1
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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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2
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Caputo A, Vipparthi K, Bazeley P, Downs-Kelly E, McIntire P, Duckworth LA, Ni Y, Hu B, Keri RA, Karaayvaz M. Spatial Transcriptomics Suggests That Alterations Occur in the Preneoplastic Breast Microenvironment of BRCA1/2 Mutation Carriers. Mol Cancer Res 2024; 22:169-180. [PMID: 37878345 PMCID: PMC10872731 DOI: 10.1158/1541-7786.mcr-23-0489] [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: 06/19/2023] [Revised: 08/28/2023] [Accepted: 10/23/2023] [Indexed: 10/26/2023]
Abstract
Breast cancer is the most common cancer in females, affecting one in every eight women and accounting for the majority of cancer-related deaths in women worldwide. Germline mutations in the BRCA1 and BRCA2 genes are significant risk factors for specific subtypes of breast cancer. BRCA1 mutations are associated with basal-like breast cancers, whereas BRCA2 mutations are associated with luminal-like disease. Defects in mammary epithelial cell differentiation have been previously recognized in germline BRCA1/2 mutation carriers even before cancer incidence. However, the underlying mechanism is largely unknown. Here, we employ spatial transcriptomics to investigate defects in mammary epithelial cell differentiation accompanied by distinct microenvironmental alterations in preneoplastic breast tissues from BRCA1/2 mutation carriers and normal breast tissues from noncarrier controls. We uncovered spatially defined receptor-ligand interactions in these tissues for the investigation of autocrine and paracrine signaling. We discovered that β1-integrin-mediated autocrine signaling in BRCA2-deficient mammary epithelial cells may differ from BRCA1-deficient mammary epithelial cells. In addition, we found that the epithelial-to-stromal paracrine signaling in the breast tissues of BRCA1/2 mutation carriers is greater than in control tissues. More integrin-ligand pairs were differentially correlated in BRCA1/2-mutant breast tissues than noncarrier breast tissues with more integrin receptor-expressing stromal cells. IMPLICATIONS These results suggest alterations in the communication between mammary epithelial cells and the microenvironment in BRCA1 and BRCA2 mutation carriers, laying the foundation for designing innovative breast cancer chemo-prevention strategies for high-risk patients.
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Affiliation(s)
- Anthony Caputo
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kavya Vipparthi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Erinn Downs-Kelly
- Department of Pathology, Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Patrick McIntire
- Department of Pathology, Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lauren A. Duckworth
- Department of Pathology, Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ying Ni
- Center for Immunotherapy & Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bo Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ruth A. Keri
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Mihriban Karaayvaz
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
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3
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Lim PX, Zaman M, Feng W, Jasin M. BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair. Mol Cell 2024; 84:447-462.e10. [PMID: 38244544 PMCID: PMC11188060 DOI: 10.1016/j.molcel.2023.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 10/10/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
Tumor suppressor BRCA2 functions in homology-directed repair (HDR), the protection of stalled replication forks, and the suppression of replicative gaps, but their relative contributions to genome integrity and chemotherapy response are under scrutiny. Here, we report that mouse and human cells require a RAD51 filament stabilization motif in BRCA2 for fork protection and gap suppression but not HDR. In mice, the loss of fork protection/gap suppression does not compromise genome stability or shorten tumor latency. By contrast, HDR deficiency increases spontaneous and replication stress-induced chromosome aberrations and tumor predisposition. Unlike with HDR, fork protection/gap suppression defects are also observed in Brca2 heterozygous cells, likely due to reduced RAD51 stabilization at stalled forks/gaps. Gaps arise from PRIMPOL activity, which is associated with 5-hydroxymethyl-2'-deoxyuridine sensitivity due to the formation of SMUG1-generated abasic sites and is exacerbated by poly(ADP-ribose) polymerase (PARP) inhibition. However, HDR proficiency has the major role in mitigating sensitivity to chemotherapeutics, including PARP inhibitors.
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Affiliation(s)
- Pei Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mahdia Zaman
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Weiran Feng
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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4
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Sengodan SK, Hu X, Peddibhotla V, Balamurugan K, Mitrophanov AY, McKennett L, Kharat SS, Sanawar R, Singh VK, Albaugh ME, Burkett SS, Zhao Y, Tran B, Malys T, Sterneck E, De S, Sharan SK. Mismatch repair protein MLH1 suppresses replicative stress in BRCA2-deficient breast tumors. J Clin Invest 2024; 134:e173718. [PMID: 38271119 PMCID: PMC10977984 DOI: 10.1172/jci173718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/22/2024] [Indexed: 01/27/2024] Open
Abstract
Loss of BRCA2 (breast cancer 2) is lethal for normal cells. Yet it remains poorly understood how, in BRCA2 mutation carriers, cells undergoing loss of heterozygosity overcome the lethality and undergo tissue-specific neoplastic transformation. Here, we identified mismatch repair gene mutL homolog 1 (MLH1) as a genetic interactor of BRCA2 whose overexpression supports the viability of Brca2-null cells. Mechanistically, we showed that MLH1 interacts with Flap endonuclease 1 (FEN1) and competes to process the RNA flaps of Okazaki fragments. Together, they restrained the DNA2 nuclease activity on the reversed forks of lagging strands, leading to replication fork (RF) stability in BRCA2-deficient cells. In these cells, MLH1 also attenuated R-loops, allowing the progression of stable RFs, which suppressed genomic instability and supported cell viability. We demonstrated the significance of their genetic interaction by the lethality of Brca2-mutant mice and inhibition of Brca2-deficient tumor growth in mice by Mlh1 loss. Furthermore, we described estrogen as inducing MLH1 expression through estrogen receptor α (ERα), which might explain why the majority of BRCA2 mutation carriers develop ER-positive breast cancer. Taken together, our findings reveal a role of MLH1 in relieving replicative stress and show how it may contribute to the establishment of BRCA2-deficient breast tumors.
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Affiliation(s)
- Satheesh K. Sengodan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Xiaoju Hu
- Rutgers Cancer Institute of New Jersey, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Vaishnavi Peddibhotla
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Kuppusamy Balamurugan
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Alexander Y. Mitrophanov
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, NIH, Frederick, Maryland, USA
| | - Lois McKennett
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Suhas S. Kharat
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Rahul Sanawar
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Vinod Kumar Singh
- Rutgers Cancer Institute of New Jersey, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Mary E. Albaugh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Sandra S. Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Yongmei Zhao
- NCI Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Bao Tran
- NCI Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Tyler Malys
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, NIH, Frederick, Maryland, USA
| | - Esta Sterneck
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Shyam K. Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
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5
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Bhat-Nakshatri P, Khatpe AS, Chen D, Batic K, Mang H, Herodotou C, McGuire PC, Xuei X, Erdogan C, Gao H, Liu Y, Sandusky G, Storniolo AM, Nakshatri H. Signaling Pathway Alterations Driven by BRCA1 and BRCA2 Germline Mutations are Sufficient to Initiate Breast Tumorigenesis by the PIK3CAH1047R Oncogene. CANCER RESEARCH COMMUNICATIONS 2024; 4:38-54. [PMID: 38059556 PMCID: PMC10774565 DOI: 10.1158/2767-9764.crc-23-0330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023]
Abstract
Single-cell transcriptomics studies have begun to identify breast epithelial cell and stromal cell specific transcriptome differences between BRCA1/2 mutation carriers and non-carriers. We generated a single-cell transcriptome atlas of breast tissues from BRCA1, BRCA2 mutation carriers and compared this single-cell atlas of mutation carriers with our previously described single-cell breast atlas of healthy non-carriers. We observed that BRCA1 but not BRCA2 mutations altered the ratio between basal (basal-myoepithelial), luminal progenitor (luminal adaptive secretory precursor, LASP), and mature luminal (luminal hormone sensing) cells in breast tissues. A unique subcluster of cells within LASP cells is underrepresented in case of BRCA1 and BRCA2 mutation carriers compared with non-carriers. Both BRCA1 and BRCA2 mutations specifically altered transcriptomes in epithelial cells which are an integral part of NFκB, LARP1, and MYC signaling. Signaling pathway alterations in epithelial cells unique to BRCA1 mutations included STAT3, BRD4, SMARCA4, HIF2A/EPAS1, and Inhibin A signaling. BRCA2 mutations were associated with upregulation of IL6, PDK1, FOXO3, and TNFSF11 signaling. These signaling pathway alterations are sufficient to alter sensitivity of BRCA1/BRCA2-mutant breast epithelial cells to transformation as epithelial cells from BRCA1 mutation carriers overexpressing hTERT + PIK3CAH1047R generated adenocarcinomas, whereas similarly modified mutant BRCA2 cells generated basal carcinomas in NSG mice. Thus, our studies provide a high-resolution transcriptome atlas of breast epithelial cells of BRCA1 and BRCA2 mutation carriers and reveal their susceptibility to PIK3CA mutation-driven transformation. SIGNIFICANCE This study provides a single-cell atlas of breast tissues of BRCA1/2 mutation carriers and demonstrates that aberrant signaling due to BRCA1/2 mutations is sufficient to initiate breast cancer by mutant PIK3CA.
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Affiliation(s)
| | - Aditi S. Khatpe
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Duojiao Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Katie Batic
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Henry Mang
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Patrick C. McGuire
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Xiaoling Xuei
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Cihat Erdogan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - George Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Anna Maria Storniolo
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
- VA Roudebush Medical Center, Indianapolis, Indiana
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6
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Minello A, Carreira A. BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele. J Mol Biol 2024; 436:168277. [PMID: 37714298 DOI: 10.1016/j.jmb.2023.168277] [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: 07/04/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Since their discovery in the late 20th century, significant progress has been made in elucidating the functions of the tumor suppressor proteins BRCA1 and BRCA2. These proteins play vital roles in maintaining genome integrity, including DNA repair, replication fork protection, and chromosome maintenance. It is well-established that germline mutations in BRCA1 and BRCA2 increase the risk of breast and ovarian cancer; however, the precise mechanism underlying tumor formation in this context is not fully understood. Contrary to the long-standing belief that the loss of the second wild-type allele is necessary for tumor development, a growing body of evidence suggests that tumorigenesis can occur despite the presence of a single functional allele. This entails that heterozygosity in BRCA1/2 confers haploinsufficiency, where a single copy of the gene is not sufficient to fully suppress tumor formation. Here we provide an overview of the findings and the ongoing debate regarding BRCA haploinsufficiency. We further put out the challenges in studying this topic and discuss its potential relevance in the prevention and treatment of BRCA-related cancers.
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Affiliation(s)
- Anna Minello
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Aura Carreira
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France; Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid 28049, Spain.
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7
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Joyce R, Pascual R, Heitink L, Capaldo BD, Vaillant F, Christie M, Tsai M, Surgenor E, Anttila CJA, Rajasekhar P, Jackling FC, Trussart M, Milevskiy MJG, Song X, Li M, Teh CE, Gray DHD, Smyth GK, Chen Y, Lindeman GJ, Visvader JE. Identification of aberrant luminal progenitors and mTORC1 as a potential breast cancer prevention target in BRCA2 mutation carriers. Nat Cell Biol 2024; 26:138-152. [PMID: 38216737 DOI: 10.1038/s41556-023-01315-5] [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: 05/25/2023] [Accepted: 11/15/2023] [Indexed: 01/14/2024]
Abstract
Inheritance of a BRCA2 pathogenic variant conveys a substantial life-time risk of breast cancer. Identification of the cell(s)-of-origin of BRCA2-mutant breast cancer and targetable perturbations that contribute to transformation remains an unmet need for these individuals who frequently undergo prophylactic mastectomy. Using preneoplastic specimens from age-matched, premenopausal females, here we show broad dysregulation across the luminal compartment in BRCA2mut/+ tissue, including expansion of aberrant ERBB3lo luminal progenitor and mature cells, and the presence of atypical oestrogen receptor (ER)-positive lesions. Transcriptional profiling and functional assays revealed perturbed proteostasis and translation in ERBB3lo progenitors in BRCA2mut/+ breast tissue, independent of ageing. Similar molecular perturbations marked tumours bearing BRCA2-truncating mutations. ERBB3lo progenitors could generate both ER+ and ER- cells, potentially serving as cells-of-origin for ER-positive or triple-negative cancers. Short-term treatment with an mTORC1 inhibitor substantially curtailed tumorigenesis in a preclinical model of BRCA2-deficient breast cancer, thus uncovering a potential prevention strategy for BRCA2 mutation carriers.
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Affiliation(s)
- Rachel Joyce
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Rosa Pascual
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Luuk Heitink
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Bianca D Capaldo
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - François Vaillant
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Michael Christie
- Department of Anatomical Pathology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Minhsuang Tsai
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Elliot Surgenor
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Casey J A Anttila
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Pradeep Rajasekhar
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Felicity C Jackling
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Marie Trussart
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Michael J G Milevskiy
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Xiaoyu Song
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Mengbo Li
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Charis E Teh
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Daniel H D Gray
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Gordon K Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Yunshun Chen
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Geoffrey J Lindeman
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia.
- Parkville Familial Cancer Centre and Department of Medical Oncology, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.
| | - Jane E Visvader
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
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8
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Xu J, Liu S. Cell origin of BRCA2-mutant breast cancer. Nat Cell Biol 2024; 26:43-44. [PMID: 38216736 DOI: 10.1038/s41556-023-01322-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Affiliation(s)
- Jiahui Xu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Cancer Institutes, State Key Laboratory of Genetic Engineering, Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Suling Liu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Cancer Institutes, State Key Laboratory of Genetic Engineering, Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- The Shanghai Key Laboratory of Medical Epigenetics, Shanghai, China.
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China.
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9
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Lee MK, Robson ME. Contralateral breast cancer risk with radiation therapy in BRCA mutation carriers: what do we tell patients? J Natl Cancer Inst 2023; 115:1243-1245. [PMID: 37603726 PMCID: PMC10637031 DOI: 10.1093/jnci/djad129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/27/2023] [Indexed: 08/23/2023] Open
Affiliation(s)
- Minna K Lee
- Breast Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark E Robson
- Breast Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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10
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Lee M, Eng G, Handte-Reinecker A, Deshpande VS, Yilmaz OH, Gala MK. Germline Determinants of Esophageal Adenocarcinoma. Gastroenterology 2023; 165:1276-1279.e7. [PMID: 37507074 PMCID: PMC10592248 DOI: 10.1053/j.gastro.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Affiliation(s)
- Minyi Lee
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; MD-PhD Program, Boston University School of Medicine, Boston, Massachusetts
| | - George Eng
- Division of Gastroenterology and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Anna Handte-Reinecker
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Vikram S Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Omer H Yilmaz
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Manish K Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
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11
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Fanale D, Corsini LR, Pedone E, Randazzo U, Fiorino A, Di Piazza M, Brando C, Magrin L, Contino S, Piraino P, Bazan Russo TD, Cipolla C, Russo A, Bazan V. Potential agnostic role of BRCA alterations in patients with several solid tumors: One for all, all for one? Crit Rev Oncol Hematol 2023; 190:104086. [PMID: 37536445 DOI: 10.1016/j.critrevonc.2023.104086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/05/2023] Open
Abstract
Germline BRCA1/2 alterations in the Homologous Recombination (HR) pathway are considered as main susceptibility biomarkers to Hereditary Breast and Ovarian Cancers (HBOC). The modern molecular biology technologies allowed to characterize germline and somatic BRCA1/2 alterations in several malignancies, broadening the landscape of BRCA1/2-alterated tumors. In the last years, BRCA genetic testing, beyond the preventive value, also assumed a predictive and prognostic significance for patient management. The approval of molecules with agnostic indication is leading to a new clinical model, defined "mutational". Among these drugs, the Poly (ADP)-Ribose Polymerase inhibitors (PARPi) for BRCA1/2-deficient tumors were widely studied leading to increasing therapeutic implications. In this Review we provided an overview of the main clinical studies describing the association between BRCA-mutated tumors and PARPi response, focusing on the controversial evidence about the potential agnostic indication based on BRCA1/2 alterations in several solid tumors.
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Affiliation(s)
- Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Lidia Rita Corsini
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Erika Pedone
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Ugo Randazzo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Marianna Di Piazza
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Luigi Magrin
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Silvia Contino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Paola Piraino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Tancredi Didier Bazan Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Calogero Cipolla
- Division of General and Oncological Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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12
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Najafabadi MG, Gray GK, Kong LR, Gupta K, Perera D, Naylor H, Brugge JS, Venkitaraman AR, Shehata M. A transcriptional response to replication stress selectively expands a subset of Brca2-mutant mammary epithelial cells. Nat Commun 2023; 14:5206. [PMID: 37626143 PMCID: PMC10457340 DOI: 10.1038/s41467-023-40956-w] [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: 09/14/2022] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Germline BRCA2 mutation carriers frequently develop luminal-like breast cancers, but it remains unclear how BRCA2 mutations affect mammary epithelial subpopulations. Here, we report that monoallelic Brca2mut/WT mammary organoids subjected to replication stress activate a transcriptional response that selectively expands Brca2mut/WT luminal cells lacking hormone receptor expression (HR-). While CyTOF analyses reveal comparable epithelial compositions among wildtype and Brca2mut/WT mammary glands, Brca2mut/WT HR- luminal cells exhibit greater organoid formation and preferentially survive and expand under replication stress. ScRNA-seq analysis corroborates the expansion of HR- luminal cells which express elevated transcript levels of Tetraspanin-8 (Tspan8) and Thrsp, plus pathways implicated in replication stress survival including Type I interferon responses. Notably, CRISPR/Cas9-mediated deletion of Tspan8 or Thrsp prevents Brca2mut/WT HR- luminal cell expansion. Our findings indicate that Brca2mut/WT cells activate a transcriptional response after replication stress that preferentially favours outgrowth of HR- luminal cells through the expression of interferon-responsive and mammary alveolar genes.
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Affiliation(s)
| | - G Kenneth Gray
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA, USA
| | - Li Ren Kong
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- The Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pharmacology, NUS School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, National University of Singapore, Singapore, Singapore
| | - Komal Gupta
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- The Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, National University of Singapore, Singapore, Singapore
| | - David Perera
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Huw Naylor
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA, USA
| | - Ashok R Venkitaraman
- MRC Cancer Unit, University of Cambridge, Cambridge, UK.
- The Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- Institute of Molecular & Cellular Biology Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore.
| | - Mona Shehata
- Department of Oncology, University of Cambridge, Cambridge, UK.
- MRC Cancer Unit, University of Cambridge, Cambridge, UK.
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13
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Caputo A, Vipparthi K, Bazeley P, Downs-Kelly E, McIntire P, Ni Y, Hu B, Keri RA, Karaayvaz M. Alterations in the preneoplastic breast microenvironment of BRCA1/ 2 mutation carriers revealed by spatial transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542078. [PMID: 37292816 PMCID: PMC10245938 DOI: 10.1101/2023.05.24.542078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Breast cancer is the most common cancer in females, affecting one in every eight women and accounting for the majority of cancer-related deaths in women worldwide. Germline mutations in the BRCA1 and BRCA2 genes are significant risk factors for specific subtypes of breast cancer. BRCA1 mutations are associated with basal-like breast cancers, whereas BRCA2 mutations are associated with luminal-like disease. There are currently few chemoprevention strategies available for BRCA1/2 mutation carriers, and irreversible prophylactic mastectomy is the primary option. Designing chemo-preventive strategies requires an in-depth understanding of the physiological processes underlying tumor initiation. Here, we employ spatial transcriptomics to investigate defects in mammary epithelial cell differentiation accompanied by distinct microenvironmental alterations in preneoplastic breast tissues from BRCA1/2 mutation carriers and normal breast tissues from non-carrier controls. We uncovered spatially defined receptor-ligand interactions in these tissues for the investigation of autocrine and paracrine signaling. We discovered that β1-integrin-mediated autocrine signaling in BRCA2-deficient mammary epithelial cells differs from BRCA1-deficient mammary epithelial cells. In addition, we found that the epithelial-to-stromal paracrine signaling in the breast tissues of BRCA1/2 mutation carriers is greater than in control tissues. More integrin-ligand pairs were differentially correlated in BRCA1/2-mutant breast tissues than non-carrier breast tissues with more integrin receptor-expressing stromal cells. These results reveal alterations in the communication between mammary epithelial cells and the microenvironment in BRCA1 and BRCA2 mutation carriers, laying the foundation for designing innovative breast cancer chemo-prevention strategies for high-risk patients.
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Affiliation(s)
- Anthony Caputo
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kavya Vipparthi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Erinn Downs-Kelly
- Department of Pathology, Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Patrick McIntire
- Department of Pathology, Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ying Ni
- Center for Immunotherapy & Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bo Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ruth A. Keri
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Mihriban Karaayvaz
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
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14
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Lim PX, Zaman M, Jasin M. BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536470. [PMID: 37090587 PMCID: PMC10120702 DOI: 10.1101/2023.04.11.536470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Highlights Gap suppression requires BRCA2 C-terminal RAD51 binding in mouse and human cells Brca2 heterozygosity in mice results in fork protection and gap suppression defects Gap suppression mitigates sensitivity to hmdU, but only when HDR is unperturbedHDR deficiency is the primary driver of chemotherapeutic sensitivity. eTOC blurb Lim et al . report that gap suppression as well as fork protection require BRCA2 stabilization of RAD51 filaments in human and mouse cells but have minimal impact on genome integrity, oncogenesis, and drug resistance. BRCA2 suppression of PRIMPOL-mediated replication gaps confers resistance to the nucleotide hmdU, incorporation of which leads to cytotoxic abasic sites.This effect is diminished when HDR is abrogated. Summary Tumor suppressor BRCA2 functions in homology-directed repair (HDR), protection of stalled replication forks, and suppression of replicative gaps. The relative contributions of these pathways to genome integrity and chemotherapy response are under scrutiny. Here, we report that mouse and human cells require a RAD51 filament stabilization motif in BRCA2 for both fork protection and gap suppression, but not HDR. Loss of fork protection and gap suppression do not compromise genome instability or shorten tumor latency in mice or cause replication stress in human mammary cells. By contrast, HDR deficiency increases spontaneous and replication stress-induced chromosome aberrations and tumor predisposition. Unlike with HDR, fork protection and gap suppression defects are also observed in Brca2 heterozygous mouse cells, likely due to reduced RAD51 stabilization at stalled forks and gaps. Gaps arise from PRIMPOL activity, which is associated with sensitivity to 5-hydroxymethyl-2’-deoxyuridine due to the formation of abasic sites by SMUG1 glycosylase and is exacerbated by poly(ADP-ribose) polymerase inhibition. However, HDR deficiency ultimately modulates sensitivity to chemotherapeutics, including PARP inhibitors.
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15
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Nukaya T, Sumitomo M, Sugihara E, Takeda M, Nohara S, Tanishima S, Takenaka M, Zennami K, Takahara K, Shiroki R, Saya H. Estimating copy number to determine BRCA2 deletion status and to expect prognosis in localized prostate cancer. Cancer Med 2023; 12:8154-8165. [PMID: 36645189 PMCID: PMC10134377 DOI: 10.1002/cam4.5617] [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: 12/05/2022] [Revised: 12/16/2022] [Accepted: 12/29/2022] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The significance of BRCA alterations has been implicated in the development of metastatic castration-resistant prostate cancer (PC). The details of the frequency and significance of BRCA alterations in localized PC remain unknown. In this study, we investigated the frequency and clinical significance of BRCA alterations in localized PCs using an in-house next-generation sequencer (NGS) system. METHODS DNA was extracted from formalin-fixed paraffin-embedded tissues of surgical specimens from 126 patients with clinically localized PC who underwent radical prostatectomy. The mutation information of 164 cancer genes was analyzed using the PleSSision-Rapid test. Both copy number (CN) variation and loss of heterozygosity of various genes, such as BRCA1 and BRCA2, were estimated and reported. RESULTS Next-generation sequencer analyses revealed that the BRCA2 CN was decreased in 17 patients (13.5%) and the BRCA1 CN in six (4.8%) patients. NGS-based CN values were shown to be highly correlated with droplet digital PCR-based CN values. Tissue-specific BRCA expression investigated using the Human Protein Atlas showed that the decreased CN of BRCA2, but not BRCA1, is responsible for the decreased BRCA activity in PC. Ten of the 22 patients with decreased BRCA2 CN were presumed to have somatic heterozygous deletion. There were no observed associations between the heterozygous deletion of BRCA2 and various clinicopathological parameters. Furthermore, three of 10 patients developed biochemical recurrence within 3 months after surgery. Multivariate analyses revealed that the initial prostate-specific antigen levels and BRCA2 CN were independent factors for biochemical recurrence. CONCLUSION Our results suggest that a decrease in BRCA2 CN may be used as a biomarker for predicting recurrence after surgery in localized PC. Early screening for somatic alterations in BRCA2 using NGS may help to broadly predict the risk of PC progression.
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Affiliation(s)
- Takuhisa Nukaya
- Fujita Cancer Center, Fujita Health University, Toyoake, Japan.,Department of Urology School of Medicine, Fujita Health University, Toyoake, Japan
| | - Makoto Sumitomo
- Fujita Cancer Center, Fujita Health University, Toyoake, Japan.,Department of Urology School of Medicine, Fujita Health University, Toyoake, Japan.,Department of Medical Research for Intractable Disease, Fujita Health University, Toyoake, Japan
| | - Eiji Sugihara
- Fujita Cancer Center, Fujita Health University, Toyoake, Japan.,Research Promotion Headquarters, Open Facility Center, Fujita Health University, Toyoake, Japan
| | - Mayu Takeda
- Fujita Cancer Center, Fujita Health University, Toyoake, Japan.,Department of Medical Research for Intractable Disease, Fujita Health University, Toyoake, Japan
| | - Sachio Nohara
- Department of Bio Informatics, Communication Engineering Center, Electronic System Business Group, Mitsubishi Electric Software Corp, Tokyo, Japan
| | - Shigeki Tanishima
- Department of Bio Informatics, Communication Engineering Center, Electronic System Business Group, Mitsubishi Electric Software Corp, Tokyo, Japan
| | - Masashi Takenaka
- Department of Urology School of Medicine, Fujita Health University, Toyoake, Japan
| | - Kenji Zennami
- Department of Urology School of Medicine, Fujita Health University, Toyoake, Japan
| | - Kiyoshi Takahara
- Department of Urology School of Medicine, Fujita Health University, Toyoake, Japan
| | - Ryoichi Shiroki
- Department of Urology School of Medicine, Fujita Health University, Toyoake, Japan
| | - Hideyuki Saya
- Fujita Cancer Center, Fujita Health University, Toyoake, Japan
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16
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Wu B, Ellisen LW. Loss of p53 and genetic evolution in pancreatic cancer: Ordered chaos after the guardian is gone. Cancer Cell 2022; 40:1276-1278. [PMID: 36379206 DOI: 10.1016/j.ccell.2022.10.020] [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] [Indexed: 11/16/2022]
Abstract
A recent Nature study delineates a stepwise genomic evolution during pancreatic cancer development, employing an engineered mutant Kras and heterozygous Trp53 mouse model that identifies cells undergoing Trp53 loss of heterozygosity (LOH). Genetic progression post-Trp53 LOH involves clonal deletions, then genome doubling and subsequent accumulation of subclonal gains and amplifications.
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Affiliation(s)
- Bogang Wu
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Leif W Ellisen
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA.
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17
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Bader AS, Luessing J, Hawley BR, Skalka GL, Lu WT, Lowndes N, Bushell M. DDX17 is required for efficient DSB repair at DNA:RNA hybrid deficient loci. Nucleic Acids Res 2022; 50:10487-10502. [PMID: 36200807 PMCID: PMC9561282 DOI: 10.1093/nar/gkac843] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022] Open
Abstract
Proteins with RNA-binding activity are increasingly being implicated in DNA damage responses (DDR). Additionally, DNA:RNA-hybrids are rapidly generated around DNA double-strand breaks (DSBs), and are essential for effective repair. Here, using a meta-analysis of proteomic data, we identify novel DNA repair proteins and characterise a novel role for DDX17 in DNA repair. We found DDX17 to be required for both cell survival and DNA repair in response to numerous agents that induce DSBs. Analysis of DSB repair factor recruitment to damage sites suggested a role for DDX17 early in the DSB ubiquitin cascade. Genome-wide mapping of R-loops revealed that while DDX17 promotes the formation of DNA:RNA-hybrids around DSB sites, this role is specific to loci that have low levels of pre-existing hybrids. We propose that DDX17 facilitates DSB repair at loci that are inefficient at forming DNA:RNA-hybrids by catalysing the formation of DSB-induced hybrids, thereby allowing propagation of the damage response.
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Affiliation(s)
- Aldo S Bader
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Janna Luessing
- Centre for Chromosome Biology, Biomedical Sciences Biulding (BSB), School of Biological & Checmical Sciences, University of Galway, Galway, H91W2TY, Ireland
| | - Ben R Hawley
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | | | - Wei-Ting Lu
- The Francis Crick Institute, London NW1 1AT, UK
| | - Noel F Lowndes
- Centre for Chromosome Biology, Biomedical Sciences Biulding (BSB), School of Biological & Checmical Sciences, University of Galway, Galway, H91W2TY, Ireland
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
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18
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Gray GK, Li CMC, Rosenbluth JM, Selfors LM, Girnius N, Lin JR, Schackmann RCJ, Goh WL, Moore K, Shapiro HK, Mei S, D'Andrea K, Nathanson KL, Sorger PK, Santagata S, Regev A, Garber JE, Dillon DA, Brugge JS. A human breast atlas integrating single-cell proteomics and transcriptomics. Dev Cell 2022; 57:1400-1420.e7. [PMID: 35617956 DOI: 10.1016/j.devcel.2022.05.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/23/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022]
Abstract
The breast is a dynamic organ whose response to physiological and pathophysiological conditions alters its disease susceptibility, yet the specific effects of these clinical variables on cell state remain poorly annotated. We present a unified, high-resolution breast atlas by integrating single-cell RNA-seq, mass cytometry, and cyclic immunofluorescence, encompassing a myriad of states. We define cell subtypes within the alveolar, hormone-sensing, and basal epithelial lineages, delineating associations of several subtypes with cancer risk factors, including age, parity, and BRCA2 germline mutation. Of particular interest is a subset of alveolar cells termed basal-luminal (BL) cells, which exhibit poor transcriptional lineage fidelity, accumulate with age, and carry a gene signature associated with basal-like breast cancer. We further utilize a medium-depletion approach to identify molecular factors regulating cell-subtype proportion in organoids. Together, these data are a rich resource to elucidate diverse mammary cell states.
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Affiliation(s)
- G Kenneth Gray
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Carman Man-Chung Li
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Jennifer M Rosenbluth
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA 02115, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura M Selfors
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Nomeda Girnius
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA; The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Jia-Ren Lin
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Ron C J Schackmann
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Walter L Goh
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Kaitlin Moore
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Hana K Shapiro
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Shaolin Mei
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Kurt D'Andrea
- Department of Medicine, Division of Translation Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katherine L Nathanson
- Department of Medicine, Division of Translation Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter K Sorger
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Sandro Santagata
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital (BWH), Boston, MA 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA 02115, USA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital (BWH), Boston, MA 02115, USA
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA.
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19
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BRCA2 Haploinsufficiency in Telomere Maintenance. Genes (Basel) 2021; 13:genes13010083. [PMID: 35052422 PMCID: PMC8775325 DOI: 10.3390/genes13010083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/13/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
Our previous studies showed an association between monoallelic BRCA2 germline mutations and dysfunctional telomeres in epithelial mammary cell lines and increased risk of breast cancer diagnosis for women with BRCA2 999del5 germline mutation and short telomeres in blood cells. In the current study, we analyzed telomere dysfunction in lymphoid cell lines from five BRCA2 999del5 mutation carriers and three Fanconi Anemia D1 patients by fluorescence in situ hybridization (FISH). Metaphase chromosomes were harvested from ten lymphoid cell lines of different BRCA2 genotype origin and analyzed for telomere loss (TL), multitelomeric signals (MTS), interstitial telomere signals (ITS) and extra chromosomal telomere signals (ECTS). TL, ITS and ECTS were separately found to be significantly increased gradually between the BRCA2+/+, BRCA2+/- and BRCA2-/- lymphoid cell lines. MTS were found to be significantly increased between the BRCA2+/+ and the BRCA2+/- heterozygous (p < 0.0001) and the BRCA2-/- lymphoid cell lines (p < 0.0001) but not between the BRCA2 mutated genotypes. Dysfunctional telomeres were found to be significantly increased in a stepwise manner between the BRCA2 genotypes indicating an effect of BRCA2 haploinsufficiency on telomere maintenance.
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20
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Srinivasan P, Bandlamudi C, Jonsson P, Kemel Y, Chavan SS, Richards AL, Penson AV, Bielski CM, Fong C, Syed A, Jayakumaran G, Prasad M, Hwee J, Sumer SO, de Bruijn I, Li X, Gao J, Schultz N, Cambria R, Galle J, Mukherjee S, Vijai J, Cadoo KA, Carlo MI, Walsh MF, Mandelker D, Ceyhan-Birsoy O, Shia J, Zehir A, Ladanyi M, Hyman DM, Zhang L, Offit K, Robson ME, Solit DB, Stadler ZK, Berger MF, Taylor BS. The context-specific role of germline pathogenicity in tumorigenesis. Nat Genet 2021; 53:1577-1585. [PMID: 34741162 PMCID: PMC8957388 DOI: 10.1038/s41588-021-00949-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 09/09/2021] [Indexed: 11/08/2022]
Abstract
Human cancers arise from environmental, heritable and somatic factors, but how these mechanisms interact in tumorigenesis is poorly understood. Studying 17,152 prospectively sequenced patients with cancer, we identified pathogenic germline variants in cancer predisposition genes, and assessed their zygosity and co-occurring somatic alterations in the concomitant tumors. Two major routes to tumorigenesis were apparent. In carriers of pathogenic germline variants in high-penetrance genes (5.1% overall), lineage-dependent patterns of biallelic inactivation led to tumors exhibiting mechanism-specific somatic phenotypes and fewer additional somatic oncogenic drivers. Nevertheless, 27% of cancers in these patients, and most tumors in patients with pathogenic germline variants in lower-penetrance genes, lacked particular hallmarks of tumorigenesis associated with the germline allele. The dependence of tumors on pathogenic germline variants is variable and often dictated by both penetrance and lineage, a finding with implications for clinical management.
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Affiliation(s)
- Preethi Srinivasan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Chaitanya Bandlamudi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Philip Jonsson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta S Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher Fong
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Prasad
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason Hwee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Selcuk Onur Sumer
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ino de Bruijn
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiang Li
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - JianJiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roy Cambria
- Research and Technology Management, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesse Galle
- Research and Technology Management, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Semanti Mukherjee
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph Vijai
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karen A Cadoo
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria I Carlo
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Walsh
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Loxo Oncology, Stamford, CT, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kenneth Offit
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark E Robson
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K Stadler
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Loxo Oncology, Stamford, CT, USA
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21
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Zimmer K, Kocher F, Puccini A, Seeber A. Targeting BRCA and DNA Damage Repair Genes in GI Cancers: Pathophysiology and Clinical Perspectives. Front Oncol 2021; 11:662055. [PMID: 34707985 PMCID: PMC8542868 DOI: 10.3389/fonc.2021.662055] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 09/15/2021] [Indexed: 12/11/2022] Open
Abstract
Mutated germline alleles in the DNA damage repair (DDR) genes “breast cancer gene 1” (BRCA1) and BRCA2 have originally been identified as major susceptibility genes in breast and ovarian cancers. With the establishment and approval of more cost-effective gene sequencing methods, germline and somatic BRCA mutations have been detected in several cancers. Since the approval of poly (ADP)-ribose polymerase inhibitors (PARPi) for BRCA-mutated cancers, BRCA mutations gained rising therapeutic implications. The impact and significance of BRCA mutations have been evaluated extensively in the last decades. Moreover, other genes involved in the DDR pathway, such as ATM, ATR, or CHK1, have emerged as potential new treatment targets, as inhibitors of these proteins are currently under clinical investigation. This review gives a concise overview on the emerging clinical implications of mutations in the DDR genes in gastrointestinal cancers with a focus on BRCA mutations.
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Affiliation(s)
- Kai Zimmer
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Kocher
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - Alberto Puccini
- Medical Oncology Unit 1, Ospedale Policlinico San Martino Istituto di ricovero e cura a carattere scientifico (IRCCS), University of Genoa, Genoa, Italy
| | - Andreas Seeber
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
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22
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Ciani Y, Fedrizzi T, Prandi D, Lorenzin F, Locallo A, Gasperini P, Franceschini GM, Benelli M, Elemento O, Fava LL, Inga A, Demichelis F. Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer. Cell Syst 2021; 13:183-193.e7. [PMID: 34731645 PMCID: PMC8856743 DOI: 10.1016/j.cels.2021.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/23/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022]
Abstract
Pan-cancer studies sketched the genomic landscape of the tumor types spectrum. We delineated the purity- and ploidy-adjusted allele-specific profiles of 4,950 patients across 27 tumor types from the Cancer Genome Atlas (TCGA). Leveraging allele-specific data, we reclassified as loss of heterozygosity (LOH) 9% and 7% of apparent copy-number wild-type and gain calls, respectively, and overall observed more than 18 million allelic imbalance somatic events at the gene level. Reclassification of copy-number events revealed associations between driver mutations and LOH, pointing out the timings between the occurrence of point mutations and copy-number events. Integrating allele-specific genomics and matched transcriptomics, we observed that allele-specific gene status is relevant in the regulation of TP53 and its targets. Further, we disclosed the role of copy-neutral LOH in the impairment of tumor suppressor genes and in disease progression. Our results highlight the role of LOH in cancer and contribute to the understanding of tumor progression.
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Affiliation(s)
- Yari Ciani
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Tarcisio Fedrizzi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Davide Prandi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesca Lorenzin
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Alessio Locallo
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Paola Gasperini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Gian Marco Franceschini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Matteo Benelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA; The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Luca L Fava
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Alberto Inga
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA; The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
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23
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Kotoula V, Papadopoulou K, Tikas I, Fostira F, Vrettou E, Chrisafi S, Fountzilas E, Koliou GA, Apostolou P, Papazisis K, Zaramboukas T, Asimaki-Vlachopoulou A, Miliaras S, Ananiadis A, Poulios C, Natsiopoulos I, Tsiftsoglou A, Demiri E, Fountzilas G. Follow-up of tissue genomics in BRCA1/2 carriers who underwent prophylactic surgeries. Breast Cancer 2021; 28:1367-1382. [PMID: 34304347 DOI: 10.1007/s12282-021-01276-3] [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: 05/17/2021] [Accepted: 07/14/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE The genomic status of non-malignant tissues from carriers of pathogenic germline BRCA1/2 (gBRCA1/2) variants may reveal information towards individualized prophylaxis. We performed spatiotemporal tissue genotype comparisons in a real-life cohort of gBRCA1/2 carriers of Greek origin, who underwent multiple risk-reducing/prophylactic surgeries at various time points. METHODS Fifty-three women (median age 36 years) within cancer families were observed for up to 37.5 years; 43 were cancer carriers and 10 were healthy carriers. Histology review and genotyping were performed for 187 paraffin tissues (average: 3.5 per carrier) including 46 carcinomas (40 breast) and 141 non-malignant breast and gynecological samples. RESULTS High allelic imbalance (AI) and somatic pathogenic TP53 variants were present in cancer carriers only (p values < 0.0001). High AI was associated with gBRCA1/2 indels (p < 0.0001) and gBRCA2 alterations (p = 0.0109). Somatic (pathogenic) variants were infrequently shared between non-malignant tissues and matched carcinomas. Aberrations of gBRCA1 variant heterozygosity were noticed in tissues from cancer carriers only (13/43, 30.2%). These pertained to classic LOH (neoplastic lesions in 9/43 carriers, 20.9%) and under-representation of the germline variants (5 samples, 4 non-malignant, all in the breast). Both aberrations coexisted in matched samples in one case. Over time, germline variant heterozygosity prevailed in non-malignant tissues; intra-carrier genomic alterations were aggravated (21.1%), ameliorated (26.3%) or remained stable. CONCLUSION This real-life case study supports the need to address tissue genotypes from prophylactic surgeries in combination with polygenic scores towards personalized prophylaxis. To this end, knowing the traditionally classified pathogenic potential of a gBRCA1/2 variant may not be enough.
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Affiliation(s)
- Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece. .,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece.
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Ioannis Tikas
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Eleni Vrettou
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | - Sofia Chrisafi
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Elena Fountzilas
- Second Department of Medical Oncology, Euromedica General Clinic of Thessaloniki, Thessaloníki, Greece.,European University of Cyprus, Nicosia, Cyprus
| | | | - Paraskevi Apostolou
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Konstantinos Papazisis
- Department of Medical Oncology, Interbalkan European Medical Center, Thessaloníki, Greece
| | - Thomas Zaramboukas
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | | | - Spyros Miliaras
- First Department of Surgery, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloníki, Greece
| | | | - Christos Poulios
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | - Ioannis Natsiopoulos
- Department of Breast Surgery, Interbalkan European Medical Center, Thessaloníki, Greece
| | - Aris Tsiftsoglou
- Department of Surgery, St. Luke's Hospital, Thessaloníki, Greece
| | - Efterpi Demiri
- Department of Plastic Surgery, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloníki, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece.,Aristotle University of Thessaloniki, Thessaloníki, Greece.,German Oncology Center, Limassol, Cyprus
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24
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Setton J, Zinda M, Riaz N, Durocher D, Zimmermann M, Koehler M, Reis-Filho JS, Powell SN. Synthetic Lethality in Cancer Therapeutics: The Next Generation. Cancer Discov 2021; 11:1626-1635. [PMID: 33795234 PMCID: PMC8295179 DOI: 10.1158/2159-8290.cd-20-1503] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/01/2021] [Accepted: 02/23/2021] [Indexed: 12/25/2022]
Abstract
Synthetic lethality (SL) provides a conceptual framework for tackling targets that are not classically "druggable," including loss-of-function mutations in tumor suppressor genes required for carcinogenesis. Recent technological advances have led to an inflection point in our understanding of genetic interaction networks and ability to identify a wide array of novel SL drug targets. Here, we review concepts and lessons emerging from first-generation trials aimed at testing SL drugs, discuss how the nature of the targeted lesion can influence therapeutic outcomes, and highlight the need to develop clinical biomarkers distinct from those based on the paradigms developed to target activated oncogenes. SIGNIFICANCE: SL offers an approach for the targeting of loss of function of tumor suppressor and DNA repair genes, as well as of amplification and/or overexpression of genes that cannot be targeted directly. A next generation of tumor-specific alterations targetable through SL has emerged from high-throughput CRISPR technology, heralding not only new opportunities for drug development, but also important challenges in the development of optimal predictive biomarkers.
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Affiliation(s)
- Jeremy Setton
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - Simon N Powell
- Memorial Sloan Kettering Cancer Center, New York, New York.
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25
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Saeki K, Chang G, Kanaya N, Wu X, Wang J, Bernal L, Ha D, Neuhausen SL, Chen S. Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis. Commun Biol 2021; 4:660. [PMID: 34079055 PMCID: PMC8172904 DOI: 10.1038/s42003-021-02201-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/11/2021] [Indexed: 01/01/2023] Open
Abstract
The female mammary epithelium undergoes reorganization during development, pregnancy, and menopause, linking higher risk with breast cancer development. To characterize these periods of complex remodeling, here we report integrated 50 K mouse and 24 K human mammary epithelial cell atlases obtained by single-cell RNA sequencing, which covers most lifetime stages. Our results indicate a putative trajectory that originates from embryonic mammary stem cells which differentiates into three epithelial lineages (basal, luminal hormone-sensing, and luminal alveolar), presumably arising from unipotent progenitors in postnatal glands. The lineage-specific genes infer cells of origin of breast cancer using The Cancer Genome Atlas data and single-cell RNA sequencing of human breast cancer, as well as the association of gland reorganization to different breast cancer subtypes. This comprehensive mammary cell gene expression atlas ( https://mouse-mammary-epithelium-integrated.cells.ucsc.edu ) presents insights into the impact of the internal and external stimuli on the mammary epithelium at an advanced resolution.
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Affiliation(s)
- Kohei Saeki
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Gregory Chang
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Noriko Kanaya
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jinhui Wang
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Lauren Bernal
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Desiree Ha
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Shiuan Chen
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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26
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Kutasovic JR, McCart Reed AE, Sokolova A, Lakhani SR, Simpson PT. Morphologic and Genomic Heterogeneity in the Evolution and Progression of Breast Cancer. Cancers (Basel) 2020; 12:E848. [PMID: 32244556 PMCID: PMC7226487 DOI: 10.3390/cancers12040848] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
: Breast cancer is a remarkably complex and diverse disease. Subtyping based on morphology, genomics, biomarkers and/or clinical parameters seeks to stratify optimal approaches for management, but it is clear that every breast cancer is fundamentally unique. Intra-tumour heterogeneity adds further complexity and impacts a patient's response to neoadjuvant or adjuvant therapy. Here, we review some established and more recent evidence related to the complex nature of breast cancer evolution. We describe morphologic and genomic diversity as it arises spontaneously during the early stages of tumour evolution, and also in the context of treatment where the changing subclonal architecture of a tumour is driven by the inherent adaptability of tumour cells to evolve and resist the selective pressures of therapy.
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Affiliation(s)
- Jamie R. Kutasovic
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- QIMR Berghofer Medical Research Institute, Herston 4006, Australia
| | - Amy E. McCart Reed
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- QIMR Berghofer Medical Research Institute, Herston 4006, Australia
| | - Anna Sokolova
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, Brisbane 4029, Australia
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, Brisbane 4029, Australia
| | - Peter T. Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
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