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Jo SY, Lee JD, Won J, Park J, Kweon T, Jo S, Sohn J, Kim SI, Kim S, Park HS. Reversion of pathogenic BRCA1 L1780P mutation confers resistance to PARP and ATM inhibitor in breast cancer. iScience 2024; 27:110469. [PMID: 39156639 PMCID: PMC11326956 DOI: 10.1016/j.isci.2024.110469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/12/2024] [Accepted: 07/03/2024] [Indexed: 08/20/2024] Open
Abstract
This study investigates the molecular characteristics and therapeutic implications of the BRCA1 L1780P mutation, a rare variant prevalent among Korean hereditary breast cancer patients. Using patient-derived xenograft (PDX) models and cell lines (PDX-derived cell line) from carriers, sequencing analyses revealed loss of heterozygosity (LOH) at the BRCA1 locus, with one patient losing the wild-type allele and the other mutated allele. This reversion mutation may cf. resistance to homologous recombination deficiency (HRD)-targeting drugs such as PARP inhibitors (PARPi) and ATM inhibitors (ATMi). Although HRDetect and CHORD analyses confirmed a strong association between the L1780P mutation and HRD, effective initially, drug resistance developed in cases with reversion mutations. These findings underscore the complexity of using HRD prediction in personalized treatment strategies for breast cancer patients with BRCA1/2 mutations, as resistance may arise in reversion cases despite high HRD scores.
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Affiliation(s)
- Se-Young Jo
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Jeong Dong Lee
- Avison Biomedical Research Center, Yonsei University College of Medicine, Seoul, Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Jeongsoo Won
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Jiho Park
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea
| | - Taeyong Kweon
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
- Department of Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Seongyeon Jo
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
- Department of Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Joohyuk Sohn
- Division of Medical Oncology, Department of Internal Medicine Yonsei University College of Medicine, Seoul, Korea
| | - Seung-Il Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
- Postech Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Hyung Seok Park
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
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Kulkarni S, Gajjar K, Madhusudan S. Poly (ADP-ribose) polymerase inhibitor therapy and mechanisms of resistance in epithelial ovarian cancer. Front Oncol 2024; 14:1414112. [PMID: 39135999 PMCID: PMC11317305 DOI: 10.3389/fonc.2024.1414112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024] Open
Abstract
Advanced epithelial ovarian cancer is the commonest cause of gynaecological cancer deaths. First-line treatment for advanced disease includes a combination of platinum-taxane chemotherapy (post-operatively or peri-operatively) and maximal debulking surgery whenever feasible. Initial response rate to chemotherapy is high (up to 80%) but most patients will develop recurrence (approximately 70-90%) and succumb to the disease. Recently, poly-ADP-ribose polymerase (PARP) inhibition (by drugs such as Olaparib, Niraparib or Rucaparib) directed synthetic lethality approach in BRCA germline mutant or platinum sensitive disease has generated real hope for patients. PARP inhibitor (PARPi) maintenance therapy can prolong survival but therapeutic response is not sustained due to intrinsic or acquired secondary resistance to PARPi therapy. Reversion of BRCA1/2 mutation can lead to clinical PARPi resistance in BRCA-germline mutated ovarian cancer. However, in the more common platinum sensitive sporadic HGSOC, the clinical mechanisms of development of PARPi resistance remains to be defined. Here we provide a comprehensive review of the current status of PARPi and the mechanisms of resistance to therapy.
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Affiliation(s)
- Sanat Kulkarni
- Department of Medicine, Sandwell and West Birmingham NHS Trust, West Bromwich, United Kingdom
| | - Ketankumar Gajjar
- Department of Gynaecological Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Srinivasan Madhusudan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, United Kingdom
- Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
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Wang Y, Ma Y, He L, Du J, Li X, Jiao P, Wu X, Xu X, Zhou W, Yang L, Di J, Zhu C, Xu L, Sun T, Li L, Liu D, Wang Z. Clinical and molecular significance of homologous recombination deficiency positive non-small cell lung cancer in Chinese population: An integrated genomic and transcriptional analysis. Chin J Cancer Res 2024; 36:282-297. [PMID: 38988485 PMCID: PMC11230889 DOI: 10.21147/j.issn.1000-9604.2024.03.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024] Open
Abstract
Objective The clinical significance of homologous recombination deficiency (HRD) in breast cancer, ovarian cancer, and prostate cancer has been established, but the value of HRD in non-small cell lung cancer (NSCLC) has not been fully investigated. This study aimed to systematically analyze the HRD status of untreated NSCLC and its relationship with patient prognosis to further guide clinical care. Methods A total of 355 treatment-naïve NSCLC patients were retrospectively enrolled. HRD status was assessed using the AmoyDx Genomic Scar Score (GSS), with a score of ≥50 considered HRD-positive. Genomic, transcriptomic, tumor microenvironmental characteristics and prognosis between HRD-positive and HRD-negative patients were analyzed. Results Of the patients, 25.1% (89/355) were HRD-positive. Compared to HRD-negative patients, HRD-positive patients had more somatic pathogenic homologous recombination repair (HRR) mutations, higher tumor mutation burden (TMB) (P<0.001), and fewer driver gene mutations (P<0.001). Furthermore, HRD-positive NSCLC had more amplifications in PI3K pathway and cell cycle genes, MET and MYC in epidermal growth factor receptor (EGFR)/anaplastic lymphoma kinase (ALK) mutant NSCLC, and more PIK3CA and AURKA in EGFR/ALK wild-type NSCLC. HRD-positive NSCLC displayed higher tumor proliferation and immunosuppression activity. HRD-negative NSCLC showed activated signatures of major histocompatibility complex (MHC)-II, interferon (IFN)-γ and effector memory CD8+ T cells. HRD-positive patients had a worse prognosis and shorter progression-free survival (PFS) to targeted therapy (first- and third-generation EGFR-TKIs) (P=0.042). Additionally, HRD-positive, EGFR/ALK wild-type patients showed a numerically lower response to platinum-free immunotherapy regimens. Conclusions Unique genomic and transcriptional characteristics were found in HRD-positive NSCLC. Poor prognosis and poor response to EGFR-TKIs and immunotherapy were observed in HRD-positive NSCLC. This study highlights potential actionable alterations in HRD-positive NSCLC, suggesting possible combinational therapeutic strategies for these patients.
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Affiliation(s)
| | | | | | | | - Xiaoguang Li
- Department of Minimally Invasive Tumor Therapies Center
| | | | | | - Xiaomao Xu
- Department of Respiratory and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Wei Zhou
- Department of Respiratory and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | | | - Changbin Zhu
- Amoy Diagnostics Co., Ltd., Xiamen 361027, China
| | - Liming Xu
- Amoy Diagnostics Co., Ltd., Xiamen 361027, China
| | - Tianlin Sun
- Amoy Diagnostics Co., Ltd., Xiamen 361027, China
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Abdelrahman Z, Abdelatty A, Luo J, McKnight AJ, Wang X. Stratification of glioma based on stemness scores in bulk and single-cell transcriptomes. Comput Biol Med 2024; 175:108304. [PMID: 38663352 DOI: 10.1016/j.compbiomed.2024.108304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 05/15/2024]
Abstract
BACKGROUND Brain tumours are known to have a high mortality and morbidity rate due to their localised and frequent invasive growth. The concept that glioma resistance could originate from the dissimilarity in the vulnerability of clonogenic glial stem cells to chemotherapeutic drugs and radiation has driven the scientific community to reexamine the comprehension of glioma growth and strategies that target these cells or modify their stemness. METHODS Based on the enrichment scores of 12 stemness signatures, we identified glioma subtypes in both tumour bulks and single cells by clustering analysis. Furthermore, we comprehensively compared molecular and clinical features among the glioma subtypes. RESULTS Consistently, in seven different datasets, hierarchical clustering uncovered three subtypes of glioma, termed Stem-H, Stem-M, and Stem-L, with high, medium, and low stemness signatures, respectively. Stem-H and Stem-L exhibited the most unfavorable and favourable overall and disease-free survival, respectively. Stem-H showed the highest enrichment scores of the EMT, invasion, proliferation, differentiation, and metastasis processes signatures, while Stem-L displayed the lowest. Stem-H harboured a greater proportion of late-stage tumours compared to Stem-L. Moreover, Stem-H manifested higher tumour mutation burden, DNA damage repair and cell cycle activity, intratumour heterogeneity, and a more frequent incidence of TP53 and EGFR mutations than Stem-L. In contrast, Stem-L had higher O6-Methylguanine-DNA Methyltransferase (MGMT) methylation levels. CONCLUSION The classification of glioma based on stemness may offer new insights into the biology of the tumour, as well as more accurate clinical management of the disease.
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Affiliation(s)
- Zeinab Abdelrahman
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK.
| | - Alaa Abdelatty
- Department of Pathology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Jiangti Luo
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Amy Jayne McKnight
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China.
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Cheo SW, Ong PY, Ow SGW, Chan GHJ, Tan DSP, Lim YW, Kong HL, Wong ALA, Lim SE, Walsh RJ, Wong ASC, Low JJH, Ngoi NYL, Lim JSL, Lee SC. Therapeutic applications of germline testing for cancer predisposition genes in Asia in the real world. ESMO Open 2024; 9:103482. [PMID: 38833967 PMCID: PMC11179091 DOI: 10.1016/j.esmoop.2024.103482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 04/28/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Germline genetic testing is traditionally carried out in patients suspected with hereditary cancer syndrome for enhanced cancer surveillance and/or preventive strategies, but is increasingly carried out for therapeutic indications. MATERIALS AND METHODS We conducted a retrospective review of patients who underwent germline genetic testing at our centre to determine the prevalence of actionable pathogenic germline variants (PGV) and their clinical utility. RESULTS From 2000 to 2022, 1154 cancer patients underwent germline testing, with the majority (945/1154) tested with multi-gene panels. Four hundred and eleven (35.6%) patients harboured a PGV and 334 (81%) were clinically actionable. BRCA1/2 accounted for 62.3% of actionable mutations, followed by mismatch repair (18%), and other homologous recombination repair (HRR) genes (19.7%). One hundred and fifty-two germline-positive patients have advanced cancers, and 79 received germline-directed therapies (poly ADP ribose polymerase inhibitors = 75; immunotherapy = 4). Median duration of immunotherapy and poly ADP ribose polymerase were 20.5 months (range 5-40 months) and 8 months (range 1-76 months), respectively. Among BRCA/HRR mutation carriers who received platinum-based chemotherapy, pathological complete response rate in the neoadjuvant setting was 53% (n = 17 breast cancers) and objective response rate was >80% in the advanced setting (n = 71). CONCLUSIONS One-third of cancer patients tested carried a PGV and ∼80% were clinically actionable. Three-quarters of germline-positive advanced cancer patients received germline-directed therapies in the real world, underscoring the practical utility of germline testing to guide cancer therapeutics.
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Affiliation(s)
- S W Cheo
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - P Y Ong
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - S G W Ow
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - G H J Chan
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - D S P Tan
- Department of Haematology-Oncology, National University Cancer Institute, Singapore; Cancer Science Institute, National University of Singapore, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore
| | - Y W Lim
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | | | - A L A Wong
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - S E Lim
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - R J Walsh
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - A S C Wong
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - J J H Low
- Department of Obstetrics and Gynaecology, National University Hospital, Singapore
| | - N Y L Ngoi
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - J S L Lim
- Department of Haematology-Oncology, National University Cancer Institute, Singapore; Cancer Science Institute, National University of Singapore, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - S C Lee
- Department of Haematology-Oncology, National University Cancer Institute, Singapore; Cancer Science Institute, National University of Singapore, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Liu Y, Bi X, Leng Y, Chen D, Wang J, Ma Y, Zhang MZ, Han BW, Li Y. A deep-learning-based genomic status estimating framework for homologous recombination deficiency detection from low-pass whole genome sequencing. Heliyon 2024; 10:e26121. [PMID: 38404843 PMCID: PMC10884843 DOI: 10.1016/j.heliyon.2024.e26121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024] Open
Abstract
Genome-wide sequencing allows for prediction of clinical treatment responses and outcomes by estimating genomic status. Here, we developed Genomic Status scan (GSscan), a long short-term memory (LSTM)-based deep-learning framework, which utilizes low-pass whole genome sequencing (WGS) data to capture genomic instability-related features. In this study, GSscan directly surveys homologous recombination deficiency (HRD) status independent of other existing biomarkers. In breast cancer, GSscan achieved an AUC of 0.980 in simulated low-pass WGS data, and obtained a higher HRD risk score in clinical BRCA-deficient breast cancer samples (p = 1.3 × 10-4, compared with BRCA-intact samples). In ovarian cancer, GSscan obtained higher HRD risk scores in BRCA-deficient samples in both simulated data and clinical samples (p = 2.3 × 10-5 and p = 0.039, respectively, compared with BRCA-intact samples). Moreover, HRD-positive patients predicted by GSscan showed longer progression-free intervals in TCGA datasets (p = 0.0011) treated with platinum-based adjuvant chemotherapy, outperforming existing low-pass WGS-based methods. Furthermore, GSscan can accurately predict HRD status using only 1 ng of input DNA and a minimum sequencing coverage of 0.02 × , providing a reliable, accessible, and cost-effective approach. In summary, GSscan effectively and accurately detected HRD status, and provide a broadly applicable framework for disease diagnosis and selecting appropriate disease treatment.
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Affiliation(s)
- Yang Liu
- Department of BC Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xiang Bi
- Department of Breast Surgery, Yantai Yuhuangding Hospital, Yantai, Shandong, China
| | - Yang Leng
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Dan Chen
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Juan Wang
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Youjia Ma
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Min-Zhe Zhang
- GeneGenieDx Corp, 160 E Tasman Dr, San Jose, CA, USA
| | - Bo-Wei Han
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Yalun Li
- Department of Breast Surgery, Yantai Yuhuangding Hospital, Yantai, Shandong, China
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Vogel A, Haupts A, Kloth M, Roth W, Hartmann N. A novel targeted NGS panel identifies numerous homologous recombination deficiency (HRD)-associated gene mutations in addition to known BRCA mutations. Diagn Pathol 2024; 19:9. [PMID: 38184614 PMCID: PMC10770950 DOI: 10.1186/s13000-023-01431-8] [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: 06/06/2022] [Accepted: 12/15/2023] [Indexed: 01/08/2024] Open
Abstract
Deleterious mutations in the BRCA1 and BRCA2 genes have significant therapeutic relevance in clinical settings regarding personalized therapy approaches. BRCA1 and BRCA2 play a pivotal role in homologous recombination (HR) and thus are sensitive for PARP inhibitors (PARPi). Beyond the narrow scope of evaluating only the BRCA mutation status, PARPi can be beneficial for HR deficient (HRD) patients, who harbor mutations in other HR-associated genes. In the present retrospective study, a novel targeted HRD gene panel was validated and implemented for use with FFPE tissue. Samples of patients with ovarian, breast, pancreatic and prostate cancer were included. Variants were robustly detected with various DNA input amounts and the use of test samples showed complete concordance between previously known mutations and HRD panel results. From all the 90 samples included in this cohort, TP53 was the most frequently altered gene (73%). Deleterious BRCA1/2 mutations were found in 20 (22%) of all samples. New pathogenic or likely pathogenic mutations in additional HR-associated genes were identified in 22 (24%) patients. Taken together, the present study proves the feasibility of a new HRD gene panel with reliable panel performance and offers the possibility to easily screen for resistance mutations acquired over treatment time.Mutations in HR-associated genes, besides BRCA1/2, might represent promising potential targets for synthetic lethality approaches. Thus, a substantial number of patients may benefit from expanding the scope of therapeutic agents like PARPi.
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Affiliation(s)
- Anne Vogel
- Institute of Pathology, University Medical Center Mainz, Langenbeckstraße 1, Mainz, 55131, Germany
| | - Anna Haupts
- Institute of Pathology, University Medical Center Mainz, Langenbeckstraße 1, Mainz, 55131, Germany
| | - Michael Kloth
- Institute of Pathology, University Medical Center Mainz, Langenbeckstraße 1, Mainz, 55131, Germany
| | - Wilfried Roth
- Institute of Pathology, University Medical Center Mainz, Langenbeckstraße 1, Mainz, 55131, Germany
| | - Nils Hartmann
- Institute of Pathology, University Medical Center Mainz, Langenbeckstraße 1, Mainz, 55131, Germany.
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Yang Y, Huang Z, Yuan M, Rui J, Chen R, Jin T, Sun Y, Deng Z, Shan H, Niu X, Liu W. Genomic and transcriptomic characterization of pre-operative chemotherapy response in patients with osteosarcoma. Sci Rep 2023; 13:20914. [PMID: 38017005 PMCID: PMC10684554 DOI: 10.1038/s41598-023-46857-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
Osteosarcoma is a heterogeneous disease with regard to its chemotherapy response and clinical outcomes. This study aims to investigate the genomic and transcriptomic characteristics related to pre-operative chemotherapy response. Samples from 25 osteosarcoma patients were collected to perform both whole exome and transcriptome sequencing. Osteosarcoma had significant amount of chromosomal copy number variants (CNVs). Chemotherapy responders showed the higher chromosomal CNV burden than non-responders (p = 0.0775), but the difference was not significant. The percentage of COSMIC signature 3, associated with homologous recombination repair deficiency, was higher in responders (56%) than in non-responders (45%). Transcriptomic analysis suggested that 11 genes were significantly up-regulated in responders and 18 genes were up-regulated in non-responders. Both GSEA and KEGG enrichment analysis indicted that four pathways related to cardiomyopathy were up-regulated in responders, while neuroactive ligand - receptor interaction was up-regulated in non-responders. Finally, a previously published chemoresistant model was validated using our dataset, with the area under the curve of 0.796 (95% CI, 0.583-1.000). Osteosarcoma had the heterogeneous mutational profile with frequent occurrence of CNVs. Transcriptomic analysis identified several signaling pathways associated with chemotherapy responsiveness to osteosarcoma. Transcriptomic signatures provides a potential research direction for predicting the chemotherapy response.
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Affiliation(s)
- Yongkun Yang
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Zhen Huang
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | | | - Jinqiu Rui
- Geneplus-Beijing, Beijing, 102206, China
| | | | - Tao Jin
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Yang Sun
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Zhiping Deng
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Huachao Shan
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Xiaohui Niu
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Weifeng Liu
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China.
- Fourth Medical College of Peking University, Beijing, 100035, China.
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Wang Y, Yan S, Liu Y, Yan Z, Deng W, Geng J, Li Z, Xia R, Zeng W, Zhao T, Fang Y, Liu N, Yang L, Cheng Z, Xu J, Wu CL, Miao Y. Dynamic viral integration patterns actively participate in the progression of BK polyomavirus-associated diseases after renal transplantation. Am J Transplant 2023; 23:1694-1708. [PMID: 37507072 DOI: 10.1016/j.ajt.2023.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
The classical lytic infection theory along with large T antigen-mediated oncogenesis cannot explain the BK polyomavirus (BKPyV)-associated tumor secondary to BKPyV-associated nephropathy (BKVAN), viremia/DNAemia, and viruria after renal transplantation. This study performed virome capture sequencing and pathological examination on regularly collected urine sediment and peripheral blood samples, and BKVAN and tumor biopsy tissues of 20 patients with BKPyV-associated diseases of different stages. In the early noncancerous stages, well-amplified integration sites were visualized by in situ polymerase chain reaction, simultaneously with BKPyV inclusion bodies and capsid protein expression. The integration intensity, the proportion of microhomology-mediated end-joining integration, and host PARP-1 and POLQ gene expression levels increased with disease progression. Furthermore, multiomics analysis was performed on BKPyV-associated urothelial carcinoma tissues, identifying tandem-like structures of BKPyV integration using long-read genome sequencing. The carcinogenicity of BKPyV integration was proven to disturb host gene expression and increase viral oncoprotein expression. Fallible DNA double-strand break repair pathways were significantly activated in the parenchyma of BKPyV-associated tumors. Olaparib showed an antitumor activity dose-response effect in the tumor organoids without BRCA1/2 genes mutation. In conclusion, the dynamic viral integration patterns actively participate in the progression of BKPyV-associated diseases and thus could be a potential target for disease monitoring and intervention.
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Affiliation(s)
- Yuchen Wang
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Susha Yan
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanna Liu
- Department of Gastroenterology and Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Ziyan Yan
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wenfeng Deng
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Geng
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhuolin Li
- KingMed Diagnostics Group Co, Ltd, Guangzhou, China
| | - Renfei Xia
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wenli Zeng
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Zhao
- Departments of Urology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yiling Fang
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Na Liu
- Mygenostics Co, Beijing, China
| | - Lingling Yang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co, Inc, Hangzhou, China
| | - Jian Xu
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chin-Lee Wu
- Departments of Urology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yun Miao
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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10
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Feng J, Lan Y, Liu F, Yuan Y, Ge J, Wei S, Luo H, Li J, Luo T, Bian X. Combination of genomic instability score and TP53 status for prognosis prediction in lung adenocarcinoma. NPJ Precis Oncol 2023; 7:110. [PMID: 37907595 PMCID: PMC10618567 DOI: 10.1038/s41698-023-00465-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023] Open
Abstract
The genomic instability (GI) /homologous recombination deficiency (HRD) score, calculated as the sum of the events of loss of heterozygosity (LOH), large-scale state transition (LST) and telomere allele imbalance (TAI), is used to guide the choice of treatment in several cancers, but its relationship with genomic features, clinicopathological characteristics and prognosis in lung cancer is poorly understood, which could lead to population bias in prospective studies. We retrospectively analyzed 1011 lung cancer patients whose tumor samples were successfully profiled by high-throughput sequencing panel including GI/HRD score. Alterations of many cancer suppressor genes were associated with higher GI/HRD scores, biallelic inactivation of TP53 was correlated with a high GI/HRD score. A combination of two gene alterations exhibited a higher GI/HRD scores than single gene alterations. The GI/HRD score was associated with advanced stages in lung adenocarcinoma but not in lung squamous cell carcinoma. Furthermore, patients with higher GI/HRD scores had significantly shorter overall survival and progression-free survival than patients with lower GI/HRD scores. Finally, patients with a combination of a higher GI/HRD scores and TP53 alteration exhibited an extremely poor prognosis compared with patients with a lower GI/HRD scores and wild-type TP53 (overall survival, training cohort, hazard ratio (HR) = 8.56, P < 0.001; validation cohort, HR = 6.47, P < 0.001; progression-free survival, HR = 4.76, P < 0.001). Our study revealed the prognostic value of the GI/HRD score in lung adenocarcinoma, but not for all lung cancer. Moreover, the combination of the GI/HRD score and TP53 status could be a promising strategy to predict the prognosis of patients with lung adenocarcinoma.
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Affiliation(s)
- Juan Feng
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Yang Lan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Feng Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Ye Yuan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Jia Ge
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Sen Wei
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Hu Luo
- Department of Respiratory and Critical Care Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Jianjun Li
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Tao Luo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China.
| | - Xiuwu Bian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China.
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11
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Abe H, Kamimura K, Okuda S, Watanabe Y, Inoue J, Aoyagi Y, Wakai T, Kominami R, Terai S. BCL11B expression in hepatocellular carcinoma relates to chemosensitivity and clinical prognosis. Cancer Med 2023; 12:15650-15663. [PMID: 37293953 PMCID: PMC10417273 DOI: 10.1002/cam4.6167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
INTRODUCTION B-cell lymphoma/leukemia 11B (BCL11B) is a subunit of SWI/SNF chromatin remodeling complexes and functions in cell cycle regulation and apoptosis upon DNA replication stress and damages via transcription. Many malignancies were reported to exhibit changes in BCL11B gene expression; however, no study has focused on the relationship between BCL11B and hepatocellular carcinoma, which potentially exhibits DNA replication stress and damages upon its oncogenesis. Thus, in this study, we examined the molecular characterization of BCL11B expression in hepatocellular carcinoma. METHODS AND RESULTS The cumulative progression-free survival and overall survival were significantly longer in the clinical cases of BCL11B-negative hepatocellular carcinoma than BCL11B-positve cases. Microarray and real-time PCR analyses in hepatocellular carcinoma cell lines indicated a correlation between BCL11B and GATA6, a gene reported to be correlated with oncogenic activities and resistance to anthracycline, which is often used for hepatocellular carcinoma chemotherapy. Consequently, BCL11B-overexpressing cell lines exhibited resistance to anthracycline in cell growth assays and the resistance has been evidenced by the increased expression of BCL-xL in cell lines. The results were supported by the analyses of human HCC samples showing the correlation between BCL11B and GATA6 expressions. DISCUSSIONS AND CONCLUSION Our results indicated that overexpression of BCL11B amplifies GATA6 expression in hepatocellular carcinoma in vitro and in vivo that leads to anti-apoptotic signal activation, and induces resistance to chemotherapy, which influenced the postoperative prognosis.
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Affiliation(s)
- Hiroyuki Abe
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Kenya Kamimura
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
- Department of General MedicineNiigata University School of MedicineNiigataNiigataJapan
| | - Shujiro Okuda
- Division of Bioinformatics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Yu Watanabe
- Division of Bioinformatics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Jun Inoue
- Department of Agricultural Chemistry, Faculty of Applied BiosciencesTokyo University of AgricultureTokyoJapan
| | - Yutaka Aoyagi
- Department of Gastroenterology and HepatologyNiigata Medical CenterNiigataNiigataJapan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Ryo Kominami
- Department of Molecular Genetics, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
| | - Shuji Terai
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental SciencesNiigata UniversityNiigataNiigataJapan
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12
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Luo LZ, Li S, Wei C, Ma J, Qian LM, Chen YX, Wang SX, Zhao Q. Unveiling the interplay between mutational signatures and tumor microenvironment: a pan-cancer analysis. Front Immunol 2023; 14:1186357. [PMID: 37283742 PMCID: PMC10239828 DOI: 10.3389/fimmu.2023.1186357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023] Open
Abstract
Background While recent studies have separately explored mutational signatures and the tumor microenvironment (TME), there is limited research on the associations of both factors in a pan-cancer context. Materials and methods We performed a pan-cancer analysis of over 8,000 tumor samples from The Cancer Genome Atlas (TCGA) project. Machine learning methods were employed to systematically explore the relationship between mutational signatures and TME and develop a risk score based on TME-associated mutational signatures to predict patient survival outcomes. We also constructed an interaction model to explore how mutational signatures and TME interact and influence cancer prognosis. Results Our analysis revealed a varied association between mutational signatures and TME, with the Clock-like signature showing the most widespread influence. Risk scores based on mutational signatures mainly induced by Clock-like and AID/APOBEC activity exhibited strong pan-cancer survival stratification ability. We also propose a novel approach to predict transcriptome decomposed infiltration levels using genome-derived mutational signatures as an alternative approach for exploring TME cell types when transcriptome data are unavailable. Our comprehensive analysis revealed that certain mutational signatures and their interaction with immune cells significantly impact clinical outcomes in particular cancer types. For instance, T cell infiltration levels only served as a prognostic biomarker in melanoma patients with high ultraviolet radiation exposure, breast cancer patients with high homologous recombination deficiency signature, and lung adenocarcinoma patients with high tobacco-associated mutational signature. Conclusion Our study comprehensively explains the complex interplay between mutational signatures and immune infiltration in cancer. The results highlight the importance of considering both mutational signatures and immune phenotypes in cancer research and their significant implications for developing personalized cancer treatments and more effective immunotherapy.
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Affiliation(s)
- Li-Zhi Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Sheng Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Chen Wei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Jiao Ma
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Li-Mei Qian
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Yan-Xing Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Shi-Xiang Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
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13
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Yao H, Li H, Wang J, Wu T, Ning W, Diao K, Wu C, Wang G, Tao Z, Zhao X, Chen J, Sun X, Liu XS. Copy number alteration features in pan-cancer homologous recombination deficiency prediction and biology. Commun Biol 2023; 6:527. [PMID: 37193789 DOI: 10.1038/s42003-023-04901-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/02/2023] [Indexed: 05/18/2023] Open
Abstract
Homologous recombination deficiency (HRD) renders cancer cells vulnerable to unrepaired double-strand breaks and is an important therapeutic target as exemplified by the clinical efficacy of poly ADP-ribose polymerase (PARP) inhibitors as well as the platinum chemotherapy drugs applied to HRD patients. However, it remains a challenge to predict HRD status precisely and economically. Copy number alteration (CNA), as a pervasive trait of human cancers, can be extracted from a variety of data sources, including whole genome sequencing (WGS), SNP array, and panel sequencing, and thus can be easily applied clinically. Here we systematically evaluate the predictive performance of various CNA features and signatures in HRD prediction and build a gradient boosting machine model (HRDCNA) for pan-cancer HRD prediction based on these CNA features. CNA features BP10MB[1] (The number of breakpoints per 10MB of DNA is 1) and SS[ > 7 & <=8] (The log10-based size of segments is greater than 7 and less than or equal to 8) are identified as the most important features in HRD prediction. HRDCNA suggests the biallelic inactivation of BRCA1, BRCA2, PALB2, RAD51C, RAD51D, and BARD1 as the major genetic basis for human HRD, and may also be applied to effectively validate the pathogenicity of BRCA1/2 variants of uncertain significance (VUS). Together, this study provides a robust tool for cost-effective HRD prediction and also demonstrates the applicability of CNA features and signatures in cancer precision medicine.
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Affiliation(s)
- Huizi Yao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyu Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wei Ning
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Kaixuan Diao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chenxu Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guangshuai Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ziyu Tao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiangyu Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jing Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiaoqin Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xue-Song Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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14
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Liu Y, Li Y, Zhang MZ, Chen D, Leng Y, Wang J, Han BW, Wang J. Homologous recombination deficiency prediction using low-pass whole genome sequencing in breast cancer. Cancer Genet 2023; 272-273:35-40. [PMID: 36758499 DOI: 10.1016/j.cancergen.2023.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/17/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
Homologous recombination repair deficiency (HRD) results in a defect in DNA repair and is a frequent driver of tumorigenesis. Poly(ADP-ribose) polymerase inhibitors (PARPi) or platinum-based therapies have increased theraputic effectiveness when treating HRD positive cancers. For breast cancer and ovairan cancer HRD companion diagnostic tests are commonly used. However, the currently used HRD tests are based on high-depth genome sequencing or hybridization-based capture sequencing, which are technically complex and costly. In this study, we modified an existing method named shallowHRD, which uses low-pass whole genome sequencing (WGS) for HRD detection, and estimated the performance of the modified shallowHRD pipeline. Our shallowHRD pipeline achieved an AUC of 0.997 in simulated low-pass WGS data, with a sensitivity of 0.981 and a specificity of 0.964; and achieved a higher HRD risk score in clinical BRCA-deficient breast cancer samples (p = 5.5 × 10-5, compared with BRCA-intact breast cancer samples). We also estimated the limit of detection the shallowHRD pipeline could accurately predict HRD status with a minimum sequencing depth of 0.1 ×, a tumor purity of > 20%, and an input DNA amount of 1 ng. Our study demostrates using low-pass sequencing, HRD status can be determined with high accuracy using a simple approach with greatly reduced cost.
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Affiliation(s)
- Yang Liu
- Department of BC Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yalun Li
- Department of Breast Surgery, Yantai Yuhuangding Hospital, Yantai, Shandong, China
| | - Min-Zhe Zhang
- GeneGenieDx Corp, 160 E Tasman Dr, San Jose, CA, USA
| | - Dan Chen
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Yang Leng
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Juan Wang
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China
| | - Bo-Wei Han
- Guangdong Jiyin Biotech Co. Ltd, Shenzhen, Guangdong, China.
| | - Ji Wang
- Department of Breast Surgery, Yantai Yuhuangding Hospital, Yantai, Shandong, China.
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15
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Feng Z, Shao D, Cai Y, Bi R, Ju X, Chen D, Song C, Chen X, Li J, An N, Li Y, Zhou Q, Xiu Z, Zhu S, Wu X, Wen H. Homologous recombination deficiency status predicts response to platinum-based chemotherapy in Chinese patients with high-grade serous ovarian carcinoma. J Ovarian Res 2023; 16:53. [PMID: 36922847 PMCID: PMC10015784 DOI: 10.1186/s13048-023-01129-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Homologous Recombination Deficiency (HRD) is a predictive biomarker for ovarian cancer treated with PARP inhibitors or for breast cancer treated with first-line platinum-based chemotherapy. However, limited research is documented on platinum-based treatment prediction with HRD as a biomarker in ovarian cancer patients, especially in the Chinese population. METHODS We investigated the association between HRD status and the response of platinum-based chemotherapy in 240 Chinese HGSOC patients. RESULTS The Pt-sensitive patients showed higher HRD scores than Pt-resistant ones, but this was not significant(median: 42.6 vs. 31.6, p = 0.086). (Pt)-sensitive rate was higher in HRD + BRCAm tumors and in HRD + BRCAwt tumors (HRD + BRCAm: 97%, p = 0.004 and HRD + BRCAwt: 90%, p = 0.04) compared with 74% in the HRD-BRCAwt tumors. We also found Pt-sensitive patients tend to be enriched in patients with BRCA mutations or non-BRCA HRR pathway gene mutations (BRCA: 93.6% vs 75.4%, p < 0.001; non-BRCA HRR: 88.6% vs 75.4%, p = 0.062). Patients with HRD status positive had significantly improved PFS compared with those with HRD status negative (median PFS: 30.5 months vs. 16.8 months, Log-rank p = 0.001). Even for BRCAwt patients, positive HRD was also associated with better PFS than the HRD-negative group (median: 27.5 months vs 16.8 months, Log-rank p = 0.010). Further, we found patients with pathogenic mutations located in the DNA-binding domain (DBD) of BRCA1 had improved FPS, compared to those with mutations in other domains. (p = 0.03). CONCLUSIONS The HRD status can be identified as an independent significance in Chinese HGSOC patients treated with first-line platinum-based chemotherapy.
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Affiliation(s)
- Zheng Feng
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 DongAn Rd, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Di Shao
- BGI Genomics, BGI-Shenzhen, BGI Genomics, Beishan Industrial Zone, Yantian District, ShenzhenShenzhen, 518083518083, China
| | - Yuhang Cai
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Rui Bi
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xingzhu Ju
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 DongAn Rd, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dongju Chen
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Chengcheng Song
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xiaojun Chen
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 DongAn Rd, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin Li
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 DongAn Rd, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Na An
- BGI Genomics, BGI-Shenzhen, BGI Genomics, Beishan Industrial Zone, Yantian District, ShenzhenShenzhen, 518083518083, China
| | - Yunjin Li
- BGI Genomics, BGI-Shenzhen, BGI Genomics, Beishan Industrial Zone, Yantian District, ShenzhenShenzhen, 518083518083, China
| | - Qing Zhou
- BGI Genomics, BGI-Shenzhen, BGI Genomics, Beishan Industrial Zone, Yantian District, ShenzhenShenzhen, 518083518083, China
| | - Zhihui Xiu
- BGI Genomics, BGI-Shenzhen, BGI Genomics, Beishan Industrial Zone, Yantian District, ShenzhenShenzhen, 518083518083, China
| | - Shida Zhu
- BGI Genomics, BGI-Shenzhen, BGI Genomics, Beishan Industrial Zone, Yantian District, ShenzhenShenzhen, 518083518083, China.
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 DongAn Rd, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Hao Wen
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 DongAn Rd, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Implementing HRD Testing in Routine Clinical Practice on Patients with Primary High-Grade Advanced Ovarian Cancer. Cancers (Basel) 2023; 15:cancers15030818. [PMID: 36765776 PMCID: PMC9913091 DOI: 10.3390/cancers15030818] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 02/01/2023] Open
Abstract
The chemotherapy backbone for patients with high-grade advanced epithelial ovarian cancer (HG-AOC) is carboplatin and paclitaxel followed by a maintenance therapy either with bevacizumab, with a PARP inhibitor, or with a combination of both, which is defined by the presence of a homologous recombination deficiency (HRD) and by the BRCA1/2 status. This study included patients with a primary diagnosis of HG-AOC treated between December 2019 and December 2021. The HRD status was measured using the Myriad myChoice® test on all the patients with an indication for tumor HRD testing. Germline testing was conducted on all the patients using the TruRisk® panel as recommended by the national guidelines. HRD testing was requested for 190 patients, and, for 163 patients (85.8%), an HRD test result was available. An HRD test result could not be reported in 27 patients due to an insufficient tumor yield. The median time that it took to receive the HRD test results was 37 days (range of 8-97). In total, an HRD was present in 44.7% (73/163) of the patients based on a GIS ≥ 42 in 42.9% of the patients and based on a tumor BRCA1/2 mutation in 3 cases (all with a GIS < 42). The germline testing results were available for 148 patients, and, in 18 patients (12.2%), a deleterious germline mutation was detected. Of the 27 patients without sufficient HRD testing, BRCA1/2 germline testing results were available for 19 patients (70.4%), and a deleterious germline mutation was detected in 2 patients (7.4%). The implementation of HRD testing is feasible, and the results become available for treatment decisions in a timely manner for most patients. The prerequisite for HRD testing with the Myriad myChoice® test is a sufficient amount of tumor tissue. The cotesting of HRD and BRCA1/2 germline testing should be aimed for in order to enable optimal and timely treatment decisions on maintenance therapy as well as to test patients on whom the HRD test will not be evaluable.
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17
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Zhang L, Wu Z, Li J, Zhu D, Yang L, Shao Y, Lin Y, Liu Z, Cao Y, Zhang G, Shang S, Zhang Y, Wang K. Impact of Homologous Recombination Deficiency on Outcomes in Patients With Triple-Negative Breast Cancer Treated With Carboplatin-Based Neoadjuvant Chemotherapy: Secondary Analysis of the NeoCART Randomized Clinical Trial. JCO Precis Oncol 2023; 7:e2200337. [PMID: 36652665 DOI: 10.1200/po.22.00337] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
PURPOSE Pathologic complete response (pCR) rates of patients with triple-negative breast cancer who were administered docetaxel plus carboplatin were significantly higher than those of patients administered epirubicin/cyclophosphamide followed by docetaxel in the neoadjuvant NeoCART trial. Here, we performed a preplanned secondary analysis of the homologous recombination deficiency (HRD) score as a predictor of the pCR in patients with triple-negative breast cancer from the NeoCART cohort. METHODS Pretherapeutic tumor tissues were assessed retrospectively by DNA extraction and sequencing. BRCA1/2 mutations were evaluated in both somatic and germline forms. HRD scores were calculated from genome-wide allele-specific copy number results and comprised telomeric allelic imbalance, loss of heterozygosity, and large-scale state transitions. High HRD scores were defined as ≥ 38, and HRD was defined as either a high HRD score or a deleterious BRCA1/2 mutation. RESULTS HRD testing was completed for 43 (79.6%) of 54 NeoCART cohort patients. Thirty of 43 (69.8%) tumors had high HRD scores, and eight patients had BRCA-mutated tumors. No significant association between BRCA1/2 mutation status and pCR was observed either in the general population or in the two treatment arms. Docetaxel plus carboplatin group patients who achieved pCR had higher HRD scores than non-pCR patients, and this difference approached significance (61.69 ± 24.26 v 39.44 ± 22.83, P = .061). No significant correlations between HRD scores and pCR (61.29 ± 24.02 v 53.21 ± 24.31, P = .480) or residual cancer burden 0/1 (62.50 ± 22.50 v 51.85 ± 24.74, P = .324) were observed in the epirubicin/cyclophosphamide followed by docetaxel group. CONCLUSION HRD is a potential predictive biomarker for clinical benefit from neoadjuvant carboplatin-based chemotherapy and provides a possibility for screening the optimum chemotherapy backbone to combine with immunotherapy.
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Affiliation(s)
- Liulu Zhang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhiyong Wu
- Diagnosis & Treatment Center of Breast Diseases, Shantou Central Hospital, Shantou, Guangdong, China
| | - Jie Li
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangdong, China
| | - Dongqin Zhu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Lingling Yang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Ying Lin
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangdong, China
| | - Zhenzhen Liu
- Department of Breast Cancer Center, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yin Cao
- Breast Central, Dongguan People's Hospital, Dongguan, Guangdong, China
| | - Gangling Zhang
- Breast Surgery, Baotou Cancer Hospital, Baotou, Inner Mongolia, China
| | - Shiyao Shang
- Department of Ultrasound, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yi Zhang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Kun Wang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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Algethami M, Kulkarni S, Sadiq MT, Tang HKC, Brownlie J, Jeyapalan JN, Mongan NP, Rakha EA, Madhusudan S. Towards Personalized Management of Ovarian Cancer. Cancer Manag Res 2022; 14:3469-3483. [PMID: 36545222 PMCID: PMC9762171 DOI: 10.2147/cmar.s366681] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022] Open
Abstract
Despite advances in surgery and chemotherapy, the overall outcomes for patients with advanced ovarian cancer remain poor. Although initial response rates to platinum-based chemotherapy is about 60-80%, most patients will have recurrence and succumb to the disease. However, a DNA repair-directed precision medicine strategy has recently generated real hope in improving survival. The clinical development of PARP inhibitors has transformed lives for many patients with BRCA germline-deficient and/or platinum-sensitive epithelial ovarian cancers. Antiangiogenic agents and intraperitoneal chemotherapy approaches may also improve outcomes in patients. Moreover, evolving immunotherapeutic opportunities could also positively impact patient outcomes. Here we review the current clinical state of PARP inhibitors and other clinically viable targeted approaches in ovarian cancer.
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Affiliation(s)
- Mashael Algethami
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Sanat Kulkarni
- Department of Medicine, City Hospital, Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, B18 7QH, UK
| | - Maaz T Sadiq
- Cancer Centre, Queen Elizabeth Hospital, University Hospitals Birmingham NHS Trust, Birmingham, B15 2GW, UK
| | - Hiu K C Tang
- Department of Oncology, Nottingham University Hospitals, Nottingham, NG51PB, UK
| | - Juliette Brownlie
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Jennie N Jeyapalan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Nigel P Mongan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Emad A Rakha
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Srinivasan Madhusudan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
- Department of Oncology, Nottingham University Hospitals, Nottingham, NG51PB, UK
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19
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Smith MA, Van Alsten SC, Walens A, Damrauer JS, Maduekwe UN, Broaddus RR, Love MI, Troester MA, Hoadley KA. DNA Damage Repair Classifier Defines Distinct Groups in Hepatocellular Carcinoma. Cancers (Basel) 2022; 14:cancers14174282. [PMID: 36077818 PMCID: PMC9454479 DOI: 10.3390/cancers14174282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary DNA repair pathways have been implicated in hepatocellular carcinoma outcomes. We found that hepatocellular carcinomas (HCC) could be separated into two groups (high and low) based on the overall expression of genes involved in DNA repair. Among the low repair group, there were three subgroups, one of which shared features of the high repair group. Given the important role of liver in metabolism and detoxification and its regenerative capacity, proliferation and DNA damage responses are critical in subdividing major biological categories of liver tumors. High repair samples showed more proliferative and regenerative signatures and had poorer outcomes versus the low repair that were more associated with the genes involved in normal liver biology. These biological groups suggest that dysregulation in endogenous liver processes promotes a pro-tumorigenic microenvironment that may facilitate tumor progression or identify tumors that require more substantial clinical intervention. Abstract DNA repair pathways have been associated with variability in hepatocellular carcinoma (HCC) clinical outcomes, but the mechanism through which DNA repair varies as a function of liver regeneration and other HCC characteristics is poorly understood. We curated a panel of 199 genes representing 15 DNA repair pathways to identify DNA repair expression classes and evaluate their associations with liver features and clinicopathologic variables in The Cancer Genome Atlas (TCGA) HCC study. We identified two groups in HCC, defined by low or high expression across all DNA repair pathways. The low-repair group had lower grade and retained the expression of classical liver markers, whereas the high-repair group had more clinically aggressive features, increased p53 mutant-like gene expression, and high liver regenerative gene expression. These pronounced features overshadowed the variation in the low-repair subset, but when considered separately, the low-repair samples included three subgroups: L1, L2, and L3. L3 had high DNA repair expression with worse progression-free (HR 1.24, 95% CI 0.81–1.91) and overall (HR 1.63, 95% CI 0.98–2.71) survival. High-repair outcomes were also significantly worse compared with the L1 and L2 groups. HCCs vary in DNA repair expression, and a subset of tumors with high regeneration profoundly disrupts liver biology and poor prognosis.
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Affiliation(s)
- Markia A. Smith
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sarah C. Van Alsten
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Andrea Walens
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeffrey S. Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ugwuji N. Maduekwe
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Russell R. Broaddus
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael I. Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melissa A. Troester
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence:
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