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Ma J, Shah R, Bell AC, McDermott N, Pei X, Selenica P, Haseltine J, Delsite R, Khan AJ, Lok BH, Ellis MJ, Aft RF, Setton J, Reis-Filho JS, Riaz N, Powell SN. Increased Synthetic Cytotoxicity of Combinatorial Chemoradiation Therapy in Homologous Recombination Deficient Tumors. Int J Radiat Oncol Biol Phys 2024:S0360-3016(24)02946-8. [PMID: 38997095 DOI: 10.1016/j.ijrobp.2024.06.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 06/10/2024] [Accepted: 06/29/2024] [Indexed: 07/14/2024]
Abstract
PURPOSE Homologous recombination deficient (HRD) tumors are exquisitely sensitive to platinum-based chemotherapy and when combined with radiation therapy (RT), leads to improved overall survival in multiple cancer types. Whether a subset of tumors with distinct molecular characteristics demonstrate increased benefit from cisplatin and RT (c-RT) is unclear. We hypothesized that HRD tumors, whether associated with BRCA mutations or genomic scars of HRD, exhibit exquisite sensitivity to c-RT, and that HRD may be a significant driver of c-RT benefit. METHODS AND MATERIALS Sensitivity to c-RT was examined using isogenic and sporadic breast cancer cell lines. HRD was assessed using 4 assays: RT-induced Rad51 foci, a DR-GFP reporter assay, a genomic scar score (large-scale state transitions [LST]), and clonogenic survival assays. Whole-genome sequencing of 4 breast tumors from a phase 2 clinical trial of neoadjuvant c-RT in triple-negative breast cancer was performed and HRD was defined using HRDetect. RESULTS BRCA1/2 deficient cell lines displayed functional HRD based on the Rad51 functional assay, with c-RT to RT or cisplatin interaction ratios (IR) of 1.11 and 26.84 for the BRCA1 isogenic pair at 2 μM cisplatin and 6 Gy, respectively. The highest LST lines demonstrated HRD and synthetic cytotoxicity to c-RT with IR at 2 Gy and cisplatin 20 μM of 7.50, and the lowest LST line with IR of 0.65. Of 4 evaluable patients in the phase 2 trial, one achieved a pathologic complete response with corresponding HRD based on multiple genomic scar scores including HRDetect and LST scores, compared with patients without a pathologic complete response. CONCLUSIONS HRD breast cancers, whether identified by BRCA1/2 mutation status, functional tests, or mutational signatures, appear to be significantly more sensitive to c-RT compared with isogenic controls or tumors without HRD mutational signatures. HRD tumors may be exquisitely sensitive to c-RT which warrants further clinical investigation to guide a precision oncology approach.
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Affiliation(s)
- Jennifer Ma
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rachna Shah
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew C Bell
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Niamh McDermott
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xin Pei
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pier Selenica
- Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Justin Haseltine
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert Delsite
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Atif J Khan
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin H Lok
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York; Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Departments of Radiation Oncology; Medical Biophysics; Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Matthew J Ellis
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Rebecca F Aft
- Department of General Surgery, Washington University, St Louis, Missouri
| | - Jeremy Setton
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Nadeem Riaz
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Simon N Powell
- Departments of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.
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2
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Al Assaad M, Michaud O, Semaan A, Sigouros M, Tranquille M, Phan A, Levine MF, Gundem G, Medina-Martínez JS, Papaemmanuil E, Manohar J, Wilkes D, Sboner A, Hoda SAF, Elemento O, Mosquera JM. Whole-Genome Sequencing Analysis of Male Breast Cancer Unveils Novel Structural Events and Potential Therapeutic Targets. Mod Pathol 2024; 37:100452. [PMID: 38369186 DOI: 10.1016/j.modpat.2024.100452] [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: 11/30/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 02/20/2024]
Abstract
The molecular characterization of male breast cancer (MaBC) has received limited attention in research, mostly because of its low incidence rate, accounting for only 0.5% to 1% of all reported cases of breast cancer each year. Managing MaBC presents significant challenges, with most treatment protocols being adapted from those developed for female breast cancer. Utilizing whole-genome sequencing (WGS) and state-of-the-art analyses, the genomic features of 10 MaBC cases (n = 10) were delineated and correlated with clinical and histopathologic characteristics. Using fluorescence in situ hybridization, an additional cohort of 18 patients was interrogated to supplement WGS findings. The genomic landscape of MaBC uncovered significant genetic alterations that could influence diagnosis and treatment. We found common somatic mutations in key driver genes, such as FAT1, GATA3, SMARCA4, and ARID2. Our study also mapped out structural variants that impact cancer-associated genes, such as ARID1A, ESR1, GATA3, NTRK1, and NF1. Using a WGS-based classifier, homologous recombination deficiency (HRD) was identified in 2 cases, both presenting with deleterious variants in BRCA2. Noteworthy was the observation of FGFR1 amplification in 21% of cases. Altogether, we identified at least 1 potential therapeutic target in 8 of the 10 cases, including high tumor mutational burden, FGFR1 amplification, and HRD. Our study is the first WGS characterization of MaBC, which uncovered potentially relevant variants, including structural events in cancer genes, HRD signatures, and germline pathogenic mutations. Our results demonstrate unique genetic markers and potential treatment targets in MaBC, thereby underlining the necessity of tailoring treatment strategies for this understudied patient population. These WGS-based findings add to the growing knowledge of MaBC genomics and highlight the need to expand research on this type of cancer.
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Affiliation(s)
- Majd Al Assaad
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Olivier Michaud
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Département de Pathologie, Université Laval, Quebec City, Quebec, Canada
| | - Alissa Semaan
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Michael Sigouros
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Marvel Tranquille
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Andy Phan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | | | | | | | | | - Jyothi Manohar
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - David Wilkes
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Syed A F Hoda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York; New York Genome Center, New York, New York.
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3
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Lin PH, Tien YW, Cheng WF, Chiang YC, Wu CH, Yang K, Huang CS. Diverse genetic spectrum among patients who met the criteria of hereditary breast, ovarian and pancreatic cancer syndrome. J Gynecol Oncol 2023; 34:e66. [PMID: 37170728 PMCID: PMC10482589 DOI: 10.3802/jgo.2023.34.e66] [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: 12/31/2022] [Revised: 03/06/2023] [Accepted: 04/16/2023] [Indexed: 05/13/2023] Open
Abstract
OBJECTIVE Genetic high-risk assessment combines hereditary breast, ovarian and pancreatic cancer into one syndrome. However, there is a lack of data for comparing the germline mutational spectrum of the cancer predisposing genes between these three cancers. METHODS Patients who met the criteria of the hereditary breast, ovarian and pancreatic cancer were enrolled and received multi-gene sequencing. RESULTS We enrolled 730 probands: 418 developed breast cancer, 185 had ovarian cancer, and 145 had pancreatic cancer. Out of the 18 patients who had two types of cancer, 16 had breast and ovarian cancer and 2 had breast and pancreatic cancer. A total of 167 (22.9%) patients had 170 mutations. Mutation frequency in breast, ovarian and pancreatic cancer was 22.3%, 33.5% and 17.2%, respectively. The mutation rate was significantly higher in patients with double cancers than those with a single cancer (p<0.001). BRCA1 and BRCA2 were the most dominant genes associated with hereditary breast and ovarian cancer, whereas ATM was the most prevalent gene related to hereditary pancreatic cancer. Genes of hereditary colon cancer such as lynch syndrome were presented in a part of patients with pancreatic or ovarian cancer but seldom in those with breast cancer. Families with a history of both ovarian and breast cancer were associated with a higher mutation rate than those with other histories. CONCLUSION The mutation spectrum varies across the three cancer types and family histories. Our analysis provides guidance for physicians, counsellors, and counselees on the offer and uptake of genetic counseling.
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Affiliation(s)
- Po-Han Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yun-Wen Tien
- Department of Surgery, National Taiwan University Hospital and Medical College of the National Taiwan University, Taipei, Taiwan
| | - Wen-Fang Cheng
- Department of Gynecology and Obstetrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ying-Cheng Chiang
- Department of Gynecology and Obstetrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Huei Wu
- Department of Surgery, National Taiwan University Hospital and Medical College of the National Taiwan University, Taipei, Taiwan
| | - Karen Yang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital and Medical College of the National Taiwan University, Taipei, Taiwan.
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4
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Andersen LVB, Larsen MJ, Davies H, Degasperi A, Nielsen HR, Jensen LA, Kroeldrup L, Gerdes AM, Lænkholm AV, Kruse TA, Nik-Zainal S, Thomassen M. Non-BRCA1/BRCA2 high-risk familial breast cancers are not associated with a high prevalence of BRCAness. Breast Cancer Res 2023; 25:69. [PMID: 37316882 DOI: 10.1186/s13058-023-01655-y] [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: 08/09/2022] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Familial breast cancer is in most cases unexplained due to the lack of identifiable pathogenic variants in the BRCA1 and BRCA2 genes. The somatic mutational landscape and in particular the extent of BRCA-like tumour features (BRCAness) in these familial breast cancers where germline BRCA1 or BRCA2 mutations have not been identified is to a large extent unknown. METHODS We performed whole-genome sequencing on matched tumour and normal samples from high-risk non-BRCA1/BRCA2 breast cancer families to understand the germline and somatic mutational landscape and mutational signatures. We measured BRCAness using HRDetect. As a comparator, we also analysed samples from BRCA1 and BRCA2 germline mutation carriers. RESULTS We noted for non-BRCA1/BRCA2 tumours, only a small proportion displayed high HRDetect scores and were characterized by concomitant promoter hypermethylation or in one case a RAD51D splice variant previously reported as having unknown significance to potentially explain their BRCAness. Another small proportion showed no features of BRCAness but had mutationally active tumours. The remaining tumours lacked features of BRCAness and were mutationally quiescent. CONCLUSIONS A limited fraction of high-risk familial non-BRCA1/BRCA2 breast cancer patients is expected to benefit from treatment strategies against homologue repair deficient cancer cells.
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Affiliation(s)
- Lars V B Andersen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Helen Davies
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Andrea Degasperi
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | | | - Louise A Jensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lone Kroeldrup
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anne-Vibeke Lænkholm
- Department of Surgical Pathology, Zealand University Hospital, 4000, Roskilde, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Serena Nik-Zainal
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- European Sperm Bank, Copenhagen, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
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5
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Glodzik D, Selenica P, Rogge RA, Silverman IM, Mandelker D, Harris S, Zhao J, Zinda M, Veloso A, Malani N, Riaz N, Koehler M, Daber RD, Johnson V, Rimkunas V, Reis-Filho JS. Detection of Biallelic Loss of DNA Repair Genes in Formalin-Fixed, Paraffin-Embedded Tumor Samples Using a Novel Tumor-Only Sequencing Panel. J Mol Diagn 2023; 25:295-310. [PMID: 36944408 PMCID: PMC10340082 DOI: 10.1016/j.jmoldx.2023.02.004] [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: 09/01/2022] [Revised: 11/21/2022] [Accepted: 02/09/2023] [Indexed: 03/23/2023] Open
Abstract
Patient selection for synthetic lethal-based cancer therapy may be improved by assessment of gene-specific loss of heterozygosity (LOH) and biallelic loss of function (LOF). This report describes SyNthetic lethal Interactions for Precision Diagnostics (SNiPDx), a targeted next-generation sequencing (NGS) panel for detection of LOH and biallelic LOF alterations in 26 target genes focused on DNA damage response pathways, in tumor-only formalin-fixed, paraffin-embedded (FFPE) samples. NGS was performed across all exons of these 26 genes and encompassed a total of 7632 genome-wide single-nucleotide polymorphisms on genomic DNA from 80 FFPE solid tumor samples. The Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing algorithm was optimized to assess tumor purity and copy number based on heterozygous single-nucleotide polymorphisms. SNiPDx demonstrated high sensitivity (95%) and specificity (91%) for LOH detection compared with whole genome sequencing. Positive agreement with local NGS-based testing in the detection of genetic alterations was 95%. SNiPDx detected 93% of biallelic ATM LOF mutations, 100% of ATM single-nucleotide variants and small insertions/deletions, and 100% of all ATM LOH status events identified by orthogonal NGS-based testing. SNiPDx is a novel, clinically feasible test for analysis of allelic status in FFPE tumor samples, which demonstrated high accuracy when compared with other NGS-based approaches in clinical use.
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Affiliation(s)
| | - Pier Selenica
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | | | | | | | | | | | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, New York
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6
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Liu W, Zheng M, Zhang R, Jiang Q, Du G, Wu Y, Yang C, Li F, Li W, Wang L, Wu J, Shi L, Li W, Zhang K, Zhou Z, Liu R, Gao Y, Huang X, Fan S, Zhi X, Jiang D, Chen C. RNF126-Mediated MRE11 Ubiquitination Activates the DNA Damage Response and Confers Resistance of Triple-Negative Breast Cancer to Radiotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203884. [PMID: 36563124 PMCID: PMC9929257 DOI: 10.1002/advs.202203884] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/05/2022] [Indexed: 05/27/2023]
Abstract
Triple-negative breast cancer (TNBC) has higher molecular heterogeneity and metastatic potential and the poorest prognosis. Because of limited therapeutics against TNBC, irradiation (IR) therapy is still a common treatment option for patients with lymph nodes or brain metastasis. Thus, it is urgent to develop strategies to enhance the sensitivity of TNBC tumors to low-dose IR. Here, the authors report that E3 ubiquitin ligase Ring finger protein 126 (RNF126) is important for IR-induced ATR-CHK1 pathway activation to enhance DNA damage repair (DDR). Mechanistically, RNF126 physically associates with the MRE11-RAD50-NBS1 (MRN) complex and ubiquitinates MRE11 at K339 and K480 to increase its DNA exonuclease activity, subsequent RPA binding, and ATR phosphorylation, promoting sustained DDR in a homologous recombination repair-prone manner. Accordingly, depletion of RNF126 leads to increased genomic instability and radiation sensitivity in both TNBC cells and mice. Furthermore, it is found that RNF126 expression is induced by IR activating the HER2-AKT-NF-κB pathway and targeting RNF126 expression with dihydroartemisinin significantly improves the sensitivity of TNBC tumors in the brain to IR treatment in vivo. Together, these results reveal that RNF126-mediated MRE11 ubiquitination is a critical regulator of the DDR, which provides a promising target for improving the sensitivity of TNBC to radiotherapy.
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Affiliation(s)
- Wenjing Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
- The Third Affiliated HospitalKunming Medical UniversityKunming650118China
| | - Min Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Rou Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
| | - Qiuyun Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Guangshi Du
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Yingying Wu
- Department of the PathologyFirst Affiliated Hospital of Kunming Medical UniversityKunming650032China
| | - Chuanyu Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Fubing Li
- Academy of Biomedical EngineeringKunming Medical UniversityKunming650500China
| | - Wei Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Luzhen Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- School of Life ScienceUniversity of Science & Technology of ChinaHefei230027China
| | - Jiao Wu
- The Third Affiliated HospitalKunming Medical UniversityKunming650118China
| | - Lei Shi
- Department of Biochemistry and Molecular BiologyTianjin Medical UniversityTianjin300070China
| | - Wenhui Li
- The Third Affiliated HospitalKunming Medical UniversityKunming650118China
| | - Kai Zhang
- Department of Biochemistry and Molecular BiologyTianjin Medical UniversityTianjin300070China
| | - Zhongmei Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
| | - Rong Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Translational Cancer Research CenterPeking University First HospitalBeijing100034China
| | - Yingzheng Gao
- Department of the Central LaboratorySecond Affiliated Hospital of Kunming Medical UniversityKunming650032China
| | - Xinwei Huang
- Department of the Central LaboratorySecond Affiliated Hospital of Kunming Medical UniversityKunming650032China
| | - Songqing Fan
- Department of Pathologythe Second Xiangya HospitalCentral South UniversityChangsha410000China
| | - Xu Zhi
- Center for Reproductive MedicineDepartment of Obstetrics and GynecologyPeking University Third HospitalBeijing100191China
| | - Dewei Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life SciencesUniversity of the Chinese Academy of SciencesKunming650204China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- The Third Affiliated HospitalKunming Medical UniversityKunming650118China
- Academy of Biomedical EngineeringKunming Medical UniversityKunming650500China
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7
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Moore G, Majumdar R, Powell SN, Khan AJ, Weinhold N, Yin S, Higginson DS. Templated Insertions Are Associated Specifically with BRCA2 Deficiency and Overall Survival in Advanced Ovarian Cancer. Mol Cancer Res 2022; 20:1061-1070. [PMID: 35385581 PMCID: PMC9372910 DOI: 10.1158/1541-7786.mcr-21-1012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/14/2022] [Accepted: 04/01/2022] [Indexed: 01/09/2023]
Abstract
Cancer cells defective in homologous recombination (HR) are responsive to DNA-crosslinking chemotherapies, PARP inhibitors, and inhibitors of polymerase theta (Pol θ), a key mediator of the backup pathway alternative end-joining. Such cancers include those with pathogenic biallelic alterations in core HR genes and another cohort of cases that exhibit sensitivity to the same agents and harbor genomic hallmarks of HR deficiency (HRD). These HRD signatures include a single-base substitution pattern, large rearrangements, characteristic tandem duplications, and small deletions. Here, we used what is now known about the backup pathway alternative end-joining (Alt-EJ) through the key factor Pol θ to design and test novel signatures of polymerase theta-mediated (TMEJ) repair. We generated two novel signatures; a signature composed of small deletions with microhomology and another consisting of small, templated insertions (TINS). We find that TINS consistent with TMEJ repair are highly specific to tumors with pathogenic biallelic mutations in BRCA2 and that high TINS genomic signature content in advanced ovarian cancers associate with overall survival following treatment with platinum agents. In addition, the combination of TINS with other HRD metrics significantly improves the association of platinum sensitivity with survival compared with current state-of-the-art signatures. IMPLICATIONS Small, templated insertions indicative of theta-mediated end-joining likely can be used in conjunction with other HRD mutational signatures as a prognostic tool for patient response to therapies targeting HR deficiency.
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Affiliation(s)
- Grace Moore
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Rahul Majumdar
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Simon N. Powell
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Atif J. Khan
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Shen Yin
- Epidemiology & Biostatistics, Memorial Sloan Kettering
Cancer Center, New York, NY 10065
| | - Daniel S. Higginson
- Department of Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, NY 10065.,Corresponding author: Daniel S.
Higginson, Department of Radiation Oncology, Memorial Sloan Kettering Cancer
Center, 1275 York Ave Box #22, New York, NY 10065; Phone: (646) 888-3567;
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8
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Mekonnen N, Yang H, Shin YK. Homologous Recombination Deficiency in Ovarian, Breast, Colorectal, Pancreatic, Non-Small Cell Lung and Prostate Cancers, and the Mechanisms of Resistance to PARP Inhibitors. Front Oncol 2022; 12:880643. [PMID: 35785170 PMCID: PMC9247200 DOI: 10.3389/fonc.2022.880643] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
Homologous recombination (HR) is a highly conserved DNA repair mechanism that protects cells from exogenous and endogenous DNA damage. Breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) play an important role in the HR repair pathway by interacting with other DNA repair proteins such as Fanconi anemia (FA) proteins, ATM, RAD51, PALB2, MRE11A, RAD50, and NBN. These pathways are frequently aberrant in cancer, leading to the accumulation of DNA damage and genomic instability known as homologous recombination deficiency (HRD). HRD can be caused by chromosomal and subchromosomal aberrations, as well as by epigenetic inactivation of tumor suppressor gene promoters. Deficiency in one or more HR genes increases the risk of many malignancies. Another conserved mechanism involved in the repair of DNA single-strand breaks (SSBs) is base excision repair, in which poly (ADP-ribose) polymerase (PARP) enzymes play an important role. PARP inhibitors (PARPIs) convert SSBs to more cytotoxic double-strand breaks, which are repaired in HR-proficient cells, but remain unrepaired in HRD. The blockade of both HR and base excision repair pathways is the basis of PARPI therapy. The use of PARPIs can be expanded to sporadic cancers displaying the “BRCAness” phenotype. Although PARPIs are effective in many cancers, their efficacy is limited by the development of resistance. In this review, we summarize the prevalence of HRD due to mutation, loss of heterozygosity, and promoter hypermethylation of 35 DNA repair genes in ovarian, breast, colorectal, pancreatic, non-small cell lung cancer, and prostate cancer. The underlying mechanisms and strategies to overcome PARPI resistance are also discussed.
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Affiliation(s)
- Negesse Mekonnen
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Department of Veterinary Science, School of Animal Science and Veterinary Medicine, Bahir Dar University, Bahir Dar, Ethiopia
| | - Hobin Yang
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
| | - Young Kee Shin
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Bio-MAX/N-Bio, Seoul National University, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University Graduate School of Convergence Science and Technology, Seoul, South Korea
- LOGONE Bio Convergence Research Foundation, Center for Companion Diagnostics, Seoul, South Korea
- *Correspondence: Young Kee Shin,
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9
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Zhang J, Wang N, Zheng T, Lu T, Zhang R, Ran R, Li K, Huang Y, Xie F, Zhang Y, Jia S, Yu J, Li H. Germline Mutational Landscape in Chinese Patients With Advanced Breast Cancer. Front Oncol 2022; 12:745796. [PMID: 35494038 PMCID: PMC9043949 DOI: 10.3389/fonc.2022.745796] [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: 07/22/2021] [Accepted: 03/09/2022] [Indexed: 11/27/2022] Open
Abstract
Background Genetic testing for breast cancer (BC) patients may shift the paradigm towards more personalized management and treatment strategies. While gene alterations may be ethnic-specific in breast cancer, our understanding of genetic epidemiology of BC remains mainly driven by data from Caucasian populations and further limited to selected handful of genes. Methods We collected whole blood samples from 356 BC patients at metastatic first line BC and primary stage IV disease at Beijing Cancer Hospital between Jan. 2013 to Dec. 2019. A comprehensive 600-gene cancer panel was used to detect germline variants in the covered genes with a median 300x sequencing depth. Variants were classified into pathogenic, likely pathogenic, variant of uncertain significance, likely benign and benign groups according to the ACMG/AMP Standards and Guidelines. Pathogenic and likely pathogenic variants were considered as deleterious mutations. Results The median age of 356 BC patients was 49 years (range, 21-87 years) at the first diagnosis of BC. Deleterious germline mutations across 48 cancer-related genes were identified in 21.6% (77/356) of the patients. The most prevalent mutations were BRCA1/2 mutations (7.0%), followed by ATM and RAD50 mutations (1.4% each). In addition, patients with family history were more likely to carry BRCA1 mutations (P=0.04). Moreover, patients with triple-negative breast cancer (TNBC) were more likely to harbor BRCA1 mutations than those with HR+ or HER2+ breast cancer (P=0.006). While there was no significant survival difference observed in BRCA1/2 carriers relative to non-carriers, patients with DNA damage repair (DDR) gene mutations (mostly frequently BRCA, ATM, RAD50) had worse disease-free survival (P=0.02). Conclusions The most prevalent germline mutations in a large cohort of Chinese patients with advanced BC were BRCA1/2 mutations, followed by ATM and RAD50 mutations. In total, approximately 16.0% (57/356) of patients carry deleterious mutations in DDR pathway. Patients with breast or ovarian cancer family history were more likely to carry BRCA1/2 mutations, and ones with DDR mutations had worse survival. These findings suggest that DDR mutations are prevalent in Chinese BC patients who may potentially benefit from treatment with Poly (ADP-ribose) polymerase inhibitors.
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Affiliation(s)
- Jiayang Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Nan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | | | - Tan Lu
- Huidu Shanghai Medical Sciences, Shanghai, China
| | - Ruyan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ran Ran
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Kun Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yong Huang
- Huidu Shanghai Medical Sciences, Shanghai, China
| | - Feng Xie
- Huidu Shanghai Medical Sciences, Shanghai, China
| | - Yue Zhang
- Huidu Shanghai Medical Sciences, Shanghai, China
| | - Shidong Jia
- Huidu Shanghai Medical Sciences, Shanghai, China
| | - Jianjun Yu
- Huidu Shanghai Medical Sciences, Shanghai, China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, China
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10
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Collet L, Péron J, Penault-Llorca F, Pujol P, Lopez J, Freyer G, You B. PARP Inhibitors: A Major Therapeutic Option in Endocrine-Receptor Positive Breast Cancers. Cancers (Basel) 2022; 14:599. [PMID: 35158866 PMCID: PMC8833594 DOI: 10.3390/cancers14030599] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 01/01/2023] Open
Abstract
Recently, OlympiAD and EMBRACA trials demonstrated the favorable efficacy/toxicity ratio of PARPi, compared to chemotherapy, in patients with HER2-negative metastatic breast cancers (mBC) carrying a germline BRCA mutation. PARPi have been largely adopted in triple-negative metastatic breast cancer, but their place has been less clearly defined in endocrine-receptor positive, HER2 negative (ER+/ HER2-) mBC. The present narrative review aims at addressing this question by identifying the patients that are more likely benefit from PARPi. Frequencies of BRCA pathogenic variant (PV) carriers among ER+/HER2- breast cancer patients have been underestimated, and many experts assume than 50% of all BRCA1/2 mutated breast cancers are of ER+/HER2- subtype. Patients with ER+/HER2- BRCA-mutated mBC seemed to have a higher risk of early disease progression while on CDK4/6 inhibitors and PARPi are effective especially when prescribed before exposure to chemotherapy. The OLYMPIA trial also highlighted the utility of PARPi in patients with early breast cancers at high risk of relapse and carrying PV of BRCA. PARPi might also be effective in patients with HRD diseases, representing up to 20% of ER+/HER2- breast cancers. Consequently, the future implementation of early genotyping strategies for identifying the patients with high-risk ER+/HER2- HRD breast cancers likely to benefit from PARPi is of high importance.
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Affiliation(s)
- Laetitia Collet
- Oncology Department, CITOHL, Lyon-Sud Hospital, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Hospices Civils de Lyon, 69495 Lyon, France; (L.C.); (J.P.); (G.F.)
- Lyon-Sud Medicine School, University of Lyon, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Julien Péron
- Oncology Department, CITOHL, Lyon-Sud Hospital, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Hospices Civils de Lyon, 69495 Lyon, France; (L.C.); (J.P.); (G.F.)
- Lyon-Sud Medicine School, University of Lyon, University Claude Bernard Lyon 1, 69008 Lyon, France
- Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, CNRS UMR 5558, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
| | - Frédérique Penault-Llorca
- Department of Pathology and Biopathology, Jean Perrin Comprehensive Cancer Center, UMR INSERM 1240, University Clermont Auvergne, 63011 Clermont-Ferrand, France;
| | - Pascal Pujol
- Department of Cancer Genetics, CHU Montpellier, UMR IRD 224-CNRS 5290, Université Montpellier, 34295 Montpellier, France;
- Centre de Recherches Écologiques et Évolutives sur le Cancer (CREEC), UMR 224 CNRS-5290, University of Montpellier, 34394 Montpellier, France
| | - Jonathan Lopez
- Biochemistry and Molecular Biology Department, Hopital Lyon Sud, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France;
| | - Gilles Freyer
- Oncology Department, CITOHL, Lyon-Sud Hospital, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Hospices Civils de Lyon, 69495 Lyon, France; (L.C.); (J.P.); (G.F.)
- Lyon-Sud Medicine School, University of Lyon, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Benoît You
- Oncology Department, CITOHL, Lyon-Sud Hospital, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Hospices Civils de Lyon, 69495 Lyon, France; (L.C.); (J.P.); (G.F.)
- Lyon-Sud Medicine School, University of Lyon, University Claude Bernard Lyon 1, 69008 Lyon, France
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11
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Abstract
Triple-negative breast cancer (TNBC) encompasses a heterogeneous group of fundamentally different diseases with different histologic, genomic, and immunologic profiles, which are aggregated under this term because of their lack of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 expression. Massively parallel sequencing and other omics technologies have demonstrated the level of heterogeneity in TNBCs and shed light into the pathogenesis of this therapeutically challenging entity in breast cancer. In this review, we discuss the histologic and molecular classifications of TNBC, the genomic alterations these different tumor types harbor, and the potential impact of these alterations on the pathogenesis of these tumors. We also explore the role of the tumor microenvironment in the biology of TNBCs and its potential impact on therapeutic response. Dissecting the biology and understanding the therapeutic dependencies of each TNBC subtype will be essential to delivering on the promise of precision medicine for patients with triple-negative disease.
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Affiliation(s)
- Fatemeh Derakhshan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA;
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA;
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12
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van Wijk LM, Nilas AB, Vrieling H, Vreeswijk MPG. RAD51 as a functional biomarker for homologous recombination deficiency in cancer: a promising addition to the HRD toolbox? Expert Rev Mol Diagn 2021; 22:185-199. [PMID: 34913794 DOI: 10.1080/14737159.2022.2020102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Carcinomas with defects in the homologous recombination (HR) pathway are sensitive to PARP inhibitors (PARPi). A robust method to identify HR-deficient (HRD) carcinomas is therefore of utmost clinical importance. Currently available DNA-based HRD tests either scan HR-related genes such as BRCA1 and BRCA2 for the presence of pathogenic variants or identify HRD-related genomic scars or mutational signatures by using whole-exome or whole-genome sequencing data. As an alternative to DNA-based tests, functional HRD tests have been developed that assess the actual ability of tumors to accumulate RAD51 protein at DNA double strand breaks as a proxy for HR proficiency. AREAS COVERED This review presents an overview of currently available HRD tests and discuss the pros and cons of the different methodologies including their sensitivity for the identification of HRD tumors, their concordance with other HRD tests, and their capacity to predict therapy response. EXPERT OPINION With the increasing use of PARP inhibitors in the treatment of several cancers there is an urgent need to implement HRD testing in routine clinical practice. To this end, calibration of HRD thresholds and clinical validation of both DNA-based and RAD51-based HRD tests should have top-priority in the coming years.
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Affiliation(s)
- Lise M van Wijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Andreea B Nilas
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
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13
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Bhat V, Pellizzari S, Allan AL, Wong E, Lock M, Brackstone M, Lohmann AE, Cescon DW, Parsyan A. Radiotherapy and radiosensitization in breast cancer: Molecular targets and clinical applications. Crit Rev Oncol Hematol 2021; 169:103566. [PMID: 34890802 DOI: 10.1016/j.critrevonc.2021.103566] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/28/2021] [Accepted: 12/06/2021] [Indexed: 12/24/2022] Open
Abstract
Relatively poor survival outcomes are observed in advanced or metastatic breast cancer, where local control of the primary or metastatic disease may be achieved by surgical resection, local ablative and radiation therapies. Radioresistance, poses a major challenge in achieving durable oncologic outcomes, mandating development of novel management strategies. Although multimodality approaches that combine radiotherapy with chemotherapy, or systemic agents, are utilized for radiosensitization and treatment of various malignancies, this approach has not yet found its clinical application in breast cancer. Some agents for breast cancer treatment can serve as radiosensitizers, creating an opportunity to enhance effects of radiation while providing systemic disease control. Hence, combination of radiotherapy with radiosensitizing agents have the potential to improve oncologic outcomes in advanced or metastatic breast cancer. This review discusses molecular targets for radiosensitization and novel systemic agents that have potential for clinical use as radiosensitizers in breast cancer.
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Affiliation(s)
- Vasudeva Bhat
- London Regional Cancer Program, London Health Science Centre, London, ON, N6A 5W9, Canada; Department of Anatomy & Cell Biology, Western University, London, ON, N6A 3K7, Canada
| | - Sierra Pellizzari
- Department of Anatomy & Cell Biology, Western University, London, ON, N6A 3K7, Canada
| | - Alison L Allan
- London Regional Cancer Program, London Health Science Centre, London, ON, N6A 5W9, Canada; Department of Anatomy & Cell Biology, Western University, London, ON, N6A 3K7, Canada; Department of Oncology, Western University, London, ON, N6A 4L6, Canada
| | - Eugene Wong
- Department of Oncology, Western University, London, ON, N6A 4L6, Canada; Department of Physics and Astronomy, Western University, London, ON, N6A 3K7, Canada; Department of Medical Biophysics, Western University, London, N6A 5C1, Canada
| | - Michael Lock
- London Regional Cancer Program, London Health Science Centre, London, ON, N6A 5W9, Canada; Department of Oncology, Western University, London, ON, N6A 4L6, Canada
| | - Muriel Brackstone
- London Regional Cancer Program, London Health Science Centre, London, ON, N6A 5W9, Canada; Department of Oncology, Western University, London, ON, N6A 4L6, Canada; Department of Surgery, Western University, London, ON, N6A 3K7, Canada
| | - Ana Elisa Lohmann
- London Regional Cancer Program, London Health Science Centre, London, ON, N6A 5W9, Canada; Department of Oncology, Western University, London, ON, N6A 4L6, Canada
| | - David W Cescon
- Department of Medical Oncology and Hematology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Armen Parsyan
- London Regional Cancer Program, London Health Science Centre, London, ON, N6A 5W9, Canada; Department of Anatomy & Cell Biology, Western University, London, ON, N6A 3K7, Canada; Department of Oncology, Western University, London, ON, N6A 4L6, Canada; Department of Surgery, Western University, London, ON, N6A 3K7, Canada.
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14
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Setton J, Selenica P, Mukherjee S, Shah R, Pecorari I, McMillan B, Pei IX, Kemel Y, Ceyhan-Birsoy O, Sheehan M, Tkachuk K, Brown DN, Zhang L, Cadoo K, Powell S, Weigelt B, Robson M, Riaz N, Offit K, Reis-Filho JS, Mandelker D. Germline RAD51B variants confer susceptibility to breast and ovarian cancers deficient in homologous recombination. NPJ Breast Cancer 2021; 7:135. [PMID: 34635660 PMCID: PMC8505423 DOI: 10.1038/s41523-021-00339-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
Pathogenic germline mutations in the RAD51 paralog genes RAD51C and RAD51D, are known to confer susceptibility to ovarian and triple-negative breast cancer. Here, we investigated whether germline loss-of-function variants affecting another RAD51 paralog gene, RAD51B, are also associated with breast and ovarian cancer. Among 3422 consecutively accrued breast and ovarian cancer patients consented to tumor/germline sequencing, the observed carrier frequency of loss-of-function germline RAD51B variants was significantly higher than control cases from the gnomAD population database (0.26% vs 0.09%), with an odds ratio of 2.69 (95% CI: 1.4-5.3). Furthermore, we demonstrate that tumors harboring biallelic RAD51B alteration are deficient in homologous recombination DNA repair deficiency (HRD), as evidenced by analysis of sequencing data and in vitro functional assays. Our findings suggest that RAD51B should be considered as an addition to clinical germline testing panels for breast and ovarian cancer susceptibility.
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Affiliation(s)
- Jeremy Setton
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- GROW School for Ontology and Developmental Biology, University of Maastricht, Maastricht, The Netherlands
| | - Semanti Mukherjee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Rachna Shah
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Isabella Pecorari
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Biko McMillan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Isaac X Pei
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yelena Kemel
- Niehaus Center of Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - David N Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Karen Cadoo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Simon Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Molecular Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Mark Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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15
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Franchet C, Hoffmann JS, Dalenc F. Recent Advances in Enhancing the Therapeutic Index of PARP Inhibitors in Breast Cancer. Cancers (Basel) 2021; 13:cancers13164132. [PMID: 34439286 PMCID: PMC8392832 DOI: 10.3390/cancers13164132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Two to three percent of breast cancer patients harbor germline mutation of either BRCA1 or BRCA2 genes. Their tumor cells are deficient in homologous recombination, a BRCA-dependent DNA repair machinery. These deficient cells survive thanks to the PARP-mediated alternative pathway. Therefore, PARP inhibitors have already shown some level of efficiency in the treatment of metastatic breast cancer patients. Unfortunately, some tumor cells inevitably resist PARP inhibitors by different mechanisms. In this review, we (i) present the notion of homologous recombination deficiency and its evaluation methods, (ii) detail the PARP inhibitor clinical trials in breast cancer, (iii) briefly describe the mechanisms to PARP inhibitors resistance, and (iv) discuss some strategies currently under evaluation to enhance the therapeutic index of PARP inhibitors in breast cancer. Abstract As poly-(ADP)-ribose polymerase (PARP) inhibition is synthetic lethal with the deficiency of DNA double-strand (DSB) break repair by homologous recombination (HR), PARP inhibitors (PARPi) are currently used to treat breast cancers with mutated BRCA1/2 HR factors. Unfortunately, the increasingly high rate of PARPi resistance in clinical practice has dented initial hopes. Multiple resistance mechanisms and acquired vulnerabilities revealed in vitro might explain this setback. We describe the mechanisms and vulnerabilities involved, including newly identified modes of regulation of DSB repair that are now being tested in large cohorts of patients and discuss how they could lead to novel treatment strategies to improve the therapeutic index of PARPi.
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Affiliation(s)
- Camille Franchet
- Laboratoire de Pathologie and Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse-Oncopole, 1 Av. Irène Joliot-Curie, 31100 Toulouse, France;
| | - Jean-Sébastien Hoffmann
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, 31037 Toulouse, France;
| | - Florence Dalenc
- Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse-Oncopole, 1 Av. Irène Joliot-Curie, 31100 Toulouse, France
- Correspondence:
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16
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Setton J, Zinda M, Riaz N, Durocher D, Zimmermann M, Koehler M, Reis-Filho JS, Powell SN. Synthetic Lethality in Cancer Therapeutics: The Next Generation. Cancer Discov 2021; 11:1626-1635. [PMID: 33795234 PMCID: PMC8295179 DOI: 10.1158/2159-8290.cd-20-1503] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/01/2021] [Accepted: 02/23/2021] [Indexed: 12/25/2022]
Abstract
Synthetic lethality (SL) provides a conceptual framework for tackling targets that are not classically "druggable," including loss-of-function mutations in tumor suppressor genes required for carcinogenesis. Recent technological advances have led to an inflection point in our understanding of genetic interaction networks and ability to identify a wide array of novel SL drug targets. Here, we review concepts and lessons emerging from first-generation trials aimed at testing SL drugs, discuss how the nature of the targeted lesion can influence therapeutic outcomes, and highlight the need to develop clinical biomarkers distinct from those based on the paradigms developed to target activated oncogenes. SIGNIFICANCE: SL offers an approach for the targeting of loss of function of tumor suppressor and DNA repair genes, as well as of amplification and/or overexpression of genes that cannot be targeted directly. A next generation of tumor-specific alterations targetable through SL has emerged from high-throughput CRISPR technology, heralding not only new opportunities for drug development, but also important challenges in the development of optimal predictive biomarkers.
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Affiliation(s)
- Jeremy Setton
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - Simon N Powell
- Memorial Sloan Kettering Cancer Center, New York, New York.
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17
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Coussy F, El-Botty R, Château-Joubert S, Dahmani A, Montaudon E, Leboucher S, Morisset L, Painsec P, Sourd L, Huguet L, Nemati F, Servely JL, Larcher T, Vacher S, Briaux A, Reyes C, La Rosa P, Lucotte G, Popova T, Foidart P, Sounni NE, Noel A, Decaudin D, Fuhrmann L, Salomon A, Reyal F, Mueller C, Ter Brugge P, Jonkers J, Poupon MF, Stern MH, Bièche I, Pommier Y, Marangoni E. BRCAness, SLFN11, and RB1 loss predict response to topoisomerase I inhibitors in triple-negative breast cancers. Sci Transl Med 2021; 12:12/531/eaax2625. [PMID: 32075943 DOI: 10.1126/scitranslmed.aax2625] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/17/2019] [Accepted: 01/16/2020] [Indexed: 12/16/2022]
Abstract
Topoisomerase I (TOP1) inhibitors trap TOP1 cleavage complexes resulting in DNA double-strand breaks (DSBs) during replication, which are repaired by homologous recombination (HR). Triple-negative breast cancer (TNBC) could be eligible for TOP1 inhibitors given the considerable proportion of tumors with a defect in HR-mediated repair (BRCAness). The TOP1 inhibitor irinotecan was tested in 40 patient-derived xenografts (PDXs) of TNBC. BRCAness was determined with a single-nucleotide polymorphism (SNP) assay, and expression of Schlafen family member 11 (SLFN11) and retinoblastoma transcriptional corepressor 1 (RB1) was evaluated by real-time polymerase chain reaction (RT-PCR) and immunohistochemistry analyses. In addition, the combination of irinotecan and the ataxia telangiectasia and Rad3-related protein (ATR) inhibitor VE-822 was tested in SLFN11-negative PDXs, and two clinical non-camptothecin TOP1 inhibitors (LMP400 and LMP776) were tested. Thirty-eight percent of the TNBC models responded to irinotecan. BRCAness combined with high SLFN11 expression and RB1 loss identified highly sensitive tumors, consistent with the notion that deficiencies in cell cycle checkpoints and DNA repair result in high sensitivity to TOP1 inhibitors. Treatment by the ATR inhibitor VE-822 increased sensitivity to irinotecan in SLFN11-negative PDXs and abolished irinotecan-induced phosphorylation of checkpoint kinase 1 (CHK1). LMP400 (indotecan) and LMP776 (indimitecan) showed high antitumor activity in BRCA1-mutated or BRCAness-positive PDXs. Last, low SLFN11 expression was associated with poor survival in 250 patients with TNBC treated with anthracycline-based chemotherapy. In conclusion, a substantial proportion of TNBC respond to irinotecan. BRCAness, high SLFN11 expression, and RB1 loss are highly predictive of response to irinotecan and the clinical indenoisoquinoline TOP1 inhibitors.
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Affiliation(s)
- Florence Coussy
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France.,Medical Oncology Department, Institut Curie, PSL Research University, 75005 Paris, France.,Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Rania El-Botty
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | | | - Ahmed Dahmani
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Elodie Montaudon
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Sophie Leboucher
- Institut Curie, PSL Research University, UMR3306, 91405 Orsay, France
| | - Ludivine Morisset
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Pierre Painsec
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Laura Sourd
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Léa Huguet
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Fariba Nemati
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Jean-Luc Servely
- BioPôle Alfort, Ecole Nationale Vétérinaire d'Alfort, 94704 Maisons Alfort, France.,INRA, PHASE Department, 37380 Nouzilly, France
| | | | - Sophie Vacher
- Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Adrien Briaux
- Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Cécile Reyes
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Philippe La Rosa
- INSERM, U900, 75005 Paris, France.,Institut Curie, PSL Research University, 75005 Paris, France
| | - Georges Lucotte
- INSERM, U900, 75005 Paris, France.,Institut Curie, PSL Research University, 75005 Paris, France
| | - Tatiana Popova
- Institut Curie, PSL Research University, 75005 Paris, France.,INSERM U830, 75005 Paris, France
| | - Pierre Foidart
- Laboratory of Tumor and Developmental Biology, Groupe Interdisciplinaire de Génoprotéomique Appliqué-Cancer (GIGA-Cancer), University of Liège, Liège 4000, Belgium
| | - Nor Eddine Sounni
- Laboratory of Tumor and Developmental Biology, Groupe Interdisciplinaire de Génoprotéomique Appliqué-Cancer (GIGA-Cancer), University of Liège, Liège 4000, Belgium
| | - Agnès Noel
- Laboratory of Tumor and Developmental Biology, Groupe Interdisciplinaire de Génoprotéomique Appliqué-Cancer (GIGA-Cancer), University of Liège, Liège 4000, Belgium
| | - Didier Decaudin
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France.,Medical Oncology Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Laetitia Fuhrmann
- Department of Pathology, Institut Curie, PSL Research University, 75005 Paris, France
| | - Anne Salomon
- Department of Pathology, Institut Curie, PSL Research University, 75005 Paris, France
| | - Fabien Reyal
- Surgery Department, Institut Curie, PSL Research University, 75005 Paris, France.,U932, Immunity and Cancer, INSERM, Institut Curie, 75005 Paris, France
| | - Christopher Mueller
- Queen's Cancer Research Institute, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Petra Ter Brugge
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, Netherlands Cancer Institute, Amsterdam, 1066 CX, Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, Netherlands Cancer Institute, Amsterdam, 1066 CX, Netherlands
| | - Marie-France Poupon
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, 75005 Paris, France.,INSERM U830, 75005 Paris, France
| | - Ivan Bièche
- Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Elisabetta Marangoni
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France.
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18
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Zhou Q, Howard ME, Tu X, Zhu Q, Denbeigh JM, Remmes NB, Herman MG, Beltran CJ, Yuan J, Greipp PT, Boughey JC, Wang L, Johnson N, Goetz MP, Sarkaria JN, Lou Z, Mutter RW. Inhibition of ATM Induces Hypersensitivity to Proton Irradiation by Upregulating Toxic End Joining. Cancer Res 2021; 81:3333-3346. [PMID: 33597272 PMCID: PMC8260463 DOI: 10.1158/0008-5472.can-20-2960] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/30/2020] [Accepted: 02/11/2021] [Indexed: 12/15/2022]
Abstract
Proton Bragg peak irradiation has a higher ionizing density than conventional photon irradiation or the entrance of the proton beam profile. Whether targeting the DNA damage response (DDR) could enhance vulnerability to the distinct pattern of damage induced by proton Bragg peak irradiation is currently unknown. Here, we performed genetic or pharmacologic manipulation of key DDR elements and evaluated DNA damage signaling, DNA repair, and tumor control in cell lines and xenografts treated with the same physical dose across a radiotherapy linear energy transfer spectrum. Radiotherapy consisted of 6 MV photons and the entrance beam or Bragg peak of a 76.8 MeV spot scanning proton beam. More complex DNA double-strand breaks (DSB) induced by Bragg peak proton irradiation preferentially underwent resection and engaged homologous recombination (HR) machinery. Unexpectedly, the ataxia-telangiectasia mutated (ATM) inhibitor, AZD0156, but not an inhibitor of ATM and Rad3-related, rendered cells hypersensitive to more densely ionizing proton Bragg peak irradiation. ATM inhibition blocked resection and shunted more DSBs to processing by toxic ligation through nonhomologous end-joining, whereas loss of DNA ligation via XRCC4 or Lig4 knockdown rescued resection and abolished the enhanced Bragg peak cell killing. Proton Bragg peak monotherapy selectively sensitized cell lines and tumor xenografts with inherent HR defects, and the repair defect induced by ATM inhibitor coadministration showed enhanced efficacy in HR-proficient models. In summary, inherent defects in HR or administration of an ATM inhibitor in HR-proficient tumors selectively enhances the relative biological effectiveness of proton Bragg peak irradiation. SIGNIFICANCE: Coadministration of an ATM inhibitor rewires DNA repair machinery to render cancer cells uniquely hypersensitive to DNA damage induced by the proton Bragg peak, which is characterized by higher density ionization.See related commentary by Nickoloff, p. 3156.
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Affiliation(s)
- Qin Zhou
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | | | - Xinyi Tu
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Janet M Denbeigh
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | | | - Michael G Herman
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Chris J Beltran
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jian Yuan
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, Minnesota
| | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Matthew P Goetz
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, Minnesota.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Robert W Mutter
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota.
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19
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Börcsök J, Diossy M, Sztupinszki Z, Prosz A, Tisza V, Spisak S, Rusz O, Stormoen DR, Pappot H, Csabai I, Brunak S, Mouw KW, Szallasi Z. Detection of Molecular Signatures of Homologous Recombination Deficiency in Bladder Cancer. Clin Cancer Res 2021; 27:3734-3743. [PMID: 33947694 DOI: 10.1158/1078-0432.ccr-20-5037] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/11/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Poly (ADP ribose)-polymerase (PARP) inhibitors are approved for use in breast, ovarian, prostate, and pancreatic cancers, which are the solid tumor types that most frequently have alterations in key homologous recombination (HR) genes, such as BRCA1/2. However, the frequency of HR deficiency (HRD) in other solid tumor types, including bladder cancer, is less well characterized. EXPERIMENTAL DESIGN Specific DNA aberration profiles (mutational signatures) are induced by HRD, and the presence of these "genomic scars" can be used to assess the presence or absence of HRD in a given tumor biopsy even in the absence of an observed alteration of an HR gene. Using whole-exome and whole-genome data, we measured various HRD-associated mutational signatures in bladder cancer. RESULTS We found that a subset of bladder tumors have evidence of HRD. In addition to a small number of tumors with biallelic BRCA1/2 events, approximately 10% of bladder tumors had significant evidence of HRD-associated mutational signatures. Increased levels of HRD signatures were associated with promoter methylation of RBBP8, which encodes CtIP, a key protein involved in HR. CONCLUSIONS A subset of bladder tumors have genomic features suggestive of HRD and therefore may be more likely to benefit from therapies such as platinum agents and PARP inhibitors that target tumor HRD.
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Affiliation(s)
- Judit Börcsök
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Miklos Diossy
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Zsofia Sztupinszki
- Danish Cancer Society Research Center, Copenhagen, Denmark.,Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
| | - Aurel Prosz
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Orsolya Rusz
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Dag R Stormoen
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Helle Pappot
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark. .,Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts.,2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
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20
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Pitter KL, Casey DL, Lu YC, Hannum M, Zhang Z, Song X, Pecorari I, McMillan B, Ma J, Samstein RM, Pei IX, Khan AJ, Braunstein LZ, Morris LGT, Barker CA, Rimner A, Alektiar KM, Romesser PB, Crane CH, Yahalom J, Zelefsky MJ, Scher HI, Bernstein JL, Mandelker DL, Weigelt B, Reis-Filho JS, Lee NY, Powell SN, Chan TA, Riaz N, Setton J. Pathogenic ATM Mutations in Cancer and a Genetic Basis for Radiotherapeutic Efficacy. J Natl Cancer Inst 2021; 113:266-273. [PMID: 32726432 PMCID: PMC7936050 DOI: 10.1093/jnci/djaa095] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 04/23/2020] [Accepted: 06/09/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Radiation therapy is one of the most commonly used cancer therapeutics but genetic determinants of clinical benefit are poorly characterized. Pathogenic germline variants in ATM are known to cause ataxia-telangiectasia, a rare hereditary syndrome notable for marked radiosensitivity. In contrast, somatic inactivation of ATM is a common event in a wide variety of cancers, but its clinical actionability remains obscure. METHODS We analyzed 20 107 consecutively treated advanced cancer patients who underwent targeted genomic sequencing as part of an institutional genomic profiling initiative and identified 1085 harboring a somatic or germline ATM mutation, including 357 who received radiotherapy (RT). Outcomes of irradiated tumors harboring ATM loss-of-function (LoF) mutations were compared with those harboring variants of unknown significance. All statistical tests were 2-sided. RESULTS Among 357 pan-cancer patients who received 727 courses of RT, genetic inactivation of ATM was associated with improved radiotherapeutic efficacy. The 2-year cumulative incidence of irradiated tumor progression was 13.2% vs 27.5% for tumors harboring an ATM LoF vs variant of unknown significance allele, respectively (hazard ratio [HR] = 0.51, 95% confidence interval [CI] = 0.34 to 0.77, P = .001). The greatest clinical benefit was seen in tumors harboring biallelic ATM inactivation (HR = 0.19, 95% CI = 0.06 to 0.60, P = .005), with statistically significant benefit also observed in tumors with monoallelic ATM inactivation (HR = 0.57, 95% CI = 0.35 to 0.92, P = .02). Notably, ATM LoF was highly predictive of outcome in TP53 wild-type tumors but not among TP53-mutant tumors. CONCLUSIONS We demonstrate that somatic ATM inactivation is associated with markedly improved tumor control following RT. The identification of a radio-sensitive tumor phenotype across multiple cancer types offers potential clinical opportunities for genomically guided RT.
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Affiliation(s)
- Kenneth L Pitter
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana L Casey
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yue C Lu
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret Hannum
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhigang Zhang
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xinmao Song
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Isabella Pecorari
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Biko McMillan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jennifer Ma
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert M Samstein
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Isaac X Pei
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Atif J Khan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lior Z Braunstein
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luc G T Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher A Barker
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaled M Alektiar
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul B Romesser
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher H Crane
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joachim Yahalom
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael J Zelefsky
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonine L Bernstein
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana L Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Y Lee
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon N Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Timothy A Chan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeremy Setton
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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21
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Ladan MM, van Gent DC, Jager A. Homologous Recombination Deficiency Testing for BRCA-Like Tumors: The Road to Clinical Validation. Cancers (Basel) 2021; 13:1004. [PMID: 33670893 PMCID: PMC7957671 DOI: 10.3390/cancers13051004] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
Germline BRCA mutations result in homologous recombination deficiency (HRD) in hereditary breast and ovarian cancer, as well as several types of sporadic tumors. The HRD phenotype makes these tumors sensitive to DNA double strand break-inducing agents, including poly-(ADP-ribose)-polymerase (PARP) inhibitors. Interestingly, a subgroup of cancers without a BRCA mutation also shows an HRD phenotype. Various methods for selecting patients with HRD tumors beyond BRCA-mutations have been explored. These methods are mainly based on DNA sequencing or functional characteristics of the tumor. We here discuss the various tests and the status of their clinical validation.
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Affiliation(s)
- Marjolijn M. Ladan
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands;
- Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Dik C. van Gent
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands;
- Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands;
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22
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DNA damage response inhibitors: An avenue for TNBC treatment. Biochim Biophys Acta Rev Cancer 2021; 1875:188521. [PMID: 33556453 DOI: 10.1016/j.bbcan.2021.188521] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/30/2021] [Accepted: 01/30/2021] [Indexed: 01/13/2023]
Abstract
The DNA damage response (DDR) is critical for the maintenance of genomic stability by sensing DNA damage, regulating cell cycle and initiating DNA repair. Drugs targeting DDR pathways have been increasingly exploited in treating various tumors. Triple negative breast cancer (TNBC) is a highly heterogeneous and aggressive tumor with constitutive activation of oncogenes, inducing replication stress and DNA damage, which require the DDR for survival. In addition, emerging studies have demonstrated that TNBC harbors aberrant genetic alterations in DDR pathways, such as a high frequency of p53 dysfunction and BRCA1/2 mutations. DDR alterations force TNBC to rely on the existing DDR pathways for survival, and make TNBC particularly sensitive to specific DDR inhibitors, such as high sensitivity of TNBC with BRCA1/2 mutations to PARP inhibitors. This review first and comprehensively covers the current status of the development of DDR inhibitors and discusses the mechanism of targeting the DDR in TNBC. Preclinical and clinical studies on inhibitors of the ATR-CHK1-WEE1 pathway and PARP inhibitors, the most studied inhibitors, and some other DDR inhibitors as monotherapy or combination therapy in TNBC are summarized. We also highlight the possible predictive biomarkers for these DDR inhibitors and their potential combination strategies with chemotherapy, radiotherapy or other targeted agents to optimize the efficacy of DDR inhibitors in TNBC treatment. In conclusion, this review discussed the recent considerations related to the use of DDR inhibitors for TNBC and provides a perspective to address future directions and potential therapeutic strategies for patients with TNBC.
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23
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Kim SJ, Sota Y, Naoi Y, Honma K, Kagara N, Miyake T, Shimoda M, Tanei T, Seno S, Matsuda H, Noguchi S, Shimazu K. Determining homologous recombination deficiency scores with whole exome sequencing and their association with responses to neoadjuvant chemotherapy in breast cancer. Transl Oncol 2021; 14:100986. [PMID: 33340887 PMCID: PMC7750421 DOI: 10.1016/j.tranon.2020.100986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/28/2020] [Accepted: 12/06/2020] [Indexed: 11/23/2022] Open
Abstract
Recent studies demonstrated that homologous repair deficiency (HRD) score is a useful marker for response to poly (ADP-ribose) polymerase inhibitors or platinum-based chemotherapy. We determined HRD scores and elucidated the clinicopathologic characteristics of HRD-high tumors and their response to non-platinum-based chemotherapy. Primary breast cancer patients (n = 120) were pre-operatively treated with paclitaxel followed by 5-fluorouracil/epirubicin/cyclophosphamide (P-FEC). Germline and somatic homologous recombination related gene mutations (gHRRm and sHRRm, respectively) and HRD scores were analyzed using whole exome sequencing (WES) in tumor tissues obtained before chemotherapy. Of 120 tumors, 30 were determined to be HRD-high tumors, significantly associated with high Ki-67 (P = 0.014), ER negativity (P = 0.007), and PR negativity (P = 0.021). Triple-negative cancers showed significantly higher HRD scores than the luminal, luminal-HER2, and HER2 subtypes (P = 0.023, 0.016, and 0.033, respectively). HRD scores were significantly higher in tumors with gHRRm than in those with sHRRm (P = 0.002) or wild-type HRR genes (P = 1.44e-4), but no significant difference was found in HRD scores between tumors with sHRRm and wild-type HRR genes (P = 0.206). HRD-high tumors had significantly (P = 0.003) higher pCR rates and higher near-pCR rates (P = 0.049) compared with those of the HRD-low tumors in all tumors and the luminal subtype, respectively. HRD-high tumors were associated with aggressive phenotypes and gHRRm, but not sHRRm. Our findings suggested that HRD scores might be useful in predicting response to P-FEC in the luminal subtype.
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Affiliation(s)
- Seung Jin Kim
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E-10 Yamadaoka, Suita City, Osaka 565-0871, Japan.
| | - Yoshiaki Sota
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E-10 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E-10 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Keiichiro Honma
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita City, Osaka 565-0871, Japan; Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka City, Osaka 541-8567, Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E-10 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Tomohiro Miyake
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E-10 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E-10 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E-10 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Shigeto Seno
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Hideo Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Shinzaburo Noguchi
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E-10 Yamadaoka, Suita City, Osaka 565-0871, Japan; Hyogo Prefectural Nishinomiya Hospital, 13-9 Rokutanji-cho, Nishinomiya City, Hyogo 662-0918, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E-10 Yamadaoka, Suita City, Osaka 565-0871, Japan
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24
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Setton J, Reis-Filho JS, Powell SN. Homologous recombination deficiency: how genomic signatures are generated. Curr Opin Genet Dev 2021; 66:93-100. [PMID: 33477018 DOI: 10.1016/j.gde.2021.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
Cancer genomes harbor mutational and structural rearrangements that are jointly shaped by DNA damage and repair mechanisms. Accumulating evidence suggests that genetic alterations in DNA repair-defective tumors reflect the scars caused by the use of backup DNA repair mechanisms needed to maintain cellular viability. Detailed analysis of the patterns of mutations and structural rearrangements present in BRCA1/2-deficient tumors has allowed for the delineation of genomic signatures that reflect alternative repair with inactive homologous recombination (HR). Here we aim to summarize recent advances in the analysis of genomic signatures associated with HR-deficiency and examine recent studies that have shed light on the backup repair mechanisms responsible for genomic scarring in HR-deficient tumors.
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Affiliation(s)
- Jeremy Setton
- Dept. of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jorge S Reis-Filho
- Dept. of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Simon N Powell
- Dept. of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Molecular Biology Program, Sloan Kettering Institute, New York, NY, United States.
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25
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de Luca XM, Newell F, Kazakoff SH, Hartel G, McCart Reed AE, Holmes O, Xu Q, Wood S, Leonard C, Pearson JV, Lakhani SR, Waddell N, Nones K, Simpson PT. Using whole-genome sequencing data to derive the homologous recombination deficiency scores. NPJ Breast Cancer 2020; 6:33. [PMID: 32818150 PMCID: PMC7414867 DOI: 10.1038/s41523-020-0172-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 06/02/2020] [Indexed: 01/03/2023] Open
Abstract
The homologous recombination deficiency (HRD) score was developed using whole-genome copy number data derived from arrays as a way to infer deficiency in the homologous recombination DNA damage repair pathway (in particular BRCA1 or BRCA2 deficiency) in breast cancer samples. The score has utility in understanding tumour biology and may be indicative of response to certain therapeutic strategies. Studies have used whole-exome sequencing to derive the HRD score, however, with increasing use of whole-genome sequencing (WGS) to characterise tumour genomes, there has yet to be a comprehensive comparison between HRD scores derived by array versus WGS. Here we demonstrate that there is both a high correlation and a good agreement between array- and WGS-derived HRD scores and between the scores derived from WGS and downsampled WGS to represent shallow WGS. For samples with an HRD score close to threshold for stratifying HR proficiency or deficiency there was however some disagreement in the HR status between array and WGS data, highlighting the importance of not relying on a single method of ascertaining the homologous recombination status of a tumour.
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Affiliation(s)
- Xavier M. de Luca
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | | | - Gunter Hartel
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Amy E. McCart Reed
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - John V. Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Sunil R. Lakhani
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD Australia
- Pathology Queensland, Royal Brisbane & Women’s Hospital, Brisbane, QLD Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Peter T. Simpson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD Australia
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26
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Min A, Kim K, Jeong K, Choi S, Kim S, Suh KJ, Lee KH, Kim S, Im SA. Homologous repair deficiency score for identifying breast cancers with defective DNA damage response. Sci Rep 2020; 10:12506. [PMID: 32719318 PMCID: PMC7385153 DOI: 10.1038/s41598-020-68176-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022] Open
Abstract
Breast cancer (BC) in patients with germline mutations of BRCA1/BRCA2 are associated with benefit from drugs targeting DNA damage response (DDR), but they account for only 5-7% of overall breast cancer. To define the characteristics of these tumors and also to identify tumors without BRCA mutation but with homologous recombination deficiency (HRD) is clinically relevant. To define characteristic features of HRD tumors and analyze the correlations between BRCA1/BRCA2 and BC subtypes, we analyzed 981 breast tumors from the TCGA database using the signature analyzer. The BRCA signature was strongly associated with the HRD score top 10% (score ≥ 57) population. This population showed a high level of mutations in DDR genes, including BRCA1/BRCA2. HRD tumors were associated with high expression levels of BARD1 and BRIP1. Besides, BRCA1/2 mutations were dominantly observed in basal and luminal subtypes, respectively. A comparison of HRD features in BC revealed that BRCA1 exerts a stronger influence inducing HRD features than BRCA2 does. It reveals genetic differences between BRCA1 and BRCA2 and provides a basis for the identification of HRD and other BRCA-associated tumors.
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Affiliation(s)
- Ahrum Min
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Kwangsoo Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kyeonghun Jeong
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seongmin Choi
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seongyeong Kim
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Koung Jin Suh
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Kyung-Hun Lee
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea
| | - Seock-Ah Im
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
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27
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Chopra N, Tovey H, Pearson A, Cutts R, Toms C, Proszek P, Hubank M, Dowsett M, Dodson A, Daley F, Kriplani D, Gevensleben H, Davies HR, Degasperi A, Roylance R, Chan S, Tutt A, Skene A, Evans A, Bliss JM, Nik-Zainal S, Turner NC. Homologous recombination DNA repair deficiency and PARP inhibition activity in primary triple negative breast cancer. Nat Commun 2020; 11:2662. [PMID: 32471999 PMCID: PMC7260192 DOI: 10.1038/s41467-020-16142-7] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 04/03/2020] [Indexed: 12/17/2022] Open
Abstract
Triple negative breast cancer (TNBC) encompasses molecularly different subgroups, with a subgroup harboring evidence of defective homologous recombination (HR) DNA repair. Here, within a phase 2 window clinical trial, RIO trial (EudraCT 2014-003319-12), we investigate the activity of PARP inhibitors in 43 patients with untreated TNBC. The primary end point, decreased Ki67, occured in 12% of TNBC. In secondary end point analyses, HR deficiency was identified in 69% of TNBC with the mutational-signature-based HRDetect assay. Cancers with HRDetect mutational signatures of HR deficiency had a functional defect in HR, assessed by impaired RAD51 foci formation on end of treatment biopsy. Following rucaparib treatment there was no association of Ki67 change with HR deficiency. In contrast, early circulating tumor DNA dynamics identified activity of rucaparib, with end of treatment ctDNA levels suppressed by rucaparib in mutation-signature HR-deficient cancers. In ad hoc analysis, rucaparib induced expression of interferon response genes in HR-deficient cancers. The majority of TNBCs have a defect in DNA repair, identifiable by mutational signature analysis, that may be targetable with PARP inhibitors.
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Affiliation(s)
- Neha Chopra
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Holly Tovey
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Alex Pearson
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Ros Cutts
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Christy Toms
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Paula Proszek
- The Centre for Molecular Pathology, The Royal Marsden Hospital, 15 Cotswold Road, Sutton, SM2 5NG, Surrey, United Kingdom
| | - Michael Hubank
- The Centre for Molecular Pathology, The Royal Marsden Hospital, 15 Cotswold Road, Sutton, SM2 5NG, Surrey, United Kingdom
| | - Mitch Dowsett
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, United Kingdom
| | - Andrew Dodson
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, United Kingdom
| | - Frances Daley
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Divya Kriplani
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Heidi Gevensleben
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Helen Ruth Davies
- Department of Medical Genetics, The Clinical School, Box 238, Level 6 Addenbrooke's Treatment Centre, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, United Kingdom
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom
| | - Andrea Degasperi
- Department of Medical Genetics, The Clinical School, Box 238, Level 6 Addenbrooke's Treatment Centre, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, United Kingdom
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom
| | - Rebecca Roylance
- University College London Hospitals NHS Foundation Trust, NIHR University College London Hospitals Biomedical Research Centre, London, United Kingdom
| | - Stephen Chan
- Nottingham University Hospital Trust (City Campus), Nottingham, United Kingdom
| | - Andrew Tutt
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
- Breast Cancer Now Research Unit, Cancer Centre, Guy's Hospital, King's College London, London, United Kingdom
| | - Anthony Skene
- Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Abigail Evans
- Poole Hospital NHS Foundation Trust, Poole, United Kingdom
| | - Judith M Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Serena Nik-Zainal
- Department of Medical Genetics, The Clinical School, Box 238, Level 6 Addenbrooke's Treatment Centre, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, United Kingdom
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom
| | - Nicholas C Turner
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom.
- Breast Unit, The Royal Marsden Hospital, Fulham Road, London, United Kingdom.
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28
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Zhou Q, Huang J, Zhang C, Zhao F, Kim W, Tu X, Zhang Y, Nowsheen S, Zhu Q, Deng M, Chen Y, Qin B, Luo K, Liu B, Lou Z, Mutter RW, Yuan J. The bromodomain containing protein BRD-9 orchestrates RAD51-RAD54 complex formation and regulates homologous recombination-mediated repair. Nat Commun 2020; 11:2639. [PMID: 32457312 PMCID: PMC7251110 DOI: 10.1038/s41467-020-16443-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
Homologous recombination (HR) is important for error-free DNA double strand break repair and maintenance of genomic stability. However, upregulated HR is also used by cancer cells to promote therapeutic resistance. Therefore, inducing HR deficiency (HRD) is a viable strategy to sensitize HR proficient cancers to DNA targeted therapies in order to overcome therapeutic resistance. A bromodomain containing protein, BRD9, was previously reported to regulate chromatin remodeling and transcription. Here, we discover that following DNA damage, the bromodomain of BRD9 binds acetylated K515 on RAD54 and facilitates RAD54's interaction with RAD51, which is essential for HR. BRD9 is overexpressed in ovarian cancer and depleting BRD9 sensitizes cancer cells to olaparib and cisplatin. In addition, inhibitor of BRD9, I-BRD9, acts synergistically with olaparib in HR-proficient cancer cells. Overall, our results elucidate a role for BRD9 in HR and identify BRD9 as a potential therapeutic target to promote synthetic lethality and overcome chemoresistance.
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Affiliation(s)
- Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Chao Zhang
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Wootae Kim
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yong Zhang
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Somaira Nowsheen
- Mayo Medical Scientist Training Program, Mayo Clinic School of Medicine and Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Qian Zhu
- Research Center for Translational Medicine, East Hospital, Tongji University School of medicine, Shanghai, 200120, China
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yuping Chen
- Research Center for Translational Medicine, East Hospital, Tongji University School of medicine, Shanghai, 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Bo Qin
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
- Research Center for Translational Medicine, East Hospital, Tongji University School of medicine, Shanghai, 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Baohua Liu
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Robert W Mutter
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University School of medicine, Shanghai, 200120, China.
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
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29
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Lin PH, Chen M, Tsai LW, Lo C, Yen TC, Huang TY, Chen CK, Fan SC, Kuo SH, Huang CS. Using next-generation sequencing to redefine BRCAness in triple-negative breast cancer. Cancer Sci 2020; 111:1375-1384. [PMID: 31958182 PMCID: PMC7156820 DOI: 10.1111/cas.14313] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 12/06/2019] [Accepted: 01/08/2020] [Indexed: 12/15/2022] Open
Abstract
BRCAness is considered a predictive biomarker to platinum and poly(ADP‐ribose) polymerase (PARP) inhibitors. However, recent trials showed that its predictive value was limited in triple‐negative breast cancer (TNBC) treated with platinum. Moreover, tumors with mutations of DNA damage response (DDR) genes, such as homologous recombination (HR) genes, could be sensitive to platinum and PARP inhibitors. Thus, we aim to explore the relationship between mutation status of DDR genes and BRCAness in TNBC. We sequenced 56 DDR genes in 120 TNBC and identified BRCAness by array comparative genomic hybridization. The sequencing results showed that 13, 14, and 14 patients had BRCA, non‐BRCA HR, and non‐HR DDR gene mutations, respectively. Array comparative genomic hybridization revealed that BRCA‐mutated and HR gene‐mutated TNBC shared similar BRCAness features, both having higher numbers and longer length of large‐scale structural aberration (LSA, >10 Mb) and similar altered chromosomal regions of LSA. These suggested non‐BRCA HR gene‐mutated TNBC shared similar characteristics with BRCA‐mutated TNBC, indicating non‐BRCA HR gene‐mutated TNBC sensitive to platinum and PARP inhibitors. Among tumors with mutation of non‐HR DDR genes, 3 PTEN and 1 MSH6 mutation also contained significant LSAs (BRCAness); however, they had different regions of genomic alteration to BRCA and HR gene‐mutated tumors, might explain prior findings that PTEN‐ and MSH6‐mutated cancer cells not sensitive to PARP inhibitors. Therefore, we hypothesize that the heterogeneous genomic background of BRCAness indicates different responsiveness to platinum and PARP inhibitors. Direct sequencing DDR genes in TNBC should be applied to predict their sensitivity toward platinum and PARP inhibitors.
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Affiliation(s)
- Po-Han Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan
| | - Li-Wei Tsai
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiao Lo
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Tzu-Chun Yen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Thomas Yoyan Huang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chih-Kai Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Sheng-Chih Fan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung-Hsin Kuo
- Department of Medical Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan.,Department of Surgery, College of Medicine, National Taiwan University, Taipei, Taiwan
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30
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Bergom C, West CM, Higginson DS, Abazeed ME, Arun B, Bentzen SM, Bernstein JL, Evans JD, Gerber NK, Kerns SL, Keen J, Litton JK, Reiner AS, Riaz N, Rosenstein BS, Sawakuchi GO, Shaitelman SF, Powell SN, Woodward WA. The Implications of Genetic Testing on Radiation Therapy Decisions: A Guide for Radiation Oncologists. Int J Radiat Oncol Biol Phys 2019; 105:698-712. [PMID: 31381960 DOI: 10.1016/j.ijrobp.2019.07.026] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 06/21/2019] [Accepted: 07/08/2019] [Indexed: 02/06/2023]
Abstract
The advent of affordable and rapid next-generation DNA sequencing technology, along with the US Supreme Court ruling invalidating gene patents, has led to a deluge of germline and tumor genetic variant tests that are being rapidly incorporated into clinical cancer decision-making. A major concern for clinicians is whether the presence of germline mutations may increase the risk of radiation toxicity or secondary malignancies. Because scarce clinical data exist to inform decisions at this time, the American Society for Radiation Oncology convened a group of radiation science experts and clinicians to summarize potential issues, review relevant data, and provide guidance for adult patients and their care teams regarding the impact, if any, that genetic testing should have on radiation therapy recommendations. During the American Society for Radiation Oncology workshop, several main points emerged, which are discussed in this manuscript: (1) variants of uncertain significance should be considered nondeleterious until functional genomic data emerge to demonstrate otherwise; (2) possession of germline alterations in a single copy of a gene critical for radiation damage responses does not necessarily equate to increased risk of radiation-induced toxicity; (3) deleterious ataxia-telangiesctasia gene mutations may modestly increase second cancer risk after radiation therapy, and thus follow-up for these patients after indicated radiation therapy should include second cancer screening; (4) conveying to patients the difference between relative and absolute risk is critical to decision-making; and (5) more work is needed to assess the impact of tumor somatic alterations on the probability of response to radiation therapy and the potential for individualization of radiation doses. Data on radiosensitivity related to specific genetic mutations is also briefly discussed.
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Affiliation(s)
- Carmen Bergom
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Catharine M West
- Division of Cancer Sciences, National Institute for Health Research Manchester Biomedical Research Centre, University of Manchester, Christie National Health Service Foundation Trust Hospital, Manchester, UK
| | - Daniel S Higginson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mohamed E Abazeed
- Department of Radiation Oncology, Cleveland Clinic, Cleveland, Ohio; Department of Translational Hematology Oncology Research, Cleveland Clinic, Cleveland, Ohio
| | - Banu Arun
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Soren M Bentzen
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Jonine L Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaden D Evans
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology and Precision Genomics, Intermountain Healthcare, Ogden, Utah
| | - Naamit K Gerber
- Department of Radiation Oncology, New York University Langone Health, New York, New York
| | - Sarah L Kerns
- Department of Radiation Oncology, University of Rochester, Rochester, New York
| | - Judy Keen
- Scientific Affairs, American Society for Radiation Oncology, Arlington, Virginia
| | - Jennifer K Litton
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anne S Reiner
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Rosenstein
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gabriel O Sawakuchi
- Department of Radiation Physics The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Simona F Shaitelman
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Simon N Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wendy A Woodward
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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31
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Abstract
Squamous cell carcinomas (SCCs) arising from aerodigestive or anogenital epithelium that are associated with the human papillomavirus (HPV) are far more readily cured with radiation therapy than HPV-negative SCCs. The mechanism behind this increased radiosensitivity has been proposed to be secondary to defects in DNA repair, although the specific repair pathways that are disrupted have not been elucidated. To gain insight into this important biomarker of radiosensitivity, we first examined genomic patterns reflective of defects in DNA double-strand break repair, comparing HPV-associated and HPV-negative head and neck cancers (HNSCC). Compared to HPV-negative HNSCC genomes, HPV+ cases demonstrated a marked increase in the proportion of deletions with flanking microhomology, a signature associated with a backup, error-prone double-strand break repair pathway known as microhomology-mediated end-joining (MMEJ). Then, using 3 different methodologies to comprehensively profile double-strand break repair pathways in isogenic paired cell lines, we demonstrate that the HPV16 E7 oncoprotein suppresses canonical nonhomologous end-joining (NHEJ) and promotes error-prone MMEJ, providing a mechanistic rationale for the clinical radiosensitivity of these cancers.
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32
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Li A, Geyer FC, Blecua P, Lee JY, Selenica P, Brown DN, Pareja F, Lee SSK, Kumar R, Rivera B, Bi R, Piscuoglio S, Wen HY, Lozada JR, Gularte-Mérida R, Cavallone L, Rezoug Z, Nguyen-Dumont T, Peterlongo P, Tondini C, Terkelsen T, Rønlund K, Boonen SE, Mannerma A, Winqvist R, Janatova M, Rajadurai P, Xia B, Norton L, Robson ME, Ng PS, Looi LM, Southey MC, Weigelt B, Soo-Hwang T, Tischkowitz M, Foulkes WD, Reis-Filho JS. Homologous recombination DNA repair defects in PALB2-associated breast cancers. NPJ Breast Cancer 2019; 5:23. [PMID: 31428676 PMCID: PMC6687719 DOI: 10.1038/s41523-019-0115-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/04/2019] [Indexed: 01/02/2023] Open
Abstract
Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD.
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Affiliation(s)
- Anqi Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
- Department of Pathology, Fudan University Shanghai Cancer Center and Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Felipe C. Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Pedro Blecua
- Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ju Youn Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - David N. Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Simon S. K. Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Barbara Rivera
- Departments of Oncology and Human Genetics, McGill University, Montreal, Quebec Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec Canada
| | - Rui Bi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
- Department of Pathology, Fudan University Shanghai Cancer Center and Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Hannah Y. Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - John R. Lozada
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | | | - Luca Cavallone
- Departments of Oncology and Human Genetics, McGill University, Montreal, Quebec Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec Canada
| | - Zoulikha Rezoug
- Cancer Prevention Center, Jewish General Hospital, Montreal, Quebec Canada
| | - Tu Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Paolo Peterlongo
- IFOM, The Italian Foundation for Cancer Research Institute of Molecular Oncology, Milan, Italy
| | | | - Thorkild Terkelsen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Karina Rønlund
- Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark
| | - Susanne E. Boonen
- Clinical Genetics Unit, Department of Pediatrics, Zealand University Hospital, Roskilde, Denmark
| | - Arto Mannerma
- Biocenter Kuopio and Cancer Center of Easter Finland, University of Eastern Finland, Kuopio, Finland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Mark E. Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Pei-Sze Ng
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Teo Soo-Hwang
- Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Marc Tischkowitz
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - William D. Foulkes
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec Canada
- Cancer Prevention Center, Jewish General Hospital, Montreal, Quebec Canada
- Cancer Program, Research Institute McGill University Health Centre, Montreal, Quebec Canada
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
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Ex vivo assays to predict enhanced chemosensitization by hyperthermia in urothelial cancer of the bladder. PLoS One 2018; 13:e0209101. [PMID: 30550547 PMCID: PMC6294360 DOI: 10.1371/journal.pone.0209101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/28/2018] [Indexed: 01/03/2023] Open
Abstract
INTRODUCTION Bladder cancer (urothelial carcinoma) is a common malignancy characterized by high recurrence rates and intense clinical follow-up, indicating the necessity for more effective therapies. Current treatment regimens include intra-vesical administration of mitomycin C (MMC) for non-muscle invasive disease and systemic cisplatin for muscle-invasive or metastatic disease. Hyperthermia, heating a tumor to 40-44°C, enhances the efficacy of these chemotherapeutics by various modes of action, one of which is inhibition of DNA repair via homologous recombination. Here, we explore whether ex vivo assays on freshly obtained bladder tumors can be applied to predict the response towards hyperthermia. MATERIAL AND METHODS The cytochrome C release assay (apoptosis) and the RAD51 focus formation assay (DNA repair) were first established in the bladder cancer cell lines RT112 and T24 as measurements for hyperthermia efficiency, and subsequently tested in freshly obtained bladder tumors (n = 59). RESULTS Hyperthermia significantly increased the fraction of apoptotic cells after cisplatin or MMC treatment in both RT112 and T24 cells and in most of the bladder tumors (8/10). The RAD51 focus formation assay detected both morphological and numerical changes of RAD51 foci upon hyperthermia in the RT112 and T24 cell lines. In 64% of 37 analyzed primary bladder tumor samples, hyperthermia induced similar morphological changes in RAD51 foci. CONCLUSION The cytochrome C assay and the RAD51 focus formation assay are both feasible on freshly obtained bladder tumors, and could serve to predict the efficacy of hyperthermia together with cytotoxic agents, such as MMC or cisplatin.
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Castroviejo-Bermejo M, Cruz C, Llop-Guevara A, Gutiérrez-Enríquez S, Ducy M, Ibrahim YH, Gris-Oliver A, Pellegrino B, Bruna A, Guzmán M, Rodríguez O, Grueso J, Bonache S, Moles-Fernández A, Villacampa G, Viaplana C, Gómez P, Vidal M, Peg V, Serres-Créixams X, Dellaire G, Simard J, Nuciforo P, Rubio IT, Dienstmann R, Barrett JC, Caldas C, Baselga J, Saura C, Cortés J, Déas O, Jonkers J, Masson JY, Cairo S, Judde JG, O'Connor MJ, Díez O, Balmaña J, Serra V. A RAD51 assay feasible in routine tumor samples calls PARP inhibitor response beyond BRCA mutation. EMBO Mol Med 2018; 10:e9172. [PMID: 30377213 PMCID: PMC6284440 DOI: 10.15252/emmm.201809172] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are effective in cancers with defective homologous recombination DNA repair (HRR), including BRCA1/2-related cancers. A test to identify additional HRR-deficient tumors will help to extend their use in new indications. We evaluated the activity of the PARPi olaparib in patient-derived tumor xenografts (PDXs) from breast cancer (BC) patients and investigated mechanisms of sensitivity through exome sequencing, BRCA1 promoter methylation analysis, and immunostaining of HRR proteins, including RAD51 nuclear foci. In an independent BC PDX panel, the predictive capacity of the RAD51 score and the homologous recombination deficiency (HRD) score were compared. To examine the clinical feasibility of the RAD51 assay, we scored archival breast tumor samples, including PALB2-related hereditary cancers. The RAD51 score was highly discriminative of PARPi sensitivity versus PARPi resistance in BC PDXs and outperformed the genomic test. In clinical samples, all PALB2-related tumors were classified as HRR-deficient by the RAD51 score. The functional biomarker RAD51 enables the identification of PARPi-sensitive BC and broadens the population who may benefit from this therapy beyond BRCA1/2-related cancers.
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Affiliation(s)
| | - Cristina Cruz
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- High Risk and Familial Cancer Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Mandy Ducy
- Genome Stability Laboratory, CHU de Québec Research Center, Québec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, Canada
- CHU de Quebec - Université Laval Research Center, Genomics Center CHUL, Québec City, QC, Canada
| | - Yasir Hussein Ibrahim
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Albert Gris-Oliver
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Benedetta Pellegrino
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, University Hospital of Parma, Parma, Italy
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Marta Guzmán
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Olga Rodríguez
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Judit Grueso
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Guillermo Villacampa
- Oncology Data Science (OdysSey Group), Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Cristina Viaplana
- Oncology Data Science (OdysSey Group), Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Patricia Gómez
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Breast Cancer and Melanoma Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Maria Vidal
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Breast Cancer and Melanoma Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Vicente Peg
- Pathology Department, Vall d'Hebron University Hospital, Barcelona, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Xavier Serres-Créixams
- Department of Radiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Jacques Simard
- CHU de Quebec - Université Laval Research Center, Genomics Center CHUL, Québec City, QC, Canada
| | - Paolo Nuciforo
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Isabel T Rubio
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
- Breast Surgical Unit, Breast Cancer Center, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rodrigo Dienstmann
- Oncology Data Science (OdysSey Group), Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Breast Cancer Programme, Cancer Research UK (CRUK) Cambridge Cancer Centre, Cambridge, UK
| | - José Baselga
- Human Oncology and Pathogenesis Program (HOPP), Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cristina Saura
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Breast Cancer and Melanoma Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Javier Cortés
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
- Department of Oncology, Ramón y Cajal University Hospital, Madrid, Spain
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Jos Jonkers
- Division of Molecular Pathology and Cancer Genomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Québec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, Canada
| | | | | | - Mark J O'Connor
- Oncology Innovative Medicines and Early Clinical Development Biotech Unit, AstraZeneca, Cambridge, UK
| | - Orland Díez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Clinical and Molecular Genetics Area, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Judith Balmaña
- High Risk and Familial Cancer Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
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Chartron E, Theillet C, Guiu S, Jacot W. Targeting homologous repair deficiency in breast and ovarian cancers: Biological pathways, preclinical and clinical data. Crit Rev Oncol Hematol 2018; 133:58-73. [PMID: 30661659 DOI: 10.1016/j.critrevonc.2018.10.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 09/25/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022] Open
Abstract
Mutation or epigenetic silencing of homologous recombination (HR) repair genes is characteristic of a growing proportion of triple-negative breast cancers (TNBCs) and high-grade serous ovarian carcinomas. Defects in HR lead to genome instability, allowing cells to acquire the multiple genetic alterations essential for cancer development. However, this deficiency can also be exploited by using DNA damaging agents or by targeting compensatory repair pathways. A noteworthy example is treatment of TNBC and epithelial ovarian cancer harboring BRCA1/2 germline mutations using platinum salts and/or PARP inhibitors. Dramatic responses to PARP inhibitors may support a wider use in the HR-deficient population beyond those with mutated germline BRCA1 and 2. In this review, we discuss HR deficiency hallmarks as predictive biomarkers for platinum salt and PARP inhibitor sensitivity for selecting patients affected by TNBC or epithelial ovarian cancer who could benefit from these therapeutic options.
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Affiliation(s)
- Elodie Chartron
- Department of medical oncology, Montpellier Academic Hospital, Montpellier, France
| | - Charles Theillet
- IRCM, INSERM, Université de Montpellier, ICM, Montpellier, France
| | - Séverine Guiu
- Department of Medical Oncology, Institut du Cancer de Montpellier, Montpellier, France
| | - William Jacot
- IRCM, INSERM, Université de Montpellier, ICM, Montpellier, France; Department of Medical Oncology, Institut du Cancer de Montpellier, Montpellier, France.
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36
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Tu X, Kahila MM, Zhou Q, Yu J, Kalari KR, Wang L, Harmsen WS, Yuan J, Boughey JC, Goetz MP, Sarkaria JN, Lou Z, Mutter RW. ATR Inhibition Is a Promising Radiosensitizing Strategy for Triple-Negative Breast Cancer. Mol Cancer Ther 2018; 17:2462-2472. [PMID: 30166399 DOI: 10.1158/1535-7163.mct-18-0470] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/22/2018] [Accepted: 08/23/2018] [Indexed: 01/28/2023]
Abstract
Triple-negative breast cancer (TNBC) is characterized by elevated locoregional recurrence risk despite aggressive local therapies. New tumor-specific radiosensitizers are needed. We hypothesized that the ATR inhibitor, VX-970 (now known as M6620), would preferentially radiosensitize TNBC. Noncancerous breast epithelial and TNBC cell lines were investigated in clonogenic survival, cell cycle, and DNA damage signaling and repair assays. In addition, patient-derived xenograft (PDX) models generated prospectively as part of a neoadjuvant chemotherapy study from either baseline tumor biopsies or surgical specimens with chemoresistant residual disease were assessed for sensitivity to fractionated radiotherapy, VX-970, or the combination. To explore potential response biomarkers, exome sequencing was assessed for germline and/or somatic alterations in homologous recombination (HR) genes and other alterations associated with ATR inhibitor sensitivity. VX-970 preferentially inhibited ATR-Chk1-CDC25a signaling, abrogated the radiotherapy-induced G2-M checkpoint, delayed resolution of DNA double-strand breaks, and reduced colony formation after radiotherapy in TNBC cells relative to normal-like breast epithelial cells. In vivo, VX-970 did not exhibit significant single-agent activity at the dose administered even in the context of genomic alterations predictive of ATR inhibitor responsiveness, but significantly sensitized TNBC PDXs to radiotherapy. Exome sequencing and functional testing demonstrated that combination therapy was effective in both HR-proficient and -deficient models. PDXs established from patients with chemoresistant TNBC were also highly radiosensitized. In conclusion, VX-970 is a tumor-specific radiosensitizer for TNBC. Patients with residual TNBC after neoadjuvant chemotherapy, a subset at particularly high risk of relapse, may be ideally suited for this treatment intensification strategy. Mol Cancer Ther; 17(11); 2462-72. ©2018 AACR.
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Affiliation(s)
- Xinyi Tu
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Mohamed M Kahila
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Qin Zhou
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - William S Harmsen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Jian Yuan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Matthew P Goetz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Robert W Mutter
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota.
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The therapeutic significance of mutational signatures from DNA repair deficiency in cancer. Nat Commun 2018; 9:3292. [PMID: 30120226 PMCID: PMC6098043 DOI: 10.1038/s41467-018-05228-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/15/2018] [Indexed: 12/19/2022] Open
Abstract
Cancer is fundamentally a disease of the genome and inherited deficiencies in DNA repair pathways are well established to increase lifetime cancer risk. Computational analysis of pan-cancer data has identified signatures of mutational processes thought to be responsible for the pattern of mutations in any given cancer. These analyses identified altered DNA repair pathways in a much broader spectrum of cancers than previously appreciated with significant therapeutic implications. The development of DNA repair deficiency biomarkers is critical to the implementation of therapeutic targeting of repair-deficient tumors, using either DNA damaging agents or immunotherapy for the personalization of cancer therapy. Targeting DNA repair-deficient tumors is one of the most promising therapeutic strategies in cancer research; however, accurately predicting which tumors will respond can be a challenge. Here the authors present a review of the current state of knowledge in DNA repair deficiency across human cancers.
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38
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Sztupinszki Z, Diossy M, Krzystanek M, Reiniger L, Csabai I, Favero F, Birkbak NJ, Eklund AC, Syed A, Szallasi Z. Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer. NPJ Breast Cancer 2018; 4:16. [PMID: 29978035 PMCID: PMC6028448 DOI: 10.1038/s41523-018-0066-6] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 02/01/2023] Open
Abstract
The first genomic scar-based homologous recombination deficiency (HRD) measures were produced using SNP arrays. As array-based technology has been largely replaced by next generation sequencing approaches, it has become important to develop algorithms that derive the same type of genomic scar scores from next generation sequencing (whole exome “WXS”, whole genome “WGS”) data. In order to perform this analysis, we introduce here the scarHRD R package and show that using this method the SNP array-based and next generation sequencing-based derivation of HRD scores show good correlation (Pearson correlation between 0.73 and 0.87 depending on the actual HRD measure) and that the NGS-based HRD scores distinguish similarly well between BRCA mutant and BRCA wild-type cases in a cohort of triple-negative breast cancer patients of the TCGA data set.
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Affiliation(s)
- Zsofia Sztupinszki
- 1Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, Lyngby, 2800 Denmark
| | - Miklos Diossy
- 1Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, Lyngby, 2800 Denmark
| | - Marcin Krzystanek
- 1Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, Lyngby, 2800 Denmark
| | - Lilla Reiniger
- 21st Department of Pathology and Experimental Research, Semmelweis University, Budapest, Hungary.,32nd Department of Pathology, MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | - István Csabai
- 4Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Francesco Favero
- 5Biotech Research & Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, DK-2200 Denmark
| | - Nicolai J Birkbak
- 6The Francis Crick Institute, London, UK.,7University College London Cancer Institute, London, UK
| | - Aron C Eklund
- 1Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, Lyngby, 2800 Denmark
| | - Ali Syed
- Danish National Life Science Supercomputing Center, Copenhagen, Denmark
| | - Zoltan Szallasi
- 1Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, Lyngby, 2800 Denmark.,32nd Department of Pathology, MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary.,9Computational Health Informatics Program, Boston Children's Hospital, Boston, MA USA.,10Harvard Medical School, Boston, MA USA
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39
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Toward A variable RBE for proton beam therapy. Radiother Oncol 2018; 128:68-75. [PMID: 29910006 DOI: 10.1016/j.radonc.2018.05.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/09/2018] [Accepted: 05/17/2018] [Indexed: 12/19/2022]
Abstract
In the clinic, proton beam therapy (PBT) is based on the use of a generic relative biological effectiveness (RBE) of 1.1 compared to photons in human cancers and normal tissues. However, the experimental basis for this RBE lacks any significant number of representative tumor models and clinically relevant endpoints for dose-limiting organs at risk. It is now increasingly appreciated that much of the variations of treatment responses in cancers are due to inter-tumoral genomic heterogeneity. Indeed, recently it has been shown that defects in certain DNA repair pathways, which are found in subsets of many cancers, are associated with a RBE increase in vitro. However, there currently exist little in vivo or clinical data that confirm the existence of similarly increased RBE values in human cancers. Furthermore, evidence for variable RBE values for normal tissue toxicity has been sparse and conflicting to date. If we could predict variable RBE values in patients, we would be able to optimally use and personalize PBT. For example, predictive tumor biomarkers may facilitate selection of patients with proton-sensitive cancers previously ineligible for PBT. Dose de-escalation may be possible to reduce normal tissue toxicity, especially in pediatric patients. Knowledge of increased tumor RBE may allow us to develop biologically optimized therapies to enhance local control while RBE biomarkers for normal tissues could lead to a better understanding and prevention of unusual PBT-associated toxicity. Here, we will review experimental data on the repair of proton damage to DNA that impact both RBE values and biophysical modeling to predict RBE variations. Experimental approaches for studying proton sensitivity in vitro and in vivo will be reviewed as well and recent clinical findings discussed. Ultimately, therapeutically exploiting the understudied biological advantages of protons and developing approaches to limit treatment toxicity should fundamentally impact the clinical use of PBT.
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40
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Tumiati M, Hietanen S, Hynninen J, Pietilä E, Färkkilä A, Kaipio K, Roering P, Huhtinen K, Alkodsi A, Li Y, Lehtonen R, Erkan EP, Tuominen MM, Lehti K, Hautaniemi SK, Vähärautio A, Grénman S, Carpén O, Kauppi L. A Functional Homologous Recombination Assay Predicts Primary Chemotherapy Response and Long-Term Survival in Ovarian Cancer Patients. Clin Cancer Res 2018; 24:4482-4493. [PMID: 29858219 DOI: 10.1158/1078-0432.ccr-17-3770] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/25/2018] [Accepted: 05/25/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Homologous recombination deficiency (HRD) correlates with platinum sensitivity in patients with ovarian cancer, which clinically is the most useful predictor of sensitivity to PARPi. To date, there are no reliable diagnostic tools to anticipate response to platinum-based chemotherapy, thus we aimed to develop an ex vivo functional HRD detection test that could predict both platinum-sensitivity and patient eligibility to targeted drug treatments.Experimental Design: We obtained a functional HR score by quantifying homologous recombination (HR) repair after ionizing radiation-induced DNA damage in primary ovarian cancer samples (n = 32). Samples clustered in 3 categories: HR-deficient, HR-low, and HR-proficient. We analyzed the HR score association with platinum sensitivity and treatment response, platinum-free interval (PFI) and overall survival (OS), and compared it with other clinical parameters. In parallel, we performed DNA-sequencing of HR genes to assess if functional HRD can be predicted by currently offered genetic screening.Results: Low HR scores predicted primary platinum sensitivity with high statistical significance (P = 0.0103), associated with longer PFI (HR-deficient vs. HR-proficient: 531 vs. 53 days), and significantly correlated with improved OS (HR score <35 vs. ≥35, hazard ratio = 0.08, P = 0.0116). At the genomic level, we identified a few unclear mutations in HR genes and the mutational signature associated with HRD, but, overall, genetic screening failed to predict functional HRD.Conclusions: We developed an ex vivo assay that detects tumor functional HRD and an HR score able to predict platinum sensitivity, which holds the clinically relevant potential to become the routine companion diagnostic in the management of patients with ovarian cancer. Clin Cancer Res; 24(18); 4482-93. ©2018 AACR.
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Affiliation(s)
- Manuela Tumiati
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland.
| | - Sakari Hietanen
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Elina Pietilä
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Anniina Färkkilä
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Katja Kaipio
- Department of Pathology, University of Turku and Turku University Hospital, Finland
| | - Pia Roering
- Department of Pathology, University of Turku and Turku University Hospital, Finland
| | - Kaisa Huhtinen
- Department of Pathology, University of Turku and Turku University Hospital, Finland
| | - Amjad Alkodsi
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Yilin Li
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Rainer Lehtonen
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Erdogan Pekcan Erkan
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Minna M Tuominen
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Kaisa Lehti
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sampsa K Hautaniemi
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Anna Vähärautio
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Seija Grénman
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Olli Carpén
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Pathology, University of Turku and Turku University Hospital, Finland
| | - Liisa Kauppi
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland.
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41
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Bartosch C, Clarke B, Bosse T. Gynaecological neoplasms in common familial syndromes (Lynch and HBOC). Pathology 2017; 50:222-237. [PMID: 29287922 DOI: 10.1016/j.pathol.2017.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 12/22/2022]
Abstract
Recognising hereditary predisposition in a cancer patient has implications both for the patient and the patient's kindred. For the latter, cascade germline testing can reassure those not-at-risk family members while carriers can be enrolled in cancer screening and prevention programs that are medically effective and economically sustainable for health care systems. Furthermore, in many of these syndromes, ramifications of molecular phenotypes are increasing, and it is now emerging that, in addition, they convey prognostic and predictive information. Although cancer predisposition syndromes are rare, these molecular phenotypes also occur as somatic events in sporadic cancer settings. The information obtained from these molecular phenotypes, regardless of germline or somatic origin, is being incorporated into clinical management in view of their manifold significance. Thus, increasingly, bespoke management of cancer patients involves testing for both germline and somatic mutations in tumours. Lynch syndrome and BRCA-1 and BRCA-2-associated hereditary breast and ovarian cancer are hereditary cancer syndromes frequently involving the gynaecological tract but tumours associated with similar molecular alterations may also occur sporadically. Thus, the molecular phenotype of mismatch repair deficiency, microsatellite instability or hypermutator phenotype may be attributable to germline or somatic events. Similarly, homologous recombination deficiency or 'BRCAness' in ovarian cancers may be syndromic or sporadic. While hereditary syndromes are well recognised, the prognostic and predictive implications of these molecular phenotypes have only recently been elucidated and these aspects will finally ensure that molecular screening may become standard of care. Thus, nowadays pathologists are asked to designate the molecular phenotype of these cancers and then determine whether it is due to hereditary or sporadic causes.
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Affiliation(s)
- Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Blaise Clarke
- Department of Laboratory Medicine and Pathobiology, University of Toronto, University Health Network, Toronto, Ontario, Canada
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, The Netherlands.
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Pan-cancer analysis of bi-allelic alterations in homologous recombination DNA repair genes. Nat Commun 2017; 8:857. [PMID: 29021619 PMCID: PMC5636842 DOI: 10.1038/s41467-017-00921-w] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/04/2017] [Indexed: 12/22/2022] Open
Abstract
BRCA1 and BRCA2 are involved in homologous recombination (HR) DNA repair and are germ-line cancer pre-disposition genes that result in a syndrome of hereditary breast and ovarian cancer (HBOC). Whether germ-line or somatic alterations in these genes or other members of the HR pathway and if mono- or bi-allelic alterations of HR-related genes have a phenotypic impact on other cancers remains to be fully elucidated. Here, we perform a pan-cancer analysis of The Cancer Genome Atlas (TCGA) data set and observe that bi-allelic pathogenic alterations in homologous recombination (HR) DNA repair-related genes are prevalent across many malignancies. These bi-allelic alterations often associate with genomic features of HR deficiency. Further, in ovarian, breast and prostate cancers, bi-allelic alterations are mutually exclusive of each other. The combination of these two properties facilitates reclassification of variants of unknown significance affecting DNA repair genes, and may help personalize HR directed therapies in the clinic.Germline mutations in homologous recombination (HR) DNA repair genes are linked to breast and ovarian cancer. Here, the authors show that mutually exclusive bi-allelic inactivation of HR genes are present in other cancer types and associated with genomic features of HR deficiency, expanding the potential use of HR-directed therapies.
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Talens F, Jalving M, Gietema JA, Van Vugt MA. Therapeutic targeting and patient selection for cancers with homologous recombination defects. Expert Opin Drug Discov 2017; 12:565-581. [PMID: 28425306 DOI: 10.1080/17460441.2017.1322061] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION DNA double-strand breaks (DSBs) are toxic DNA lesions that can be repaired by non-homologous end-joining (NHEJ) or homologous recombination (HR). Mutations in HR genes elicit a predisposition to cancer; yet, they also result in increased sensitivity to certain DNA damaging agents and poly (ADP-ribose) polymerase (PARP) inhibitors. To optimally implement PARP inhibitor treatment, it is important that patients with HR-deficient tumors are adequately selected. Areas covered: Herein, the authors describe the HR pathway mechanistically and review the treatment of HR-deficient cancers, with a specific focus on PARP inhibition for BRCA1/2-mutated breast and ovarian cancer. In addition, mechanisms of acquired PARP inhibitor resistance are discussed. Furthermore, combination therapies with PARP inhibitors are reviewed, in the context of both HR-deficient and HR-proficient tumors and methods for proper patient selection are also discussed. Expert opinion: Currently, only patients with germline or somatic BRCA1/2 mutations are eligible for PARP inhibitor treatment and only a proportion of patients respond. Patients with HR-deficient tumors caused by other (epi)genetic events may also benefit from PARP inhibitor treatment. Ideally, selection of eligible patients for PARP inhibitor treatment include a functional HR read-out, in which cancer cells are interrogated for their ability to perform HR repair and maintain replication fork stability.
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Affiliation(s)
- Francien Talens
- a Department of Medical Oncology , University Medical Center Groningen, University of Groningen , Groningen , The Netherlands
| | - Mathilde Jalving
- a Department of Medical Oncology , University Medical Center Groningen, University of Groningen , Groningen , The Netherlands
| | - Jourik A Gietema
- a Department of Medical Oncology , University Medical Center Groningen, University of Groningen , Groningen , The Netherlands
| | - Marcel A Van Vugt
- a Department of Medical Oncology , University Medical Center Groningen, University of Groningen , Groningen , The Netherlands
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