1
|
Shahrouzi P, Forouz F, Mathelier A, Kristensen VN, Duijf PHG. Copy number alterations: a catastrophic orchestration of the breast cancer genome. Trends Mol Med 2024:S1471-4914(24)00120-5. [PMID: 38772764 DOI: 10.1016/j.molmed.2024.04.017] [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: 02/26/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/23/2024]
Abstract
Breast cancer (BCa) is a prevalent malignancy that predominantly affects women around the world. Somatic copy number alterations (CNAs) are tumor-specific amplifications or deletions of DNA segments that often drive BCa development and therapy resistance. Hence, the complex patterns of CNAs complement BCa classification systems. In addition, understanding the precise contributions of CNAs is essential for tailoring personalized treatment approaches. This review highlights how tumor evolution drives the acquisition of CNAs, which in turn shape the genomic landscapes of BCas. It also discusses advanced methodologies for identifying recurrent CNAs, studying CNAs in BCa and their clinical impact.
Collapse
Affiliation(s)
- Parastoo Shahrouzi
- Department of Medical Genetics, Institute of Basic Medical Science, Faculty of Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Farzaneh Forouz
- School of Pharmacy, University of Queensland, Woolloongabba, Brisbane, Australia
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway; Center for Bioinformatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway; Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Vessela N Kristensen
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Division of Medicine, Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University Hospital, Lørenskog, Norway; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Pascal H G Duijf
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Centre for Cancer Biology, UniSA Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, Australia.
| |
Collapse
|
2
|
O’Connor TN, Schultz E, Wang J, O’Connor T, Levine E, Knudsen ES, Witkiewicz AK. Real-World Experience among Elderly Metastatic Breast Cancer Patients Treated with CDK4/6 Inhibitor-Based Therapy. Cancers (Basel) 2024; 16:1749. [PMID: 38730702 PMCID: PMC11083425 DOI: 10.3390/cancers16091749] [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: 03/21/2024] [Revised: 04/22/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
The largest portion of breast cancer patients diagnosed after 70 years of age present with hormone receptor-positive (HR+) breast cancer subtypes. Cyclin-dependent kinase (CDK) 4/6 inhibitor treatment, in conjunction with endocrine therapy, has become standard-of-care for metastatic HR+ breast cancer. In total, 320 patients with metastatic breast cancer receiving CDK4/6 inhibitor combined with fulvestrant or an aromatase inhibitor were enrolled in an ongoing observational study or were included in an IRB-approved retrospective study. All patients receiving CDK4/6 inhibitor-based therapy that were ≥70 years of age (n = 111) displayed prolonged progression-free survival (27.6 months) as compared to patients <70 years of age (n = 209, 21.1 months, HR = 1.38, p < 0.05). Specifically, patients receiving a CDK4/6 inhibitor with an aromatase inhibitor who were ≥70 years of age (n = 79) displayed exceptionally prolonged progression-free survival (46.0 months) as compared to patients receiving the same treatment who were <70 years of age (n = 161, 21.8 months, HR = 1.71, p < 0.01). However, patients ≥70 years of age also experienced more frequent adverse responses to CDK4/6 inhibitor-based treatment leading to dose reduction, hold, or discontinuation than the younger cohort (69% and 53%, respectively). Treatment strategies that may decrease toxicity without affecting efficacy (such as dose titration) are worth further exploration.
Collapse
Affiliation(s)
- Thomas N. O’Connor
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA (E.S.); (J.W.)
| | - Emily Schultz
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA (E.S.); (J.W.)
| | - Jianxin Wang
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA (E.S.); (J.W.)
| | - Tracey O’Connor
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (T.O.); (E.L.)
| | - Ellis Levine
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (T.O.); (E.L.)
| | - Erik S. Knudsen
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA (E.S.); (J.W.)
| | - Agnieszka K. Witkiewicz
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA (E.S.); (J.W.)
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| |
Collapse
|
3
|
Hata AN, Larijani M. Targeting APOBECs in cancer: It's about timing. Cancer Cell 2024; 42:497-501. [PMID: 38593778 DOI: 10.1016/j.ccell.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
APOBEC3 cytidine deaminases have emerged as key drivers of mutagenesis in a wide spectrum of tumor types and are now appreciated to play a causal role in driving tumor evolution and drug resistance. As efforts to develop APOBEC3 inhibitors progress, understanding the timing and consequences of APOBEC3-mediated mutagenesis in distinct clinical contexts will be critical for guiding the development of anti-cancer therapeutic strategies.
Collapse
Affiliation(s)
- Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
| |
Collapse
|
4
|
Lin CC, Chang TC, Wang Y, Guo L, Gao Y, Bikorimana E, Lemoff A, Fang YV, Zhang H, Zhang Y, Ye D, Soria-Bretones I, Servetto A, Lee KM, Luo X, Otto JJ, Akamatsu H, Napolitano F, Mani R, Cescon DW, Xu L, Xie Y, Mendell JT, Hanker AB, Arteaga CL. PRMT5 is an actionable therapeutic target in CDK4/6 inhibitor-resistant ER+/RB-deficient breast cancer. Nat Commun 2024; 15:2287. [PMID: 38480701 PMCID: PMC10937713 DOI: 10.1038/s41467-024-46495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
CDK4/6 inhibitors (CDK4/6i) have improved survival of patients with estrogen receptor-positive (ER+) breast cancer. However, patients treated with CDK4/6i eventually develop drug resistance and progress. RB1 loss-of-function alterations confer resistance to CDK4/6i, but the optimal therapy for these patients is unclear. Through a genome-wide CRISPR screen, we identify protein arginine methyltransferase 5 (PRMT5) as a molecular vulnerability in ER+/RB1-knockout breast cancer cells. Inhibition of PRMT5 blocks the G1-to-S transition in the cell cycle independent of RB, leading to growth arrest in RB1-knockout cells. Proteomics analysis uncovers fused in sarcoma (FUS) as a downstream effector of PRMT5. Inhibition of PRMT5 results in dissociation of FUS from RNA polymerase II, leading to hyperphosphorylation of serine 2 in RNA polymerase II, intron retention, and subsequent downregulation of proteins involved in DNA synthesis. Furthermore, treatment with the PRMT5 inhibitor pemrametostat and a selective ER degrader fulvestrant synergistically inhibits growth of ER+/RB-deficient cell-derived and patient-derived xenografts. These findings highlight dual ER and PRMT5 blockade as a potential therapeutic strategy to overcome resistance to CDK4/6i in ER+/RB-deficient breast cancer.
Collapse
Affiliation(s)
- Chang-Ching Lin
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tsung-Cheng Chang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yunguan Wang
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yunpeng Gao
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Emmanuel Bikorimana
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Andrew Lemoff
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yisheng V Fang
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yanfeng Zhang
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dan Ye
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | | | - Alberto Servetto
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Kyung-Min Lee
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Life Science, Hanyang University, Seoul, South Korea
| | - Xuemei Luo
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joseph J Otto
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Hiroaki Akamatsu
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Third Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Fabiana Napolitano
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Ram Mani
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - David W Cescon
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joshua T Mendell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ariella B Hanker
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Carlos L Arteaga
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
5
|
Tinsley E, Bredin P, Toomey S, Hennessy BT, Furney SJ. KMT2C and KMT2D aberrations in breast cancer. Trends Cancer 2024:S2405-8033(24)00029-3. [PMID: 38453563 DOI: 10.1016/j.trecan.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
KMT2C and KMT2D are histone lysine methyltransferases responsible for the monomethylation of histone 3 lysine 4 (H3K4) residues at gene enhancer sites. KMT2C/D are the most frequently mutated histone methyltransferases (HMTs) in breast cancer, occurring at frequencies of 10-20% collectively. Frequent damaging and truncating somatic mutations indicate a tumour-suppressive role of KMT2C/D in breast oncogenesis. Recent studies using cell lines and mouse models to replicate KMT2C/D loss show that these genes contribute to oestrogen receptor (ER)-driven transcription in ER+ breast cancers through the priming of gene enhancer regions. This review provides an overview of the functions of KMT2C/D and outlines the recent clinical and experimental evidence of the roles of KMT2C and KMT2D in breast cancer development.
Collapse
Affiliation(s)
- Emily Tinsley
- Genomic Oncology Research Group, Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Philip Bredin
- Medical Oncology Group, Department of Molecular Medicine, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Sinead Toomey
- Medical Oncology Group, Department of Molecular Medicine, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Bryan T Hennessy
- Medical Oncology Group, Department of Molecular Medicine, RCSI University of Medicine and Health Sciences, Dublin, Ireland; Department of Medical Oncology, Beaumont Hospital, Dublin, Ireland.
| | - Simon J Furney
- Genomic Oncology Research Group, Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
| |
Collapse
|
6
|
Dananberg A, Striepen J, Rozowsky JS, Petljak M. APOBEC Mutagenesis in Cancer Development and Susceptibility. Cancers (Basel) 2024; 16:374. [PMID: 38254863 PMCID: PMC10814203 DOI: 10.3390/cancers16020374] [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: 12/20/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
APOBEC cytosine deaminases are prominent mutators in cancer, mediating mutations in over 50% of cancers. APOBEC mutagenesis has been linked to tumor heterogeneity, persistent cell evolution, and therapy responses. While emerging evidence supports the impact of APOBEC mutagenesis on cancer progression, the understanding of its contribution to cancer susceptibility and malignant transformation is limited. We examine the existing evidence for the role of APOBEC mutagenesis in carcinogenesis on the basis of the reported associations between germline polymorphisms in genes encoding APOBEC enzymes and cancer risk, insights into APOBEC activities from sequencing efforts of both malignant and non-malignant human tissues, and in vivo studies. We discuss key knowledge gaps and highlight possible ways to gain a deeper understanding of the contribution of APOBEC mutagenesis to cancer development.
Collapse
Affiliation(s)
- Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Josefine Striepen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jacob S Rozowsky
- Medical Scientist Training Program, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Mia Petljak
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| |
Collapse
|
7
|
Knudsen ES, Witkiewicz AK, Rubin SM. Cancer takes many paths through G1/S. Trends Cell Biol 2023:S0962-8924(23)00211-8. [PMID: 37953123 PMCID: PMC11082069 DOI: 10.1016/j.tcb.2023.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 11/14/2023]
Abstract
In the commonly accepted paradigm for control of the mammalian cell cycle, sequential cyclin-dependent kinase (CDK) and cyclin activities drive the orderly transition from G1 to S phase. However, recent studies using different technological approaches and examining a broad range of cancer cell types are challenging this established paradigm. An alternative model is evolving in which cell cycles utilize different drivers and take different trajectories through the G1/S transition. We are discovering that cancer cells in particular can adapt their drivers and trajectories, which has important implications for antiproliferative therapies. These studies have helped to refine an understanding of how CDK inhibition impinges on proliferation and have significance for understanding fundamental features of cell biology and cancer.
Collapse
Affiliation(s)
- Erik S Knudsen
- Molecular and Cellular Biology, Roswell Park Cancer Center, Buffalo, NY, USA.
| | - Agnieszka K Witkiewicz
- Molecular and Cellular Biology, Roswell Park Cancer Center, Buffalo, NY, USA; Department of Pathology, Roswell Park Cancer Center, Buffalo, NY, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA.
| |
Collapse
|
8
|
Rusmini M, Lantieri F. Editorial: Elucidation of the causes of human disease by multi-omics integration. Front Genet 2023; 14:1271406. [PMID: 37621705 PMCID: PMC10446758 DOI: 10.3389/fgene.2023.1271406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023] Open
Affiliation(s)
- Marta Rusmini
- Laboratory of Genetics and Genomics of Rare Diseases, Giannina Gaslini Institute (IRCCS), Genova, Italy
| | - Francesca Lantieri
- Department of Health Sciences, School of Medical and Pharmaceutical Sciences, University of Genoa, Genoa, Italy
| |
Collapse
|