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Wang Y, Douville C, Chien YW, Wang BG, Chen CL, Pinto A, Smith SA, Drapkin R, Chui MH, Numan T, Vang R, Papadopoulos N, Wang TL, Shih IM. Aneuploidy Landscape in Precursors of Ovarian Cancer. Clin Cancer Res 2024; 30:600-615. [PMID: 38048050 DOI: 10.1158/1078-0432.ccr-23-0932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/21/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
PURPOSE Serous tubal intraepithelial carcinoma (STIC) is now recognized as the main precursor of ovarian high-grade serous carcinoma (HGSC). Other potential tubal lesions include p53 signatures and tubal intraepithelial lesions. We aimed to investigate the extent and pattern of aneuploidy in these epithelial lesions and HGSC to define the features that characterize stages of tumor initiation and progression. EXPERIMENTAL DESIGN We applied RealSeqS to compare genome-wide aneuploidy patterns among the precursors, HGSC (cases, n = 85), and histologically unremarkable fallopian tube epithelium (HU-FTE; control, n = 65). On the basis of a discovery set (n = 67), we developed an aneuploidy-based algorithm, REAL-FAST (Repetitive Element AneupLoidy Sequencing Fallopian Tube Aneuploidy in STIC), to correlate the molecular data with pathology diagnoses. We validated the result in an independent validation set (n = 83) to determine its performance. We correlated the molecularly defined precursor subgroups with proliferative activity and histology. RESULTS We found that nearly all p53 signatures lost the entire Chr17, offering a "two-hit" mechanism involving both TP53 and BRCA1 in BRCA1 germline mutation carriers. Proliferatively active STICs harbor gains of 19q12 (CCNE1), 19q13.2, 8q24 (MYC), or 8q arm, whereas proliferatively dormant STICs show 22q loss. REAL-FAST classified HU-FTE and STICs into 5 clusters and identified a STIC subgroup harboring unique aneuploidy that is associated with increased proliferation and discohesive growth. On the basis of a validation set, REAL-FAST showed 95.8% sensitivity and 97.1% specificity in detecting STIC/HGSC. CONCLUSIONS Morphologically similar STICs are molecularly distinct. The REAL-FAST assay identifies a potentially "aggressive" STIC subgroup harboring unique DNA aneuploidy that is associated with increased cellular proliferation and discohesive growth. REAL-FAST offers a highly reproducible adjunct technique to assist the diagnosis of STIC lesions.
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Affiliation(s)
- Yeh Wang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Christopher Douville
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Yen-Wei Chien
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Brant G Wang
- Department of Pathology, Inova Fairfax Hospital, Falls Church, Virginia
- School of Medicine Inova Campus, University of Virginia, Falls Church, Virginia
- Department of Pathology, Georgetown University Medical Center, Washington, DC
| | - Chi-Long Chen
- Department of Pathology, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Andre Pinto
- University of Miami Sylvester Comprehensive Cancer Center, Miami, Florida
| | - Saron Ann Smith
- Cascade Pathology Services, Legacy Health System, Portland, Oregon
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology and Basser Center for BRCA, University of Pennsylvania, Philadelphia, Pennsylvania
| | - M Herman Chui
- Department of Pathology and Laboratory Medicine, Sloan-Kettering Cancer Center, New York, New York
| | - Tricia Numan
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Pathology, Sibley Memorial Hospital, Washington, DC
| | - Russell Vang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Nickolas Papadopoulos
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, Maryland
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Cen Y, Fang Y, Ren Y, Hong S, Lu W, Xu J. Global characterization of extrachromosomal circular DNAs in advanced high grade serous ovarian cancer. Cell Death Dis 2022; 13:342. [PMID: 35418185 PMCID: PMC9007969 DOI: 10.1038/s41419-022-04807-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 03/21/2022] [Accepted: 03/30/2022] [Indexed: 01/02/2023]
Abstract
High grade serous ovarian cancer (HGSOC) is the most aggressive subtype of ovarian cancer and HGSOC patients often appear with metastasis, leading to the poor prognosis. Up to date, the extrachromosomal circular DNAs (eccDNAs) have been shown to be involved in cancer genome remodeling but the roles of eccDNAs in metastatic HGSOC are still not clear. Here we explored eccDNA profiles in HGSOC by Circle-Sequencing analysis using four pairs of primary and metastatic tissues of HGSOC patients. Within the differentially expressed eccDNAs screened out by our analysis, eight candidates were validated by outward PCR and qRT-PCR analysis. Among them, DNMT1circle10302690-10302961 was further confirmed by FISH assay and BaseScope assay, as the most significantly down-regulated eccDNA in metastatic tumors of HGSOC. Lower expression of DNMT1circle10302690-10302961 in both primary and metastatic tumors was associated with worse prognosis of HGSOC. Taken together, our finding firstly demonstrated the eccDNAs landscape of primary and metastatic tissues of HGSOC. The eccDNA DNMT1circle10302690-10302961 can be considered as a potential biomarker or a therapeutically clinical target of HGSOC metastasis and prognosis.
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Affiliation(s)
- Yixuan Cen
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Yifeng Fang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Yan Ren
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Shiyuan Hong
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China.
| | - Weiguo Lu
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China. .,Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China. .,Cancer Center, Zhejiang University, Hangzhou, 310058, China.
| | - Junfen Xu
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China. .,Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
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Złowocka-Perłowska E, Tołoczko-Grabarek A, Lubiński J. Germline HOXB13 mutation p.G84E do not confer an increased bladder or kidney cancer risk in polish population. Hered Cancer Clin Pract 2022; 20:1. [PMID: 34983599 PMCID: PMC8728939 DOI: 10.1186/s13053-021-00208-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/09/2021] [Indexed: 11/10/2022] Open
Abstract
Introduction The role of HOXB13 in bladder and renal tumorigenesis is unclear. Our goal was to determine the prevalence of HOXB13 p.G84E mutation in bladder and kidney cancer patients from Poland. Materials and methods 1418 patients with bladder cancer and 813 cases with kidney cancer and 4497 controls were genotyped for HOXB13 p.G84E. Results p.G84E mutation of HOXB13 gene was detected in three of 1418 (0.2%) bladder cancer cases and in six of 4497 controls (odds ratio [OR], 1.6; 95% CI 0.39–6.36; p = 0.8). Among 813 kidney cancer cases HOXB13 mutations was reported in three patients (0,4%) (odds ratio [OR], (OR = 2,8; 95% CI 0.69–11.11; p = 0.3). In cases with mutations in the HOXB13 gene, the family history of cancer was negative. Conclusion HOXB13 mutation was not associated with bladder or kidney cancer. Mutation p.G84E in HOXB13 seem not to play a role in bladder and kidney cancer development in Polish patients.
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Affiliation(s)
- Elżbieta Złowocka-Perłowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland.
| | - Aleksandra Tołoczko-Grabarek
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
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Wang Y, Bernhardy AJ, Nacson J, Krais JJ, Tan YF, Nicolas E, Radke MR, Handorf E, Llop-Guevara A, Balmaña J, Swisher EM, Serra V, Peri S, Johnson N. BRCA1 intronic Alu elements drive gene rearrangements and PARP inhibitor resistance. Nat Commun 2019; 10:5661. [PMID: 31827092 PMCID: PMC6906494 DOI: 10.1038/s41467-019-13530-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 11/14/2019] [Indexed: 12/28/2022] Open
Abstract
BRCA1 mutant carcinomas are sensitive to PARP inhibitor (PARPi) therapy; however, resistance arises. BRCA1 BRCT domain mutant proteins do not fold correctly and are subject to proteasomal degradation, resulting in PARPi sensitivity. In this study, we show that cell lines and patient-derived tumors, with highly disruptive BRCT domain mutations, have readily detectable BRCA1 protein expression, and are able to proliferate in the presence of PARPi. Peptide analyses reveal that chemo-resistant cancers contain residues encoded by BRCA1 intron 15. Mechanistically, cancers with BRCT domain mutations harbor BRCA1 gene breakpoints within or adjacent to Alu elements in intron 15; producing partial gene duplications, inversions and translocations, and terminating transcription prior to the mutation-containing BRCT domain. BRCA1 BRCT domain-deficient protein isoforms avoid mutation-induced proteasomal degradation, support homology-dependent DNA repair, and promote PARPi resistance. Taken together, Alu-mediated BRCA1 gene rearrangements are responsible for generating hypomorphic proteins, and may represent a biomarker of PARPi resistance.
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Affiliation(s)
- Yifan Wang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Andrea J Bernhardy
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Joseph Nacson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19111, USA
| | - John J Krais
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Yin-Fei Tan
- Genomics Facility, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Emmanuelle Nicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Genomics Facility, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Marc R Radke
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Elizabeth Handorf
- Bioinformatics and Statistics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Suraj Peri
- Bioinformatics and Statistics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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Trombetta D, Mertens F, Lonoce A, D'Addabbo P, Rennstam K, Mandahl N, Storlazzi CT. Characterization of a hotspot region on chromosome 12 for amplification in ring chromosomes in atypical lipomatous tumors. Genes Chromosomes Cancer 2010; 48:993-1001. [PMID: 19691106 DOI: 10.1002/gcc.20700] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ring chromosomes are cytogenetic hallmarks of genomic amplification in several bone and soft tissue tumors, in particular atypical lipomatous tumors (ALT). In ALT, the ring chromosomes invariably contain amplified material from the central part of the long arm of chromosome 12, mainly 12q12-->15, but often also segments from other chromosomes are involved. Previous studies have shown that one of the recurrent amplicons in ALT, located in 12q13.3-14.1 and harboring the candidate target genes TSPAN31 and CDK4, often has a sharp centromeric border. To characterize this breakpoint region in more detail, 12 cases of ALT with ring chromosomes were analyzed by array comparative genomic hybridization and fluorescence in situ hybridization. In the seven cases showing a sharply delineated amplicon in 12q13.3-14.1, the breakpoint region was further investigated by real time quantitative polymerase chain reaction and Vectorette PCR. The breakpoints clustered to a 146-kb region containing 11 genes. Whereas there was no indication that the breakpoints gave rise to fusion genes, in silico analysis revealed that the breakpoint region was enriched for repeated elements that could be important for ring chromosome formation in ALT.
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Affiliation(s)
- Domenico Trombetta
- Department of Genetics and Microbiology, University of Bari, Bari, Italy.
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Loss of heterozygosity atBRCA1/2 loci in hereditary and sporadic ovarian cancers. J Appl Genet 2009; 50:379-84. [DOI: 10.1007/bf03195697] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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