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Möller K, Kluth M, Ahmed M, Burkhardt L, Möller-Koop C, Büscheck F, Weidemann S, Tsourlakis MC, Minner S, Heinzer H, Huland H, Graefen M, Sauter G, Schlomm T, Dum D, Simon R. Chromosome 5 harbors two independent deletion hotspots at 5q13 and 5q21 that characterize biologically different subsets of aggressive prostate cancer. Int J Cancer 2020; 148:748-758. [PMID: 33045100 DOI: 10.1002/ijc.33344] [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: 06/15/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022]
Abstract
Deletion of chromosome 5q is common in prostate cancer and is linked to aggressive disease. Most previous studies focused on 5q21 where CHD1 is located, but deletion of mapping studies has identified a second deletion hotspot at 5q13. To clarify the prevalence and clinical relevance of 5q13 deletions and to determine the relative importance of 5q13 and 5q21 abnormalities, a tissue microarray containing samples from 12 427 prostate cancers was analyzed by fluorescence in situ hybridization. Deletion of 5q13 and 5q21 was found in 13.5% and 10%, respectively, of 7932 successfully analyzed cancers. Deletion was restricted to 5q13 in 49.4% and to 5q21 in 32.0% of cancers with a 5q deletion. Only 18.6% of 5q-deleted cancers had deletions of both loci. Both 5q13 and 5q21 deletions were significantly linked to advanced tumor stage, high Gleason grade, nodal metastasis and early biochemical recurrence (P < .005 each). Cancers with co-deletion of 5q13 and 5q21 had a worse prognosis than cancers with isolated 5q13 or 5q21 deletion (P = .0080). Comparison with TMPRSS2:ERG fusion status revealed that 5q21 deletions were tightly linked to ERG negativity (P < .0001) while 5q13 deletions were unrelated to the ERG status. In summary, 5q13 deletion and 5q21 deletion are common, but independent genomic alterations with different functional effects lead to aggressive prostate cancer.
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Affiliation(s)
- Katharina Möller
- Institute of Pathology, University Medical Center, Hamburg-Eppendorf, Germany
| | - Martina Kluth
- Institute of Pathology, University Medical Center, Hamburg-Eppendorf, Germany
| | - Malik Ahmed
- Institute of Pathology, University Medical Center, Hamburg-Eppendorf, Germany
| | - Lia Burkhardt
- Institute of Pathology, University Medical Center, Hamburg-Eppendorf, Germany
| | | | - Franziska Büscheck
- Institute of Pathology, University Medical Center, Hamburg-Eppendorf, Germany
| | - Sören Weidemann
- Institute of Pathology, University Medical Center, Hamburg-Eppendorf, Germany
| | | | - Sarah Minner
- Institute of Pathology, University Medical Center, Hamburg-Eppendorf, Germany
| | - Hans Heinzer
- Martini-Clinic, Prostate Cancer Center at University Medical Center, Hamburg-Eppendorf, Germany
| | - Hartwig Huland
- Martini-Clinic, Prostate Cancer Center at University Medical Center, Hamburg-Eppendorf, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Center at University Medical Center, Hamburg-Eppendorf, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center, Hamburg-Eppendorf, Germany
| | - Thorsten Schlomm
- Department of Urology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - David Dum
- Institute of Pathology, University Medical Center, Hamburg-Eppendorf, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center, Hamburg-Eppendorf, Germany
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2
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Deletion of 8p is an independent prognostic parameter in prostate cancer. Oncotarget 2018; 8:379-392. [PMID: 27880722 PMCID: PMC5352127 DOI: 10.18632/oncotarget.13425] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 11/12/2016] [Indexed: 11/25/2022] Open
Abstract
Deletion of chromosome 8p is the second most frequent genomic alteration in prostate cancer. To better understand its clinical significance, 8p deletion was analyzed by fluorescence in-situ hybridization on a prostate cancer tissue microarray. 8p deletion was found in 2,581 of 7,017 cancers (36.8%), and was linked to unfavorable tumor phenotype. 8p deletion increased from 29.5% in 4,456 pT2 and 47.8% in 1,598 pT3a to 53.0% in 931 pT3b-pT4 cancers (P < 0,0001). Deletions of 8p were detected in 25.5% of 1,653 Gleason ≤ 3 + 3, 36.6% of 3,880 Gleason 3 + 4, 50.2% of 1,090 Gleason 4 + 3, and 51.1% of 354 Gleason ≥ 4 + 4 tumors (P < 0,0001). 8p deletions were strongly linked to biochemical recurrence (P < 0.0001) independently from established pre- and postoperative prognostic factors (P = 0.0100). However, analysis of morphologically defined subgroups revealed, that 8p deletion lacked prognostic significance in subgroups with very good (Gleason ≤ 3 + 3, 3 + 4 with ≤ 5% Gleason 4) or very poor prognosis (pT3b, Gleason ≥ 8, pN1). 8p deletions were markedly more frequent in cancers with (53.5%) than without PTEN deletions (36.4%; P < 0,0001) and were slightly more frequent in ERG-positive (40.9%) than in ERG-negative cancers (34.7%, P < 0.0001) due to the association with the ERG-associated PTEN deletion. Cancers with 8p/PTEN co-deletions had a strikingly worse prognosis than cancers with deletion of PTEN or 8p alone (P ≤ 0.0003). In summary, 8p deletion is an independent prognostic parameter in prostate cancer that may act synergistically with PTEN deletions. Even statistically independent prognostic biomarkers like 8p may have limited clinical impact in morphologically well defined high or low risk cancers.
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Kluth M, Ahrary R, Hube-Magg C, Ahmed M, Volta H, Schwemin C, Steurer S, Wittmer C, Wilczak W, Burandt E, Krech T, Adam M, Michl U, Heinzer H, Salomon G, Graefen M, Koop C, Minner S, Simon R, Sauter G, Schlomm T. Genomic deletion of chromosome 12p is an independent prognostic marker in prostate cancer. Oncotarget 2016; 6:27966-79. [PMID: 26293672 PMCID: PMC4695038 DOI: 10.18632/oncotarget.4626] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/03/2015] [Indexed: 11/25/2022] Open
Abstract
Deletion of 12p is a recurrent alteration in prostate cancer, but the prevalence and clinical consequences of this alteration have not been studied in detail. Dual labeling fluorescence in situ hybridization using probes for 12p13 (CDKN1B; p27) and centromere 12 as a reference was used to successfully analyze more than 3700 prostate cancers with clinical follow-up data assembled in a tissue microarray format. CDKN1B was selected as a probe because it is located in the center of the deletion, which spans > 10 Mb and includes > 50 genes in 80% of cancers with 12p deletion. Deletion of 12p was found in 13.7% of cancers and included 13.5% heterozygous and 0.2% homozygous deletions. 12p deletion were linked to advanced tumor stage (p < 0.0001), high Gleason grade (p < 0.0001), rapid tumor cell proliferation (p < 0.0001), lymph node metastasis (p = 0.0004), and biochemical recurrence (p = 0.0027). Multivariate analysis including pT stage (p < 0.0001), Gleason grade (p < 0.0001), pN status (p = 0.0001), preoperative PSA levels (p = 0.0001), and resection margin status (p = 0.0001) revealed an independent prognostic value of 12p deletion (p = 0.0014). Deletion of 12p was unrelated to the ERG fusion status. Deletion of 12p was only marginally linked to reduced p27 expression, which by itself was unrelated to clinical outcome. This argues against p27 as the key target gene of 12p deletions. In summary, the results of our study demonstrate that 12p deletion is frequent in prostate cancer and provides independent prognostic information. 12p deletion analysis alone, or in combination with other prognostic parameters may thus have clinical utility.
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Affiliation(s)
- Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Ramin Ahrary
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Malik Ahmed
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Heinke Volta
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Catina Schwemin
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Corinna Wittmer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Waldemar Wilczak
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Eike Burandt
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Till Krech
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Meike Adam
- Martini-Klinik, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Uwe Michl
- Martini-Klinik, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Hans Heinzer
- Martini-Klinik, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Georg Salomon
- Martini-Klinik, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Markus Graefen
- Martini-Klinik, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Christina Koop
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Thorsten Schlomm
- Martini-Klinik, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany.,Department of Urology, Section for Translational Prostate Cancer Research, University Medical Center Hamburg-Eppendorf, Germany
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Bacolla A, Tainer JA, Vasquez KM, Cooper DN. Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences. Nucleic Acids Res 2016; 44:5673-88. [PMID: 27084947 PMCID: PMC4937311 DOI: 10.1093/nar/gkw261] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/30/2016] [Indexed: 12/13/2022] Open
Abstract
Gross chromosomal rearrangements (including translocations, deletions, insertions and duplications) are a hallmark of cancer genomes and often create oncogenic fusion genes. An obligate step in the generation of such gross rearrangements is the formation of DNA double-strand breaks (DSBs). Since the genomic distribution of rearrangement breakpoints is non-random, intrinsic cellular factors may predispose certain genomic regions to breakage. Notably, certain DNA sequences with the potential to fold into secondary structures [potential non-B DNA structures (PONDS); e.g. triplexes, quadruplexes, hairpin/cruciforms, Z-DNA and single-stranded looped-out structures with implications in DNA replication and transcription] can stimulate the formation of DNA DSBs. Here, we tested the postulate that these DNA sequences might be found at, or in close proximity to, rearrangement breakpoints. By analyzing the distribution of PONDS-forming sequences within ±500 bases of 19 947 translocation and 46 365 sequence-characterized deletion breakpoints in cancer genomes, we find significant association between PONDS-forming repeats and cancer breakpoints. Specifically, (AT)n, (GAA)n and (GAAA)n constitute the most frequent repeats at translocation breakpoints, whereas A-tracts occur preferentially at deletion breakpoints. Translocation breakpoints near PONDS-forming repeats also recur in different individuals and patient tumor samples. Hence, PONDS-forming sequences represent an intrinsic risk factor for genomic rearrangements in cancer genomes.
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Affiliation(s)
- Albino Bacolla
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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5
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Kluth M, Runte F, Barow P, Omari J, Abdelaziz ZM, Paustian L, Steurer S, Christina Tsourlakis M, Fisch M, Graefen M, Tennstedt P, Huland H, Michl U, Minner S, Sauter G, Simon R, Adam M, Schlomm T. Concurrent deletion of 16q23 and PTEN is an independent prognostic feature in prostate cancer. Int J Cancer 2015; 137:2354-63. [PMID: 26009879 DOI: 10.1002/ijc.29613] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/13/2015] [Accepted: 04/22/2015] [Indexed: 01/14/2023]
Abstract
The deletion of 16q23-q24 belongs to the most frequent chromosomal changes in prostate cancer, but the clinical consequences of this alteration have not been studied in detail. We performed fluorescence in situ hybridization analysis using a 16q23 probe in more than 7,400 prostate cancers with clinical follow-up data assembled in a tissue microarray format. Chromosome 16q deletion was found in 21% of cancers, and was linked to advanced tumor stage, high Gleason grade, accelerated cell proliferation, the presence of lymph node metastases (p < 0.0001 each) and positive surgical margin (p = 0.0004). 16q Deletion was more frequent in ERG fusion-positive (27%) as compared to ERG fusion-negative cancers (16%, p < 0.0001), and was linked to other ERG-associated deletions including phosphatase and tensin homolog (PTEN) (p < 0.0001) and 3p13 (p = 0.0303). In univariate analysis, the deletion of 16q was linked to early biochemical recurrence independently from the ERG status (p < 0.0001). Tumors with codeletions of 16q and PTEN had a worse prognosis (p = 0.0199) than those with PTEN or the deletion of 16q alone. Multivariate modeling revealed that the prognostic value of 16q/PTEN deletion patterns was independent from the established prognostic factors. In summary, the results of our study demonstrate that the deletion of 16q and PTEN cooperatively drives prostate cancer progression, and suggests that deletion analysis of 16q and PTEN could be of important clinical value particularly for preoperative risk assessment of the clinically most challenging group of low- and intermediated grade prostate cancers.
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Affiliation(s)
- Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Frederic Runte
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philipp Barow
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jazan Omari
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Zaid M Abdelaziz
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lisa Paustian
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Margit Fisch
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pierre Tennstedt
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartwig Huland
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Uwe Michl
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Meike Adam
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Schlomm
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Urology, Section for Translational Prostate Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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