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Wang Z, Lu Y, Han M, Li A, Ruan M, Tong Y, Yang C, Zhang X, Zhu C, Wang C, Shen K, Dong L, Chen X. Association between homologous recombination deficiency status and carboplatin treatment response in early triple-negative breast cancer. Breast Cancer Res Treat 2024:10.1007/s10549-024-07436-1. [PMID: 39048852 DOI: 10.1007/s10549-024-07436-1] [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: 03/27/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND The aim of this study was to assess homologous recombination deficiency (HRD) status and its correlation with carboplatin treatment response in early triple-negative breast cancer (TNBC) patients. METHODS Tumor tissues from 225 consecutive TNBC patients were evaluated with an HRD panel and homologous recombination-related (HRR) gene expression data. HRD positivity was defined as a high HRD score and/or BRCA1/2 pathogenic or likely pathogenic mutation. Clinicopathological factors, neoadjuvant treatment response, and prognosis were analyzed with respect to HRD status in these TNBC patients. RESULTS HRD positivity was found in 53.3% of patients and was significantly related to high Ki67 levels (P = 0.001). In patients who received neoadjuvant chemotherapy, HRD positivity (P = 0.005) or a high HRD score (P = 0.003) was significantly associated with a greater pathological complete response (pCR) rate, especially in those treated with carboplatin-containing neoadjuvant regimens (HRD positivity vs. negativity: 50.00% vs. 17.65%, P = 0.040). HRD positivity was associated with favorable distant metastasis-free survival (hazard ratio HR 0.49, 95% confidence interval CI 0.26-0.90, P = 0.022) and overall survival (HR 0.45, 95% CI 0.20-0.99, P = 0.049), irrespective of carboplatin treatment. CONCLUSION TNBC patients with high HRDs had high Ki67 levels and BRCA mutations. HRD-positive TNBC patients treated with carboplatin had a higher pCR rate. Patients with HRD positivity had a better prognosis, irrespective of carboplatin treatment, warranting further evaluation.
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Affiliation(s)
- Zheng Wang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Yujie Lu
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Mengyuan Han
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Anqi Li
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Miao Ruan
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Yiwei Tong
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Cuiyan Yang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Xiaotian Zhang
- Department of Translational Oncology, Amoy Diagnostics Co., Ltd., Xiamen, 361026, China
| | - Changbin Zhu
- Department of Translational Oncology, Amoy Diagnostics Co., Ltd., Xiamen, 361026, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
| | - Kunwei Shen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
| | - Lei Dong
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
| | - Xiaosong Chen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
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2
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Pan JW, Tan ZC, Ng PS, Zabidi MMA, Nur Fatin P, Teo JY, Hasan SN, Islam T, Teoh LY, Jamaris S, See MH, Yip CH, Rajadurai P, Looi LM, Taib NAM, Rueda OM, Caldas C, Chin SF, Lim J, Teo SH. Gene expression signature for predicting homologous recombination deficiency in triple-negative breast cancer. NPJ Breast Cancer 2024; 10:60. [PMID: 39030225 PMCID: PMC11271517 DOI: 10.1038/s41523-024-00671-1] [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: 08/16/2023] [Accepted: 07/10/2024] [Indexed: 07/21/2024] Open
Abstract
Triple-negative breast cancers (TNBCs) are a subset of breast cancers that have remained difficult to treat. A proportion of TNBCs arising in non-carriers of BRCA pathogenic variants have genomic features that are similar to BRCA carriers and may also benefit from PARP inhibitor treatment. Using genomic data from 129 TNBC samples from the Malaysian Breast Cancer (MyBrCa) cohort, we developed a gene expression-based machine learning classifier for homologous recombination deficiency (HRD) in TNBCs. The classifier identified samples with HRD mutational signature at an AUROC of 0.93 in MyBrCa validation datasets and 0.84 in TCGA TNBCs. Additionally, the classifier strongly segregated HRD-associated genomic features in TNBCs from TCGA, METABRIC, and ICGC. Thus, our gene expression classifier may identify triple-negative breast cancer patients with homologous recombination deficiency, suggesting an alternative method to identify individuals who may benefit from treatment with PARP inhibitors or platinum chemotherapy.
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Affiliation(s)
- Jia-Wern Pan
- Cancer Research Malaysia, Subang Jaya, Malaysia.
| | | | - Pei-Sze Ng
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | | | | | | | | | - Tania Islam
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Li-Ying Teoh
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Suniza Jamaris
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Mee-Hoong See
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | | | - Pathmanathan Rajadurai
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Nur Aishah Mohd Taib
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Oscar M Rueda
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Joanna Lim
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
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3
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Abbasi A, Steele CD, Bergstrom EN, Khandekar A, Farswan A, Mckay RR, Pillay N, Alexandrov LB. Detecting HRD in whole-genome and whole-exome sequenced breast and ovarian cancers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.14.24310383. [PMID: 39040162 PMCID: PMC11261949 DOI: 10.1101/2024.07.14.24310383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Breast and ovarian cancers harboring homologous recombination deficiency (HRD) are sensitive to PARP inhibitors and platinum chemotherapy. Conventionally, detecting HRD involves screening for defects in BRCA1, BRCA2, and other relevant genes. Recent analyses have shown that HRD cancers exhibit characteristic mutational patterns due to the activities of HRD-associated mutational signatures. At least three machine learning tools exist for detecting HRD based on mutational patterns. Here, using sequencing data from 1,043 breast and 182 ovarian cancers, we trained Homologous Recombination Proficiency Profiler (HRProfiler), a machine learning method for detecting HRD using six mutational features. HRProfiler's performance is assessed against prior approaches using additional independent datasets of 417 breast and 115 ovarian cancers, including retrospective data from a clinical trial involving patients treated with PARP inhibitors. Our results demonstrate that HRProfiler is the only tool that robustly and consistently predicts clinical response from whole-exome sequenced breast and ovarian cancers.
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Affiliation(s)
- Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
- Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, CA, 92093, USA
- Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA 92037
| | - Christopher D. Steele
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
- Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, CA, 92093, USA
| | - Akanksha Farswan
- Research Department of Pathology, Cancer Institute, University College London, London, WC1E 6BT, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, HA7 4LP, UK
| | - Rana R. Mckay
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London, WC1E 6BT, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, HA7 4LP, UK
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
- Bioinformatics and Systems Biology Graduate Program, UC San Diego, La Jolla, CA, 92093, USA
- Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA 92037
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4
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Godina C, Khazaei S, Belting M, Vallon-Christersson J, Nodin B, Jirström K, Isaksson K, Bosch A, Jernström H. High Caveolin-1 mRNA expression in triple-negative breast cancer is associated with an aggressive tumor microenvironment, chemoresistance, and poor clinical outcome. PLoS One 2024; 19:e0305222. [PMID: 38959243 PMCID: PMC11221642 DOI: 10.1371/journal.pone.0305222] [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: 02/13/2024] [Accepted: 05/28/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Currently, there are few treatment-predictive and prognostic biomarkers in triple-negative breast cancer (TNBC). Caveolin-1 (CAV1) is linked to chemoresistance and several important processes involved in tumor progression and metastasis, such as epithelial-mesenchymal transition (EMT). Herein, we report that high CAV1 gene expression is an independent factor of poor prognosis in TNBC. METHODS CAV1 gene expression was compared across different molecular features (e.g., PAM50 subtypes). CAV1 expression was assessed in relation to clinical outcomes using Cox regression adjusted for clinicopathological predictors. Differential gene expression and gene set enrichment analyses were applied to compare high- and low-expressing CAV1 tumors. Tumor microenvironment composition of high- and low-expressing CAV1 tumors was estimated using ECOTYPER. Tumor tissue microarrays were used to evaluate CAV1 protein levels in stromal and malignant cells. RESULTS In the SCAN-B (n = 525) and GSE31519 (n = 327) cohorts, patients with CAV1-high tumors had an increased incidence of early recurrence adjusted HR 1.78 (95% CI 1.12-2.81) and 2.20 (95% CI 1.39-3.47), respectively. In further analysis, high CAV1 gene expression was associated with a molecular profile indicating altered metabolism, neovascularization, chemoresistance, EMT, suppressed immune response, and active tumor microenvironment. Protein levels of CAV1 in malignant and stromal cells were not correlated with CAV1 gene expression. CONCLUSION CAV1 gene expression in TNBC is a biomarker that merits further investigation in clinical trials and as a therapeutic target.
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Affiliation(s)
- Christopher Godina
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Somayeh Khazaei
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Mattias Belting
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Sweden
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Vallon-Christersson
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Björn Nodin
- Department of Clinical Sciences Lund, Oncology and Therapeutic Pathology, Lund University, Lund, Sweden
| | - Karin Jirström
- Department of Clinical Sciences Lund, Oncology and Therapeutic Pathology, Lund University, Lund, Sweden
| | - Karolin Isaksson
- Department of Clinical Sciences Lund, Surgery, Lund University and Kristianstad Hospital, Kristianstad, Sweden
| | - Ana Bosch
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Sweden
| | - Helena Jernström
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Lund, Sweden
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5
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Németh E, Szüts D. The mutagenic consequences of defective DNA repair. DNA Repair (Amst) 2024; 139:103694. [PMID: 38788323 DOI: 10.1016/j.dnarep.2024.103694] [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: 03/22/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Multiple separate repair mechanisms safeguard the genome against various types of DNA damage, and their failure can increase the rate of spontaneous mutagenesis. The malfunction of distinct repair mechanisms leads to genomic instability through different mutagenic processes. For example, defective mismatch repair causes high base substitution rates and microsatellite instability, whereas homologous recombination deficiency is characteristically associated with deletions and chromosome instability. This review presents a comprehensive collection of all mutagenic phenotypes associated with the loss of each DNA repair mechanism, drawing on data from a variety of model organisms and mutagenesis assays, and placing greatest emphasis on systematic analyses of human cancer datasets. We describe the latest theories on the mechanism of each mutagenic process, often explained by reliance on an alternative repair pathway or the error-prone replication of unrepaired, damaged DNA. Aided by the concept of mutational signatures, the genomic phenotypes can be used in cancer diagnosis to identify defective DNA repair pathways.
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Affiliation(s)
- Eszter Németh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
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6
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Sueangoen N, Thuwajit P, Yenchitsomanus PT, Thuwajit C. Public neoantigens in breast cancer immunotherapy (Review). Int J Mol Med 2024; 54:65. [PMID: 38904202 PMCID: PMC11188978 DOI: 10.3892/ijmm.2024.5388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Among women globally, breast cancer is the most prevalent cancer and the leading cause of cancer‑related death. Interestingly, though genetic mutations contribute to the disease, <15% of women diagnosed with breast cancer have a family history of the disease, suggesting a prevalence of sporadic genetic mutations in breast cancer development. In the rapidly rising field of cancer genomics, neoantigen‑based immunotherapy has come to the fore. The investigation of novel proteins arising from unique somatic mutations or neoantigens have opened a new pathway for both individualized and public cancer treatments. Because they are shared among individuals with similar genetic changes, public neoantigens provide an opportunity for 'off‑the‑shelf' anticancer therapies, potentially extending the benefits to a wider patient group. The present review aimed to highlight the role of shared or public neoantigens as therapeutic targets for patients with breast cancer, emphasizing common hotspot mutations of certain genes identified in breast cancer. The clinical utilization of public neoantigen‑based therapies for breast cancer treatment were also discussed.
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Affiliation(s)
- Natthaporn Sueangoen
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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7
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Hanssen F, Garcia MU, Folkersen L, Pedersen A, Lescai F, Jodoin S, Miller E, Seybold M, Wacker O, Smith N, Gabernet G, Nahnsen S. Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery. NAR Genom Bioinform 2024; 6:lqae031. [PMID: 38666213 PMCID: PMC11044436 DOI: 10.1093/nargab/lqae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO2 emissions low. The code is available at https://nf-co.re/sarek.
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Affiliation(s)
- Friederike Hanssen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, 72076 Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
| | - Maxime U Garcia
- Seqera Labs, Carrer de Marià Aguilò, 28, Barcelona 08005, Spain
- Barntumörbanken, Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Visionsgatan 4, Solna 17164, Sweden
- National Genomics Infrastructure, SciLifeLab, SciLifeLab, Tomtebodavägen 23, Solna 17165, Sweden
| | | | | | - Francesco Lescai
- Department of Biology and Biotechnology ”L. Spallanzani”, University of Pavia, via Ferrata, 9, Pavia, 27100 PV, Italy
| | - Susanne Jodoin
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Edmund Miller
- Department of Biological Sciences and Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX 75080, USA
| | - Matthias Seybold
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Oskar Wacker
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Nicholas Smith
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, Garching, 85748 Bavaria, Germany
| | - Gisela Gabernet
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Pathology, Yale School of Medicine, 300 George, New Haven, CT 06510, USA
| | - Sven Nahnsen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, 72076 Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
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8
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Lee M, Yoo TK, Chae BJ, Lee A, Cha YJ, Lee J, Ahn SG, Kang J. Luminal androgen receptor subtype and tumor-infiltrating lymphocytes groups based on triple-negative breast cancer molecular subclassification. Sci Rep 2024; 14:11278. [PMID: 38760384 PMCID: PMC11101432 DOI: 10.1038/s41598-024-61640-z] [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: 09/22/2023] [Accepted: 05/08/2024] [Indexed: 05/19/2024] Open
Abstract
In our previous study, we developed a triple-negative breast cancer (TNBC) subtype classification that correlated with the TNBC molecular subclassification. In this study, we aimed to evaluate the predictor variables of this subtype classification on the whole slide and to validate the model's performance by using an external test set. We explored the characteristics of this subtype classification and investigated genomic alterations, including genomic scar signature scores. First, TNBC was classified into the luminal androgen receptor (LAR) and non-luminal androgen receptor (non-LAR) subtypes based on the AR Allred score (≥ 6 and < 6, respectively). Then, the non-LAR subtype was further classified into the lymphocyte-predominant (LP), lymphocyte-intermediate (LI), and lymphocyte-depleted (LD) groups based on stromal tumor-infiltrating lymphocytes (TILs) (< 20%, > 20% but < 60%, and ≥ 60%, respectively). This classification showed fair agreement with the molecular classification in the test set. The LAR subtype was characterized by a high rate of PIK3CA mutation, CD274 (encodes PD-L1) and PDCD1LG2 (encodes PD-L2) deletion, and a low homologous recombination deficiency (HRD) score. The non-LAR LD TIL group was characterized by a high frequency of NOTCH2 and MYC amplification and a high HRD score.
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Affiliation(s)
- Miseon Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Tae-Kyung Yoo
- Division of Breast Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Byung Joo Chae
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ahwon Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yoon Jin Cha
- Department of Pathology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
- Institute of Breast Cancer Precision Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jieun Lee
- Cancer Research Institute, The Catholic University of Korea, Seoul, Republic of Korea
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sung Gwe Ahn
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Institute for Breast Cancer Precision Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Jun Kang
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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9
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Abraham JE, Pinilla K, Dayimu A, Grybowicz L, Demiris N, Harvey C, Drewett LM, Lucey R, Fulton A, Roberts AN, Worley JR, Chhabra A, Qian W, Vallier AL, Hardy RM, Chan S, Hickish T, Tripathi D, Venkitaraman R, Persic M, Aslam S, Glassman D, Raj S, Borley A, Braybrooke JP, Sutherland S, Staples E, Scott LC, Davies M, Palmer CA, Moody M, Churn MJ, Newby JC, Mukesh MB, Chakrabarti A, Roylance RR, Schouten PC, Levitt NC, McAdam K, Armstrong AC, Copson ER, McMurtry E, Tischkowitz M, Provenzano E, Earl HM. The PARTNER trial of neoadjuvant olaparib with chemotherapy in triple-negative breast cancer. Nature 2024; 629:1142-1148. [PMID: 38588696 PMCID: PMC11136660 DOI: 10.1038/s41586-024-07384-2] [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: 02/06/2024] [Accepted: 04/04/2024] [Indexed: 04/10/2024]
Abstract
PARTNER is a prospective, phase II-III, randomized controlled clinical trial that recruited patients with triple-negative breast cancer1,2, who were germline BRCA1 and BRCA2 wild type3. Here we report the results of the trial. Patients (n = 559) were randomized on a 1:1 basis to receive neoadjuvant carboplatin-paclitaxel with or without 150 mg olaparib twice daily, on days 3 to 14, of each of four cycles (gap schedule olaparib, research arm) followed by three cycles of anthracycline-based chemotherapy before surgery. The primary end point was pathologic complete response (pCR)4, and secondary end points included event-free survival (EFS) and overall survival (OS)5. pCR was achieved in 51% of patients in the research arm and 52% in the control arm (P = 0.753). Estimated EFS at 36 months in the research and control arms was 80% and 79% (log-rank P > 0.9), respectively; OS was 90% and 87.2% (log-rank P = 0.8), respectively. In patients with pCR, estimated EFS at 36 months was 90%, and in those with non-pCR it was 70% (log-rank P < 0.001), and OS was 96% and 83% (log-rank P < 0.001), respectively. Neoadjuvant olaparib did not improve pCR rates, EFS or OS when added to carboplatin-paclitaxel and anthracycline-based chemotherapy in patients with triple-negative breast cancer who were germline BRCA1 and BRCA2 wild type. ClinicalTrials.gov ID: NCT03150576 .
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Affiliation(s)
- Jean E Abraham
- Precision Breast Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK.
| | - Karen Pinilla
- Precision Breast Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Alimu Dayimu
- Cambridge Cancer Trials Centre, University of Cambridge, Cambridge, UK
| | - Louise Grybowicz
- Cambridge Cancer Trials Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nikolaos Demiris
- Department of Statistics, Athens University of Economics and Business, Athens, Greece
| | - Caron Harvey
- Cambridge Cancer Trials Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lynsey M Drewett
- Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Rebecca Lucey
- Precision Breast Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Alexander Fulton
- Precision Breast Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Anne N Roberts
- Cambridge Cancer Trials Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Joanna R Worley
- Precision Breast Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Anita Chhabra
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Wendi Qian
- Cambridge Clinical Trials Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Anne-Laure Vallier
- Cambridge Cancer Trials Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Richard M Hardy
- Cambridge Cancer Trials Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Steve Chan
- The City Hospital, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | | | - Devashish Tripathi
- Royal Wolverhampton NHS Trust, Wolverhampton, UK
- Russells Hall Hospital, Dudley, UK
| | | | - Mojca Persic
- University Hospital of Derby and Burton, Derby, UK
| | - Shahzeena Aslam
- Bedford Hospital, Bedfordshire Hospitals NHS Foundation Trust, Bedford, UK
| | - Daniel Glassman
- Pinderfields Hospital, Mid Yorkshire Teaching NHS Trust, Wakefield, UK
| | - Sanjay Raj
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Basingstoke & North Hampshire Hospital, Basingstoke, UK
- Royal Hampshire Hospital, Winchester, UK
| | | | | | | | - Emma Staples
- Queens Hospital, Barking, Havering and Redbridge University Hospitals NHS Trust, Romford, UK
| | - Lucy C Scott
- Beatson West Of Scotland Cancer Centre, Glasgow, UK
| | - Mark Davies
- Swansea Bay University Health Board, Swansea, UK
| | - Cheryl A Palmer
- Hinchingbrooke Hospital, North West Anglia NHS Foundation Trust, Huntingdon, UK
| | - Margaret Moody
- Macmillan Unit, West Suffolk Hospital NHS Foundation Trust, Bury Saint Edmunds, UK
| | - Mark J Churn
- Worcestershire Acute Hospitals NHS Trust, Worcester, UK
- Alexandra Redditch Hospital, Redditch, UK
- Kidderminster Hospital, Kidderminster, Worcestershire, UK
| | | | - Mukesh B Mukesh
- Oncology Department, Colchester General Hospital, East Suffolk & North Essex NHS Trust, Colchester, UK
| | | | | | - Philip C Schouten
- Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Karen McAdam
- Peterborough City Hospital, North West Anglia NHS Foundation Trust, Peterborough, UK
| | - Anne C Armstrong
- The Christie NHS Foundation Trust and Division of Cancer Sciences, Manchester, UK
| | - Ellen R Copson
- Cancer Sciences Academic Unit, University of Southampton, Southampton, UK
| | | | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research, Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Elena Provenzano
- Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Helena M Earl
- Precision Breast Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
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10
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Veerla S, Staaf J. Kataegis in clinical and molecular subgroups of primary breast cancer. NPJ Breast Cancer 2024; 10:32. [PMID: 38658600 PMCID: PMC11043427 DOI: 10.1038/s41523-024-00640-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/13/2024] [Indexed: 04/26/2024] Open
Abstract
Kataegis is a hypermutation phenomenon characterized by localized clusters of single base pair substitution (SBS) reported in multiple cancer types. Despite a high frequency in breast cancer, large-scale analyses of kataegis patterns and associations with clinicopathological and molecular variables in established breast cancer subgroups are lacking. Therefore, WGS profiled primary breast cancers (n = 791) with associated clinical and molecular data layers, like RNA-sequencing data, were analyzed for kataegis frequency, recurrence, and associations with genomic contexts and functional elements, transcriptional patterns, driver alterations, homologous recombination deficiency (HRD), and prognosis in tumor subgroups defined by ER, PR, and HER2/ERBB2 status. Kataegis frequency was highest in the HER2-positive(p) subgroups, including both ER-negative(n)/positive(p) tumors (ERnHER2p/ERpHER2p). In TNBC, kataegis was neither associated with PAM50 nor TNBC mRNA subtypes nor with distant relapse in chemotherapy-treated patients. In ERpHER2n tumors, kataegis was associated with aggressive characteristics, including PR-negativity, molecular Luminal B subtype, higher mutational burden, higher grade, and expression of proliferation-associated genes. Recurrent kataegis loci frequently targeted regions commonly amplified in ER-positive tumors, while few recurrent loci were observed in TNBC. SBSs in kataegis loci appeared enriched in regions of open chromatin. Kataegis status was not associated with HRD in any subgroup or with distinct transcriptional patterns in unsupervised or supervised analysis. In summary, kataegis is a common hypermutation phenomenon in established breast cancer subgroups, particularly in HER2p subgroups, coinciding with an aggressive tumor phenotype in ERpHER2n disease. In TNBC, the molecular implications and associations of kataegis are less clear, including its prognostic value.
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Affiliation(s)
- Srinivas Veerla
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden.
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11
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Tuppurainen H, Laurila N, Nätynki M, Eshraghi L, Tervasmäki A, Erichsen L, Sørensen CS, Pylkäs K, Winqvist R, Peltoketo H. PALB2-mutated human mammary cells display a broad spectrum of morphological and functional abnormalities induced by increased TGFβ signaling. Cell Mol Life Sci 2024; 81:173. [PMID: 38597967 PMCID: PMC11006627 DOI: 10.1007/s00018-024-05183-6] [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: 06/02/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 04/11/2024]
Abstract
Heterozygous mutations in any of three major genes, BRCA1, BRCA2 and PALB2, are associated with high-risk hereditary breast cancer susceptibility frequently seen as familial disease clustering. PALB2 is a key interaction partner and regulator of several vital cellular activities of BRCA1 and BRCA2, and is thus required for DNA damage repair and alleviation of replicative and oxidative stress. Little is however known about how PALB2-deficiency affects cell function beyond that, especially in the three-dimensional setting, and also about its role during early steps of malignancy development. To answer these questions, we have generated biologically relevant MCF10A mammary epithelial cell lines with mutations that are comparable to certain clinically important PALB2 defects. We show in a non-cancerous background how both mono- and biallelically PALB2-mutated cells exhibit gross spontaneous DNA damage and mitotic aberrations. Furthermore, PALB2-deficiency disturbs three-dimensional spheroid morphology, increases the migrational capacity and invasiveness of the cells, and broadly alters their transcriptome profiles. TGFβ signaling and KRT14 expression are enhanced in PALB2-mutated cells and their inhibition and knock down, respectively, lead to partial restoration of cell functions. KRT14-positive cells are also more abundant with DNA damage than KRT14-negative cells. The obtained results indicate comprehensive cellular changes upon PALB2 mutations, even in the presence of half dosage of wild type PALB2 and demonstrate how PALB2 mutations may predispose their carriers to malignancy.
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Affiliation(s)
- Hanna Tuppurainen
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Niina Laurila
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Marjut Nätynki
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Leila Eshraghi
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Garvan Institute of Medical Research, Sydney, Australia
| | - Anna Tervasmäki
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Louisa Erichsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Northern Finland Laboratory Centre, Oulu, Finland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland.
| | - Hellevi Peltoketo
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland.
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12
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Harvey-Jones E, Raghunandan M, Robbez-Masson L, Magraner-Pardo L, Alaguthurai T, Yablonovitch A, Yen J, Xiao H, Brough R, Frankum J, Song F, Yeung J, Savy T, Gulati A, Alexander J, Kemp H, Starling C, Konde A, Marlow R, Cheang M, Proszek P, Hubank M, Cai M, Trendell J, Lu R, Liccardo R, Ravindran N, Llop-Guevara A, Rodriguez O, Balmana J, Lukashchuk N, Dorschner M, Drusbosky L, Roxanis I, Serra V, Haider S, Pettitt SJ, Lord CJ, Tutt ANJ. Longitudinal profiling identifies co-occurring BRCA1/2 reversions, TP53BP1, RIF1 and PAXIP1 mutations in PARP inhibitor-resistant advanced breast cancer. Ann Oncol 2024; 35:364-380. [PMID: 38244928 DOI: 10.1016/j.annonc.2024.01.003] [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] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Resistance to therapies that target homologous recombination deficiency (HRD) in breast cancer limits their overall effectiveness. Multiple, preclinically validated, mechanisms of resistance have been proposed, but their existence and relative frequency in clinical disease are unclear, as is how to target resistance. PATIENTS AND METHODS Longitudinal mutation and methylation profiling of circulating tumour (ct)DNA was carried out in 47 patients with metastatic BRCA1-, BRCA2- or PALB2-mutant breast cancer treated with HRD-targeted therapy who developed progressive disease-18 patients had primary resistance and 29 exhibited response followed by resistance. ctDNA isolated at multiple time points in the patient treatment course (before, on-treatment and at progression) was sequenced using a novel >750-gene intron/exon targeted sequencing panel. Where available, matched tumour biopsies were whole exome and RNA sequenced and also used to assess nuclear RAD51. RESULTS BRCA1/2 reversion mutations were present in 60% of patients and were the most prevalent form of resistance. In 10 cases, reversions were detected in ctDNA before clinical progression. Two new reversion-based mechanisms were identified: (i) intragenic BRCA1/2 deletions with intronic breakpoints; and (ii) intragenic BRCA1/2 secondary mutations that formed novel splice acceptor sites, the latter being confirmed by in vitro minigene reporter assays. When seen before commencing subsequent treatment, reversions were associated with significantly shorter time to progression. Tumours with reversions retained HRD mutational signatures but had functional homologous recombination based on RAD51 status. Although less frequent than reversions, nonreversion mechanisms [loss-of-function (LoF) mutations in TP53BP1, RIF1 or PAXIP1] were evident in patients with acquired resistance and occasionally coexisted with reversions, challenging the notion that singular resistance mechanisms emerge in each patient. CONCLUSIONS These observations map the prevalence of candidate drivers of resistance across time in a clinical setting, information with implications for clinical management and trial design in HRD breast cancers.
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Affiliation(s)
- E Harvey-Jones
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK; The City of London Cancer Research UK Centre at King's College London, UK
| | - M Raghunandan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - L Robbez-Masson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - L Magraner-Pardo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - T Alaguthurai
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | | | - J Yen
- Guardant Health Inc., Redwood City, USA
| | - H Xiao
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - R Brough
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Frankum
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - F Song
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Yeung
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - T Savy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - A Gulati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Alexander
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - H Kemp
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - C Starling
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - A Konde
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - R Marlow
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - M Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - P Proszek
- Clinical Genomics, The Royal Marsden Hospital, London, UK
| | - M Hubank
- Clinical Genomics, The Royal Marsden Hospital, London, UK
| | - M Cai
- Guardant Health Inc., Redwood City, USA
| | - J Trendell
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - R Lu
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - R Liccardo
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - N Ravindran
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - O Rodriguez
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - J Balmana
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | | | | | - I Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - V Serra
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - S Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - S J Pettitt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - C J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - A N J Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK; The City of London Cancer Research UK Centre at King's College London, UK.
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13
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Cavanagh RJ, Monteiro PF, Moloney C, Travanut A, Mehradnia F, Taresco V, Rahman R, Martin SG, Grabowska AM, Ashford MB, Alexander C. Free drug and ROS-responsive nanoparticle delivery of synergistic doxorubicin and olaparib combinations to triple negative breast cancer models. Biomater Sci 2024; 12:1822-1840. [PMID: 38407276 DOI: 10.1039/d3bm01931d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Combinations of the topoisomerase II inhibitor doxorubicin and the poly (ADP-ribose) polymerase inhibitor olaparib offer potential drug-drug synergy for the treatment of triple negative breast cancers (TNBC). In this study we performed in vitro screening of combinations of these drugs, administered directly or encapsulated within polymer nanoparticles, in both 2D and in 3D spheroid models of breast cancer. A variety of assays were used to evaluate drug potency, and calculations of combination index (CI) values indicated that synergistic effects of drug combinations occurred in a molar-ratio dependent manner. It is suggested that the mechanisms of synergy were related to enhancement of DNA damage as shown by the level of double-strand DNA breaks, and mechanisms of antagonism associated with mitochondrial mediated cell survival, as indicated by reactive oxygen species (ROS) generation. Enhanced drug delivery and potency was observed with nanoparticle formulations, with a greater extent of doxorubicin localised to cell nuclei as evidenced by microscopy, and higher cytotoxicity at the same time points compared to free drugs. Together, the work presented identifies specific combinations of doxorubicin and olaparib which were most effective in a panel of TNBC cell lines, explores the mechanisms by which these combined agents might act, and shows that formulation of these drug combinations into polymeric nanoparticles at specific ratios conserves synergistic action and enhanced potency in vitro compared to the free drugs.
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Affiliation(s)
| | - Patrícia F Monteiro
- School of Pharmacy, University of Nottingham, NG7 2RD, UK.
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Cara Moloney
- School of Pharmacy, University of Nottingham, NG7 2RD, UK.
- School of Medicine, BioDiscovery Institute, University of Nottingham, NG7 2RD, UK
| | | | | | | | - Ruman Rahman
- School of Medicine, BioDiscovery Institute, University of Nottingham, NG7 2RD, UK
| | - Stewart G Martin
- School of Medicine, BioDiscovery Institute, University of Nottingham, NG7 2RD, UK
| | - Anna M Grabowska
- School of Medicine, BioDiscovery Institute, University of Nottingham, NG7 2RD, UK
| | - Marianne B Ashford
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
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14
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Zhang H, Lee S, Muthakana RR, Lu B, Boone DN, Lee D, Wang XS. Intragenic Rearrangement Burden Associates with Immune Cell Infiltration and Response to Immune Checkpoint Blockade in Cancer. Cancer Immunol Res 2024; 12:287-295. [PMID: 38345376 PMCID: PMC11107381 DOI: 10.1158/2326-6066.cir-22-0637] [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: 08/28/2022] [Revised: 02/27/2023] [Accepted: 12/21/2023] [Indexed: 03/06/2024]
Abstract
Immune checkpoint blockade (ICB) can induce durable cancer remission. However, only a small subset of patients gains benefits. While tumor mutation burden (TMB) differentiates responders from nonresponders in some cases, it is a weak predictor in tumor types with low mutation rates. Thus, there is an unmet need to discover a new class of genetic aberrations that predict ICB responses in these tumor types. Here, we report analyses of pan-cancer whole genomes which revealed that intragenic rearrangement (IGR) burden is significantly associated with immune infiltration in breast, ovarian, esophageal, and endometrial cancers, particularly with increased M1 macrophage and CD8+ T-cell signatures. Multivariate regression against spatially counted tumor-infiltrating lymphocytes in breast, endometrial, and ovarian cancers suggested that IGR burden is a more influential covariate than other genetic aberrations in these cancers. In the MEDI4736 trial evaluating durvalumab in esophageal adenocarcinoma, IGR burden correlated with patient benefits. In the IMVigor210 trial evaluating atezolizumab in urothelial carcinoma, IGR burden increased with platinum exposure and predicted patient benefit among TMB-low, platinum-exposed tumors. Altogether, we have demonstrated that IGR burden correlates with T-cell inflammation and predicts ICB benefit in TMB-low, IGR-dominant tumors, and in platinum-exposed tumors.
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Affiliation(s)
- Han Zhang
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Biomedical Informatics, University of
Pittsburgh, Pittsburgh, PA
| | - Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Biomedical Informatics, University of
Pittsburgh, Pittsburgh, PA
| | - Renee R. Muthakana
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Biological Sciences, University of
Pittsburgh, PA
| | - Binfeng Lu
- Center for Discovery and Innovation, Hackensack Meridian
Health
| | - David N Boone
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Biomedical Informatics, University of
Pittsburgh, Pittsburgh, PA
| | - Daniel Lee
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Medicine, University of Pittsburgh,
Pittsburgh, PA
| | - Xiao-Song Wang
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Pathology, University of Pittsburgh,
Pittsburgh, PA
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15
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Garikapati K, Young IC, Hong S, Rai P, Jain C, Briegel KJ. Blocking LBH expression causes replication stress and sensitizes triple-negative breast cancer cells to ATR inhibitor treatment. Oncogene 2024; 43:851-865. [PMID: 38297083 DOI: 10.1038/s41388-024-02951-3] [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: 08/30/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Triple-negative (ER-PR-HER2-) breast cancers (TNBC) are highly aggressive and difficult to treat. TNBC exhibit high genomic instability, which enables them to adapt and become resistant to chemo/radiation therapy, leading to rapid disease relapse and mortality. The pro-survival factors that safeguard genome integrity in TNBC cells are poorly understood. LBH is an essential mammary stem cell-specific transcription regulator in the WNT pathway that is aberrantly overexpressed in TNBC, correlating with poor prognosis. Herein, we demonstrate a novel role for LBH in promoting TNBC cell survival. Depletion of LBH in multiple TNBC cell models triggered apoptotic cell death both in vitro and in vivo and led to S-G2M cell cycle delays. Mechanistically, LBH loss causes replication stress due to DNA replication fork stalling, leading to ssDNA breaks, ɣH2AX and 53BP1 nuclear foci formation, and activation of the ATR/CHK1 DNA damage response. Notably, ATR inhibition in combination with LBH downmodulation had a synergistic effect, boosting TNBC cell killing and blocking in vivo tumor growth. Our findings demonstrate, for the first time, that LBH protects the genome integrity of cancer cells by preventing replicative stress. Importantly, they uncover new synthetic lethal vulnerabilities in TNBC that could be exploited for future multi-modal precision medicine.
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Affiliation(s)
- Koteswararao Garikapati
- DeWitt Daugherty Department of Surgery, Molecular Oncology Program, University of Miami Miller School of Medicine, Miami, FL, USA
- Braman Family Breast Cancer Institute at the Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - In-Chi Young
- DeWitt Daugherty Department of Surgery, Molecular Oncology Program, University of Miami Miller School of Medicine, Miami, FL, USA
- Braman Family Breast Cancer Institute at the Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sunhwa Hong
- DeWitt Daugherty Department of Surgery, Molecular Oncology Program, University of Miami Miller School of Medicine, Miami, FL, USA
- Braman Family Breast Cancer Institute at the Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Priyamvada Rai
- Department of Radiation Oncology and Tumor Biology Program at the Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Chaitanya Jain
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Karoline J Briegel
- DeWitt Daugherty Department of Surgery, Molecular Oncology Program, University of Miami Miller School of Medicine, Miami, FL, USA.
- Braman Family Breast Cancer Institute at the Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA.
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16
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Jin H, Gulhan DC, Geiger B, Ben-Isvy D, Geng D, Ljungström V, Park PJ. Accurate and sensitive mutational signature analysis with MuSiCal. Nat Genet 2024; 56:541-552. [PMID: 38361034 PMCID: PMC10937379 DOI: 10.1038/s41588-024-01659-0] [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: 04/16/2022] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. Here we present Mutational Signature Calculator (MuSiCal), a rigorous analytical framework with algorithms that solve major problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing more than 2,700 cancer genomes, we provide an improved catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous 'flat' signatures and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.
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Affiliation(s)
- Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Benedikt Geiger
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Daniel Ben-Isvy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - David Geng
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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17
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Huang Y, Qiu Y, Ding L, Ren S, Jiang Y, Luo J, Huang J, Yin X, Fu S, Zhao J, Hu K, Liao J. Somatic mutations in four novel genes contribute to homologous recombination deficiency in breast cancer: a real-world clinical tumor sequencing study. J Pathol Clin Res 2024; 10:e12367. [PMID: 38504382 PMCID: PMC10951049 DOI: 10.1002/2056-4538.12367] [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: 08/08/2023] [Revised: 01/31/2024] [Accepted: 02/13/2024] [Indexed: 03/21/2024]
Abstract
Breast cancers involving mutations in homologous recombination (HR) genes, most commonly BRCA1 and BRCA2 (BRCA1/2), respond well to PARP inhibitors and platinum-based chemotherapy. However, except for these specific HR genes, it is not clear which other mutations contribute to homologous recombination defects (HRD). Here, we performed next-generation sequencing of tumor tissues and matched blood samples from 119 breast cancer patients using the OncoScreen Plus panel. Genomic mutation characteristics and HRD scores were analyzed. In the HR genes, we found that BRCA1/2 and PLAB2 mutations were related to HRD. HRD was also detected in a subset of patients without germline or somatic mutations in BRCA1/2, PLAB2, or other HR-related genes. Notably, LRP1B, NOTCH3, GATA2, and CARD11 (abbreviated as LNGC) mutations were associated with high HRD scores in breast cancer patients. Furthermore, functional experiments demonstrated that silencing CARD11 and GATA2 impairs HR repair efficiency and enhances the sensitivity of tumor cells to olaparib treatment. In summary, in the absence of mutations in the HR genes, the sensitivity of tumor cells to PARP inhibitors and platinum-based chemotherapy may be enhanced in a subset of breast cancer patients with LNGC somatic mutations.
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Affiliation(s)
- Yongsheng Huang
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationGuangzhouPR China
| | - Yuntan Qiu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationGuangzhouPR China
| | - Linxiaoxiao Ding
- Breast Tumor Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Shuwei Ren
- Department of Clinical LaboratoryThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Yuanling Jiang
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Jiahuan Luo
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Jinghua Huang
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Xinke Yin
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Sha Fu
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Jianli Zhao
- Breast Tumor Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
- Guangzhou Regenerative Medicine and Health, Guangdong Laboratory, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationGuangzhouPR China
| | - Jianwei Liao
- Cellular & Molecular Diagnostics CenterSun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPR China
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18
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Meng P, Dalal H, Chen Y, Brueffer C, Gladchuk S, Alcaide M, Ehinger A, Saal LH. Digital PCR quantification of ultrahigh ERBB2 copy number identifies poor breast cancer survival after trastuzumab. NPJ Breast Cancer 2024; 10:14. [PMID: 38374091 PMCID: PMC10876644 DOI: 10.1038/s41523-024-00621-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
HER2/ERBB2 evaluation is necessary for treatment decision-making in breast cancer (BC), however current methods have limitations and considerable variability exists. DNA copy number (CN) evaluation by droplet digital PCR (ddPCR) has complementary advantages for HER2/ERBB2 diagnostics. In this study, we developed a single-reaction multiplex ddPCR assay for determination of ERBB2 CN in reference to two control regions, CEP17 and a copy-number-stable region of chr. 2p13.1, validated CN estimations to clinical in situ hybridization (ISH) HER2 status, and investigated the association of ERBB2 CN with clinical outcomes. 909 primary BC tissues were evaluated and the area under the curve for concordance to HER2 status was 0.93 and 0.96 for ERBB2 CN using either CEP17 or 2p13.1 as reference, respectively. The accuracy of ddPCR ERBB2 CN was 93.7% and 94.1% in the training and validation groups, respectively. Positive and negative predictive value for the classic HER2 amplification and non-amplification groups was 97.2% and 94.8%, respectively. An identified biological "ultrahigh" ERBB2 ddPCR CN group had significantly worse survival within patients treated with adjuvant trastuzumab for both recurrence-free survival (hazard ratio, HR: 3.3; 95% CI 1.1-9.6; p = 0.031, multivariable Cox regression) and overall survival (HR: 3.6; 95% CI 1.1-12.6; p = 0.041). For validation using RNA-seq data as a surrogate, in a population-based SCAN-B cohort (NCT02306096) of 682 consecutive patients receiving adjuvant trastuzumab, the ultrahigh-ERBB2 mRNA group had significantly worse survival. Multiplex ddPCR is useful for ERBB2 CN estimation and ultrahigh ERBB2 may be a predictive factor for decreased long-term survival after trastuzumab treatment.
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Affiliation(s)
- Pei Meng
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
| | - Hina Dalal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
| | - Yilun Chen
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Christian Brueffer
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Sergii Gladchuk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Miguel Alcaide
- SAGA Diagnostics AB, Scheelevägen 2, MV406, SE-22381, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Skåne University Hospital Comprehensive Cancer Center, SE-22381, Lund, Sweden.
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19
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van de Kooij B, Schreuder A, Pavani R, Garzero V, Uruci S, Wendel TJ, van Hoeck A, San Martin Alonso M, Everts M, Koerse D, Callen E, Boom J, Mei H, Cuppen E, Luijsterburg MS, van Vugt MATM, Nussenzweig A, van Attikum H, Noordermeer SM. EXO1 protects BRCA1-deficient cells against toxic DNA lesions. Mol Cell 2024; 84:659-674.e7. [PMID: 38266640 DOI: 10.1016/j.molcel.2023.12.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/14/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Inactivating mutations in the BRCA1 and BRCA2 genes impair DNA double-strand break (DSB) repair by homologous recombination (HR), leading to chromosomal instability and cancer. Importantly, BRCA1/2 deficiency also causes therapeutically targetable vulnerabilities. Here, we identify the dependency on the end resection factor EXO1 as a key vulnerability of BRCA1-deficient cells. EXO1 deficiency generates poly(ADP-ribose)-decorated DNA lesions during S phase that associate with unresolved DSBs and genomic instability in BRCA1-deficient but not in wild-type or BRCA2-deficient cells. Our data indicate that BRCA1/EXO1 double-deficient cells accumulate DSBs due to impaired repair by single-strand annealing (SSA) on top of their HR defect. In contrast, BRCA2-deficient cells retain SSA activity in the absence of EXO1 and hence tolerate EXO1 loss. Consistent with a dependency on EXO1-mediated SSA, we find that BRCA1-mutated tumors show elevated EXO1 expression and increased SSA-associated genomic scars compared with BRCA1-proficient tumors. Overall, our findings uncover EXO1 as a promising therapeutic target for BRCA1-deficient tumors.
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Affiliation(s)
- Bert van de Kooij
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Anne Schreuder
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Veronica Garzero
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Sidrit Uruci
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Tiemen J Wendel
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Arne van Hoeck
- Oncode Institute, Utrecht 3521 AL, the Netherlands; Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584 CG, the Netherlands
| | - Marta San Martin Alonso
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Marieke Everts
- Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Dana Koerse
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jasper Boom
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Edwin Cuppen
- Oncode Institute, Utrecht 3521 AL, the Netherlands; Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584 CG, the Netherlands; Hartwig Medical Foundation, Amsterdam 1098 XH, the Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands.
| | - Sylvie M Noordermeer
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands.
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20
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Lehmann BD, Abramson VG, Dees EC, Shah PD, Ballinger TJ, Isaacs C, Santa-Maria CA, An H, Gonzalez-Ericsson PI, Sanders ME, Newsom KC, Abramson RG, Sheng Q, Hsu CY, Shyr Y, Wolff AC, Pietenpol JA. Atezolizumab in Combination With Carboplatin and Survival Outcomes in Patients With Metastatic Triple-Negative Breast Cancer: The TBCRC 043 Phase 2 Randomized Clinical Trial. JAMA Oncol 2024; 10:193-201. [PMID: 38095878 PMCID: PMC10722391 DOI: 10.1001/jamaoncol.2023.5424] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 08/29/2023] [Indexed: 12/17/2023]
Abstract
Importance Agents targeting programmed death ligand 1 (PD-L1) have demonstrated efficacy in triple-negative breast cancer (TNBC) when combined with chemotherapy and are now the standard of care in patients with PD-L1-positive metastatic disease. In contrast to microtubule-targeting agents, the effect of combining platinum compounds with programmed cell death 1 (PD-1)/PD-L1 immunotherapy has not been extensively determined. Objective To evaluate the efficacy of atezolizumab with carboplatin in patients with metastatic TNBC. Design, Setting, and Participants This phase 2 randomized clinical trial was conducted in 6 centers from August 2017 to June 2021. Interventions Patients with metastatic TNBC were randomized to receive carboplatin area under the curve (AUC) 6 alone or with atezolizumab, 1200 mg, every 3 weeks until disease progression or unacceptable toxic effects with a 3-year duration of follow-up. Main Outcome and Measures The primary end point was investigator-assessed progression-free survival (PFS). Secondary end points included overall response rate (ORR), clinical benefit rate (CBR), and overall survival (OS). Other objectives included correlation of response with tumor PD-L1 levels, tumor-infiltrating lymphocytes (TILs), tumor DNA- and RNA-sequenced biomarkers, TNBC subtyping, and multiplex analyses of immune markers. Results All 106 patients with metastatic TNBC who were enrolled were female with a mean (range) age of 55 (27-79) years, of which 12 (19%) identified as African American/Black, 1 (1%) as Asian, 73 (69%) as White, and 11 (10%) as unknown. Patients were randomized and received either carboplatin (n = 50) or carboplatin and atezolizumab (n = 56). The combination improved PFS (hazard ratio [HR], 0.66; 95% CI, 0.44-1.01; P = .05) from a median of 2.2 to 4.1 months, increased ORR from 8.0% (95% CI, 3.2%-18.8%) to 30.4% (95% CI, 19.9%-43.3%), increased CBR at 6 months from 18.0% (95% CI, 9.8%-30.1%) to 37.5% (95% CI, 26.0%-50.6%), and improved OS (HR, 0.60; 95% CI, 0.37-0.96; P = .03) from a median of 8.6 to 12.6 months. Subgroup analysis showed PD-L1-positive tumors did not benefit more from adding atezolizumab (HR, 0.62; 95% CI, 0.23-1.65; P = .35). Patients with high TILs (HR, 0.12; 95% CI, 0.30-0.50), high mutation burden (HR, 0.50; 95% CI, 0.23-1.06), and prior chemotherapy (HR, 0.59; 95% CI, 0.36-0.95) received greater benefit on the combination. Patients with obesity and patients with more than 125 mg/dL on-treatment blood glucose levels were associated with better PFS (HR, 0.35; 95% CI, 0.10-1.80) on the combination. TNBC subtypes benefited from adding atezolizumab, except the luminal androgen receptor subtype. Conclusions and Relevance In this randomized clinical trial, the addition of atezolizumab to carboplatin significantly improved survival of patients with metastatic TNBC regardless of PD-L1 status. Further, lower risk of disease progression was associated with increased TILs, higher mutation burden, obesity, and uncontrolled blood glucose levels. Trial Registration ClinicalTrials.gov Identifier: NCT03206203.
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Affiliation(s)
- Brian D Lehmann
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Tennessee
| | - Vandana G Abramson
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Tennessee
| | - E Claire Dees
- Department of Medicine and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill
| | - Payal D Shah
- Department of Medicine, University of Pennsylvania, Philadelphia
| | | | - Claudine Isaacs
- Department of Medical Oncology, Lombardi Cancer Center, Georgetown University, Washington, DC
| | - Cesar A Santa-Maria
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Hanbing An
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Paula I Gonzalez-Ericsson
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Tennessee
- Breast Cancer Research Program, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Melinda E Sanders
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Tennessee
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee
| | - Kimberly C Newsom
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Tennessee
| | - Richard G Abramson
- Department of Biomedical Engineering, Vanderbilt University School of Engineering, Nashville, Tennessee
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Chih-Yuan Hsu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Antonio C Wolff
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jennifer A Pietenpol
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Tennessee
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
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21
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Hafstað V, Häkkinen J, Larsson M, Staaf J, Vallon-Christersson J, Persson H. Improved detection of clinically relevant fusion transcripts in cancer by machine learning classification. BMC Genomics 2023; 24:783. [PMID: 38110872 PMCID: PMC10726539 DOI: 10.1186/s12864-023-09889-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 12/10/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Genomic rearrangements in cancer cells can create fusion genes that encode chimeric proteins or alter the expression of coding and non-coding RNAs. In some cancer types, fusions involving specific kinases are used as targets for therapy. Fusion genes can be detected by whole genome sequencing (WGS) and targeted fusion panels, but RNA sequencing (RNA-Seq) has the advantageous capability of broadly detecting expressed fusion transcripts. RESULTS We developed a pipeline for validation of fusion transcripts identified in RNA-Seq data using matched WGS data from The Cancer Genome Atlas (TCGA) and applied it to 910 tumors from 11 different cancer types. This resulted in 4237 validated gene fusions, 3049 of them with at least one identified genomic breakpoint. Utilizing validated fusions as true positive events, we trained a machine learning classifier to predict true and false positive fusion transcripts from RNA-Seq data. The final precision and recall metrics of the classifier were 0.74 and 0.71, respectively, in an independent dataset of 249 breast tumors. Application of this classifier to all samples with RNA-Seq data from these cancer types vastly extended the number of likely true positive fusion transcripts and identified many potentially targetable kinase fusions. Further analysis of the validated gene fusions suggested that many are created by intrachromosomal amplification events with microhomology-mediated non-homologous end-joining. CONCLUSIONS A classifier trained on validated fusion events increased the accuracy of fusion transcript identification in samples without WGS data. This allowed the analysis to be extended to all samples with RNA-Seq data, facilitating studies of tumor biology and increasing the number of detected kinase fusions. Machine learning could thus be used in identification of clinically relevant fusion events for targeted therapy. The large dataset of validated gene fusions generated here presents a useful resource for development and evaluation of fusion transcript detection algorithms.
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Affiliation(s)
- Völundur Hafstað
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Jari Häkkinen
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Malin Larsson
- Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Linköping University, Linköping, Sweden
| | - Johan Staaf
- Faculty of Medicine, Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Centre, Lund, Sweden
| | - Johan Vallon-Christersson
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Helena Persson
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden.
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22
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Ring A, Kilburn LS, Pearson A, Moretti L, Afshari-Mehr A, Wardley AM, Gurel B, Macpherson IR, Riisnaes R, Baird RD, Martin S, Roylance R, Johnson H, Ferreira A, Winter MC, Dunne K, Copson E, Hickish T, Burcombe R, Randle K, Serra V, Llop-Guevara A, Bliss JM, Turner NC. Olaparib and Ceralasertib (AZD6738) in Patients with Triple-Negative Advanced Breast Cancer: Results from Cohort E of the plasmaMATCH Trial (CRUK/15/010). Clin Cancer Res 2023; 29:4751-4759. [PMID: 37773077 PMCID: PMC10690092 DOI: 10.1158/1078-0432.ccr-23-1696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/16/2023] [Accepted: 09/26/2023] [Indexed: 09/30/2023]
Abstract
PURPOSE Approximately 10% to 15% of triple-negative breast cancers (TNBC) have deleterious mutations in BRCA1 and BRCA2 and may benefit from PARP inhibitor treatment. PARP inhibitors may also increase exogenous replication stress and thereby increase sensitivity to inhibitors of ataxia telangiectasia and Rad3-related (ATR) protein. This phase II study examined the activity of the combination of PARP inhibitor, olaparib, and ATR inhibitor, ceralasertib (AZD6738), in patients with advanced TNBC. PATIENTS AND METHODS Patients with TNBC on most recent biopsy who had received 1 or 2 lines of chemotherapy for advanced disease or had relapsed within 12 months of (neo)adjuvant chemotherapy were eligible. Treatment was olaparib 300 mg twice a day continuously and celarasertib 160 mg on days 1-7 on a 28-day cycle until disease progression. The primary endpoint was confirmed objective response rate (ORR). Tissue and plasma biomarker analyses were preplanned to identify predictors of response. RESULTS 70 evaluable patients were enrolled. Germline BRCA1/2 mutations were present in 10 (14%) patients and 3 (4%) patients had somatic BRCA mutations. The confirmed ORR was 12/70; 17.1% (95% confidence interval, 10.4-25.5). Responses were observed in patients without germline or somatic BRCA1/2 mutations, including patients with mutations in other homologous recombination repair genes and tumors with functional homologous recombination deficiency by RAD51 foci. CONCLUSIONS The response rate to olaparib and ceralasertib did not meet prespecified criteria for activity in the overall evaluable population, but responses were observed in patients who would not be expected to respond to olaparib monotherapy.
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Affiliation(s)
- Alistair Ring
- Breast Unit, The Royal Marsden Hospital, Sutton, United Kingdom
- Division of Breast Cancer Research, Institute of Cancer Research, London, United Kingdom
| | - Lucy S. Kilburn
- Clinical Trials and Statistics Unit at The Institute of Cancer Research, London, United Kingdom
| | - Alex Pearson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Laura Moretti
- Clinical Trials and Statistics Unit at The Institute of Cancer Research, London, United Kingdom
| | - Angelica Afshari-Mehr
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | - Bora Gurel
- Clinical Studies – Cancer Biomarkers, The Institute of Cancer Research, London, United Kingdom
| | - Iain R. Macpherson
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ruth Riisnaes
- Clinical Studies – Cancer Biomarkers, The Institute of Cancer Research, London, United Kingdom
| | | | - Sue Martin
- Clinical Trials and Statistics Unit at The Institute of Cancer Research, London, United Kingdom
| | - Rebecca Roylance
- University College London Hospitals NHS Foundation Trust & NIHR University College London Hospitals Biomedical Research Centre, London, United Kingdom
| | - Hannah Johnson
- Clinical Trials and Statistics Unit at The Institute of Cancer Research, London, United Kingdom
| | - Ana Ferreira
- Clinical Studies – Cancer Biomarkers, The Institute of Cancer Research, London, United Kingdom
| | - Matthew C. Winter
- Weston Park Hospital, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - Kathryn Dunne
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, United Kingdom
| | - Ellen Copson
- Cancer Sciences Academic Unit, University of Southampton, Southampton, United Kingdom
| | - Tamas Hickish
- Royal Bournemouth Hospital, University Hospitals Dorset NHS Foundation Trust, Bournemouth, United Kingdom
| | - Russell Burcombe
- Maidstone and Tunbridge Wells NHS Trust, Maidstone, Kent, United Kingdom
| | - Kat Randle
- Independent Cancer Patients’ Voice, London, United Kingdom
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Judith M. Bliss
- Clinical Trials and Statistics Unit at The Institute of Cancer Research, London, United Kingdom
| | - Nicolas C. Turner
- Breast Unit, The Royal Marsden Hospital, Sutton, United Kingdom
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
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23
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Llinàs-Arias P, Ensenyat-Mendez M, Íñiguez-Muñoz S, Orozco JIJ, Valdez B, Salomon MP, Matsuba C, Solivellas-Pieras M, Bedoya-López AF, Sesé B, Mezger A, Ormestad M, Unzueta F, Strand SH, Boiko AD, Hwang ES, Cortés J, DiNome ML, Esteller M, Lupien M, Marzese DM. Chromatin insulation orchestrates matrix metalloproteinase gene cluster expression reprogramming in aggressive breast cancer tumors. Mol Cancer 2023; 22:190. [PMID: 38017545 PMCID: PMC10683115 DOI: 10.1186/s12943-023-01906-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is an aggressive subtype that exhibits a high incidence of distant metastases and lacks targeted therapeutic options. Here we explored how the epigenome contributes to matrix metalloprotease (MMP) dysregulation impacting tumor invasion, which is the first step of the metastatic process. METHODS We combined RNA expression and chromatin interaction data to identify insulator elements potentially associated with MMP gene expression and invasion. We employed CRISPR/Cas9 to disrupt the CCCTC-Binding Factor (CTCF) binding site on an insulator element downstream of the MMP8 gene (IE8) in two TNBC cellular models. We characterized these models by combining Hi-C, ATAC-seq, and RNA-seq with functional experiments to determine invasive ability. The potential of our findings to predict the progression of ductal carcinoma in situ (DCIS), was tested in data from clinical specimens. RESULTS We explored the clinical relevance of an insulator element located within the Chr11q22.2 locus, downstream of the MMP8 gene (IE8). This regulatory element resulted in a topologically associating domain (TAD) boundary that isolated nine MMP genes into two anti-correlated expression clusters. This expression pattern was associated with worse relapse-free (HR = 1.57 [1.06 - 2.33]; p = 0.023) and overall (HR = 2.65 [1.31 - 5.37], p = 0.005) survival of TNBC patients. After CRISPR/Cas9-mediated disruption of IE8, cancer cells showed a switch in the MMP expression signature, specifically downregulating the pro-invasive MMP1 gene and upregulating the antitumorigenic MMP8 gene, resulting in reduced invasive ability and collagen degradation. We observed that the MMP expression pattern predicts DCIS that eventually progresses into invasive ductal carcinomas (AUC = 0.77, p < 0.01). CONCLUSION Our study demonstrates how the activation of an IE near the MMP8 gene determines the regional transcriptional regulation of MMP genes with opposing functional activity, ultimately influencing the invasive properties of aggressive forms of breast cancer.
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Affiliation(s)
- Pere Llinàs-Arias
- Cancer Epigenetics Laboratory, Health Research Institute of the Balearic Islands (IdISBa), Palma, 07120, Spain
| | - Miquel Ensenyat-Mendez
- Cancer Epigenetics Laboratory, Health Research Institute of the Balearic Islands (IdISBa), Palma, 07120, Spain
| | - Sandra Íñiguez-Muñoz
- Cancer Epigenetics Laboratory, Health Research Institute of the Balearic Islands (IdISBa), Palma, 07120, Spain
| | - Javier I J Orozco
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Betsy Valdez
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Matthew P Salomon
- Keck School of Medicine, USC Research Center for Liver Diseases, University of Southern California, Los Angeles, CA, USA
| | - Chikako Matsuba
- Keck School of Medicine, USC Research Center for Liver Diseases, University of Southern California, Los Angeles, CA, USA
| | - Maria Solivellas-Pieras
- Cancer Epigenetics Laboratory, Health Research Institute of the Balearic Islands (IdISBa), Palma, 07120, Spain
| | - Andrés F Bedoya-López
- Cancer Epigenetics Laboratory, Health Research Institute of the Balearic Islands (IdISBa), Palma, 07120, Spain
| | - Borja Sesé
- Cancer Epigenetics Laboratory, Health Research Institute of the Balearic Islands (IdISBa), Palma, 07120, Spain
| | - Anja Mezger
- Science for Life Laboratory, Solna, 17665, Sweden
| | | | - Fernando Unzueta
- Advanced Optical Microscopy Facility Scientific and Technological Centres of University of Barcelona, Barcelona, Spain
| | - Siri H Strand
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alexander D Boiko
- Department of Medicine, Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, 90048, USA
| | - E Shelley Hwang
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Javier Cortés
- Pangaea Oncology, Quiron Group, International Breast Cancer Center (IBCC), Barcelona, 08017, Spain
- Medica Scientia Innovation Research SL (MEDSIR), Barcelona, 08018, Spain
- Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, 28670, Spain
| | - Maggie L DiNome
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red Cancer (CIBERONC), Madrid, 28029, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada
| | - Diego M Marzese
- Cancer Epigenetics Laboratory, Health Research Institute of the Balearic Islands (IdISBa), Palma, 07120, Spain.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
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Chu C, Lin EW, Tran A, Jin H, Ho NI, Veit A, Cortes-Ciriano I, Burns KH, Ting DT, Park PJ. The landscape of human SVA retrotransposons. Nucleic Acids Res 2023; 51:11453-11465. [PMID: 37823611 PMCID: PMC10681720 DOI: 10.1093/nar/gkad821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons are evolutionarily young and still-active transposable elements (TEs) in the human genome. Several pathogenic SVA insertions have been identified that directly mutate host genes to cause neurodegenerative and other types of diseases. However, due to their sequence heterogeneity and complex structures as well as limitations in sequencing techniques and analysis, SVA insertions have been less well studied compared to other mobile element insertions. Here, we identified polymorphic SVA insertions from 3646 whole-genome sequencing (WGS) samples of >150 diverse populations and constructed a polymorphic SVA insertion reference catalog. Using 20 long-read samples, we also assembled reference and polymorphic SVA sequences and characterized the internal hexamer/variable-number-tandem-repeat (VNTR) expansions as well as differing SVA activity for SVA subfamilies and human populations. In addition, we developed a module to annotate both reference and polymorphic SVA copies. By characterizing the landscape of both reference and polymorphic SVA retrotransposons, our study enables more accurate genotyping of these elements and facilitate the discovery of pathogenic SVA insertions.
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Affiliation(s)
- Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Eric W Lin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Antuan Tran
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Natalie I Ho
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Alexander Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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25
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Qin Y, Yuan X, Cui Z, Chen W, Xu S, Chen K, Wang F, Zheng F, Ni H, Shen HM, Wu Y, Xia D. Low dose PFDA induces DNA damage and DNA repair inhibition by promoting nuclear cGAS accumulation in ovarian epithelial cells. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 265:115503. [PMID: 37742570 DOI: 10.1016/j.ecoenv.2023.115503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS), the versatile anthropogenic chemicals, are popular with the markets and manufactured in large quantities yearly. Accumulation of PFAS has various adverse health effects on human. Albeit certain members of PFAS were found to have genotoxicity in previous studies, the mechanisms underlying their effects on DNA damage repair remain unclear. Here, we investigated the effects of Perfluorodecanoic acid (PFDA) on DNA damage and DNA damage repair in ovarian epithelial cells through a series of in vivo and in vitro experiments. At environmentally relevant concentration, we firstly found that PFDA can cause DNA damage in primary mouse ovarian epithelial cells and IOSE-80 cells. Moreover, nuclear cGAS increased in PFDA-treated cells, which leaded to the efficiency of DNA homologous recombination (HR) decreased and DNA double-strand breaks perpetuated. In vivo experiments also verified that PFDA can induce more DNA double-strand breaks lesions and nuclear cGAS in ovarian tissue. Taken together, our results unveiled that low dose PFDA can cause deleterious effects on DNA and DNA damage repair (DDR) in ovarian epithelial cells and induce genomic instability.
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Affiliation(s)
- Yuheng Qin
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaoyu Yuan
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhenyan Cui
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wenhan Chen
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Sinan Xu
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kelie Chen
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fang Wang
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fang Zheng
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Heng Ni
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Han-Ming Shen
- Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau, China
| | - Yihua Wu
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences, Hangzhou, Zhejiang, China.
| | - Dajing Xia
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
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26
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Sigurjonsdottir G, De Marchi T, Ehinger A, Hartman J, Bosch A, Staaf J, Killander F, Niméus E. Comparison of SP142 and 22C3 PD-L1 assays in a population-based cohort of triple-negative breast cancer patients in the context of their clinically established scoring algorithms. Breast Cancer Res 2023; 25:123. [PMID: 37817263 PMCID: PMC10566164 DOI: 10.1186/s13058-023-01724-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/02/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Immunohistochemical (IHC) PD-L1 expression is commonly employed as predictive biomarker for checkpoint inhibitors in triple-negative breast cancer (TNBC). However, IHC evaluation methods are non-uniform and further studies are needed to optimize clinical utility. METHODS We compared the concordance, prognostic value and gene expression between PD-L1 IHC expression by SP142 immune cell (IC) score and 22C3 combined positive score (CPS; companion IHC diagnostic assays for atezolizumab and pembrolizumab, respectively) in a population-based cohort of 232 early-stage TNBC patients. RESULTS The expression rates of PD-L1 for SP142 IC ≥ 1%, 22C3 CPS ≥ 10, 22C3 CPS ≥ 1 and 22C3 IC ≥ 1% were 50.9%, 27.2%, 53.9% and 41.8%, respectively. The analytical concordance (kappa values) between SP142 IC+ and these three different 22C3 scorings were 73.7% (0.48, weak agreement), 81.5% (0.63) and 86.6% (0.73), respectively. The SP142 assay was better at identifying 22C3 positive tumors than the 22C3 assay was at detecting SP142 positive tumors. PD-L1 (CD274) gene expression (mRNA) showed a strong positive association with all two-categorical IHC scorings of the PD-L1 expression, irrespective of antibody and cut-off (Spearman Rho ranged from 0.59 to 0.62; all p-values < 0.001). PD-L1 IHC positivity and abundance of tumor infiltrating lymphocytes were of positive prognostic value in univariable regression analyses in patients treated with (neo)adjuvant chemotherapy, where it was strongest for 22C3 CPS ≥ 10 and distant relapse-free interval (HR = 0.18, p = 0.019). However, PD-L1 status was not independently prognostic when adjusting for abundance of tumor infiltrating lymphocytes in multivariable analyses. CONCLUSION Our findings support that the SP142 and 22C3 IHC assays, with their respective clinically applied scoring algorithms, are not analytically equivalent where they identify partially non-overlapping subpopulations of TNBC patients and cannot be substituted with one another regarding PD-L1 detection. Trial registration The Swedish Cancerome Analysis Network - Breast (SCAN-B) study, retrospectively registered 2nd Dec 2014 at ClinicalTrials.gov; ID NCT02306096.
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Affiliation(s)
- Gudbjörg Sigurjonsdottir
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Tommaso De Marchi
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Laboratory Medicine, Region Skåne, Lund, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Ana Bosch
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, Sweden
| | - Fredrika Killander
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Emma Niméus
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
- Divison of Surgery, Department of Clinical Sciences Lund, Lund University, Sölvegatan 19 - BMC I12, 22184, Lund, Sweden.
- Department of Surgery, Skåne University Hospital, Malmö, Sweden.
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27
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Edsjö A, Holmquist L, Geoerger B, Nowak F, Gomon G, Alix-Panabières C, Ploeger C, Lassen U, Le Tourneau C, Lehtiö J, Ott PA, von Deimling A, Fröhling S, Voest E, Klauschen F, Dienstmann R, Alshibany A, Siu LL, Stenzinger A. Precision cancer medicine: Concepts, current practice, and future developments. J Intern Med 2023; 294:455-481. [PMID: 37641393 DOI: 10.1111/joim.13709] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Precision cancer medicine is a multidisciplinary team effort that requires involvement and commitment of many stakeholders including the society at large. Building on the success of significant advances in precision therapy for oncological patients over the last two decades, future developments will be significantly shaped by improvements in scalable molecular diagnostics in which increasingly complex multilayered datasets require transformation into clinically useful information guiding patient management at fast turnaround times. Adaptive profiling strategies involving tissue- and liquid-based testing that account for the immense plasticity of cancer during the patient's journey and also include early detection approaches are already finding their way into clinical routine and will become paramount. A second major driver is the development of smart clinical trials and trial concepts which, complemented by real-world evidence, rapidly broaden the spectrum of therapeutic options. Tight coordination with regulatory agencies and health technology assessment bodies is crucial in this context. Multicentric networks operating nationally and internationally are key in implementing precision oncology in clinical practice and support developing and improving the ecosystem and framework needed to turn invocation into benefits for patients. The review provides an overview of the diagnostic tools, innovative clinical studies, and collaborative efforts needed to realize precision cancer medicine.
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Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Genomic Medicine Sweden (GMS), Kristianstad, Sweden
| | - Louise Holmquist
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Genomic Medicine Sweden (GMS), Kristianstad, Sweden
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | | | - Georgy Gomon
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Department of Medical Oncology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells, University Medical Center of Montpellier, Montpellier, France
- CREEC, MIVEGEC, University of Montpellier, Montpellier, France
| | - Carolin Ploeger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Centers for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Ulrik Lassen
- Department of Oncology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
- INSERM U900 Research Unit, Saint-Cloud, France
- Faculty of Medicine, Paris-Saclay University, Paris, France
| | - Janne Lehtiö
- Department of Oncology Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Emile Voest
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Frederick Klauschen
- Institute of Pathology, Charite - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- BIFOLD - Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute of Pathology, Ludwig-Maximilians-University, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Munich Partner Site, Heidelberg, Germany
| | | | | | - Lillian L Siu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Centers for Personalized Medicine (ZPM), Heidelberg, Germany
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28
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Tovey H, Sipos O, Parker JS, Hoadley KA, Quist J, Kernaghan S, Kilburn L, Salgado R, Loi S, Kennedy RD, Roxanis I, Gazinska P, Pinder SE, Bliss J, Perou CM, Haider S, Grigoriadis A, Tutt A, Cheang MCU. Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727). Clin Cancer Res 2023; 29:3691-3705. [PMID: 37574209 PMCID: PMC10502473 DOI: 10.1158/1078-0432.ccr-23-0370] [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: 02/08/2023] [Revised: 05/23/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023]
Abstract
PURPOSE The TNT trial (NCT00532727) showed no evidence of carboplatin superiority over docetaxel in metastatic triple-negative breast cancer (mTNBC), but carboplatin benefit was observed in the germline BRCA1/2 mutation subgroup. Broader response-predictive biomarkers are needed. We explored the predictive ability of DNA damage response (DDR) and immune markers. EXPERIMENTAL DESIGN Tumor-infiltrating lymphocytes were evaluated for 222 of 376 patients. Primary tumors (PT) from 186 TNT participants (13 matched recurrences) were profiled using total RNA sequencing. Four transcriptional DDR-related and 25 immune-related signatures were evaluated. We assessed their association with objective response rate (ORR) and progression-free survival (PFS). Conditional inference forest clustering was applied to integrate multimodal data. The biology of subgroups was characterized by 693 gene expression modules and other markers. RESULTS Transcriptional DDR-related biomarkers were not predictive of ORR to either treatment overall. Changes from PT to recurrence were demonstrated; in chemotherapy-naïve patients, transcriptional DDR markers separated carboplatin responders from nonresponders (P values = 0.017; 0.046). High immune infiltration was associated with docetaxel ORR (interaction P values < 0.05). Six subgroups were identified; the immune-enriched cluster had preferential docetaxel response [62.5% (D) vs. 29.4% (C); P = 0.016]. The immune-depleted cluster had preferential carboplatin response [8.0% (D) vs. 40.0% (C); P = 0.011]. DDR-related subgroups were too small to assess ORR. CONCLUSIONS High immune features predict docetaxel response, and high DDR signature scores predict carboplatin response in treatment-naïve mTNBC. Integrating multimodal DDR and immune-related markers identifies subgroups with differential treatment sensitivity. Treatment options for patients with immune-low and DDR-proficient tumors remains an outstanding need. Caution is needed using PT-derived transcriptional signatures to direct treatment in mTNBC, particularly DDR-related markers following prior chemotherapy.
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Affiliation(s)
- Holly Tovey
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Orsolya Sipos
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Joel S. Parker
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Katherine A. Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jelmar Quist
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Sarah Kernaghan
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Lucy Kilburn
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Sherene Loi
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Ioannis Roxanis
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Patrycja Gazinska
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
- Biobank Research Group, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Wroclaw, Poland
| | - Sarah E. Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Judith Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Charles M. Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Syed Haider
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Anita Grigoriadis
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Andrew Tutt
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Maggie Chon U. Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
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29
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Yang F, Wei W, Li G, Lan Q, Liu X, Gao L, Zhang C, Fan J, Li J. A novel marker integrating multiple genetic alterations better predicts platinum sensitivity in ovarian cancer than HRD score. Front Genet 2023; 14:1240068. [PMID: 37732324 PMCID: PMC10508345 DOI: 10.3389/fgene.2023.1240068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/17/2023] [Indexed: 09/22/2023] Open
Abstract
Introduction: Platinum-based chemotherapy is the first-line treatment strategy for ovarian cancer patients. The dismal prognosis of ovarian cancer was shown to be stringently associated with the heterogeneity of tumor cells in response to this therapy, therefore understanding platinum sensitivity in ovarian cancer would be helpful for improving patients' quality of life and clinical outcomes. HRDetect, utilized to characterize patients' homologous recombination repair deficiency, was used to predict patients' response to platinum-based chemotherapy. However, whether each of the single features contributing to HRD score is associated with platinum sensitivity remains elusive. Methods: We analyzed the whole-exome sequencing data of 196 patients who received platinum-based chemotherapy from the TCGA database. Genetic features were determined individually to see if they could indicate patients' response to platinum-based chemotherapy and prognosis, then integrated into a Pt-score employing LASSO regression model to assess its predictive performance. Results and discussion: Multiple genetic features, including bi-allelic inactivation of BRCA1/2 genes and genes involved in HR pathway, multiple somatic mutations in genes involved in DNA damage repair (DDR), and previously reported HRD-related features, were found to be stringently associated with platinum sensitivity and improved prognosis. Higher contributions of mutational signature SBS39 or ID6 predicted improved overall survival. Besides, arm-level loss of heterozygosity (LOH) of either chr4p or chr5q predicted significantly better disease-free survival. Notably, some of these features were found independent of HRD. And SBS3, an HRD-related feature, was found irrelevant to platinum sensitivity. Integrated all candidate markers using the LASSO model to yield a Pt-score, which showed better predictive ability compared to HRDetect in determining platinum sensitivity and predicting patients' prognosis, and this performance was validated in an independent cohort. The outcomes of our study will be instrumental in devising effective strategies for treating ovarian cancer with platinum-based chemotherapy.
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Affiliation(s)
- Fan Yang
- Department of Gynecologic Oncology, Sun Yat-sen University Cancer Centre, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, China
| | - Wei Wei
- Department of Gynecologic Oncology, Sun Yat-sen University Cancer Centre, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, China
| | - Ganghua Li
- GenePlus-Shenzhen, Shenzhen, Guangdong, China
| | - Qiongyu Lan
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiwei Liu
- GenePlus-Shenzhen, Shenzhen, Guangdong, China
| | - Lin Gao
- GenePlus-Shenzhen, Shenzhen, Guangdong, China
| | - Chao Zhang
- GenePlus-Shenzhen, Shenzhen, Guangdong, China
| | - Jiangtao Fan
- Department of Gynecology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jundong Li
- Department of Gynecologic Oncology, Sun Yat-sen University Cancer Centre, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, China
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Wang F, Xu Y, Wang R, Zhang B, Smith N, Notaro A, Gaerlan S, Kutschera E, Kadash-Edmondson KE, Xing Y, Lin L. TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing. Nat Commun 2023; 14:4760. [PMID: 37553321 PMCID: PMC10409798 DOI: 10.1038/s41467-023-40083-6] [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: 12/03/2022] [Accepted: 07/11/2023] [Indexed: 08/10/2023] Open
Abstract
Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. One strategy for overcoming this bottleneck is targeted long-read RNA-seq for preselected gene panels. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq utilizing isothermally linear-amplified capture probes. When performed on the Oxford nanopore platform with multiple gene panels of varying sizes, TEQUILA-seq consistently and substantially enriches transcript coverage while preserving transcript quantification. We profile full-length transcript isoforms of 468 actionable cancer genes across 40 representative breast cancer cell lines. We identify transcript isoforms enriched in specific subtypes and discover novel transcript isoforms in extensively studied cancer genes such as TP53. Among cancer genes, tumor suppressor genes (TSGs) are significantly enriched for aberrant transcript isoforms targeted for degradation via mRNA nonsense-mediated decay, revealing a common RNA-associated mechanism for TSG inactivation. TEQUILA-seq reduces the per-reaction cost of targeted capture by 2-3 orders of magnitude, as compared to a standard commercial solution. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.
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Affiliation(s)
- Feng Wang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yang Xu
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert Wang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Beatrice Zhang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Noah Smith
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amber Notaro
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Samantha Gaerlan
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric Kutschera
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kathryn E Kadash-Edmondson
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Lan Lin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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31
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Yao H, Li H, Wang J, Wu T, Ning W, Diao K, Wu C, Wang G, Tao Z, Zhao X, Chen J, Sun X, Liu XS. Copy number alteration features in pan-cancer homologous recombination deficiency prediction and biology. Commun Biol 2023; 6:527. [PMID: 37193789 DOI: 10.1038/s42003-023-04901-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/02/2023] [Indexed: 05/18/2023] Open
Abstract
Homologous recombination deficiency (HRD) renders cancer cells vulnerable to unrepaired double-strand breaks and is an important therapeutic target as exemplified by the clinical efficacy of poly ADP-ribose polymerase (PARP) inhibitors as well as the platinum chemotherapy drugs applied to HRD patients. However, it remains a challenge to predict HRD status precisely and economically. Copy number alteration (CNA), as a pervasive trait of human cancers, can be extracted from a variety of data sources, including whole genome sequencing (WGS), SNP array, and panel sequencing, and thus can be easily applied clinically. Here we systematically evaluate the predictive performance of various CNA features and signatures in HRD prediction and build a gradient boosting machine model (HRDCNA) for pan-cancer HRD prediction based on these CNA features. CNA features BP10MB[1] (The number of breakpoints per 10MB of DNA is 1) and SS[ > 7 & <=8] (The log10-based size of segments is greater than 7 and less than or equal to 8) are identified as the most important features in HRD prediction. HRDCNA suggests the biallelic inactivation of BRCA1, BRCA2, PALB2, RAD51C, RAD51D, and BARD1 as the major genetic basis for human HRD, and may also be applied to effectively validate the pathogenicity of BRCA1/2 variants of uncertain significance (VUS). Together, this study provides a robust tool for cost-effective HRD prediction and also demonstrates the applicability of CNA features and signatures in cancer precision medicine.
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Affiliation(s)
- Huizi Yao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyu Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wei Ning
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Kaixuan Diao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chenxu Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guangshuai Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ziyu Tao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiangyu Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jing Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiaoqin Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xue-Song Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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Nacer DF, Vallon-Christersson J, Nordborg N, Ehrencrona H, Kvist A, Borg Å, Staaf J. Molecular characteristics of breast tumors in patients screened for germline predisposition from a population-based observational study. Genome Med 2023; 15:25. [PMID: 37060015 PMCID: PMC10103478 DOI: 10.1186/s13073-023-01177-4] [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: 10/26/2022] [Accepted: 04/05/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Pathogenic germline variants (PGVs) in certain genes are linked to higher lifetime risk of developing breast cancer and can influence preventive surgery decisions and therapy choices. Public health programs offer genetic screening based on criteria designed to assess personal risk and identify individuals more likely to carry PGVs, dividing patients into screened and non-screened groups. How tumor biology and clinicopathological characteristics differ between these groups is understudied and could guide refinement of screening criteria. METHODS Six thousand six hundred sixty breast cancer patients diagnosed in South Sweden during 2010-2018 were included with available clinicopathological and RNA sequencing data, 900 (13.5%) of which had genes screened for PGVs through routine clinical screening programs. We compared characteristics of screened patients and tumors to non-screened patients, as well as between screened patients with (n = 124) and without (n = 776) PGVs. RESULTS Broadly, breast tumors in screened patients showed features of a more aggressive disease. However, few differences related to tumor biology or patient outcome remained significant after stratification by clinical subgroups or PAM50 subtypes. Triple-negative breast cancer (TNBC), the subgroup most enriched for PGVs, showed the most differences between screening subpopulations (e.g., higher tumor proliferation in screened cases). Significant differences in PGV prevalence were found between clinical subgroups/molecular subtypes, e.g., TNBC cases were enriched for BRCA1 PGVs. In general, clinicopathological differences between screened and non-screened patients mimicked those between patients with and without PGVs, e.g., younger age at diagnosis for positive cases. However, differences in tumor biology/microenvironment such as immune cell composition were additionally seen within PGV carriers/non-carriers in ER + /HER2 - cases, but not between screening subpopulations in this subgroup. CONCLUSIONS Characterization of molecular tumor features in patients clinically screened and not screened for PGVs represents a relevant read-out of guideline criteria. The general lack of molecular differences between screened/non-screened patients after stratification by relevant breast cancer subsets questions the ability to improve the identification of screening candidates based on currently used patient and tumor characteristics, pointing us towards universal screening. Nevertheless, while that is not attained, molecular differences identified between PGV carriers/non-carriers suggest the possibility of further refining patient selection within certain patient subsets using RNA-seq through, e.g., gene signatures. TRIAL REGISTRATION The Sweden Cancerome Analysis Network - Breast (SCAN-B) was prospectively registered at ClinicalTrials.gov under the identifier NCT02306096.
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Affiliation(s)
- Deborah F Nacer
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, SE-22381, Sweden
| | | | - Nicklas Nordborg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Hans Ehrencrona
- Department of Genetics and Pathology, Laboratory Medicine, Region Skåne, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Kvist
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, SE-22381, Sweden.
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Patterson A, Elbasir A, Tian B, Auslander N. Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications. Cancers (Basel) 2023; 15:cancers15071958. [PMID: 37046619 PMCID: PMC10093138 DOI: 10.3390/cancers15071958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
Since the rise of next-generation sequencing technologies, the catalogue of mutations in cancer has been continuously expanding. To address the complexity of the cancer-genomic landscape and extract meaningful insights, numerous computational approaches have been developed over the last two decades. In this review, we survey the current leading computational methods to derive intricate mutational patterns in the context of clinical relevance. We begin with mutation signatures, explaining first how mutation signatures were developed and then examining the utility of studies using mutation signatures to correlate environmental effects on the cancer genome. Next, we examine current clinical research that employs mutation signatures and discuss the potential use cases and challenges of mutation signatures in clinical decision-making. We then examine computational studies developing tools to investigate complex patterns of mutations beyond the context of mutational signatures. We survey methods to identify cancer-driver genes, from single-driver studies to pathway and network analyses. In addition, we review methods inferring complex combinations of mutations for clinical tasks and using mutations integrated with multi-omics data to better predict cancer phenotypes. We examine the use of these tools for either discovery or prediction, including prediction of tumor origin, treatment outcomes, prognosis, and cancer typing. We further discuss the main limitations preventing widespread clinical integration of computational tools for the diagnosis and treatment of cancer. We end by proposing solutions to address these challenges using recent advances in machine learning.
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Affiliation(s)
- Andrew Patterson
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- The Wistar Institute, Philadelphia, PA 19104, USA
| | | | - Bin Tian
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Noam Auslander
- The Wistar Institute, Philadelphia, PA 19104, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence:
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Velazquez C, Orhan E, Tabet I, Fenou L, Orsetti B, Adélaïde J, Guille A, Thézénas S, Crapez E, Colombo PE, Chaffanet M, Birnbaum D, Sardet C, Jacot W, Theillet C. BRCA1-methylated triple negative breast cancers previously exposed to neoadjuvant chemotherapy form RAD51 foci and respond poorly to olaparib. Front Oncol 2023; 13:1125021. [PMID: 37007122 PMCID: PMC10064050 DOI: 10.3389/fonc.2023.1125021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/03/2023] [Indexed: 03/19/2023] Open
Abstract
BackgroundAbout 15% of Triple-Negative-Breast-Cancer (TNBC) present silencing of the BRCA1 promoter methylation and are assumed to be Homologous Recombination Deficient (HRD). BRCA1-methylated (BRCA1-Me) TNBC could, thus, be eligible to treatment based on PARP-inhibitors or Platinum salts. However, their actual HRD status is discussed, as these tumors are suspected to develop resistance after chemotherapy exposure.MethodsWe interrogated the sensitivity to olaparib vs. carboplatin of 8 TNBC Patient-Derived Xenografts (PDX) models. Four PDX corresponded to BRCA1-Me, of which 3 were previously exposed to NeoAdjuvant-Chemotherapy (NACT). The remaining PDX models corresponded to two BRCA1-mutated (BRCA1-Mut) and two BRCA1-wild type PDX that were respectively included as positive and negative controls. The HRD status of our PDX models was assessed using both genomic signatures and the functional BRCA1 and RAD51 nuclear foci formation assay. To assess HR restoration associated with olaparib resistance, we studied pairs of BRCA1 deficient cell lines and their resistant subclones.ResultsThe 3 BRCA1-Me PDX that had been exposed to NACT responded poorly to olaparib, likewise BRCA1-WT PDX. Contrastingly, 3 treatment-naïve BRCA1-deficient PDX (1 BRCA1-Me and 2 BRCA1-mutated) responded to olaparib. Noticeably, the three olaparib-responsive PDX scored negative for BRCA1- and RAD51-foci, whereas all non-responsive PDX models, including the 3 NACT-exposed BRCA1-Me PDX, scored positive for RAD51-foci. This suggested HRD in olaparib responsive PDX, while non-responsive models were HR proficient. These results were consistent with observations in cell lines showing a significant increase of RAD51-foci in olaparib-resistant subclones compared with sensitive parental cells, suggesting HR restoration in these models.ConclusionOur results thus support the notion that the actual HRD status of BRCA1-Me TNBC, especially if previously exposed to chemotherapy, may be questioned and should be verified using the BRCA1- and RAD51-foci assay.
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Affiliation(s)
- Carolina Velazquez
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Esin Orhan
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Imene Tabet
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Lise Fenou
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Béatrice Orsetti
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - José Adélaïde
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Arnaud Guille
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Simon Thézénas
- Biometry Unit, Institut du Cancer de Montpellier, Montpellier, France
| | - Evelyne Crapez
- Unité de Recherche Translationnelle, Institut du Cancer de Montpellier, Montpellier, France
| | - Pierre-Emmanuel Colombo
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
- Oncological Surgery, Institut du Cancer de Montpellier, Montpellier, France
| | - Max Chaffanet
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Daniel Birnbaum
- Centre de Recherche en Cancérologie de Marseille, CRCM UMR1068, Aix-Marseille University, IPC, CNRS, Marseille, France
| | - Claude Sardet
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - William Jacot
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
- Clinical Oncology, Institut du Cancer de Montpellier, Montpellier, France
| | - Charles Theillet
- Institut de Recherche en Cancérologie de Montpellier, IRCM U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
- *Correspondence: Charles Theillet,
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Guillén-Mancina E, Jiménez-Alonso JJ, Calderón-Montaño JM, Jiménez-González V, Díaz-Ortega P, Burgos-Morón E, López-Lázaro M. Artificial Diets with Selective Restriction of Amino Acids and Very Low Levels of Lipids Induce Anticancer Activity in Mice with Metastatic Triple-Negative Breast Cancer. Cancers (Basel) 2023; 15:cancers15051540. [PMID: 36900331 PMCID: PMC10000978 DOI: 10.3390/cancers15051540] [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: 12/20/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Patients with metastatic triple negative breast cancer (TNBC) need new therapies to improve the low survival rates achieved with standard treatments. In this work, we show for the first time that the survival of mice with metastatic TNBC can be markedly increased by replacing their normal diet with artificial diets in which the levels of amino acids (AAs) and lipids are strongly manipulated. After observing selective anticancer activity in vitro, we prepared five artificial diets and evaluated their anticancer activity in a challenging model of metastatic TNBC. The model was established by injecting 4T1 murine TNBC cells into the tail vein of immunocompetent BALB/cAnNRj mice. First-line drugs doxorubicin and capecitabine were also tested in this model. AA manipulation led to modest improvements in mice survival when the levels of lipids were normal. Reducing lipid levels to 1% markedly improved the activity of several diets with different AA content. Some mice fed the artificial diets as monotherapy lived much longer than mice treated with doxorubicin and capecitabine. An artificial diet without 10 non-essential AAs, with reduced levels of essential AAs, and with 1% lipids improved the survival not only of mice with TNBC but also of mice with other types of metastatic cancers.
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van de Kooij B, Schreuder A, Pavani RS, Garzero V, Van Hoeck A, San Martin Alonso M, Koerse D, Wendel TJ, Callen E, Boom J, Mei H, Cuppen E, Nussenzweig A, van Attikum H, Noordermeer SM. EXO1-mediated DNA repair by single-strand annealing is essential for BRCA1-deficient cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529205. [PMID: 37720033 PMCID: PMC10503826 DOI: 10.1101/2023.02.24.529205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Deficiency for the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR) leads to chromosomal instability and diseases such as cancer. Yet, defective HR also results in vulnerabilities that can be exploited for targeted therapy. Here, we identify such a vulnerability and show that BRCA1-deficient cells are dependent on the long-range end-resection factor EXO1 for survival. EXO1 loss results in DNA replication-induced lesions decorated by poly(ADP-ribose)-chains. In cells that lack both BRCA1 and EXO1, this is accompanied by unresolved DSBs due to impaired single-strand annealing (SSA), a DSB repair process that requires the activity of both proteins. In contrast, BRCA2-deficient cells have increased SSA, also in the absence of EXO1, and hence are not dependent on EXO1 for survival. In agreement with our mechanistic data, BRCA1-mutated tumours have elevated EXO1 expression and contain more genomic signatures of SSA compared to BRCA1-proficient tumours. Collectively, our data indicate that EXO1 is a promising novel target for treatment of BRCA1-deficient tumours.
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37
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Systemic Therapy for Hereditary Breast Cancers. Hematol Oncol Clin North Am 2023; 37:203-224. [PMID: 36435611 DOI: 10.1016/j.hoc.2022.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Approximately 5% to 10% of all breast cancers are hereditary; many of which are caused by pathogenic variants in genes required for homologous recombination, including BRCA1 and BRCA2. Here we discuss systemic treatment for such breast cancers, including approved chemotherapeutic approaches and also targeted treatment approaches using poly-(ADP ribose) polymerase inhibitors. We also discuss experimental approaches to treating hereditary breast cancer, including new small molecule DNA repair inhibitors and also immunomodulatory agents. Finally, we discuss how drug resistance emerges in patients with hereditary breast cancer, how this might be delayed or prevented, and how biomarker-adapted treatment is molding the future management of hereditary breast cancer.
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38
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Vezain M, Thauvin-Robinet C, Vial Y, Coutant S, Drunat S, Urtizberea JA, Rolland A, Jacquin-Piques A, Fehrenbach S, Nicolas G, Lecoquierre F, Saugier-Veber P. Retrotransposon insertion as a novel mutational cause of spinal muscular atrophy. Hum Genet 2023; 142:125-138. [PMID: 36138164 DOI: 10.1007/s00439-022-02473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/15/2022] [Indexed: 01/18/2023]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder resulting from biallelic alterations of the SMN1 gene: deletion, gene conversion or, in rare cases, intragenic variants. The disease severity is mainly influenced by the copy number of SMN2, a nearly identical gene, which produces only low amounts of full-length (FL) mRNA. Here we describe the first example of retrotransposon insertion as a pathogenic SMN1 mutational event. The 50-year-old patient is clinically affected by SMA type III with a diagnostic odyssey spanning nearly 30 years. Despite a mild disease course, he carries a single SMN2 copy. Using Exome Sequencing and Sanger sequencing, we characterized a SINE-VNTR-Alu (SVA) type F retrotransposon inserted in SMN1 intron 7. Using RT-PCR and RNASeq experiments on lymphoblastoid cell lines, we documented the dramatic decrease of FL transcript production in the patient compared to subjects with the same SMN1 and SMN2 copy number, thus validating the pathogenicity of this SVA insertion. We described the mutant FL-SMN1-SVA transcript characterized by exon extension and showed that it is subject to degradation by nonsense-mediated mRNA decay. The stability of the SMN-SVA protein may explain the mild course of the disease. This observation exemplifies the role of retrotransposons in human genetic disorders.
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Affiliation(s)
- Myriam Vezain
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Christel Thauvin-Robinet
- INSERM UMR1231 GAD-Génétique des Anomalies du Développement, Bourgogne Franche-Comté University, F-21000 , Dijon, France.,Genetics Center, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Yoann Vial
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, 48 boulevard Sérurier, 75019 , Paris, France
| | - Sophie Coutant
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Séverine Drunat
- INSERM UMR 1141, PROTECT, Paris University, F-75019, Paris, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, F-75019, Paris, France
| | - Jon Andoni Urtizberea
- Myology Institute, AP-HP Pitié-Salpêtrière University Hospital, F-75013, Paris, France
| | - Anne Rolland
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Pediatrics Department, Valence Hospital, 179 boulevard du Maréchal Juin, 26000, Valence, France
| | - Agnès Jacquin-Piques
- Department of Neurology, Clinical Neurophysiology, Competence Center of Neuromuscular Diseases, Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Séverine Fehrenbach
- Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Gaël Nicolas
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - François Lecoquierre
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France. .,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France. .,Laboratoire de Génétique Moléculaire, UFR-Santé, 22 boulevard Gambetta, 76183, Rouen, France.
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39
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Oswald AJ, Gourley C. Development of Homologous Recombination Functional Assays for Targeting the DDR. Cancer Treat Res 2023; 186:43-70. [PMID: 37978130 DOI: 10.1007/978-3-031-30065-3_4] [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] [Indexed: 11/19/2023]
Abstract
Identification of tumours that have homologous recombination deficiency (HRD) has become of increasing interest following the licensing of PARP inhibitors. Potential methods to assess HRD status include; clinical selection for platinum sensitive disease, mutational/methylation status, genomic scars/signature and functional RAD51 assays. Homologous recombination (HR) is a dynamic process with the potential to evolve over a disease course, particularly in relation to previous treatment. This is one of the major drawbacks of genomic scars/signatures, as they only demonstrate historic HR status. Functional HR assays have the benefit of giving a real time HR status readout and therefore have the potential for clearer identification of patients who may benefit from PARP inhibitors at that specific time point. However, the development of RAD51 foci assays ready for clinical practice has been challenging. Pre-clinical considerations have included; controlling for variation in tumour proliferation, tissue type and whether DNA damage induction is required. Furthermore, the assays require correlation with clinical outcomes, an understanding of how they complement current testing modalities and validation of test performance in large cohorts. Despite these challenges, given the profound benefit from PARP inhibitors seen in those with an HRD phenotype to date, the ongoing development and validation of these functional HR assays remains of high clinical importance.
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Affiliation(s)
- Ailsa J Oswald
- Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK.
| | - Charlie Gourley
- Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK
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40
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Pandey A, L'Yi S, Wang Q, Borkin MA, Gehlenborg N. GenoREC: A Recommendation System for Interactive Genomics Data Visualization. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2023; 29:570-580. [PMID: 36191105 PMCID: PMC10067538 DOI: 10.1109/tvcg.2022.3209407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Interpretation of genomics data is critically reliant on the application of a wide range of visualization tools. A large number of visualization techniques for genomics data and different analysis tasks pose a significant challenge for analysts: which visualization technique is most likely to help them generate insights into their data? Since genomics analysts typically have limited training in data visualization, their choices are often based on trial and error or guided by technical details, such as data formats that a specific tool can load. This approach prevents them from making effective visualization choices for the many combinations of data types and analysis questions they encounter in their work. Visualization recommendation systems assist non-experts in creating data visualization by recommending appropriate visualizations based on the data and task characteristics. However, existing visualization recommendation systems are not designed to handle domain-specific problems. To address these challenges, we designed GenoREC, a novel visualization recommendation system for genomics. GenoREC enables genomics analysts to select effective visualizations based on a description of their data and analysis tasks. Here, we present the recommendation model that uses a knowledge-based method for choosing appropriate visualizations and a web application that enables analysts to input their requirements, explore recommended visualizations, and export them for their usage. Furthermore, we present the results of two user studies demonstrating that GenoREC recommends visualizations that are both accepted by domain experts and suited to address the given genomics analysis problem. All supplemental materials are available at https://osf.io/y73pt/.
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41
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Tsang JY, Tse GM. Update on triple-negative breast cancers - highlighting subtyping update and treatment implication. Histopathology 2023; 82:17-35. [PMID: 36468263 DOI: 10.1111/his.14784] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/14/2022] [Accepted: 08/19/2022] [Indexed: 12/12/2022]
Abstract
Triple-negative breast cancer (TNBC) remains a major challenge in breast cancer management. Continuing research in the past years aimed at understanding the biology of this tumour and developing more effective therapeutic options. It is now clear that TNBC is vastly heterogeneous with diverse histological, molecular, immunological profiles and clinical differences. Current evidence suggested the existence of at least four predominant subtypes based on expression profiling across studies. These subtypes exhibited specific genomic alterations and tumour microenvironment. Subtype-specific therapeutic strategies were identified. Recognising these subtypes allows not only an improved prognostication but also a better treatment decision. Herein, we provide an overview of the recent findings on TNBC heterogeneity at different levels and corresponding subtyping. The characteristic of subtypes and the implication of these subtypings in therapeutic approaches are also discussed.
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Affiliation(s)
- Julia Y Tsang
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Gary M Tse
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
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42
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Preclinical evaluation of Insulin-like growth factor receptor 1 (IGF1R) and Insulin Receptor (IR) as a therapeutic targets in triple negative breast cancer. PLoS One 2023; 18:e0282512. [PMID: 36920947 PMCID: PMC10016661 DOI: 10.1371/journal.pone.0282512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023] Open
Abstract
Triple Negative Breast Cancer (TNBC), a subtype of breast cancer, has fewer successful therapeutic therapies than other types of breast cancer. Insulin-like growth factor receptor 1 (IGF1R) and the Insulin receptor (IR) are associated with poor outcomes in TNBC. Targeting IGF1R has failed clinically. We aimed to test if inhibiting both IR/IGF1R was a rationale therapeutic approach to treat TNBC. We showed that despite IGF1R and IR being expressed in TNBC, their expression is not associated with a negative survival outcome. Furthermore, targeting both IR/IGF1R with inhibitors in multiple TNBC cell lines did not inhibit cell growth. Linsitinib, a small molecule inhibitor of both IGF1R and IR, did not block tumour formation and had no effect on tumour growth in vivo. Cumulatively these data suggest that while IGF1R and IR are expressed in TNBC, they are not good therapeutic targets. A potential reason for the limited anti-cancer impact when IR/IGF1R was targeted may be because multiple signalling pathways are altered in TNBC. Therefore, targeting individual signalling pathways may not be sufficient to inhibit cancer growth.
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43
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Optimized detection of homologous recombination deficiency improves the prediction of clinical outcomes in cancer. NPJ Precis Oncol 2022; 6:96. [PMID: 36581696 PMCID: PMC9800569 DOI: 10.1038/s41698-022-00339-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
Homologous recombination DNA-repair deficiency (HRD) is a common driver of genomic instability and confers a therapeutic vulnerability in cancer. The accurate detection of somatic allelic imbalances (AIs) has been limited by methods focused on BRCA1/2 mutations and using mixtures of cancer types. Using pan-cancer data, we revealed distinct patterns of AIs in high-grade serous ovarian cancer (HGSC). We used machine learning and statistics to generate improved criteria to identify HRD in HGSC (ovaHRDscar). ovaHRDscar significantly predicted clinical outcomes in three independent patient cohorts with higher precision than previous methods. Characterization of 98 spatiotemporally distinct metastatic samples revealed low intra-patient variation and indicated the primary tumor as the preferred site for clinical sampling in HGSC. Further, our approach improved the prediction of clinical outcomes in triple-negative breast cancer (tnbcHRDscar), validated in two independent patient cohorts. In conclusion, our tumor-specific, systematic approach has the potential to improve patient selection for HR-targeted therapies.
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44
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Funnell T, O’Flanagan CH, Williams MJ, McPherson A, McKinney S, Kabeer F, Lee H, Salehi S, Vázquez-García I, Shi H, Leventhal E, Masud T, Eirew P, Yap D, Zhang AW, Lim JLP, Wang B, Brimhall J, Biele J, Ting J, Au V, Van Vliet M, Liu YF, Beatty S, Lai D, Pham J, Grewal D, Abrams D, Havasov E, Leung S, Bojilova V, Moore RA, Rusk N, Uhlitz F, Ceglia N, Weiner AC, Zaikova E, Douglas JM, Zamarin D, Weigelt B, Kim SH, Da Cruz Paula A, Reis-Filho JS, Martin SD, Li Y, Xu H, de Algara TR, Lee SR, Llanos VC, Huntsman DG, McAlpine JN, Shah SP, Aparicio S, Cannell IG, Casbolt H, Jauset C, Kovačević T, Mulvey CM, Nugent F, Ribes MP, Pearson I, Qosaj F, Sawicka K, Wild SA, Williams E, Laks E, Smith A, Lai D, Roth A, Balasubramanian S, Lee M, Bodenmiller B, Burger M, Kuett L, Tietscher S, Windhager J, Boyden ES, Alon S, Cui Y, Emenari A, Goodwin DR, Karagiannis ED, Sinha A, Wassie AT, Caldas C, Bruna A, Callari M, Greenwood W, Lerda G, Eyal-Lubling Y, Rueda OM, Shea A, Harris O, Becker R, Grimaldo F, Harris S, Vogl SL, Joyce JA, Watson SS, Tavare S, Dinh KN, Fisher E, Kunes R, Walton NA, Al Sa’d M, Chornay N, Dariush A, González-Solares EA, González-Fernández C, Yoldaş AK, Miller N, Zhuang X, Fan J, Lee H, Sepúlveda LA, Xia C, Zheng P, Shah SP, Aparicio S. Single-cell genomic variation induced by mutational processes in cancer. Nature 2022; 612:106-115. [PMID: 36289342 PMCID: PMC9712114 DOI: 10.1038/s41586-022-05249-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/17/2022] [Indexed: 12/15/2022]
Abstract
How cell-to-cell copy number alterations that underpin genomic instability1 in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer2, remains understudied. Here, by applying scaled single-cell whole-genome sequencing3 to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient mammary epithelial cells (13,818 genomes), and to primary triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSC) cells (22,057 genomes), we identify three distinct 'foreground' mutational patterns that are defined by cell-to-cell structural variation. Cell- and clone-specific high-level amplifications, parallel haplotype-specific copy number alterations and copy number segment length variation (serrate structural variations) had measurable phenotypic and evolutionary consequences. In TNBC and HGSC, clone-specific high-level amplifications in known oncogenes were highly prevalent in tumours bearing fold-back inversions, relative to tumours with homologous recombination deficiency, and were associated with increased clone-to-clone phenotypic variation. Parallel haplotype-specific alterations were also commonly observed, leading to phylogenetic evolutionary diversity and clone-specific mono-allelic expression. Serrate variants were increased in tumours with fold-back inversions and were highly correlated with increased genomic diversity of cellular populations. Together, our findings show that cell-to-cell structural variation contributes to the origins of phenotypic and evolutionary diversity in TNBC and HGSC, and provide insight into the genomic and mutational states of individual cancer cells.
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Affiliation(s)
- Tyler Funnell
- grid.5386.8000000041936877XTri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY USA ,grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ciara H. O’Flanagan
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Marc J. Williams
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Andrew McPherson
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Steven McKinney
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Farhia Kabeer
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Hakwoo Lee
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Sohrab Salehi
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ignacio Vázquez-García
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Hongyu Shi
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Emily Leventhal
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Tehmina Masud
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Peter Eirew
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Damian Yap
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Allen W. Zhang
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Jamie L. P. Lim
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Beixi Wang
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Jazmine Brimhall
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Justina Biele
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Jerome Ting
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Vinci Au
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Michael Van Vliet
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Yi Fei Liu
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Sean Beatty
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Daniel Lai
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Jenifer Pham
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Diljot Grewal
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Douglas Abrams
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Eliyahu Havasov
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Samantha Leung
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Viktoria Bojilova
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Richard A. Moore
- grid.434706.20000 0004 0410 5424Michael Smith Genome Sciences Centre, Vancouver, British Columbia Canada
| | - Nicole Rusk
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Florian Uhlitz
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Nicholas Ceglia
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Adam C. Weiner
- grid.5386.8000000041936877XTri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY USA ,grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Elena Zaikova
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - J. Maxwell Douglas
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Dmitriy Zamarin
- grid.51462.340000 0001 2171 9952GYN Medical Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Britta Weigelt
- grid.51462.340000 0001 2171 9952Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Sarah H. Kim
- grid.51462.340000 0001 2171 9952Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Arnaud Da Cruz Paula
- grid.51462.340000 0001 2171 9952Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Jorge S. Reis-Filho
- grid.51462.340000 0001 2171 9952Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Spencer D. Martin
- grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Yangguang Li
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Hong Xu
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Teresa Ruiz de Algara
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - So Ra Lee
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Viviana Cerda Llanos
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - David G. Huntsman
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Jessica N. McAlpine
- grid.17091.3e0000 0001 2288 9830Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, British Columbia Canada
| | | | - Sohrab P. Shah
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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Abstract
DNA polymerase θ (Pol θ) is a DNA repair enzyme widely conserved in animals and plants. Pol θ uses short DNA sequence homologies to initiate repair of double-strand breaks by theta-mediated end joining. The DNA polymerase domain of Pol θ is at the C terminus and is connected to an N-terminal DNA helicase-like domain by a central linker. Pol θ is crucial for maintenance of damaged genomes during development, protects DNA against extensive deletions, and limits loss of heterozygosity. The cost of using Pol θ for genome protection is that a few nucleotides are usually deleted or added at the repair site. Inactivation of Pol θ often enhances the sensitivity of cells to DNA strand-breaking chemicals and radiation. Since some homologous recombination-defective cancers depend on Pol θ for growth, inhibitors of Pol θ may be useful in treating such tumors.
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Affiliation(s)
- Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, Texas, USA;
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA;
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46
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Ainsworth C. Three ways genomics is already helping NHS patients-and three ways it will soon. BMJ 2022; 379:o2643. [PMID: 36423916 DOI: 10.1136/bmj.o2643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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47
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Zeng Q, Saghafinia S, Chryplewicz A, Fournier N, Christe L, Xie YQ, Guillot J, Yucel S, Li P, Galván JA, Karamitopoulou E, Zlobec I, Ataca D, Gallean F, Zhang P, Rodriguez-Calero JA, Rubin M, Tichet M, Homicsko K, Hanahan D. Aberrant hyperexpression of the RNA binding protein FMRP in tumors mediates immune evasion. Science 2022; 378:eabl7207. [DOI: 10.1126/science.abl7207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Many human cancers manifest the capability to circumvent attack by the adaptive immune system. In this work, we identified a component of immune evasion that involves frequent up-regulation of fragile X mental retardation protein (FMRP) in solid tumors. FMRP represses immune attack, as revealed by cancer cells engineered to lack its expression. FMRP-deficient tumors were infiltrated by activated T cells that impaired tumor growth and enhanced survival in mice. Mechanistically, FMRP’s immunosuppression was multifactorial, involving repression of the chemoattractant C-C motif chemokine ligand 7 (CCL7) concomitant with up-regulation of three immunomodulators—interleukin-33 (IL-33), tumor-secreted protein S (PROS1), and extracellular vesicles. Gene signatures associate FMRP’s cancer network with poor prognosis and response to therapy in cancer patients. Collectively, FMRP is implicated as a regulator that orchestrates a multifaceted barrier to antitumor immune responses.
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Affiliation(s)
- Qiqun Zeng
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
- Opna Bio SA, Biopole, 1066 Epalinges, Lausanne, Switzerland
| | - Sadegh Saghafinia
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
- Opna Bio SA, Biopole, 1066 Epalinges, Lausanne, Switzerland
| | - Agnieszka Chryplewicz
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
- Agora Cancer Research Center, 1011 Lausanne, Switzerland
| | - Nadine Fournier
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Lucine Christe
- Institute of Pathology, University of Bern, 3008 Bern, Switzerland
| | - Yu-Qing Xie
- Institute of Bioengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Jeremy Guillot
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
- Agora Cancer Research Center, 1011 Lausanne, Switzerland
| | - Simge Yucel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
- Agora Cancer Research Center, 1011 Lausanne, Switzerland
| | - Pumin Li
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
- Agora Cancer Research Center, 1011 Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - José A. Galván
- Institute of Pathology, University of Bern, 3008 Bern, Switzerland
| | | | - Inti Zlobec
- Institute of Pathology, University of Bern, 3008 Bern, Switzerland
| | - Dalya Ataca
- Opna Bio SA, Biopole, 1066 Epalinges, Lausanne, Switzerland
| | | | - Peng Zhang
- Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing 100045, China
| | | | - Mark Rubin
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Mélanie Tichet
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
- Agora Cancer Research Center, 1011 Lausanne, Switzerland
- Lausanne Branch, Ludwig Institute for Cancer Research, 1011 Lausanne, Switzerland
| | - Krisztian Homicsko
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
- Agora Cancer Research Center, 1011 Lausanne, Switzerland
- Lausanne Branch, Ludwig Institute for Cancer Research, 1011 Lausanne, Switzerland
- Department of Oncology, University Hospital of Lausanne (CHUV), 1011 Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), 1011 Lausanne, Switzerland
| | - Douglas Hanahan
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland
- Agora Cancer Research Center, 1011 Lausanne, Switzerland
- Lausanne Branch, Ludwig Institute for Cancer Research, 1011 Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), 1011 Lausanne, Switzerland
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Anurag M, Jaehnig EJ, Krug K, Lei JT, Bergstrom EJ, Kim BJ, Vashist TD, Huynh AMT, Dou Y, Gou X, Huang C, Shi Z, Wen B, Korchina V, Gibbs RA, Muzny DM, Doddapaneni H, Dobrolecki LE, Rodriguez H, Robles AI, Hiltke T, Lewis MT, Nangia JR, Nemati Shafaee M, Li S, Hagemann IS, Hoog J, Lim B, Osborne CK, Mani D, Gillette MA, Zhang B, Echeverria GV, Miles G, Rimawi MF, Carr SA, Ademuyiwa FO, Satpathy S, Ellis MJ. Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer. Cancer Discov 2022; 12:2586-2605. [PMID: 36001024 PMCID: PMC9627136 DOI: 10.1158/2159-8290.cd-22-0200] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 01/12/2023]
Abstract
Microscaled proteogenomics was deployed to probe the molecular basis for differential response to neoadjuvant carboplatin and docetaxel combination chemotherapy for triple-negative breast cancer (TNBC). Proteomic analyses of pretreatment patient biopsies uniquely revealed metabolic pathways, including oxidative phosphorylation, adipogenesis, and fatty acid metabolism, that were associated with resistance. Both proteomics and transcriptomics revealed that sensitivity was marked by elevation of DNA repair, E2F targets, G2-M checkpoint, interferon-gamma signaling, and immune-checkpoint components. Proteogenomic analyses of somatic copy-number aberrations identified a resistance-associated 19q13.31-33 deletion where LIG1, POLD1, and XRCC1 are located. In orthogonal datasets, LIG1 (DNA ligase I) gene deletion and/or low mRNA expression levels were associated with lack of pathologic complete response, higher chromosomal instability index (CIN), and poor prognosis in TNBC, as well as carboplatin-selective resistance in TNBC preclinical models. Hemizygous loss of LIG1 was also associated with higher CIN and poor prognosis in other cancer types, demonstrating broader clinical implications. SIGNIFICANCE Proteogenomic analysis of triple-negative breast tumors revealed a complex landscape of chemotherapy response associations, including a 19q13.31-33 somatic deletion encoding genes serving lagging-strand DNA synthesis (LIG1, POLD1, and XRCC1), that correlate with lack of pathologic response, carboplatin-selective resistance, and, in pan-cancer studies, poor prognosis and CIN. This article is highlighted in the In This Issue feature, p. 2483.
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Affiliation(s)
- Meenakshi Anurag
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Eric J. Jaehnig
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Jonathan T. Lei
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Erik J. Bergstrom
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Beom-Jun Kim
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Tanmayi D. Vashist
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Anh Minh Tran Huynh
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Yongchao Dou
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Xuxu Gou
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Chen Huang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Zhiao Shi
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Bo Wen
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Viktoriya Korchina
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A. Gibbs
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Donna M. Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | | | - Lacey E. Dobrolecki
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, Maryland
| | - Ana I. Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, Maryland
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, Maryland
| | - Michael T. Lewis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Julie R. Nangia
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Maryam Nemati Shafaee
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Shunqiang Li
- Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, Missouri
| | - Ian S. Hagemann
- Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, Missouri
| | - Jeremy Hoog
- Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, Missouri
| | - Bora Lim
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - C. Kent Osborne
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - D.R. Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Michael A. Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Bing Zhang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Gloria V. Echeverria
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - George Miles
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Mothaffar F. Rimawi
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Steven A. Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Foluso O. Ademuyiwa
- Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, Missouri
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Matthew J. Ellis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
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Taurelli Salimbeni B, Corvaja C, Valenza C, Zagami P, Curigliano G. The triple negative breast cancer drugs graveyard: a review of failed clinical trials 2017-2022. Expert Opin Investig Drugs 2022; 31:1203-1226. [PMID: 36413823 DOI: 10.1080/13543784.2022.2151433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
INTRODUCTION Triple-negative breast cancer (TNBC) accounts for 15-20% of breast cancers (BC) and has the worst prognosis. It is characterized by the absence of both hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2). TNBC has more limited therapeutic options compared to other subtypes, meaning that there is still a long way to go to discover target treatments. AREAS COVERED Our review aims to summarize phase II/III clinical trials enrolling patients with TNBC that have been published between 2017 and 2022 but failed to reach their primary endpoint. We here try to emphasize the limitations and weaknesses noted in negative studies and to point out unexpected results which might be useful to enhance the therapeutic approach to TNBC disease. EXPERT OPINION A deeper understanding of the mechanisms behind TNBC heterogeneity allowed to enhance the knowledge of new prognostic and predictive biomarkers of response. However, it is also through several failed clinical trials that we were able to define new therapeutic approaches which improved TNBC patients' clinical outcomes. Nowadays, we still need to overcome several difficulties to fully recognize different intracellular and extracellular pathways that crosstalk in TNBC and the mechanisms of resistance to identify novel tailored-patients' therapies.
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Affiliation(s)
- Beatrice Taurelli Salimbeni
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, Irccs, Milan, Italy.,Department of Clinical and Molecular Medicine, Oncology Unit, "la Sapienza" University of Rome, Azienda Ospedaliera Sant'Andrea, Rome, Italy
| | - Carla Corvaja
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, Irccs, Milan, Italy.,Department of Medicine, University of Udine, Udine, Italy
| | - Carmine Valenza
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, Irccs, Milan, Italy.,Department of Oncology and Haematology, University of Milan, Milan, Italy
| | - Paola Zagami
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, Irccs, Milan, Italy.,Department of Oncology and Haematology, University of Milan, Milan, Italy.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, Irccs, Milan, Italy.,Department of Oncology and Haematology, University of Milan, Milan, Italy
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Lobanova O, Medvedieva N, Fishchuk L, Dubitska O, Cheshuk V, Vereshchako R, Zakhartseva L, Rossokha Z, Gorovenko N. Methylation of promoter region of BRCA1 gene versus pathogenic variants of gene: risk factor or clinical marker of breast cancer. Breast Cancer Res Treat 2022; 196:505-515. [DOI: 10.1007/s10549-022-06774-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022]
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