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Spiliopoulou P, Yang SC, Bruce JP, Wang BX, Berman HK, Pugh TJ, Siu LL. All is not lost: learning from 9p21 loss in cancer. Trends Immunol 2022; 43:379-390. [DOI: 10.1016/j.it.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 12/11/2022]
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Eichenauer T, Simmendinger L, Kluth M, Chirico V, Luebke AM, Höflmayer D, Hinsch A, Jacobsen F, Hube-Magg C, Möller-Koop C, Dahlem R, Fisch M, Rink M, Riechardt S, Tsourlakis MC, Büscheck F, Bernreuther C, Clauditz T, Lebok P, Simon R, Sauter G, Wilczak W, Fraune C. Chromosomal deletion of 9p21 is linked to poor patient prognosis in papillary and clear cell kidney cancer. Urol Oncol 2020; 38:605.e1-605.e8. [PMID: 32241691 DOI: 10.1016/j.urolonc.2020.02.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/07/2020] [Accepted: 02/19/2020] [Indexed: 01/27/2023]
Abstract
BACKGROUND The ongoing approval of adjuvant systemic therapy in high-risk kidney tumor will increase the demand for prognostic assessment in these tumors. 9p21 deletion has been suggested as a possible prognostic feature in clear cell kidney cancer. MATERIAL AND METHODS To learn more on the prognostic relevance of 9p21 deletions in clear cell and other kidney tumors, 1,809 kidney tumor specimens were analyzed by dual-labeling fluorescence in situ hybridization (FISH) with probes for 9p21 and centromere 9 in a tissue microarray format. Results were compared to histologic tumor type, pT stage, grade, and patient outcome. RESULTS A total of 1,341 (74%) of tumor samples had interpretable FISH results. 9p21 deletion was found in 4.4% of 894 clear cell, 5.1% of 197 papillary, and 4.2% of 71 chromophobe carcinomas. 9p21 deletions were not found in 112 oncocytomas and in 21 clear cell tubulo-papillary cancers. In clear cell carcinomas, 9p deletions were associated with advanced stage (P = 0.009) and nodal metastasis (P = 0.0067), but not with ISUP grade (P = 0.1039) and distant metastasis (P = 0.4809). Also, in papillary carcinomas, 9p deletions were associated with advanced stage (P = 0.0008) and nodal metastasis (P = 0.0202) but not with ISUP grade (0.0904) and distant metastasis (P = 0.2022). Follow-up data were available for 789 clear cell and 177 papillary cancers. In both tumor entities, 9p21 deletions were associated with shortened overall survival, tumor-specific death, and progression-free survival in univariate analysis (P < 0.02 each). In a multivariate analysis, 9p21 deletion was an independent predictor of early tumor recurrence (P = 0.04). CONCLUSION 9p21 deletions, 9p21 deletions identify a small subset of aggressive renal carcinomas. 9p deletion assessment may be clinically useful to identify high-risk renal cell carcinomas.
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Affiliation(s)
- Till Eichenauer
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Luca Simmendinger
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Victoria Chirico
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas M Luebke
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Doris Höflmayer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrea Hinsch
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Frank Jacobsen
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christina Möller-Koop
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roland Dahlem
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Margit Fisch
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Rink
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Silke Riechardt
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Franziska Büscheck
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Bernreuther
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Clauditz
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Patrick Lebok
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Waldemar Wilczak
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Fraune
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Correlation between Chromosome 9p21 Locus Deletion and Prognosis in Clinically Localized Prostate Cancer. Int J Biol Markers 2017; 32:e248-e254. [DOI: 10.5301/jbm.5000242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2016] [Indexed: 01/16/2023]
Abstract
Background Some studies have reported that deletions at chromosome arm 9p occur frequently and represent a critical step in carcinogenesis of some neoplasms. Our aim was to evaluate the deletion of locus 9p21 and chromosomes 3, 7 and 17 in localized prostate cancer (PC) and correlate these alterations with prognostic factors and biochemical recurrence after surgery. Methods We retrospectively evaluated surgical specimens from 111 patients with localized PC who underwent radical prostatectomy. Biochemical recurrence was defined as a prostate-specific antigen (PSA) >0.2 ng/mL and the mean postoperative follow-up was 123 months. The deletions were evaluated using fluorescence in situ hybridization with centromeric and locus-specific probes in a tissue microarray containing 2 samples from each patient. We correlated the occurrence of any deletion with pathological stage, Gleason score, ISUP grade group, PSA and biochemical recurrence. Results We observed a loss of any probe in only 8 patients (7.2%). The most common deletion was the loss of locus 9p21, which occurred in 6.4% of cases. Deletions of chromosomes 3, 7 and 17 were observed in 2.3%, 1.2% and 1.8% patients, respectively. There was no correlation between chromosome loss and Gleason score, ISUP, PSA or stage. Biochemical recurrence occurred in 83% cases involving 9p21 deletions. Loss of 9p21 locus was significantly associated with time to recurrence (p = 0.038). Conclusions We found low rates of deletion in chromosomes 3, 7 and 17 and 9p21 locus. We observed that 9p21 locus deletion was associated with worse prognosis in localized PC treated by radical prostatectomy.
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Chen X, Xiong W, Li H. Comparison of microRNA expression profiles in K562-cells-derived microvesicles and parental cells, and analysis of their roles in leukemia. Oncol Lett 2016; 12:4937-4948. [PMID: 28105201 PMCID: PMC5228523 DOI: 10.3892/ol.2016.5308] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/20/2016] [Indexed: 02/07/2023] Open
Abstract
Microvesicles (MVs) are 30-1,000-nm extracellular vesicles that are released from a multitude of cell types and perform diverse cellular functions, including intercellular communication, antigen presentation, and transfer of proteins, messenger RNA and microRNA (also known as miR). MicroRNAs have been demonstrated to be aberrantly expressed in leukemia, and the overall microRNA expression profile may differentiate normal blood cells vs. leukemia cells. MVs containing microRNAs may enable intercellular cross-talk in vivo. This prompted us to investigate specific variations of microRNA expression patterns in MVs derived from leukemia cells. The present study examined the microRNA expression profile of MVs from chronic myeloid leukemia K562 cells and that of MVs from normal human volunteers' peripheral blood cells. The potential targets of the differentially expressed microRNAs were predicted using computational searches. Bioinformatic analyses of the predicted target genes were performed for further evaluation. The present study analyzed microRNAs of MVs derived from leukemia and normal cells, and characterized specific microRNAs expression. The results revealed that MVs derived from K562 cells expressed 181 microRNAs of the 888 microRNAs assessed. Further analysis revealed that 16 microRNAs were downregulated, while 7 were upregulated in these MVs. In addition, significant differences in microRNA expression profiles between MVs derived from K562 cells and K562 cells were identified. The present results revealed that 77 and 122 microRNAs were only expressed in MVs derived from K562 cells and in K562 cells, respectively. There were 104 microRNAs co-expressed in MVs derived from K562 cells and in K562 cells. Target gene-related pathway analyses demonstrated that the majority of the dysregulated microRNAs were involved in pathways associated with leukemia, particularly the mitogen-activated protein kinase (MAPK) and the p53 signaling pathways. By further conducting microRNA gene network analysis, the present study revealed that the miR-15a/b, miR-16, miR-17 and miR-30 families were likely to play a role in the regulation of the MAPK signaling pathway. Since K562 cells presented the t(9;22) translocation, the current study further examined the predicted function of 12 microRNAs located in chromosomes 9 [Homo sapiens (hsa)-let-7a, hsa-let-7f, miR-126, miR-126*, miR-23b, miR-24, miR-27b and miR-7] and 22 (hsa-let-7b, miR-1249, miR-130b and miR-185), which were expressed both in MVs derived from K562 cells and in K562 cells. The present study identified microRNAs of MVs from leukemia and normal cells, and characterized the expression of specific microRNAs. The current study is also the first to identify and characterize distinct microRNA expression between MVs derived from K562 cells and K562 cells. These findings highlight that a number of microRNAs from leukemia-derived MVs may contribute to the development of hematopoietic malignancies. Further investigation may reveal the function of these differentially expressed microRNAs and may provide potential targets for novel therapeutic strategies.
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Affiliation(s)
- Xiaomei Chen
- Center for Biotherapy, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Wei Xiong
- Center of Clinical Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine at Binjiang, Hangzhou, Zhejiang 310009, P.R. China
| | - Huiyu Li
- Center for Stem Cell Research and Application, Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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El-Mokadem I, Lim A, Kidd T, Garret K, Pratt N, Batty D, Fleming S, Nabi G. Microsatellite alteration and immunohistochemical expression profile of chromosome 9p21 in patients with sporadic renal cell carcinoma following surgical resection. BMC Cancer 2016; 16:546. [PMID: 27465101 PMCID: PMC4963937 DOI: 10.1186/s12885-016-2514-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 06/27/2016] [Indexed: 11/20/2022] Open
Abstract
Background Long-term prognostic significance of loss of heterozygosity on chromosome 9p21 for localized renal cell carcinoma following surgery remains unreported. The study assessed the frequency of deletions of different loci of chromosome 9p along with immunohistochemical profile of proteins in surgically resected renal cancer tissue and correlated this with long-term outcomes. Methods DNA was extracted from renal tumours and corresponding normal kidney tissues in prospectively collected samples of 108 patients who underwent surgical resection for clinically localized disease between January 2001 and December 2005, providing a minimum of 9 years follow-up for each participant. After checking quality of DNA, amplified by PCR, loss of heterozygosity (LOH) on chromosome 9p was assessed using 6 microsatellite markers in 77 clear cell carcinoma. Only 5 of the markers showed LOH (D9S1814, D9S916, D9S974, D9S942, and D9S171). Protein expression of p15(INK4b), p16(INK4a), p14(ARF), CAIX, and adipose related protein (ADFP) were demonstrated by immunostaining in normal and cancer tissues. Loss of heterozygosity for microsatellite analysis was correlated with tumour characteristics, recurrence free, cancer specific, and overall survival, including significance of immunohistochemical profile of protein expressions. Results The main deletion was found at loci telomeric to CDKN2A region at D9S916. There was a significant correlation between frequency of LOH stage (p = 0.005) and metastases (p = 0.006) suggesting a higher LOH for advanced and aggressive renal cell carcinoma. Most commonly observed LOH in the 3 markers: D9S916, D9S974, and D9S942 were associated with poor survival, and were statistically significant on multivariate analysis. Immunohistochemical expression of p14, p15, and p16 proteins were either low or absent in cancer tissue compared to normal. Conclusions Loss of heterozygosity of p921 chromosome is associated with aggressive tumours, and predicts cancer specific or recurrence free survival on long-term follow-up. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2514-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ismail El-Mokadem
- Academic Section of Urology, Division of Cancer Research, Ninewells Hospital, University of Dundee, Dundee, DD1 9SY, UK
| | - Alison Lim
- Academic Section of Urology, Division of Cancer Research, Ninewells Hospital, University of Dundee, Dundee, DD1 9SY, UK
| | - Thomas Kidd
- Department of Pathology, Ninewells Hospital, University of Dundee, Dundee, DD1 9SY, UK
| | - Katherine Garret
- Department of Pathology, Ninewells Hospital, University of Dundee, Dundee, DD1 9SY, UK
| | - Norman Pratt
- Department of Cytogenetic, Ninewells Hospital, University of Dundee, Dundee, DD1 9SY, UK
| | - David Batty
- Department of Cytogenetic, Ninewells Hospital, University of Dundee, Dundee, DD1 9SY, UK
| | - Stewart Fleming
- Department of Pathology, Ninewells Hospital, University of Dundee, Dundee, DD1 9SY, UK
| | - Ghulam Nabi
- Academic Section of Urology, Division of Cancer Research, Ninewells Hospital, University of Dundee, Dundee, DD1 9SY, UK.
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Genetic and Chromosomal Aberrations and Their Clinical Significance in Renal Neoplasms. BIOMED RESEARCH INTERNATIONAL 2015; 2015:476508. [PMID: 26448938 PMCID: PMC4584050 DOI: 10.1155/2015/476508] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/23/2015] [Accepted: 05/25/2015] [Indexed: 12/16/2022]
Abstract
The most common form of malignant renal neoplasms is renal cell carcinoma (RCC), which is classified into several different subtypes based on the histomorphological features. However, overlaps in these characteristics may present difficulties in the accurate diagnosis of these subtypes, which have different clinical outcomes. Genomic and molecular studies have revealed unique genetic aberrations in each subtype. Knowledge of these genetic changes in hereditary and sporadic renal neoplasms has given an insight into the various proteins and signalling pathways involved in tumour formation and progression. In this review, the genetic aberrations characteristic to each renal neoplasm subtype are evaluated along with the associated protein products and affected pathways. The potential applications of these genetic aberrations and proteins as diagnostic tools, prognostic markers, or therapeutic targets are also assessed.
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Li WQ, Pfeiffer RM, Hyland PL, Shi J, Gu F, Wang Z, Bhattacharjee S, Luo J, Xiong X, Yeager M, Deng X, Hu N, Taylor PR, Albanes D, Caporaso NE, Gapstur SM, Amundadottir L, Chanock SJ, Chatterjee N, Landi MT, Tucker MA, Goldstein AM, Yang XR. Genetic polymorphisms in the 9p21 region associated with risk of multiple cancers. Carcinogenesis 2014; 35:2698-705. [PMID: 25239644 DOI: 10.1093/carcin/bgu203] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The chromosome 9p21 region has been implicated in the pathogenesis of multiple cancers. We analyzed 9p21 single nucleotide polymorphisms (SNPs) from eight genome-wide association studies (GWAS) with data deposited in dbGaP, including studies of esophageal squamous cell carcinoma (ESCC), gastric cancer (GC), pancreatic cancer, renal cell carcinoma (RCC), lung cancer (LC), breast cancer (BrC), bladder cancer (BC) and prostate cancer (PrC). The number of subjects ranged from 2252 (PrC) to 7619 (LC). SNP-level analyses for each cancer were conducted by logistic regression or random-effects meta-analysis. A subset-based statistical approach (ASSET) was performed to combine SNP-level P values across multiple cancers. We calculated gene-level P values using the adaptive rank truncated product method. We identified that rs1063192 and rs2157719 in the CDKN2A/2B region were significantly associated with ESCC and rs2764736 (3' of TUSC1) was associated with BC (P ≤ 2.59 × 10(-6)). ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2A intronic) with ESCC, GC and BC (P = 3.96 × 10(-) (4)); rs10811474 (3' of IFNW1) with RCC and BrC (P = 0.001); rs12683422 (LINGO2 intronic) with RCC and BC (P = 5.93 × 10(-) (4)) and rs10511729 (3' of ELAVL2) with LC and BrC (P = 8.63 × 10(-) (4)). At gene level, CDKN2B, CDKN2A and CDKN2B-AS1 were significantly associated with ESCC (P ≤ 4.70 × 10(-) (5)). Rs10511729 and rs10811474 were associated with cis-expression of 9p21 genes in corresponding cancer tissues in the expression quantitative trait loci analysis. In conclusion, we identified several genetic variants in the 9p21 region associated with the risk of multiple cancers, suggesting that this region may contribute to a shared susceptibility across different cancer types.
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Affiliation(s)
- Wen-Qing Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Department of Dermatology, Warren Alpert Medical School, Brown University, Providence, RI, USA,
| | - Ruth M Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Paula L Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Fangyi Gu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | | | - Jun Luo
- Information Management Services, Inc., Calverton, MD, USA and
| | - Xiaoqin Xiong
- Information Management Services, Inc., Calverton, MD, USA and
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | - Xiang Deng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Laufey Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
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El-Mokadem I, Fitzpatrick J, Bondad J, Rauchhaus P, Cunningham J, Pratt N, Fleming S, Nabi G. Chromosome 9p deletion in clear cell renal cell carcinoma predicts recurrence and survival following surgery. Br J Cancer 2014; 111:1381-90. [PMID: 25137021 PMCID: PMC4183850 DOI: 10.1038/bjc.2014.420] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/25/2014] [Accepted: 07/01/2014] [Indexed: 11/23/2022] Open
Abstract
Background: Wider clinical applications of 9p status in clear cell renal cell carcinoma (ccRCC) are limited owing to the lack of validation and consensus for interphase fluorescent in situ hybridisation (I-FISH) scoring technique. The aim of this study was to analytically validate the applicability of I-FISH in assessing 9p deletion in ccRCC and to clinically assess its long-term prognostic impact following surgical excision of ccRCC. Methods: Tissue microarrays were constructed from 108 renal cell carcinoma (RCC) tumour paraffin blocks. Interphase fluorescent in situ hybridisation analysis was undertaken based on preset criteria by two independent observers to assess interobserver variability. 9p status in ccRCC tumours was determined and correlated to clinicopathological variables, recurrence-free survival and disease-specific survival. Results: There were 80 ccRCCs with valid 9p scoring and a median follow-up of 95 months. Kappa statistic for interobserver variability was 0.71 (good agreement). 9p deletion was detected in 44% of ccRCCs. 9p loss was associated with higher stage, larger tumours, necrosis, microvascular and renal vein invasion, and higher SSIGN (stage, size, grade and necrosis) score. Patients with 9p-deleted ccRCC were at a higher risk of recurrence (P=0.008) and RCC-specific mortality (P=0.001). On multivariate analysis, 9p deletion was an independent predictor of recurrence (hazard ratio 4.323; P=0.021) and RCC-specific mortality (hazard ratio 4.603; P=0.007). The predictive accuracy of SSIGN score improved from 87.7% to 93.1% by integrating 9p status to the model (P=0.001). Conclusions: Loss of 9p is associated with aggressive ccRCC and worse prognosis in patients following surgery. Our findings independently confirm the findings of previous reports relying on I-FISH to detect 9p (CDKN2A) deletion.
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Affiliation(s)
- I El-Mokadem
- Academic section of Urology, Medical Research Institute, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - J Fitzpatrick
- Academic section of Urology, Medical Research Institute, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - J Bondad
- Academic section of Urology, Medical Research Institute, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - P Rauchhaus
- Division of Population Sciences, Medical Research Institute, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - J Cunningham
- Department of Clinical Genetics, NHS Tayside Health Board, Dundee DD1 9SY, UK
| | - N Pratt
- Department of Clinical Genetics, NHS Tayside Health Board, Dundee DD1 9SY, UK
| | - S Fleming
- Department of Pathology, Medical Research Institute, School of Medicine, Dundee DD1 9SY, UK
| | - G Nabi
- Academic section of Urology, Medical Research Institute, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
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Significance of chromosome 9p status in renal cell carcinoma: a systematic review and quality of the reported studies. BIOMED RESEARCH INTERNATIONAL 2014; 2014:521380. [PMID: 24877109 PMCID: PMC4022119 DOI: 10.1155/2014/521380] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/02/2014] [Indexed: 01/03/2023]
Abstract
Defining the prognosis of renal cell carcinoma (RCC) using genetic tests is an evolving area. The prognostic significance of 9p status in RCC, although described in the literature, remains underutilised in clinical practice. The study explored the causes of this translational gap. A systematic review on the significance of 9p status in RCC was performed to assess its clinical applicability and impact on clinical decision-making. Medline, Embase, and other electronic searches were made for studies reporting on 9p status in RCC. We collected data on: genetic techniques, pathological parameters, clinical outcomes, and completeness of follow-up assessment. Eleven studies reporting on 1,431 patients using different genetic techniques were included. The most commonly used genetic technique for the assessment of 9p status in RCC was fluorescence in situ hybridization. Combined genomic hybridisation (CGH), microsatellite analysis, karyotyping, and sequencing were other reported techniques. Various thresholds and cut-off values were used for the diagnosis of 9p deletion in different studies. Standardization, interobserver agreement, and consensus on the interpretation of test remained poor. The studies lacked validation and had high risk of bias and poor clinical applicability as assessed by two independent reviewers using a modified quality assessment tool. Further protocol driven studies with standardised methodology including use of appropriate positive and negative controls, assessment of interobserver variations, and evidenced based follow-up protocols are needed to clarify the role of 9p status in predicting oncological outcomes in renal cell cancer.
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Hosseini SA, Horton S, Saldivar JC, Miuma S, Stampfer MR, Heerema NA, Huebner K. Common chromosome fragile sites in human and murine epithelial cells and FHIT/FRA3B loss-induced global genome instability. Genes Chromosomes Cancer 2013; 52:1017-29. [PMID: 23929738 PMCID: PMC4293015 DOI: 10.1002/gcc.22097] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/06/2013] [Indexed: 01/21/2023] Open
Abstract
Chromosomal positions of common fragile sites differ in lymphoblasts and fibroblasts, with positions dependent on the epigenetically determined density of replication origins at these loci. Because rearrangement of fragile loci and associated loss of fragile gene products are hallmarks of cancers, we aimed to map common fragile sites in epithelial cells, from which most cancers derive. Among the five most frequently activated sites in human epithelial cells were chromosome bands 2q33 and Xq22.1, which are not among top fragile sites identified in lymphoblasts or fibroblasts. FRA16D at 16q23 was among the top three fragile sites in the human epithelial cells examined, as it is in lymphoblasts and fibroblasts, while FRA3B at 3p14.2, the top fragile locus in lymphoblasts, was not fragile in most epithelial cell lines tested. Epithelial cells exhibited varying hierarchies of fragile sites; some frequent epithelial cell fragile sites are apparently not frequently altered in epithelial cancers and sites that are frequently deleted in epithelial cancers are not necessarily among the most fragile. Since we have reported that loss of expression of the FRA3B-encoded FHIT protein causes increased replication stress-induced DNA damage, we also examined the effect of FHIT-deficiency on markers of genome instability in epithelial cells. FHIT-deficient cells exhibited increases in fragile breaks and in γH2AX and 53BP1 foci in G1 phase cells, confirming in epithelial cells that the FHIT gene and encompassing FRA3B, is a "caretaker gene" necessary for maintenance of genome stability.
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Affiliation(s)
- Seyed Ali Hosseini
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Susan Horton
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Joshua C. Saldivar
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Satoshi Miuma
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Martha R. Stampfer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Nyla A. Heerema
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Kay Huebner
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Wexner Medical Center, Columbus, OH
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11
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Du Y, Su T, Tan X, Li X, Xie J, Wang G, Shen J, Hou J, Cao G. Polymorphism in protein tyrosine phosphatase receptor delta is associated with the risk of clear cell renal cell carcinoma. Gene 2013; 512:64-9. [DOI: 10.1016/j.gene.2012.09.094] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/28/2012] [Accepted: 09/27/2012] [Indexed: 10/27/2022]
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12
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Shen C, Kaelin WG. The VHL/HIF axis in clear cell renal carcinoma. Semin Cancer Biol 2012; 23:18-25. [PMID: 22705278 DOI: 10.1016/j.semcancer.2012.06.001] [Citation(s) in RCA: 284] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 06/05/2012] [Indexed: 02/08/2023]
Abstract
Inactivation of the VHL tumor suppressor protein (pVHL) is a common event in clear cell renal carcinoma, which is the most common form of kidney cancer. pVHL performs many functions, including serving as the substrate recognition module of an ubiquitin ligase complex that targets the alpha subunits of the heterodimeric HIF transcription factor for proteasomal degradation. Deregulation of HIF2α appears to be a driving force in pVHL-defective clear cell renal carcinomas. In contrast, genetic and functional studies suggest that HIF1α serves as a tumor suppressor and is a likely target of the 14q deletions that are characteristic of this tumor type. Drugs that inhibit HIF2α, or its downstream targets such as VEGF, are in various stages of clinical testing. Indeed, clear cell renal carcinomas are exquisitely sensitive to VEGF deprivation and four VEGF inhibitors have now been approved for the treatment of this disease.
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Affiliation(s)
- Chuan Shen
- Howard Hughes Medical Insititute, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, United States
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13
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Li X, Tan X, Yu Y, Chen H, Chang W, Hou J, Xu D, Ma L, Cao G. D9S168 microsatellite alteration predicts a poor prognosis in patients with clear cell renal cell carcinoma and correlates with the down-regulation of protein tyrosine phosphatase receptor delta. Cancer 2011; 117:4201-11. [DOI: 10.1002/cncr.26028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 01/12/2011] [Accepted: 01/18/2011] [Indexed: 11/09/2022]
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14
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Halat S, Eble JN, Grignon DJ, Lopez-Beltran A, Montironi R, Tan PH, Wang M, Zhang S, MacLennan GT, Cheng L. Multilocular cystic renal cell carcinoma is a subtype of clear cell renal cell carcinoma. Mod Pathol 2010; 23:931-6. [PMID: 20348877 DOI: 10.1038/modpathol.2010.78] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Multilocular cystic renal cell carcinoma is an uncommon low grade renal cell carcinoma with unique morphologic features. Its cytogenetic characteristics have not been fully investigated. Its relationship to typical clear cell renal cell carcinoma is uncertain. We evaluated 19 cases of multilocular cystic renal cell carcinoma diagnosed by strict morphologic criteria using the 2004 WHO classification system. The control group consisted of 19 low grade (Fuhrman grades 1 or 2) clear cell renal cell carcinomas. Chromosome 3p deletion status was determined by dual color interphase fluorescence in situ hybridization analysis. Chromosome 3p deletion was identified in 17 out of 19 (89%) of the clear cell renal cell carcinoma cases and 14 out of 19 (74%) of the multilocular cystic renal cell carcinoma cases, respectively. There was no difference in the status of chromosome 3p deletion between clear cell renal cell carcinoma and multilocular cystic renal cell carcinoma (P=0.40). These results support the concept that multilocular cystic renal cell carcinoma as a subtype of clear cell renal cell carcinoma.
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Affiliation(s)
- Shams Halat
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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15
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Cheng L, Williamson SR, Zhang S, MacLennan GT, Montironi R, Lopez-Beltran A. Understanding the molecular genetics of renal cell neoplasia: implications for diagnosis, prognosis and therapy. Expert Rev Anticancer Ther 2010; 10:843-864. [DOI: 10.1586/era.10.72] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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16
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Chyhrai A, Sanjmyatav J, Gajda M, Reichelt O, Wunderlich H, Steiner T, Tanović E, Junker K. Multi-colour FISH on preoperative renal tumour biopsies to confirm the diagnosis of uncertain renal masses. World J Urol 2010; 28:269-74. [DOI: 10.1007/s00345-010-0551-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 03/31/2010] [Indexed: 10/19/2022] Open
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17
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Nord H, Hartmann C, Andersson R, Menzel U, Pfeifer S, Piotrowski A, Bogdan A, Kloc W, Sandgren J, Olofsson T, Hesselager G, Blomquist E, Komorowski J, von Deimling A, Bruder CEG, Dumanski JP, Díaz de Ståhl T. Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array. Neuro Oncol 2010; 11:803-18. [PMID: 19304958 DOI: 10.1215/15228517-2009-013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Glioblastomas (GBs) are malignant CNS tumors often associated with devastating symptoms. Patients with GB have a very poor prognosis, and despite treatment, most of them die within 12 months from diagnosis. Several pathways, such as the RAS, tumor protein 53 (TP53), and phosphoinositide kinase 3 (PIK3) pathways, as well as the cell cycle control pathway, have been identified to be disrupted in this tumor. However, emerging data suggest that these aberrations represent only a fraction of the genetic changes involved in gliomagenesis. In this study, we have applied a 32K clone-based genomic array, covering 99% of the current assembly of the human genome, to the detailed genetic profiling of a set of 78 GBs. Complex patterns of aberrations, including high and narrow copy number amplicons, as well as a number of homozygously deleted loci, were identified. Amplicons that varied both in number (three on average) and in size (1.4 Mb on average) were frequently detected (81% of the samples). The loci encompassed not only previously reported oncogenes (EGFR, PDGFRA, MDM2, and CDK4) but also numerous novel oncogenes as GRB10, MKLN1, PPARGC1A, HGF, NAV3, CNTN1, SYT1, and ADAMTSL3. BNC2, PTPLAD2, and PTPRE, on the other hand, represent novel candidate tumor suppressor genes encompassed within homozygously deleted loci. Many of these genes are already linked to several forms of cancer; others represent new candidate genes that may serve as prognostic markers or even as therapeutic targets in the future. The large individual variation observed between the samples demonstrates the underlying complexity of the disease and strengthens the demand for an individualized therapy based on the genetic profile of the patient.
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Affiliation(s)
- Helena Nord
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden
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18
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Cheng L, Zhang S, MacLennan GT, Lopez-Beltran A, Montironi R. Molecular and cytogenetic insights into the pathogenesis, classification, differential diagnosis, and prognosis of renal epithelial neoplasms. Hum Pathol 2009; 40:10-29. [PMID: 19027455 DOI: 10.1016/j.humpath.2008.09.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 09/10/2008] [Accepted: 09/12/2008] [Indexed: 10/21/2022]
Abstract
Renal cell carcinomas comprise a heterogeneous group of epithelial neoplasms with diverse biologic potential and variable clinical outcomes. The application of molecular and cytogenetic techniques to the study of renal neoplasms has improved our understanding of the molecular mechanisms responsible for tumor initiation and progression. Molecular classification of renal cell carcinomas has also provided new avenues for diagnosis, clinical outcome, and therapy response prediction. In this article, we review the molecular markers for various renal epithelial neoplasms and discuss the mechanisms underlying the development of these neoplasms. We also evaluate the use of molecular and cytogenetic techniques in establishing an accurate diagnosis in difficult cases and their potential usefulness in accurately classifying renal neoplasms, assessing prognosis, and selecting appropriate therapy.
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Affiliation(s)
- Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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19
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Brunelli M, Eccher A, Gobbo S, Ficarra V, Novara G, Cossu-Rocca P, Bonetti F, Menestrina F, Cheng L, Eble JN, Martignoni G. Loss of chromosome 9p is an independent prognostic factor in patients with clear cell renal cell carcinoma. Mod Pathol 2008; 21:1-6. [PMID: 17906617 DOI: 10.1038/modpathol.3800967] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Loss of chromosome 9p has been implicated in the progression of renal cell carcinoma. We evaluated the clinical utility of fluorescence in situ hybridization analysis of loss of chromosome 9p in 73 patients with clear cell renal cell carcinomas with varied stage, size, grade, necrosis (SSIGN) scores. Loss of chromosome 9p was observed in 13 tumors (18%). The 5-year cancer-specific survival of patients without loss of chromosome 9p was 88% and was 43% in those with loss of chromosome 9p (P<0.001). Local extension of the primary tumor according to the 2002 TNM staging system, lymph node involvement, the presence of distant metastases, and the SSIGN score were the other variables that predicted cancer-specific survival in univariate analysis. Loss of chromosome 9p was an independent prognostic factor in multivariate analysis. Our data indicate that the detection of chromosome 9p loss by fluorescence in situ hybridization analysis of clear cell renal cell carcinoma adds prognostic information beyond the pathological factors included in the current predictive models for renal cell carcinoma, such as SSIGN score.
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Affiliation(s)
- Matteo Brunelli
- Department of Pathology, University of Verona, Verona, Italy
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20
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Shimazui T, Ami Y, Yoshikawa K, Uchida K, Kojima T, Oikawa T, Nakamura K, Honda N, Hinotsu S, Miyazaki J, Kunita N, Akaza H. Prediction of in vitro response to interferon-alpha in renal cell carcinoma cell lines. Cancer Sci 2007; 98:529-34. [PMID: 17284252 PMCID: PMC11159908 DOI: 10.1111/j.1349-7006.2007.00421.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
We analyzed the correlation between interferon-alpha (IFNalpha) response and gene expression profiles to predict IFNalpha sensitivity and identified key molecules regulating the IFNalpha response in renal cell carcinoma (RCC) cell lines. To classify eight RCC cell lines of the SKRC series into three subgroups according to IFNalpha sensitivity, that is, sensitive, resistant and intermediate group, responses to IFNalpha (300-3000 IU/mL) were quantified by WST-1 assay. Microarray, followed by supervised hierarchical clustering analysis, was applied to selected genes according to IFNalpha sensitivity. In order to find alteration of expression profiles induced by IFNalpha, sequential microarray analyses were performed at 3, 6, and 12 h after IFNalpha treatment of RCC cell lines and mRNA expression level was confirmed using quantitative real time polymerase chain reaction. According to the sequential microarray analysis between IFNalpha-sensitive and -resistant line, seven genes were selected as candidates for IFNalpha-sensitivity-related genes in RCC cell lines. Among these seven genes, we further developed a model to predict tumor inhibition with four genes, that is, adipose differentiation-related protein, microphthalmia associated transcription factor, mitochondrial tumor suppressor 1, and troponin T1 using multiple linear regression analysis (coefficient=0.948, P=0.0291) and validated the model using other RCC cell lines including six primary cultured RCC cells. The expression levels of the combined selected genes may provide predictive information on the IFNalpha response in RCC. Furthermore, the IFNalpha response to RCC might be modulated by regulation of the expression level of these molecules.
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Affiliation(s)
- Toru Shimazui
- Department of Urology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
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21
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Jones TD, Eble JN, Wang M, MacLennan GT, Delahunt B, Brunelli M, Martignoni G, Lopez-Beltran A, Bonsib SM, Ulbright TM, Zhang S, Nigro K, Cheng L. Molecular Genetic Evidence for the Independent Origin of Multifocal Papillary Tumors in Patients with Papillary Renal Cell Carcinomas. Clin Cancer Res 2005; 11:7226-33. [PMID: 16243792 DOI: 10.1158/1078-0432.ccr-04-2597] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE In patients with papillary renal cell carcinoma, it is not uncommon to find two or more anatomically distinct and histologically similar tumors at radical nephrectomy. Whether these multiple papillary lesions result from intrarenal metastasis or arise independently is unknown. Previous studies have shown that multifocal clear cell renal cell carcinomas express identical allelic loss and shift patterns in the different tumors within the same kidney, consistent with a clonal origin. However, similar clonality assays for multifocal papillary renal cell neoplasia have not been done. Molecular analysis of microsatellite and chromosome alterations and X-chromosome inactivation status in separate tumors in the same patient can be used to study the genetic relationships among the coexisting multiple tumors. EXPERIMENTAL DESIGN We examined specimens from 21 patients who underwent radical nephrectomy for renal cell carcinoma. All patients had multiple separate papillary lesions (ranging from 2 to 5). Eighteen patients had multiple papillary renal cell carcinomas. Seven had one or more papillary renal cell carcinomas with coexisting papillary adenomas. Genomic DNA samples were prepared from formalin-fixed, paraffin-embedded tissue sections using laser-capture microdissection. Loss of heterozygosity assays were done for six microsatellite polymorphic markers for putative tumor suppressor genes on chromosomes 3p14 (D3S1285), 7q31 (D7S522), 9p21 (D9S171), 16q23 (D16S507), 17q21 (D17S1795), and 17p13 (TP53). X-chromosome inactivation analyses were done on the papillary kidney tumors from three female patients. Fluorescence in situ hybridization analysis was done on the tumors of selected patients showing allelic loss at loci on chromosome 7 and/or chromosome 17. RESULTS Twenty of 21 (95%) cases showed allelic loss in one or more of the papillary lesions in at least one of the six polymorphic markers analyzed. A concordant allelic loss pattern between each coexisting kidney tumor was seen in only 1 of 21 (5%) cases. A concordant pattern of nonrandom X-chromosome inactivation in the coexisting multiple papillary lesions was seen in two of three female patients. A discordant pattern of X-chromosome inactivation was seen in the tumors of the other female patient. Fluorescence in situ hybridization showed that the majority of tumors analyzed had gains of chromosomes 7 and 17. Two patients had one tumor with chromosomal gain and another separate tumor that did not. CONCLUSION Our data suggest that, unlike multifocal clear cell renal cell carcinomas, the multiple tumors in patients with papillary renal cell carcinoma arise independently. Thus, intrarenal metastasis does not seem to play an important role in the spread of papillary renal cell carcinoma, a finding that has surgical, therapeutic, and prognostic implications.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Papillary/genetics
- Carcinoma, Papillary/pathology
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/pathology
- Chromosomes, Human, Pair 16/genetics
- Chromosomes, Human, Pair 17/genetics
- Chromosomes, Human, Pair 3/genetics
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 9/genetics
- Female
- Gene Frequency
- Humans
- In Situ Hybridization, Fluorescence
- Kidney Neoplasms/genetics
- Kidney Neoplasms/pathology
- Loss of Heterozygosity
- Male
- Microsatellite Repeats
- Middle Aged
- Models, Genetic
- Neoplasms, Multiple Primary/genetics
- Neoplasms, Multiple Primary/pathology
- Nephrectomy
- Trisomy
- X Chromosome Inactivation/genetics
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Affiliation(s)
- Timothy D Jones
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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22
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Jones TD, Eble JN, Wang M, Maclennan GT, Jain S, Cheng L. Clonal divergence and genetic heterogeneity in clear cell renal cell carcinomas with sarcomatoid transformation. Cancer 2005; 104:1195-203. [PMID: 16047350 DOI: 10.1002/cncr.21288] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Approximately 5% of clear cell renal cell carcinomas contain components with sarcomatoid differentiation. It has been suggested that the sarcomatoid elements arise from the clear cell tumors as a consequence of clonal expansions of neoplastic cells with progressively more genetic alterations. Analysis of the pattern of allelic loss and X-chromosome inactivation in both the clear cell and sarcomatoid components of the same tumor allows assessment of the genetic relationship of these tumor elements. METHODS The authors of the current study examined the pattern of allelic loss in clear cell and sarcomatoid components of renal cell carcinomas from 22 patients who had tumors with both components. DNA samples were prepared from formalin-fixed, paraffin-embedded renal tissue sections using laser-capture microdissection. Five microsatellite polymorphic markers for putative tumor suppressor genes on 5 different chromosomes were analyzed. These included D3S1300 (3p14), D7S522 (7q31), D8S261 (8p21), D9S171 (9p21), and TP53 (17p13). In addition, X-chromosome inactivation analysis was performed in 14 tumors from female patients. RESULTS The clear cell components showed loss of heterozygosity (LOH) at the D3S1300, D7S522, D8S261, D9S171, and TP53 loci in 18% (4/22), 18% (4/22), 50% (10/20), 15% (3/20), and 20% (4/20) of informative cases, respectively. LOH in the sarcomatoid components was seen at the D3S1300, D7S522, D8S261, D9S171, and TP53 loci in 18% (4/22), 41% (9/22), 70% (14/20), 35% (7/20), and 20% (4/20) of informative cases, respectively. Six cases demonstrated an LOH pattern in the clear cell component that was not seen in the sarcomatoid component. Different patterns of allelic loss were seen in the clear cell and sarcomatoid components in 15 cases. Clonality analysis showed the same pattern of nonrandom X-chromosome inactivation in both clear cell and sarcomatoid components in 13 of the 14 cases studied. One case showed a random pattern of X-chromosome inactivation. CONCLUSION X-chromosome inactivation analysis data suggest that both clear cell and sarcomatoid components of renal cell carcinomas are derived from the same progenitor cell. Different patterns of allelic loss in multiple chromosomal regions were observed in clear cell and sarcomatoid components from the same patient. This genetic heterogeneity indicates genetic divergence during the clonal evolution of renal cell carcinoma.
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Affiliation(s)
- Timothy D Jones
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, 46202, USA
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23
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Kashyap MK, Kumar A, Emelianenko N, Kashyap A, Kaushik R, Huang R, Khullar M, Sharma SK, Singh SK, Bhargave AK, Upadhyaya SK. Biochemical and molecular markers in renal cell carcinoma: an update and future prospects. Biomarkers 2005; 10:258-94. [PMID: 16191485 DOI: 10.1080/13547500500218534] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cancer is a big problem in the developed world as well as in developing countries. Renal cell carcinoma (RCC) accounts for approximately 3% of adult malignancies and 90-95% of neoplasms arising from the kidney. RCC is more common in men than in women (2:1), and it most often occurs in patients between the ages of 50-70 years. In all cancers the cancerous cells release particular kind of proteins (called tumour markers) and blood tests are used to detect the presence of these markers. These tumour markers nowadays are an area of interest for oncologists who search for a possible solution in the detection and treatment of RCC. Different kinds of biochemical and molecular markers such as ferritin, MN/CA9, apoptotic index, p53, IL-2, gamma-enolase, CD44, CD95, chromosome instability and loss of heterozygosity have been tested in RCC, but so far no marker fulfils one or the other criteria to be considered as an ideal marker for RCC. This review gives basic and updated information about the different kinds of biomarkers studied in RCC and about the role implementation of genomics and proteomics in RCC.
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Affiliation(s)
- M K Kashyap
- Department of Veterinary Biosciences, University of Illinois, Urbana-Champaign, IL 61802, USA.
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24
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Jones TD, Eble JN, Cheng L. Application of molecular diagnostic techniques to renal epithelial neoplasms. Clin Lab Med 2005; 25:279-303. [PMID: 15848737 DOI: 10.1016/j.cll.2005.01.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The application of molecular and cytogenetic techniques to the study of renal neoplasia has resulted in improved understanding of the biologic mechanisms that are responsible for tumor development and progression. It also revealed that several different and specific genetic events are responsible for tumorigenesis in the various categories and subcategories of renal tumors. The ultimate goal of research on the molecular pathology of renal neoplasms is a complete understanding of the genetics of these tumors, which will, in turn, aid in making the correct diagnosis, accurately assessing prognosis, and selecting appropriate and targeted therapeutic options.
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MESH Headings
- Adenocarcinoma, Clear Cell/diagnosis
- Adenocarcinoma, Clear Cell/genetics
- Adenocarcinoma, Clear Cell/pathology
- Adenoma, Oxyphilic/diagnosis
- Adenoma, Oxyphilic/genetics
- Adenoma, Oxyphilic/pathology
- Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
- Carcinoma, Papillary/diagnosis
- Carcinoma, Papillary/genetics
- Carcinoma, Papillary/pathology
- Carcinoma, Renal Cell/diagnosis
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/pathology
- DNA-Binding Proteins/genetics
- Gene Dosage
- Humans
- Kidney Neoplasms/diagnosis
- Kidney Neoplasms/genetics
- Kidney Neoplasms/pathology
- Loss of Heterozygosity
- Transcription Factors/genetics
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Affiliation(s)
- Timothy D Jones
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indiana University Medical Center, University Hospital, Indianapolis, IN 46202, USA
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25
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Misra A, Pellarin M, Nigro J, Smirnov I, Moore D, Lamborn KR, Pinkel D, Albertson DG, Feuerstein BG. Array Comparative Genomic Hybridization Identifies Genetic Subgroups in Grade 4 Human Astrocytoma. Clin Cancer Res 2005; 11:2907-18. [PMID: 15837741 DOI: 10.1158/1078-0432.ccr-04-0708] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Alterations of DNA copy number are believed to be important indicators of tumor progression in human astrocytoma. We used an array of bacterial artificial chromosomes to map relative DNA copy number in 50 primary glioblastoma multiforme tumors at approximately 1.4-Mb resolution. We identified 33 candidate sites for amplification and homozygous deletion in these tumors. We identified three major genetic subgroups within these glioblastoma multiforme tumors: tumors with chromosome 7 gain and chromosome 10 loss, tumors with only chromosome 10 loss in the absence of chromosome 7 gain, and tumors without copy number change in chromosomes 7 or 10. The significance of these genetic groups to therapeutics needs further study.
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Affiliation(s)
- Anjan Misra
- Brain Tumor Research Center, Department of Neurosurgery, University of California San Francisco, San Francisco, California, USA.
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26
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Receveur AO, Couturier J, Molinié V, Vieillefond A, Desangles F, Guillaud-Bataille M, Danglot G, Coullin P, Bernheim A. Characterization of quantitative chromosomal abnormalities in renal cell carcinomas by interphase four-color fluorescence in situ hybridization. ACTA ACUST UNITED AC 2005; 158:110-8. [PMID: 15796957 DOI: 10.1016/j.cancergencyto.2004.08.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2004] [Revised: 08/09/2004] [Accepted: 08/10/2004] [Indexed: 11/27/2022]
Abstract
Renal cell carcinomas (RCC) in adults are histologically heterogeneous solid tumors with specific chromosomal abnormality patterns included in the World Health Organization (WHO) classification. To overcome some of the drawbacks of cytogenetic and comparative genomic hybridization (CGH) analyses, we designed a first-generation cytogenetic diagnostic test using four-color fluorescence in situ hybridization (FISH) on interphase nuclei. We selected 51 bacterial artificial chromosome and P1-derived artificial chromosome clones covering 17 chromosomal regions involved in the abnormalities of the adult RCC histologic subtypes. An initial set of probes allowed the identification of clear-cell RCC, papillary RCC, and other RCC on a single slide. A second test allowed the detection of additional chromosomal abnormalities or aberrations specific to chromophobic RCC and oncocytomas. We tested 25 cases of RCC, and the results were in agreement with those of cytogenetic techniques and/or CGH methods. The techniques appeared to be very sensitive, because small tumoral cell clones that were undetected by other cytogenetic methods were identified with this method. It was concluded that the multicolor FISH test was specific and sensitive, easy to perform, and could be part of the investigation process in RCC.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Renal Cell/classification
- Carcinoma, Renal Cell/diagnosis
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/pathology
- Carcinoma, Renal Cell/surgery
- Chromosome Aberrations
- Chromosome Deletion
- Clone Cells/pathology
- Cytogenetic Analysis
- Diagnosis, Differential
- Female
- Humans
- In Situ Hybridization, Fluorescence
- Interphase
- Karyotyping
- Kidney Neoplasms/classification
- Kidney Neoplasms/diagnosis
- Kidney Neoplasms/genetics
- Kidney Neoplasms/pathology
- Kidney Neoplasms/surgery
- Male
- Middle Aged
- Neoplasm Staging
- Sensitivity and Specificity
- Translocation, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- Aline Ossard Receveur
- Laboratoire de Cytogénomique des cancers CNRS UMR 8125, Institut Gustave Roussy, 39 rue Camille Desmoulins 94805, Villejuif cedex 5, France
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27
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Yang L, Leung ACC, Ko JMY, Lo PHY, Tang JCO, Srivastava G, Oshimura M, Stanbridge EJ, Daigo Y, Nakamura Y, Tang CMC, Lau KW, Law S, Lung ML. Tumor suppressive role of a 2.4 Mb 9q33-q34 critical region and DEC1 in esophageal squamous cell carcinoma. Oncogene 2005; 24:697-705. [PMID: 15580306 DOI: 10.1038/sj.onc.1208179] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The key genes involved in the development of esophageal squamous cell carcinoma (ESCC) remain to be elucidated. Previous studies indicate extensive genomic alterations occur on chromosome 9 in ESCC. Using a monochromosome transfer approach, this study provides functional evidence and narrows down the critical region (CR) responsible for chromosome 9 tumor suppressing activity to a 2.4 Mb region mapping to 9q33-q34 between markers D9S1798 and D9S61. Interestingly, a high prevalence of allelic loss in this CR is also observed in primary ESCC tumors by microsatellite typing. Allelic loss is found in 30/34 (88%) tumors and the loss of heterozygosity (LOH) frequency ranges from 67 to 86%. Absent to low expression of a 9q32 candidate tumor suppressor gene (TSG), DEC1 (deleted in esophageal cancer 1), is detected in four Asian ESCC cell lines. Stably expressing DEC1 transfectants provide functional evidence for inhibition of tumor growth in nude mice and DEC1 expression is decreased in tumor segregants arising after long-term selection in vivo. There is 74% LOH in the DEC1 region of ESCC primary tumors. This study provides the first functional evidence for the presence of critical tumor suppressive regions on 9q33-q34. DEC1 is a candidate TSG that may be involved in ESCC development.
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MESH Headings
- Animals
- Carcinogenicity Tests
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Chromosome Deletion
- Chromosomes, Human, Pair 18/genetics
- Chromosomes, Human, Pair 9/genetics
- DNA, Complementary/genetics
- Esophageal Neoplasms/genetics
- Esophageal Neoplasms/metabolism
- Esophageal Neoplasms/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- In Situ Hybridization, Fluorescence
- Mice
- Mice, Nude
- Neoplasm Transplantation
- Tumor Cells, Cultured
- Tumor Suppressor Proteins/genetics
- Tumor Suppressor Proteins/metabolism
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Affiliation(s)
- Lichun Yang
- Department of Biology, Hong Kong University of Science and Technology, Hong Kong, China
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Kawakami T, Okamoto K, Ogawa O, Okada Y. Multipoint methylation and expression analysis of tumor suppressor genes in human renal cancer cells. Urology 2003; 61:226-30. [PMID: 12559313 DOI: 10.1016/s0090-4295(02)02110-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To analyze the methylation status and expression profiles of multiple tumor suppressor genes in renal cell carcinoma-derived cell lines. Aberrant promoter methylation is commonly found in human cancers. Nonetheless, it is challenging to demonstrate that methylation of a specific gene results in gene inactivation. METHODS We simultaneously analyzed methylation and expression profiles of five putative tumor suppressor genes (p15, p16, Rb, BRCA1, and E-cadherin) in 14 different cell lines using bisulfite genomic sequencing and reverse transcriptase-polymerase chain reaction. We also used multiplex polymerase chain reaction to identify homozygous deletions at the p15 and p16 loci. RESULTS Expression of p16, BRCA1, and E-cadherin was maintained in 4 (29%) of 14 cell lines, regardless of the presence of methylation. Aberrant methylation of p16 was observed in 2 (14%), of BRCA1 in 1 (7%), and of E-cadherin in 9 (64%) of 14 cell lines. Concurrent methylation was observed among p16 and BRCA1 (1 [7%] of 14 cell lines) and among p16 and E-cadherin (1 [7%] of 14 cell lines). We detected homozygous deletion of p16 and p15 in 11 (78%) and 6 (43%) cell lines, respectively. CONCLUSIONS The present data shows the presence of methylation does not always contribute to the loss of expression of tumor suppressor genes. Therefore, we must be cautious in interpreting the results of methylation assays--in particular, detection of methylation by nonquantitative methods. The data also demonstrated that multiple tumor suppressor genes are simultaneously inactivated in renal cell carcinoma-derived cell lines by distinctive mechanisms.
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Affiliation(s)
- Takahiro Kawakami
- Department of Urology, Shiga University of Medical Science, Otsu, Shiga, Japan
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29
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Meloni-Ehrig AM. Renal cancer: cytogenetic and molecular genetic aspects. AMERICAN JOURNAL OF MEDICAL GENETICS 2002; 115:164-72. [PMID: 12407697 DOI: 10.1002/ajmg.10697] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To date, much progress has been made in the fields of cytogenetics and molecular genetics of renal tumors. The previous and recent findings have delineated the characteristics of the various tumors, particularly the cytogenetic and molecular differences that exist between papillary and nonpapillary clear cell renal cell carcinomas (RCCs). At the same time, new cytogenetic subtypes have emerged [e.g., t(X;1)] in subtypes of RCC, while in others (e.g., Wilms tumors) several new cytogenetic abnormalities and consequent molecular involvement have been found. In addition to Wilms tumor, papillary RCC, and clear-cell RCC, cytogenetic and fluorescence in situ hybridization analyses have been performed on several other tumors of the kidney, including chromophobic carcinoma, metanephric adenoma, collecting duct carcinoma, transitional cell carcinoma, congenital mesoblastic nephroma, and malignant rhabdoid tumors of the kidney. This review is therefore intended to present a concise update on the cytogenetic and molecular data on renal tumors, focusing mainly on the clinical usefulness of the findings reported in the literature.
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Affiliation(s)
- Aurelia M Meloni-Ehrig
- University of Utah, School of Medicine, Department of Pediatrics, Salt Lake City, Utah 84132, USA.
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Hashimoto Y, Akita H, Hibino M, Kohri K, Nakanishi M. Identification and characterization of Nek6 protein kinase, a potential human homolog of NIMA histone H3 kinase. Biochem Biophys Res Commun 2002; 293:753-8. [PMID: 12054534 DOI: 10.1016/s0006-291x(02)00297-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In Aspergillus nidulans, the kinase activity of NIMA (never in mitosis, gene A) is critical for the initiation of mitosis. NIMA regulates mitotic chromatin condensation through phosphorylation of histone H3 at serine 10. In the present study, we identified human Nek6 (hNek6), a member of the mammalian NIMA-related kinases. The predicted hNek6 protein is comprised of 338 amino acids. Northern blot analysis revealed that hNek6 transcripts are ubiquitously expressed with the highest expression found in the heart and skeletal muscle. Lower cell cycle-dependent expression of hNek6 transcripts was observed in the early G1 phase. GFP-fused hNek6 protein showed both nuclear and cytoplasmic localizations in HeLa cells. Fluorescence in situ hybridization using full-length hNek6 cDNA as a probe showed that the hNek6 gene is localized to human chromosome 9q33-34, a region at which the loss of heterozygosity is associated with transitional cell carcinomas. Importantly, recombinant hNek6 protein produced in insect cells effectively phosphorylated histones H1 and H3, but not casein. Thus, these results suggest that, unlike other mammalian NIMA-related kinases, Nek6 is a mitotic histone kinase which regulates chromatin condensation in mammalian cells.
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Affiliation(s)
- Yoshihiro Hashimoto
- Department of Biochemistry, Nagoya City University Medical School, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
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