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Barnett ES, Schultz N, Stopsack KH, Lam ET, Arfe A, Lee J, Zhao JL, Schonhoft JD, Carbone EA, Keegan NM, Wibmer A, Wang Y, Solit DB, Abida W, Wenstrup R, Scher HI. Analysis of BRCA2 Copy Number Loss and Genomic Instability in Circulating Tumor Cells from Patients with Metastatic Castration-resistant Prostate Cancer. Eur Urol 2023; 83:112-120. [PMID: 36123219 PMCID: PMC10228632 DOI: 10.1016/j.eururo.2022.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/13/2022] [Accepted: 08/10/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND BRCA2 alterations predict for a response to poly-ADP-ribose polymerase inhibition in metastatic castration-resistant prostate cancer (mCRPC). However, detection is hindered by insufficient tumor tissue and low sensitivity of cell-free DNA for detecting copy number loss. OBJECTIVE To evaluate the BRCA2 loss detection using single-cell, shallow whole-genome sequencing (sWGS) of circulating tumor cells (CTCs) in patients with mCRPC. DESIGN, SETTING, AND PARTICIPANTS We analyzed CTC samples collected concurrently with tumor biopsies intended for clinical sequencing in patients with progressing mCRPC. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Differences in proportions were evaluated using the chi-square test. Correlations between assays were analyzed in linear regression models. Associations between alterations and genomic instability were assessed on the single-cell level using mixed-effect negative binomial models. RESULTS AND LIMITATIONS We identified 138 patients with concurrent CTC and biopsy samples. CTC sWGS generated copy number profiles in a similar proportion of patients to biopsy samples (83% vs 78%, p = 0.23), but was more effective than bone biopsies (79% vs 50%; p = 0.009). CTC sWGS detected BRCA2 loss in more patients than tissue at the ≥1 (42% vs 16%; p < 0.001) and ≥2 (27% vs 16%; p = 0.028) CTC thresholds. The overall prevalence of BRCA2 loss was not increased in CTCs using sample-level composite z scores (p = 0.4), but was significantly increased compared with a lower-than-expected prevalence in bone samples (21% vs 3%, p = 0.014). Positive/negative predictive values for CTC BRCA2 loss were 89%/96% using the ≥1 CTC threshold and 67%/92% using the composite z score. CTC BRCA2 loss was associated with higher genomic instability in univariate (1.4-fold large-scale transition difference, 95% confidence interval [CI]: 1.2-1.6; p < 0.001) and multivariable analysis (1.4-fold difference, 95% CI: 1.2-1.6; p < 0.001). CONCLUSIONS Copy number profiles can reliably be generated using CTC sWGS, which detected a majority of tissue-confirmed BRCA2 loss and "CTC-only" losses. BRCA2 losses were supported by increases in genomic instability. PATIENT SUMMARY Current testing strategies have limitations in their ability to detect BRCA2 loss, a relatively common alteration in prostate cancer that is used to identify patients who may benefit from targeted therapy. In this paper, we evaluated whether we could detect BRCA2 loss in individual tumor cells isolated from patient blood samples and found this method to be suitable for further analysis.
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Affiliation(s)
- Ethan S Barnett
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Konrad H Stopsack
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Andrea Arfe
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Jimmy L Zhao
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Emily A Carbone
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Niamh M Keegan
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andreas Wibmer
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - David B Solit
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wassim Abida
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Howard I Scher
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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Pouyiourou M, Wohlfromm T, Kraft B, Hielscher T, Stichel D, von Deimling A, Delorme S, Endris V, Neumann O, Stenzinger A, Krämer A, Bochtler T. Local ablative treatment with surgery and/or radiotherapy in single-site and oligometastatic carcinoma of unknown primary. Eur J Cancer 2021; 157:179-189. [PMID: 34521064 DOI: 10.1016/j.ejca.2021.08.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/08/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Single-site carcinoma of unknown primary (CUP) is recognised as a distinct favourable subtype in the European Society of Medical Oncology (ESMO) classification. There is broad consensus that these patients are candidates for local ablative treatment strategies with surgery and/or radiotherapy, but data on their outcomes are scarce. PATIENTS AND METHODS In this study, we have addressed the prospects of cure and prognostic factors in a retrospective cohort of 63 patients who were eligible for local treatment at our centre. RESULTS Median event-free (EFS) and overall survival (OS) were 15.6 months and 52.5 months, respectively. Of 61 patients who received local treatment, 20 (32.8%) remained event-free over a median follow-up of 28 months. Baseline clinical parameters including affected organ, number, volume and histology of metastases had no significant impact on prognosis, whereas deleterious TP53 mutations and DNA copy number loss emerged as independent adverse risk factors with respect to EFS. Surgical treatment was associated with improved OS as compared to radiation-based therapy. CONCLUSION Our study advocates to pursue localised treatment with surgery and/or radiotherapy whenever feasible and implies that genetic parameters might additionally determine the clinical course of single-site CUP patients.
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Affiliation(s)
- Maria Pouyiourou
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany; Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Timothy Wohlfromm
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Bianca Kraft
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Institute of Neuropathology, University of Heidelberg, Heidelberg, Germany
| | | | - Stefan Delorme
- Division of Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Endris
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | | | - Alwin Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany; Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Tilmann Bochtler
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany; Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany; Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany.
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Abstract
Background Tumor suppressor genes (TSGs) encode the guardian molecules to control cell growth. The genomic alteration of TSGs may cause tumorigenesis and promote cancer progression. So far, investigators have mainly studied the functional effects of somatic single nucleotide variants in TSGs. Copy number variation (CNV) is another important form of genetic variation, and is often involved in cancer biology and drug treatment, but studies of CNV in TSGs are less represented in literature. In addition, there is a lack of a combinatory analysis of gene expression and CNV in this important gene set. Such a study may provide more insights into the relationship between gene dosage and tumorigenesis. To meet this demand, we performed a systematic analysis of CNVs and gene expression in TSGs to provide a systematic view of CNV and gene expression change in TSGs in pan-cancer. Results We identified 1170 TSGs with copy number gain or loss in 5846 tumor samples. Among them, 207 TSGs tended to have copy number loss (CNL), from which fifteen CNL hotspot regions were identified. The functional enrichment analysis revealed that the 207 TSGs were enriched in cancer-related pathways such as P53 signaling pathway and the P53 interactome. We further performed integrative analyses of CNV with gene expression using the data from the matched tumor samples. We found 81 TSGs with concordant CNL events and decreased gene expression in the tumor samples we examined. Remarkably, seven TSGs displayed concordant CNL and gene down-regulation in at least 50 tumor samples: MTAP (212 samples), PTEN (139), MCPH1 (85), FBXO25 (67), SMAD4 (64), TRIM35 (57), and RB1 (54). Specifically to MTAP, this concordance was found in 14 cancer types, an observation that is not much reported in literature yet. Further network-based analysis revealed that these TSGs with concordant CNL and gene down-regulation were highly connected. Conclusions This study provides a draft landscape of CNV in pan-cancer. Our findings of systematic concordance between CNL and down-regulation of gene expression may help better understand the TSG biology in tumorigenesis and cancer progression. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2904-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Zhao
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA. .,Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. .,Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, 37212, USA. .,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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