dieker syndrome: analysis of a human contiguous gene syndrome in the mouse. Am J Hum Genet 2003; 73:475-88. [PMID: 12905154 PMCID: PMC1180674 DOI: 10.1086/378096] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2002] [Accepted: 06/30/2003] [Indexed: 11/03/2022] Open
Affiliation(s)
- Jessica Yingling
- Departments of Pediatrics and Medicine, University of California at San Diego School of Medicine, La Jolla, CA, 92093, USA
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Zhao X, He M, Wan D, Ye Y, He Y, Han L, Guo M, Huang Y, Qin W, Wang MW, Chong W, Chen J, Zhang L, Yang N, Xu B, Wu M, Zuo L, Gu J. The minimum LOH region defined on chromosome 17p13.3 in human hepatocellular carcinoma with gene content analysis. Cancer Lett 2003; 190:221-32. [PMID: 12565177 DOI: 10.1016/s0304-3835(02)00622-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common human cancers in Asia. Previous studies have shown that in addition to aberrations of the p53 gene on chromosome 17p13.1, other gene(s) on chromosome 17p13.3 may also play a role in HCC. To detect the status of loss of heterozygosity (LOH) in HCC and to determine the minimum region of LOH on 17p13.3, we analyzed 22 paired HCC and non-cancerous liver samples with 14 polymorphic markers plus TP53 (p53 gene) as a comparison. The data revealed a high level of LOH (>68%) in a minimum region between D17S1866 and D17S1574, spanning over a 1.5 Mb region. Genomic library screening using markers in the region has resulted in the isolation of a cluster of BAC/PAC clones. We created a physical map in this region. Using large-scale genome sequencing, gene annotation, cDNA screening, and exon trapping, we identified 17 known genes and 13 novel genes in the minimum region. The function of these genes was analyzed and the possibility of several putative tumor suppressor genes was discussed.
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Affiliation(s)
- Xintai Zhao
- National Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, 2200 Xie Tu Road, 200032, Shanghai, China
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Shostak KO, Dmitrenko VV, Garifulin OM, Rozumenko VD, Khomenko OV, Zozulya YA, Zehetner G, Kavsan VM. Downregulation of putative tumor suppressor gene TSC-22 in human brain tumors. J Surg Oncol 2003; 82:57-64. [PMID: 12501169 DOI: 10.1002/jso.10180] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND AND OBJECTIVES Our objective was to identify differentially expressed genes involved in the pathogenesis of glioblastoma multiforme (GBM). METHODS Screening of arrayed human fetal brain and human postnatal brain cDNA libraries was performed by differential hybridization with glioblastoma multiforme and human normal brain cDNAs. RESULTS Repeated differential hybridization of more than 100 cDNA clones selected by primary screening and analysis of RNA from adult normal brain and glial tumors showed 16 nucleotide sequences differentially expressed between normal brain and brain tumors. Among others, decreased content in astrocytic tumors was determined for TSC-22 mRNA corresponding to cDNA in the ICRFp507J1041 clone from human fetal brain cDNA library. Northern blot hybridization of RNA from different human brain tumors showed very low amounts of TSC-22 mRNA in most investigated samples of GBM, anaplastic astrocytoma, and some other tumors. Complete lack of expression of TSC-22 occurred in one sample of anaplastic astrocytoma, as well as in meningioma, brain sarcoma, sarcomatous meningioma, and oligodendroglioma. The differential expression of TSC-22 gene was confirmed by semiquantitative RT-PCR in 15 samples of astrocytomas WHO grade II-IV and three samples of normal brain. CONCLUSIONS Significantly decreased levels of TSC-22 mRNA in human brain and salivary gland tumors and antiproliferative role of TSC-22 strongly suggest a tumor suppressor role for TSC-22. J.
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Smith JS, Tachibana I, Pohl U, Lee HK, Thanarajasingam U, Portier BP, Ueki K, Ramaswamy S, Billings SJ, Mohrenweiser HW, Louis DN, Jenkins RB. A transcript map of the chromosome 19q-arm glioma tumor suppressor region. Genomics 2000; 64:44-50. [PMID: 10708517 DOI: 10.1006/geno.1999.6101] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Allelic loss of the chromosome 19q arm is a frequent event in human diffuse gliomas, suggesting that it contains a tumor suppressor gene. Recent deletion mapping studies have broadly implicated a 1.6-Mb interval between D19S241E and D19S596, with a limited subset of tumors, suggesting that the region may be as narrow as 150 kb. Focusing on this smaller interval, we have used cDNA selection, exon amplification, and genomic sequencing to identify three novel transcripts (EHD2, GLTSCR1, and GLTSCR2) and to map two known genes (SEPW1 and CRX). A partial transcript map of 19 transcripts and two EST markers has been constructed for the 1.6-Mb interval D19S241E-D19S596. Ten of these transcripts, including the 5 mapped to the 150-kb deletion interval, have been examined for alterations in a panel of gliomas with allelic loss of 19q. Tumor-specific alterations have not been identified in the transcripts examined thus far. Collectively, these data should facilitate subsequent efforts to identify and characterize the remaining transcripts in the 1.6-Mb interval.
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Affiliation(s)
- J S Smith
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic and Foundation, Rochester, MN, 55905, USA
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Fr�hwald MC, O'Dorisio MS, Dai Z, Rush LJ, Krahe R, Smiraglia DJ, Pietsch T, Elsea SH, Plass C. Aberrant hypermethylation of the major breakpoint cluster region in 17p11.2 in medulloblastomas but not supratentorial PNETs. Genes Chromosomes Cancer 2000. [DOI: 10.1002/1098-2264(2000)9999:9999<::aid-gcc1052>3.0.co;2-s] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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