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Hong R, Cao B, Chen D, Wu W, Luo T, Lv D, Zhang W, Wang S, Shao K. Multi-omics portrait of ductal carcinoma in situ in young women. Breast Cancer Res Treat 2024; 206:105-118. [PMID: 38704773 DOI: 10.1007/s10549-024-07254-5] [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: 10/19/2023] [Accepted: 01/08/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Young patients with breast ductal carcinoma in situ (DCIS) often face a poorer prognosis. The genomic intricacies in young-onset DCIS, however, remain underexplored. METHODS To address this gap, we undertook a comprehensive study encompassing exome, transcriptome, and vmethylome analyses. Our investigation included 20 DCIS samples (including 15 young-onset DCIS) and paired samples of normal breast tissue and blood. RESULTS Through RNA sequencing, we identified two distinct DCIS subgroups: "immune hot" and "immune cold". The "immune hot" subgroup was characterized by increased infiltration of lymphocytes and macrophages, elevated expression of PDCD1 and CTLA4, and reduced GATA3 expression. This group also exhibited active immunerelated transcriptional regulators. Mutational analysis revealed alterations in TP53 (38%), GATA3 (25%), and TTN (19%), with two cases showing mutations in APC, ERBB2, and SMARCC1. Common genomic alterations, irrespective of immune status, included gains in copy numbers at 1q, 8q, 17q, and 20q, and losses at 11q, 17p, and 22q. Signature analysis highlighted the predominance of signatures 2 and 1, with "immune cold" samples showing a significant presence of signature 8. Our methylome study on 13 DCIS samples identified 328 hyperdifferentially methylated regions (DMRs) and 521 hypo-DMRs, with "immune cold" cases generally showing lower levels of methylation. CONCLUSION In summary, the molecular characteristics of young-onset DCIS share similarities with invasive breast cancer (IBC), potentially indicating a poor prognosis. Understanding these characteristics, especially the immune microenvironment of DCIS, could be pivotal in identifying new therapeutic targets and preventive strategies for breast cancer.
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Affiliation(s)
- Ruoxi Hong
- State Key Laboratory of Oncology in South China, Department of Medical Oncology, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China
| | - Boyang Cao
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, BGI Research, Hangzhou, 310030, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Research, Shenzhen, 518083, China
| | - Dongshao Chen
- State Key Laboratory of Oncology in South China, Department of Medical Oncology, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China
| | - Wei Wu
- State Key Laboratory of Oncology in South China, Department of Medical Oncology, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China
| | - Tian Luo
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, BGI Research, Hangzhou, 310030, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Research, Shenzhen, 518083, China
| | - Dian Lv
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, BGI Research, Hangzhou, 310030, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Research, Shenzhen, 518083, China
| | - Weimin Zhang
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, 518083, China.
| | - Shusen Wang
- State Key Laboratory of Oncology in South China, Department of Medical Oncology, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China.
| | - Kang Shao
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, BGI Research, Hangzhou, 310030, China.
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Research, Shenzhen, 518083, China.
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Wang W, Zhang X, Li Y, Shen J, Li Y, Xing W, Bai J, Shi J, Zhou Y. Generation and Characterization of Induced Pluripotent Stem Cells Carrying An ASXL1 Mutation. Stem Cell Rev Rep 2024:10.1007/s12015-024-10737-z. [PMID: 38884929 DOI: 10.1007/s12015-024-10737-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2024] [Indexed: 06/18/2024]
Abstract
Additional sex combs-like 1 (ASXL1) is an epigenetic modulator frequently mutated in myeloid malignancies, generally associated with poor prognosis. Current models for ASXL1-mutated diseases are mainly based on the complete deletion of Asxl1 or overexpression of C-terminal truncations in mice models. However, these models cannot fully recapitulate the pathogenesis of myeloid malignancies. Patient-derived induced pluripotent stem cells (iPSCs) provide valuable disease models that allow us to understand disease-related molecular pathways and develop novel targeted therapies. Here, we generated iPSCs from a patient with myeloproliferative neoplasm carrying a heterozygous ASXL1 mutation. The iPSCs we generated exhibited the morphology of pluripotent cells, highly expressed pluripotent markers, excellent differentiation potency in vivo, and normal karyotype. Subsequently, iPSCs with or without ASXL1 mutation were induced to differentiate into hematopoietic stem/progenitor cells, and we found that ASXL1 mutation led to myeloid-biased output and impaired erythroid differentiation. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that terms related to embryonic development, myeloid differentiation, and immune- and neural-related processes were most enriched in the differentially expressed genes. Western blot demonstrated that the global level of H2AK119ub was significantly decreased when mutant ASXL1 was present. Chromatin Immunoprecipitation Sequencing showed that most genes associated with stem cell maintenance were upregulated, whereas occupancies of H2AK119ub around these genes were significantly decreased. Thus, the iPSC model carrying ASXL1 mutation could serve as a potential tool to study the pathogenesis of myeloid malignancies and to screen targeted therapy for patients.
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Affiliation(s)
- Wenjun Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology &Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaoru Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology &Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yunan Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology &Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jun Shen
- State Key Laboratory of Experimental Hematology, Institute of Hematology &Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Yihan Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology &Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Wen Xing
- State Key Laboratory of Experimental Hematology, Institute of Hematology &Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Jie Bai
- Department of Hematology, The Second Affiliated Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Jun Shi
- State Key Laboratory of Experimental Hematology, Institute of Hematology &Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Yuan Zhou
- State Key Laboratory of Experimental Hematology, Institute of Hematology &Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
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3
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Chen S, Tse K, Lu Y, Chen S, Tian Y, Tan KT, Li C. Comprehensive genomic profiling and therapeutic implications for Taiwanese patients with treatment-naïve breast cancer. Cancer Med 2024; 13:e7384. [PMID: 38895905 PMCID: PMC11187859 DOI: 10.1002/cam4.7384] [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: 11/06/2023] [Revised: 03/29/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Breast cancer is a heterogeneous disease categorized based on molecular characteristics, including hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) expression levels. The emergence of profiling technology has revealed multiple driver genomic alterations within each breast cancer subtype, serving as biomarkers to predict treatment outcomes. This study aimed to explore the genomic landscape of breast cancer in the Taiwanese population through comprehensive genomic profiling (CGP) and identify diagnostic and predictive biomarkers. METHODS Targeted next-generation sequencing-based CGP was performed on 116 archived Taiwanese breast cancer specimens, assessing genomic alterations (GAs), including single nucleotide variants, copy number variants, fusion genes, tumor mutation burden (TMB), and microsatellite instability (MSI) status. Predictive variants for FDA-approved therapies were evaluated within each subtype. RESULTS In the cohort, frequent mutations included PIK3CA (39.7%), TP53 (36.2%), KMT2C (9.5%), GATA3 (8.6%), and SF3B1 (6.9%). All subtypes had low TMB, with no MSI-H tumors. Among HR + HER2- patients, 42% (27/65) harbored activating PIK3CA mutations, implying potential sensitivity to PI3K inhibitors and resistance to endocrine therapies. HR + HER2- patients exhibited intrinsic hormonal resistance via FGFR1 gene gain/amplification (15%), exclusive of PI3K/AKT pathway alterations. Aberrations in the PI3K/AKT/mTOR and FGFR pathways were implicated in chemoresistance, with a 52.9% involvement in triple-negative breast cancer. In HER2+ tumors, 50% harbored GAs potentially conferring resistance to anti-HER2 therapies, including PIK3CA mutations (32%), MAP3K1 (2.9%), NF1 (2.9%), and copy number gain/amplification of FGFR1 (18%), FGFR3 (2.9%), EGFR (2.9%), and AKT2 (2.9%). CONCLUSION This study presents CGP findings for treatment-naïve Taiwanese breast cancer, emphasizing its value in routine breast cancer management, disease classification, and treatment selection.
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Affiliation(s)
- Shang‐Hung Chen
- National Institute of Cancer Research, National Health Research InstitutesTainanTaiwan
- Department of OncologyNational Cheng Kung University Hospital, College of Medicine, National Cheng Kung UniversityTainanTaiwan
| | | | | | | | - Yu‐Feng Tian
- Division of Colorectal Surgery, Department of SurgeryChi Mei Medical CenterTainanTaiwan
- Department of Health and NutritionChia‐Nan University of Pharmacy and ScienceTainanTaiwan
| | - Kien Thiam Tan
- ACT Genomics, Co. Ltd.TaipeiTaiwan
- Anbogen Therapeutics, Inc.TaipeiTaiwan
| | - Chien‐Feng Li
- National Institute of Cancer Research, National Health Research InstitutesTainanTaiwan
- Department of Medical ResearchChi Mei Medical CenterTainanTaiwan
- Institute of Precision MedicineNational Sun Yat‐Sen UniversityKaohsiungTaiwan
- Department of Clinical Pathology and Laboratory MedicineChi Mei Medical CenterTainanTaiwan
- Trans‐omic Laboratory for Precision MedicineChi Mei Medical CenterTainanTaiwan
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Rysenkova KD, Gaboriaud J, Fokin AI, Toubiana R, Bense A, Mirdass C, Jin M, Ho MCN, Glading E, Vacher S, Courtois L, Bièche I, Gautreau AM. PI 3-Kinase and the Histone Methyl-Transferase KMT2D Collaborate to Induce Arp2/3-Dependent Migration of Mammary Epithelial Cells. Cells 2024; 13:876. [PMID: 38786098 PMCID: PMC11119607 DOI: 10.3390/cells13100876] [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: 02/13/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024] Open
Abstract
Breast cancer develops upon sequential acquisition of driver mutations in mammary epithelial cells; however, how these mutations collaborate to transform normal cells remains unclear in most cases. We aimed to reconstitute this process in a particular case. To this end, we combined the activated form of the PI 3-kinase harboring the H1047R mutation with the inactivation of the histone lysine methyl-transferase KMT2D in the non-tumorigenic human mammary epithelial cell line MCF10A. We found that PI 3-kinase activation promoted cell-cycle progression, especially when growth signals were limiting, as well as cell migration, both in a collective monolayer and as single cells. Furthermore, we showed that KMT2D inactivation had relatively little influence on these processes, except for single-cell migration, which KMT2D inactivation promoted in synergy with PI 3-kinase activation. The combination of these two genetic alterations induced expression of the ARPC5L gene that encodes a subunit of the Arp2/3 complex. ARPC5L depletion fully abolished the enhanced migration persistence exhibited by double-mutant cells. Our reconstitution approach in MCF10A has thus revealed both the cell function and the single-cell migration, and the underlying Arp2/3-dependent mechanism, which are synergistically regulated when KMT2D inactivation is combined with the activation of the PI 3-kinase.
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Affiliation(s)
- Karina D. Rysenkova
- Laboratoire de Biologie Structurale de la Cellule, CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France; (K.D.R.); (J.G.); (A.I.F.); (R.T.); (A.B.); (C.M.); (M.J.); (M.C.N.H.); (E.G.)
| | - Julia Gaboriaud
- Laboratoire de Biologie Structurale de la Cellule, CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France; (K.D.R.); (J.G.); (A.I.F.); (R.T.); (A.B.); (C.M.); (M.J.); (M.C.N.H.); (E.G.)
| | - Artem I. Fokin
- Laboratoire de Biologie Structurale de la Cellule, CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France; (K.D.R.); (J.G.); (A.I.F.); (R.T.); (A.B.); (C.M.); (M.J.); (M.C.N.H.); (E.G.)
| | - Raphaëlle Toubiana
- Laboratoire de Biologie Structurale de la Cellule, CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France; (K.D.R.); (J.G.); (A.I.F.); (R.T.); (A.B.); (C.M.); (M.J.); (M.C.N.H.); (E.G.)
| | - Alexandre Bense
- Laboratoire de Biologie Structurale de la Cellule, CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France; (K.D.R.); (J.G.); (A.I.F.); (R.T.); (A.B.); (C.M.); (M.J.); (M.C.N.H.); (E.G.)
| | - Camil Mirdass
- Laboratoire de Biologie Structurale de la Cellule, CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France; (K.D.R.); (J.G.); (A.I.F.); (R.T.); (A.B.); (C.M.); (M.J.); (M.C.N.H.); (E.G.)
| | - Mélissa Jin
- Laboratoire de Biologie Structurale de la Cellule, CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France; (K.D.R.); (J.G.); (A.I.F.); (R.T.); (A.B.); (C.M.); (M.J.); (M.C.N.H.); (E.G.)
| | - Minh Chau N. Ho
- Laboratoire de Biologie Structurale de la Cellule, CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France; (K.D.R.); (J.G.); (A.I.F.); (R.T.); (A.B.); (C.M.); (M.J.); (M.C.N.H.); (E.G.)
| | - Elizabeth Glading
- Laboratoire de Biologie Structurale de la Cellule, CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France; (K.D.R.); (J.G.); (A.I.F.); (R.T.); (A.B.); (C.M.); (M.J.); (M.C.N.H.); (E.G.)
| | - Sophie Vacher
- Pharmacogenomics Unit, Department of Genetics, Institut Curie, Paris Descartes University, 75005 Paris, France; (S.V.); (L.C.); (I.B.)
| | - Laura Courtois
- Pharmacogenomics Unit, Department of Genetics, Institut Curie, Paris Descartes University, 75005 Paris, France; (S.V.); (L.C.); (I.B.)
| | - Ivan Bièche
- Pharmacogenomics Unit, Department of Genetics, Institut Curie, Paris Descartes University, 75005 Paris, France; (S.V.); (L.C.); (I.B.)
| | - Alexis M. Gautreau
- Laboratoire de Biologie Structurale de la Cellule, CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France; (K.D.R.); (J.G.); (A.I.F.); (R.T.); (A.B.); (C.M.); (M.J.); (M.C.N.H.); (E.G.)
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Arumugam M, Tovar EA, Essenburg CJ, Dischinger PS, Beddows I, Wolfrum E, Madaj ZB, Turner L, Feenstra K, Gallik KL, Cohen L, Nichols M, Sheridan RTC, Esquibel CR, Mouneimne G, Graveel CR, Steensma MR. Nf1 deficiency modulates the stromal environment in the pretumorigenic rat mammary gland. Front Cell Dev Biol 2024; 12:1375441. [PMID: 38799507 PMCID: PMC11116614 DOI: 10.3389/fcell.2024.1375441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024] Open
Abstract
Background Neurofibromin, coded by the NF1 tumor suppressor gene, is the main negative regulator of the RAS pathway and is frequently mutated in various cancers. Women with Neurofibromatosis Type I (NF1)-a tumor predisposition syndrome caused by a germline NF1 mutation-have an increased risk of developing aggressive breast cancer with poorer prognosis. The mechanism by which NF1 mutations lead to breast cancer tumorigenesis is not well understood. Therefore, the objective of this work was to identify stromal alterations before tumor formation that result in the increased risk and poorer outcome seen among NF1 patients with breast cancer. Approach To accurately model the germline monoallelic NF1 mutations in NF1 patients, we utilized an Nf1-deficient rat model with accelerated mammary development before presenting with highly penetrant breast cancer. Results We identified increased collagen content in Nf1-deficient rat mammary glands before tumor formation that correlated with age of tumor onset. Additionally, gene expression analysis revealed that Nf1-deficient mature adipocytes in the rat mammary gland have increased collagen expression and shifted to a fibroblast and preadipocyte expression profile. This alteration in lineage commitment was also observed with in vitro differentiation, however, flow cytometry analysis did not show a change in mammary adipose-derived mesenchymal stem cell abundance. Conclusion Collectively, this study uncovered the previously undescribed role of Nf1 in mammary collagen deposition and regulating adipocyte differentiation. In addition to unraveling the mechanism of tumor formation, further investigation of adipocytes and collagen modifications in preneoplastic mammary glands will create a foundation for developing early detection strategies of breast cancer among NF1 patients.
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Affiliation(s)
- Menusha Arumugam
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Elizabeth A. Tovar
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Curt J. Essenburg
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Patrick S. Dischinger
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Ian Beddows
- Biostatistics ad Bioinformatics Core, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Emily Wolfrum
- Biostatistics ad Bioinformatics Core, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Zach B. Madaj
- Biostatistics ad Bioinformatics Core, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Lisa Turner
- Pathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Kristin Feenstra
- Pathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Kristin L. Gallik
- Optical Imaging Core, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Lorna Cohen
- Optical Imaging Core, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Madison Nichols
- Flow Cytometry Core, Van Andel Research Institute, Grand Rapids, MI, United States
| | | | - Corinne R. Esquibel
- Optical Imaging Core, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Ghassan Mouneimne
- University of Arizona Cancer Center, Tucson, AZ, United States
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, United States
| | - Carrie R. Graveel
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, United States
| | - Matthew R. Steensma
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, United States
- Helen DeVos Children’s Hospital, Spectrum Health System, Grand Rapids, MI, United States
- Michigan State University College of Human Medicine, Grand Rapids, MI, United States
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6
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Williams MJ, Oliphant MU, Au V, Liu C, Baril C, O'Flanagan C, Lai D, Beatty S, Van Vliet M, Yiu JC, O'Connor L, Goh WL, Pollaci A, Weiner AC, Grewal D, McPherson A, Moore M, Prabhakar V, Agarwal S, Garber JE, Dillon D, Shah SP, Brugge J, Aparicio S. Luminal breast epithelial cells from wildtype and BRCA mutation carriers harbor copy number alterations commonly associated with breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.591587. [PMID: 38746396 PMCID: PMC11092623 DOI: 10.1101/2024.05.01.591587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Cancer-associated mutations have been documented in normal tissues, but the prevalence and nature of somatic copy number alterations and their role in tumor initiation and evolution is not well understood. Here, using single cell DNA sequencing, we describe the landscape of CNAs in >42,000 breast epithelial cells from women with normal or high risk of developing breast cancer. Accumulation of individual cells with one or two of a specific subset of CNAs (e.g. 1q gain and 16q, 22q, 7q, and 10q loss) is detectable in almost all breast tissues and, in those from BRCA1 or BRCA2 mutations carriers, occurs prior to loss of heterozygosity (LOH) of the wildtype alleles. These CNAs, which are among the most common associated with ductal carcinoma in situ (DCIS) and malignant breast tumors, are enriched almost exclusively in luminal cells not basal myoepithelial cells. Allele-specific analysis of the enriched CNAs reveals that each allele was independently altered, demonstrating convergent evolution of these CNAs in an individual breast. Tissues from BRCA1 or BRCA2 mutation carriers contain a small percentage of cells with extreme aneuploidy, featuring loss of TP53 , LOH of BRCA1 or BRCA2 , and multiple breast cancer-associated CNAs in addition to one or more of the common CNAs in 1q, 10q or 16q. Notably, cells with intermediate levels of CNAs are not detected, arguing against a stepwise gradual accumulation of CNAs. Overall, our findings demonstrate that chromosomal alterations in normal breast epithelium partially mirror those of established cancer genomes and are chromosome- and cell lineage-specific.
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7
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Goto K, Kiniwa Y, Kukita Y, Ohe S, Hiraki T, Hishima T, Takai T, Honma K. Recurrent GATA3 P409Afs*99 Frameshift Extension Mutations in Sweat-gland Carcinoma With Neuroendocrine Differentiation. Am J Surg Pathol 2024; 48:528-537. [PMID: 38353459 DOI: 10.1097/pas.0000000000002195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Sweat-gland carcinoma with neuroendocrine differentiation (SCAND) was recently proposed as a new cutaneous adnexal neoplasm with neuroendocrine differentiation; however, its genetics are not well known. Herein, we performed clinicopathologic and genetic analyses of 13 SCAND cases and 5 control cases of endocrine mucin-producing sweat gland carcinoma (EMPSGC). The SCAND group included 11 males and 2 females with a median age of 68 years (range, 50 to 80 y). All SCAND lesions occurred in the ventral trunk or genital area. Of the 13 SCAND cases, 9 and 5 exhibited lymph node and distant metastases, respectively. Three (23.1%) patients with SCAND died of the disease. In contrast, neither metastasis nor mortality was confirmed in the EMPSGC cases. Immunoexpression of the androgen receptor, c-Myb, and MUC2 was limited in SCAND, whereas EMPSGC frequently expressed these immunomarkers. GATA3 P409Afs*99 extension mutations were detected in 7 (53.8%) of the 13 SCAND cases, using Sanger or panel sequencing. All 7 SCAND cases with GATA3 mutations were located in the genital, inguinal, or lower abdominal regions, whereas 5 of the other 6 SCAND cases were located in the anterior upper to mid-trunk. No GATA3 mutations were detected in the EMPSGC cases (0/5, 0%). These clinicopathologic and genetic findings support SCAND as a tumor entity distinguishable from EMPSGC. In addition, the characteristic frameshift extension mutations in GATA3 contribute to the establishment of the tumor-type concept of SCAND.
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Affiliation(s)
- Keisuke Goto
- Department of Diagnostic Pathology and Cytology
- Department of Diagnostic Pathology, Osaka National Hospital, Osaka
- Department of Diagnostic Pathology, Shizuoka Cancer Center Hospital, Sunto
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Disease Center Komagome Hospital
- Department of Pathology, Itabashi Central Clinical Laboratory
- Department of Anatomic Pathology, Tokyo Medical University, Tokyo
- Department of Dermatology, Hyogo Cancer Center, Akashi
- Department of Diagnostic Pathology, Chutoen General Medical Center, Kakegawa
- Department of Dermato-Oncology/Dermatology, National Hospital Organization Kagoshima Medical Center, Kagoshima
| | - Yukiko Kiniwa
- Department of Dermatology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yoji Kukita
- Laboratory of Genomic Pathology, Research Center
| | - Shuichi Ohe
- Department of Dermatologic Oncology, Osaka International Cancer Institute
| | - Tsubasa Hiraki
- Department of Diagnostic Pathology, Shizuoka Cancer Center Hospital, Sunto
| | - Tsunekazu Hishima
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Disease Center Komagome Hospital
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8
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Toska E. Epigenetic mechanisms of cancer progression and therapy resistance in estrogen-receptor (ER+) breast cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189097. [PMID: 38518961 DOI: 10.1016/j.bbcan.2024.189097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Estrogen receptor-positive (ER+) breast cancer is the most frequent breast cancer subtype. Agents targeting the ER signaling pathway have been successful in reducing mortality from breast cancer for decades. However, mechanisms of resistance to these treatments arise, especially in the metastatic setting. Recently, it has been recognized that epigenetic dysregulation is a common feature that facilitates the acquisition of cancer hallmarks across cancer types, including ER+ breast cancer. Alterations in epigenetic regulators and transcription factors (TF) coupled with changes to the chromatin landscape have been found to orchestrate breast oncogenesis, metastasis, and the development of a resistant phenotype. Here, we review recent advances in our understanding of how the epigenome dictates breast cancer tumorigenesis and resistance to targeted therapies and discuss novel therapeutic interventions for overcoming resistance.
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Affiliation(s)
- Eneda Toska
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University, Baltimore, MD, USA; Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA.
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9
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Kuzmin E, Baker TM, Lesluyes T, Monlong J, Abe KT, Coelho PP, Schwartz M, Del Corpo J, Zou D, Morin G, Pacis A, Yang Y, Martinez C, Barber J, Kuasne H, Li R, Bourgey M, Fortier AM, Davison PG, Omeroglu A, Guiot MC, Morris Q, Kleinman CL, Huang S, Gingras AC, Ragoussis J, Bourque G, Van Loo P, Park M. Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring. Cell Rep 2024; 43:113988. [PMID: 38517886 PMCID: PMC11063629 DOI: 10.1016/j.celrep.2024.113988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/02/2024] [Accepted: 03/07/2024] [Indexed: 03/24/2024] Open
Abstract
The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. Analysis of The Cancer Genome Atlas data shows recurrent deletion of chr4p in basal breast cancer. Phylogenetic analysis of a panel of 23 primary tumor/patient-derived xenograft basal breast cancers reveals early evolution of chr4p deletion. Mechanistically we show that chr4p loss is associated with enhanced proliferation. Gene function studies identify an unknown gene, C4orf19, within chr4p, which suppresses proliferation when overexpressed-a member of the PDCD10-GCKIII kinase module we name PGCKA1. Genome-wide pooled overexpression screens using a barcoded library of human open reading frames identify chromosomal regions, including chr4p, that suppress proliferation when overexpressed in a context-dependent manner, implicating network interactions. Together, these results shed light on the early emergence of complex aneuploid karyotypes involving chr4p and adaptive landscapes shaping breast cancer genomes.
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Affiliation(s)
- Elena Kuzmin
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada.
| | | | | | - Jean Monlong
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Kento T Abe
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Paula P Coelho
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Michael Schwartz
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Joseph Del Corpo
- Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Dongmei Zou
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Genevieve Morin
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Alain Pacis
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Yang Yang
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Constanza Martinez
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
| | - Jarrett Barber
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA
| | - Hellen Kuasne
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Rui Li
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Mathieu Bourgey
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Anne-Marie Fortier
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Peter G Davison
- Department of Surgery, McGill University, Montreal, QC H3G 1A4, Canada; McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Atilla Omeroglu
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada
| | - Sidong Huang
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Peter Van Loo
- The Francis Crick Institute, NW1 1AT London, UK; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada.
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10
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Bertucci F, Lerebours F, Ceccarelli M, Guille A, Syed N, Finetti P, Adélaïde J, Van Laere S, Goncalves A, Viens P, Birnbaum D, Mamessier E, Callens C, Bedognetti D. Mutational landscape of inflammatory breast cancer. J Transl Med 2024; 22:374. [PMID: 38637846 PMCID: PMC11025259 DOI: 10.1186/s12967-024-05198-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Inflammatory breast cancer (IBC) is the most pro-metastatic form of BC. Better understanding of its enigmatic pathophysiology is crucial. We report here the largest whole-exome sequencing (WES) study of clinical IBC samples. METHODS We retrospectively applied WES to 54 untreated IBC primary tumor samples and matched normal DNA. The comparator samples were 102 stage-matched non-IBC samples from TCGA. We compared the somatic mutational profiles, spectra and signatures, copy number alterations (CNAs), HRD and heterogeneity scores, and frequencies of actionable genomic alterations (AGAs) between IBCs and non-IBCs. The comparisons were adjusted for the molecular subtypes. RESULTS The number of somatic mutations, TMB, and mutational spectra were not different between IBCs and non-IBCs, and no gene was differentially mutated or showed differential frequency of CNAs. Among the COSMIC signatures, only the age-related signature was more frequent in non-IBCs than in IBCs. We also identified in IBCs two new mutational signatures not associated with any environmental exposure, one of them having been previously related to HIF pathway activation. Overall, the HRD score was not different between both groups, but was higher in TN IBCs than TN non-IBCs. IBCs were less frequently classified as heterogeneous according to heterogeneity H-index than non-IBCs (21% vs 33%), and clonal mutations were more frequent and subclonal mutations less frequent in IBCs. More than 50% of patients with IBC harbored at least one high-level of evidence (LOE) AGA (OncoKB LOE 1-2, ESCAT LOE I-II), similarly to patients with non-IBC. CONCLUSIONS We provide the largest mutational landscape of IBC. Only a few subtle differences were identified with non-IBCs. The most clinically relevant one was the higher HRD score in TN IBCs than in TN non-IBCs, whereas the most intriguing one was the smaller intratumor heterogeneity of IBCs.
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Affiliation(s)
- François Bertucci
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France.
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France.
| | - Florence Lerebours
- Department of Medical Oncology, Institut Curie Saint-Cloud, Paris, France
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, USA
- Department of Public Health Sciences, University of Miami, Miami, USA
| | - Arnaud Guille
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Najeeb Syed
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, Wilrijk, Belgium
| | - Pascal Finetti
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - José Adélaïde
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Steven Van Laere
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, Wilrijk, Belgium
| | - Anthony Goncalves
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Patrice Viens
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Daniel Birnbaum
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Emilie Mamessier
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Céline Callens
- Department of Medical Oncology, Institut Curie Saint-Cloud, Paris, France
| | - Davide Bedognetti
- Tumor Biology and Immunology Laboratory, Research Branch, Sidra Medicine, Doha, Qatar
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11
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Nakauma-González JA, Rijnders M, Noordsij MTW, Martens JWM, van der Veldt AAM, Lolkema MPJ, Boormans JL, van de Werken HJG. Whole-genome mapping of APOBEC mutagenesis in metastatic urothelial carcinoma identifies driver hotspot mutations and a novel mutational signature. CELL GENOMICS 2024; 4:100528. [PMID: 38552621 PMCID: PMC11019362 DOI: 10.1016/j.xgen.2024.100528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 04/13/2024]
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) enzymes mutate specific DNA sequences and hairpin-loop structures, challenging the distinction between passenger and driver hotspot mutations. Here, we characterized 115 whole genomes of metastatic urothelial carcinoma (mUC) to identify APOBEC mutagenic hotspot drivers. APOBEC-associated mutations were detected in 92% of mUCs and were equally distributed across the genome, while APOBEC hotspot mutations (ApoHMs) were enriched in open chromatin. Hairpin loops were frequent targets of didymi (twins in Greek), two hotspot mutations characterized by the APOBEC SBS2 signature, in conjunction with an uncharacterized mutational context (Ap[C>T]). Next, we developed a statistical framework that identified ApoHMs as drivers in coding and non-coding genomic regions of mUCs. Our results and statistical framework were validated in independent cohorts of 23 non-metastatic UCs and 3,744 samples of 17 metastatic cancers, identifying cancer-type-specific drivers. Our study highlights the role of APOBEC in cancer development and may contribute to developing novel targeted therapy options for APOBEC-driven cancers.
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Affiliation(s)
- J Alberto Nakauma-González
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands.
| | - Maud Rijnders
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Minouk T W Noordsij
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Astrid A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Martijn P J Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Immunology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands.
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12
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Al Assaad M, Michaud O, Semaan A, Sigouros M, Tranquille M, Phan A, Levine MF, Gundem G, Medina-Martínez JS, Papaemmanuil E, Manohar J, Wilkes D, Sboner A, Hoda SAF, Elemento O, Mosquera JM. Whole-Genome Sequencing Analysis of Male Breast Cancer Unveils Novel Structural Events and Potential Therapeutic Targets. Mod Pathol 2024; 37:100452. [PMID: 38369186 DOI: 10.1016/j.modpat.2024.100452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 02/20/2024]
Abstract
The molecular characterization of male breast cancer (MaBC) has received limited attention in research, mostly because of its low incidence rate, accounting for only 0.5% to 1% of all reported cases of breast cancer each year. Managing MaBC presents significant challenges, with most treatment protocols being adapted from those developed for female breast cancer. Utilizing whole-genome sequencing (WGS) and state-of-the-art analyses, the genomic features of 10 MaBC cases (n = 10) were delineated and correlated with clinical and histopathologic characteristics. Using fluorescence in situ hybridization, an additional cohort of 18 patients was interrogated to supplement WGS findings. The genomic landscape of MaBC uncovered significant genetic alterations that could influence diagnosis and treatment. We found common somatic mutations in key driver genes, such as FAT1, GATA3, SMARCA4, and ARID2. Our study also mapped out structural variants that impact cancer-associated genes, such as ARID1A, ESR1, GATA3, NTRK1, and NF1. Using a WGS-based classifier, homologous recombination deficiency (HRD) was identified in 2 cases, both presenting with deleterious variants in BRCA2. Noteworthy was the observation of FGFR1 amplification in 21% of cases. Altogether, we identified at least 1 potential therapeutic target in 8 of the 10 cases, including high tumor mutational burden, FGFR1 amplification, and HRD. Our study is the first WGS characterization of MaBC, which uncovered potentially relevant variants, including structural events in cancer genes, HRD signatures, and germline pathogenic mutations. Our results demonstrate unique genetic markers and potential treatment targets in MaBC, thereby underlining the necessity of tailoring treatment strategies for this understudied patient population. These WGS-based findings add to the growing knowledge of MaBC genomics and highlight the need to expand research on this type of cancer.
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Affiliation(s)
- Majd Al Assaad
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Olivier Michaud
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Département de Pathologie, Université Laval, Quebec City, Quebec, Canada
| | - Alissa Semaan
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Michael Sigouros
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Marvel Tranquille
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Andy Phan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | | | | | | | | | - Jyothi Manohar
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - David Wilkes
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Syed A F Hoda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York; New York Genome Center, New York, New York.
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13
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Ma Y, Li J, Zhao X, Ji C, Hu W, Ma Y, Qu F, Sun Y, Zhang X. Multi-omics cluster defines the subtypes of CRC with distinct prognosis and tumor microenvironment. Eur J Med Res 2024; 29:207. [PMID: 38549156 PMCID: PMC10976740 DOI: 10.1186/s40001-024-01805-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a complex malignancy characterized by diverse molecular profiles, clinical outcomes, and limited precision in prognostic markers. Addressing these challenges, this study utilized multi-omics data to define consensus molecular subtypes in CRC and elucidate their association with clinical outcomes and underlying biological processes. METHODS Consensus molecular subtypes were obtained by applying ten integrated multi-omics clustering algorithms to analyze TCGA-CRC multi-omics data, including mRNA, lncRNA, miRNA, DNA methylation CpG sites, and somatic mutation data. The association of subtypes with prognoses, enrichment functions, immune status, and genomic alterations were further analyzed. Next, we conducted univariate Cox and Lasso regression analyses to investigate the potential prognostic application of biomarkers associated with multi-omics subtypes derived from weighted gene co-expression network analysis (WGCNA). The function of one of the biomarkers MID2 was validated in CRC cell lines. RESULTS Two CRC subtypes linked to distinct clinical outcomes were identified in TCGA-CRC cohort and validated with three external datasets. The CS1 subtype exhibited a poor prognosis and was characterized by higher tumor-related Hallmark pathway activity and lower metabolism pathway activity. In addition, the CS1 was predicted to have less immunotherapy responder and exhibited more genomic alteration compared to CS2. Then a prognostic model comprising five genes was established, with patients in the high-risk group showing substantial concordance with the CS1 subtype, and those in the low-risk group with the CS2 subtype. The gene MID2, included in the prognostic model, was found to be correlated with epithelial-mesenchymal transition (EMT) pathway and distinct DNA methylation patterns. Knockdown of MID2 in CRC cells resulted in reduced colony formation, migration, and invasion capacities. CONCLUSION The integrative multi-omics subtypes proposed potential biomarkers for CRC and provided valuable knowledge for precision oncology.
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Affiliation(s)
- Yuan Ma
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Jing Li
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Xu Zhao
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Chao Ji
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Weibin Hu
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - YanFang Ma
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Fengyi Qu
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Yuchen Sun
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Xiaozhi Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China.
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14
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Li K, Wang B, Hu H. Research progress of SWI/SNF complex in breast cancer. Epigenetics Chromatin 2024; 17:4. [PMID: 38365747 PMCID: PMC10873968 DOI: 10.1186/s13072-024-00531-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
In the past decade, numerous epigenetic mechanisms have been discovered to be associated with cancer. The mammalian SWI/SNF complex is an ATP-dependent chromatin remodeling complex whose mutations are associated with various malignancies including breast cancer. As the SWI/SNF complex has become one of the most commonly mutated complexes in cancer, targeting epigenetic mutations acquired during breast cancer progress is a potential means of improving clinical efficacy in treatment strategies. This article reviews the composition of the SWI/SNF complex, its main roles and research progress in breast cancer, and links these findings to the latest discoveries in cancer epigenomics to discuss the potential mechanisms and therapeutic potential of SWI/SNF in breast cancer.
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Affiliation(s)
- Kexuan Li
- School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Baocai Wang
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
| | - Haolin Hu
- Breast Center, Zhongda Hospital, School of Medicine, Southeast University, 87 Dingjiaqiao Road, Nanjing, 210009, Jiangsu, China.
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15
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Rijnders M, Nakauma-González JA, Robbrecht DGJ, Gil-Jimenez A, Balcioglu HE, Oostvogels AAM, Aarts MJB, Boormans JL, Hamberg P, van der Heijden MS, Szabados BE, van Leenders GJLH, Mehra N, Voortman J, Westgeest HM, de Wit R, van der Veldt AAM, Debets R, Lolkema MP. Gene-expression-based T-Cell-to-Stroma Enrichment (TSE) score predicts response to immune checkpoint inhibitors in urothelial cancer. Nat Commun 2024; 15:1349. [PMID: 38355607 PMCID: PMC10866910 DOI: 10.1038/s41467-024-45714-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Immune checkpoint inhibitors (ICI) improve overall survival in patients with metastatic urothelial cancer (mUC), but therapeutic success at the individual patient level varies significantly. Here we identify predictive markers of response, based on whole-genome DNA (n = 70) and RNA-sequencing (n = 41) of fresh metastatic biopsy samples, collected prior to treatment with pembrolizumab. We find that PD-L1 combined positivity score does not, whereas tumor mutational burden and APOBEC mutagenesis modestly predict response. In contrast, T cell-to-stroma enrichment (TSE) score, computed from gene expression signature data to capture the relative abundance of T cells and stromal cells, predicts response to immunotherapy with high accuracy. Patients with a positive and negative TSE score show progression free survival rates at 6 months of 67 and 0%, respectively. The abundance of T cells and stromal cells, as reflected by the TSE score is confirmed by immunofluorescence in tumor tissue, and its good performance in two independent ICI-treated cohorts of patients with mUC (IMvigor210) and muscle-invasive UC (ABACUS) validate the predictive power of the TSE score. In conclusion, the TSE score represents a clinically applicable metric that potentially supports the prospective selection of patients with mUC for ICI treatment.
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Affiliation(s)
- Maud Rijnders
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - J Alberto Nakauma-González
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Debbie G J Robbrecht
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alberto Gil-Jimenez
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Hayri E Balcioglu
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Astrid A M Oostvogels
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Maureen J B Aarts
- Department of Medical Oncology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Paul Hamberg
- Department of Medical Oncology, Franciscus Gasthuis & Vlietland Hospital, Rotterdam/Schiedam, The Netherlands
| | - Michiel S van der Heijden
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Geert J L H van Leenders
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jens Voortman
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Hans M Westgeest
- Department of Internal Medicine, Amphia Hospital Breda, Breda, The Netherlands
| | - Ronald de Wit
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Astrid A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Reno Debets
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Amgen Inc., Breda, The Netherlands
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16
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Wang F, Wang W, Wang M, Chen D. Genetic landscape of breast cancer subtypes following radiation therapy: insights from comprehensive profiling. Front Oncol 2024; 14:1291509. [PMID: 38380359 PMCID: PMC10878167 DOI: 10.3389/fonc.2024.1291509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/17/2024] [Indexed: 02/22/2024] Open
Abstract
Background In breast cancer, in the era of precision cancer therapy, different patterns of genetic mutations dictate different treatments options. However, it is not clear whether the genetic profiling of breast cancer patients undergoing breast-conserving surgery is related to the adverse reactions caused by radiotherapy. Methods We collected formalin-fixed paraffin-embedded (FFPE) tumor tissue samples from 54 breast cancer patients treated with radiation after breast-conserving surgery and identified comprehensive molecular information in hundreds of cancer-associated genes by FoundationOne CDx (F1CDx), a next-generation sequencing (NGS)-based assay. Results Among our cohort of 54 breast cancer patients, we found high-frequency mutations in cancer-related genes such as TP53 (56%), RAD21 (39%), PIK3CA (35%), ERBB2 (24%), and MYC (22%). Strikingly, we detected that the WNT pathway appears to be a signaling pathway with specific high-frequency mutations in the HER2 subtype. We also compared the mutation frequencies of the two groups of patients with and without cutaneous radiation injury (CRI) after radiotherapy and found that the mutation frequencies of two genes, FGFR1 and KLHL6, were significantly higher in patients with CRI : No subgroup than in those with CRI : Yes. Conclusion Different breast cancer subtypes have their own type-specific mutation patterns. FGFR1 and KLHL6 mutations are protective factors for radiation-induced skin toxicity in breast cancer patients.
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Affiliation(s)
- Fang Wang
- School of Clinical Medicine, Shandong Second Medical University, Weifang, China
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Jinan, China
| | - Weiyan Wang
- Department of Hematology, Taian Central Hospital, Taian, China
| | - Minglei Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Jinan, China
- Department of Oncology, Shandong Cancer Hospital and Institute Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Dawei Chen
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Jinan, China
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17
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House RRJ, Tovar EA, Redlon LN, Essenburg CJ, Dischinger PS, Ellis AE, Beddows I, Sheldon RD, Lien EC, Graveel CR, Steensma MR. NF1 deficiency drives metabolic reprogramming in ER+ breast cancer. Mol Metab 2024; 80:101876. [PMID: 38216123 PMCID: PMC10844973 DOI: 10.1016/j.molmet.2024.101876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/28/2023] [Accepted: 01/08/2024] [Indexed: 01/14/2024] Open
Abstract
OBJECTIVE NF1 is a tumor suppressor gene and its protein product, neurofibromin, is a negative regulator of the RAS pathway. NF1 is one of the top driver mutations in sporadic breast cancer such that 27 % of breast cancers exhibit damaging NF1 alterations. NF1 loss-of-function is a frequent event in the genomic evolution of estrogen receptor (ER)+ breast cancer metastasis and endocrine resistance. Individuals with Neurofibromatosis type 1 (NF) - a disorder caused by germline NF1 mutations - have an increased risk of dying from breast cancer [1-4]. NF-related breast cancers are associated with decreased overall survival compared to sporadic breast cancer. Despite numerous studies interrogating the role of RAS mutations in tumor metabolism, no study has comprehensively profiled the NF1-deficient breast cancer metabolome to define patterns of energetic and metabolic reprogramming. The goals of this investigation were (1) to define the role of NF1 deficiency in estrogen receptor-positive (ER+) breast cancer metabolic reprogramming and (2) to identify potential targeted pathway and metabolic inhibitor combination therapies for NF1-deficient ER + breast cancer. METHODS We employed two ER+ NF1-deficient breast cancer models: (1) an NF1-deficient MCF7 breast cancer cell line to model sporadic breast cancer, and (2) three distinct, Nf1-deficient rat models to model NF-related breast cancer [1]. IncuCyte proliferation analysis was used to measure the effect of NF1 deficiency on cell proliferation and drug response. Protein quantity was assessed by Western Blot analysis. We then used RNAseq to investigate the transcriptional effect of NF1 deficiency on global and metabolism-related transcription. We measured cellular energetics using Agilent Seahorse XF-96 Glyco Stress Test and Mito Stress Test assays. We performed stable isotope labeling and measured [U-13C]-glucose and [U-13C]-glutamine metabolite incorporation and measured total metabolite pools using mass spectrometry. Lastly, we used a Bliss synergy model to investigate NF1-driven changes in targeted and metabolic inhibitor synergy. RESULTS Our results revealed that NF1 deficiency enhanced cell proliferation, altered neurofibromin expression, and increased RAS and PI3K/AKT pathway signaling while constraining oxidative ATP production and restricting energetic flexibility. Neurofibromin deficiency also increased glutamine influx into TCA intermediates and dramatically increased lipid pools, especially triglycerides (TG). Lastly, NF1 deficiency alters the synergy between metabolic inhibitors and traditional targeted inhibitors. This includes increased synergy with inhibitors targeting glycolysis, glutamine metabolism, mitochondrial fatty acid transport, and TG synthesis. CONCLUSIONS NF1 deficiency drives metabolic reprogramming in ER+ breast cancer. This reprogramming is characterized by oxidative ATP constraints, glutamine TCA influx, and lipid pool expansion, and these metabolic changes introduce novel metabolic-to-targeted inhibitor synergies.
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Affiliation(s)
- Rachel Rae J House
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Elizabeth A Tovar
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Luke N Redlon
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Curt J Essenburg
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | | | - Abigail E Ellis
- Mass Spectrometry Core, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Ian Beddows
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Ryan D Sheldon
- Mass Spectrometry Core, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Evan C Lien
- Department of Metabolism and Nutritional Programming, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Carrie R Graveel
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Matthew R Steensma
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA; Helen DeVos Children's Hospital, Spectrum Health System, Grand Rapids, MI, USA; Michigan State University College of Human Medicine, Grand Rapids, MI, USA.
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18
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Wang SSY. Advancing biomarker development for diagnostics and therapeutics using solid tumour cancer stem cell models. TUMORI JOURNAL 2024; 110:10-24. [PMID: 36964664 DOI: 10.1177/03008916231158411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The cancer stem cell model hopes to explain solid tumour carcinogenesis, tumour progression and treatment failure in cancers. However, the cancer stem cell model has led to minimal clinical translation to cancer stem cell biomarkers and targeted therapies in solid tumours. Many reasons underlie the challenges, one being the imperfect understanding of the cancer stem cell model. This review hopes to spur further research into clinically translatable cancer stem cell biomarkers through first defining cancer stem cells and their associated models. With a better understanding of these models there would be a development of more accurate biomarkers. Making the clinical translation of biomarkers into diagnostic tools and therapeutic agents more feasible.
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Xu J, Gan C, Yu S, Yao S, Li W, Cheng H. Analysis of Immune Resistance Mechanisms in TNBC: Dual Effects Inside and Outside the Tumor. Clin Breast Cancer 2024; 24:e91-e102. [PMID: 38016911 DOI: 10.1016/j.clbc.2023.10.011] [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: 09/06/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023]
Abstract
Triple-negative breast cancer (TNBC) is a unique subtype of breast cancer characterized by the lack of expression of the estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. TNBC exhibits a high degree of aggressiveness, metastatic potential, and a poor prognosis. Despite the limited success of conventional treatments, immune checkpoint inhibitors (ICIs) have emerged as promising therapeutics for TNBC. Therefore, understanding the mechanisms underlying innate and acquired resistance to ICIs in TNBC is essential. Numerous studies suggest that intrinsic and extrinsic factors significantly contribute to the development of ICI resistance in TNBC. Intrinsic resistance may result from alterations in tumor-intrinsic signaling pathways, such as dysregulation of interferon (IFN) signaling or other signaling pathways. In contrast, extratumoral mechanisms may develop due to alterations in the tumor microenvironment, changes in T cell-related factors or adaptations within the immune system itself. In this paper, we endeavor to elucidate the underlying mechanisms of immune resistance by systematically examining immune mechanisms, the present state of immunotherapy, and the processes of immune resistance. Nonetheless, enhancing our understanding of the mechanisms underlying intratumoral and extratumoral resistance to ICIs in TNBC is crucial for optimizing patient outcomes in this challenging disease. Persistent efforts to identify novel targets for combination therapies, biomarkers that can predict the response to immunotherapy, and resistance mechanisms will be instrumental in achieving this objective.
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Affiliation(s)
- Jian Xu
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; The Second Clinical College of Anhui Medical University, Hefei, Anhui, China
| | - Chen Gan
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; The Second Clinical College of Anhui Medical University, Hefei, Anhui, China
| | - Sheng Yu
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; The Second Clinical College of Anhui Medical University, Hefei, Anhui, China
| | - Senbang Yao
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; The Second Clinical College of Anhui Medical University, Hefei, Anhui, China
| | - Wen Li
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; The Second Clinical College of Anhui Medical University, Hefei, Anhui, China
| | - Huaidong Cheng
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; Shenzhen Clinical Medical School of Southern Medical University, Shenzhen, Guangdong, China; Department of Oncology, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China.
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20
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Wang Y, Sun J, Sun B, Zhang C, Tian Z, Wang L, Li J. The genetic and immune features of salivary gland secretory carcinoma with high-grade transformation. Oral Dis 2024. [PMID: 38263601 DOI: 10.1111/odi.14876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/26/2023] [Accepted: 01/11/2024] [Indexed: 01/25/2024]
Abstract
OBJECTIVES To compare the clinicopathological, molecular, and immune features of conventional and high-grade transformation (HGT) secretory carcinoma (SC) in salivary glands. MATERIALS AND METHODS The clinicopathological data of 88 cases including 74 conventional SCs and 14 SCs with HGT were reviewed. Targeted next-generation sequencing was performed in 11 SCs with HGT and 7 conventional SCs. The level of PD-L1 and CD8+ TILs was determined by immunohistochemistry. RESULTS Compared with the conventional group, the rates of nodal metastasis, local recurrence, distant metastasis and mortality were significantly higher in the HGT cohort. Mutations of ARID1A/B, KMT2A, HOXD13, NRG1 and ETV6 genes were identified in HGT SCs. A recurrent E307G mutation in GATA6 gene was also observed in two cases. Two deceased HGT patients with distant metastasis harboured NOTCH3 mutations. ETV6-RET translocation was prone to occur in the HGT SCs. Additionally, PD-L1 expression was low, and CD8+ TILs were sparse in most HGT cases. CONCLUSION Our findings reveal novel gene alterations involved in the progression of HGT in SCs. Most HGT SCs patients cannot benefit from PD-L1 blocking and may be approached with a distinct treatment strategy including the lymph node dissection and application of molecular target drugs in precision oncology.
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Affiliation(s)
- Yu Wang
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingjing Sun
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bao Sun
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunye Zhang
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen Tian
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lizhen Wang
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiang Li
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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21
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Ido M, Fujii K, Mishima H, Kubo A, Saito M, Banno H, Ito Y, Goto M, Ando T, Mouri Y, Kousaka J, Imai T, Nakano S. Comprehensive genomic evaluation of advanced and recurrent breast cancer patients for tailored precision treatments. BMC Cancer 2024; 24:85. [PMID: 38229073 DOI: 10.1186/s12885-023-11442-9] [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: 04/06/2023] [Accepted: 09/25/2023] [Indexed: 01/18/2024] Open
Abstract
AIM The aim of this study was to investigate genetic alterations within breast cancer in the setting of recurrent or de novo stage IV disease. PATIENTS AND METHODS This study included 22 patients with recurrent breast cancer (n = 19) and inoperable de novo stage IV breast cancer (n = 3). For next generation sequencing, FoundationOneCDx (F1CDx) (Foundation Medicine Inc., Cambridge, MA, USA) was performed in 21 patients and FoundationOneLiquid CDx was performed in 1 patient. RESULTS Median age was 62.9 years (range, 33.4-82.1). Pathological diagnoses of specimens included invasive ductal carcinoma (n = 19), invasive lobular carcinoma (n = 2), and invasive micropapillary carcinoma (n = 1). F1CDx detected a median of 4.5 variants (range, 1-11). The most commonly altered gene were PIK3CA (n = 9), followed by TP53 (n = 7), MYC (n = 4), PTEN (n = 3), and CDH1 (n = 3). For hormone receptor-positive patients with PIK3CA mutations, hormonal treatment plus a phosphoinositide 3-kinase inhibitor was recommended as the treatment of choice. Patients in the hormone receptor-negative and no human epidermal growth factor receptor 2 expression group had significantly higher tumor mutational burden than patients in the hormone receptor-positive group. A BRCA2 reversion mutation was revealed by F1CDx in a patient with a deleterious germline BRCA2 mutation during poly ADP ribose polymerase inhibitor treatment. CONCLUSION Guidance on tailored precision therapy with consideration of genomic mutations was possible for some patients with information provided by F1CDx. Clinicians should consider using F1CDx at turning points in the course of the disease.
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Affiliation(s)
- Mirai Ido
- Department of Surgery, Division of Breast and Endocrine Surgery, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute city, 480-1195, Japan
| | - Kimihito Fujii
- Department of Surgery, Division of Breast and Endocrine Surgery, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute city, 480-1195, Japan.
| | - Hideyuki Mishima
- Cancer Center, Aichi Medical University Hospital, Nagakute city, Japan
| | - Akihito Kubo
- Cancer Center, Aichi Medical University Hospital, Nagakute city, Japan
| | - Masayuki Saito
- Department of Surgery, Division of Breast and Endocrine Surgery, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute city, 480-1195, Japan
| | - Hirona Banno
- Department of Surgery, Division of Breast and Endocrine Surgery, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute city, 480-1195, Japan
| | - Yukie Ito
- Department of Surgery, Division of Breast and Endocrine Surgery, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute city, 480-1195, Japan
| | - Manami Goto
- Department of Surgery, Division of Breast and Endocrine Surgery, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute city, 480-1195, Japan
| | - Takahito Ando
- Department of Surgery, Division of Breast and Endocrine Surgery, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute city, 480-1195, Japan
| | - Yukako Mouri
- Department of Surgery, Division of Breast and Endocrine Surgery, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute city, 480-1195, Japan
| | - Junko Kousaka
- Department of Surgery, Division of Breast and Endocrine Surgery, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute city, 480-1195, Japan
| | - Tsuneo Imai
- Department of Surgery, Division of Breast and Endocrine Surgery, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute city, 480-1195, Japan
| | - Shogo Nakano
- Department of Surgery, Division of Breast and Endocrine Surgery, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute city, 480-1195, Japan
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22
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Abdel-Maksoud MA, Ullah S, Nadeem A, Shaikh A, Zia MK, Zakri AM, Almanaa TN, Alfuraydi AA, Mubarak A, Hameed Y. Unlocking the diagnostic, prognostic roles, and immune implications of BAX gene expression in pan-cancer analysis. Am J Transl Res 2024; 16:63-74. [PMID: 38322551 PMCID: PMC10839381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/20/2023] [Indexed: 02/08/2024]
Abstract
OBJECTIVES Cancer, a formidable disease, continues to challenge our understanding and therapeutic approaches. This study delves into the pan-cancer analysis of BCL2 Associated X (BAX) gene expression, seeking to unravel its significance in cancer development, prognosis, and potential therapeutic strategies. METHODS A combination of bioinformatics and molecular experiments. RESULTS Our pan-cancer investigation into BAX expression encompassed 33 distinct cancer types, revealing a remarkable and uniform increase in BAX expression. This groundbreaking finding emphasizes the potential universality of BAX's role in cancer development and progression. Further, our study explored the prognostic implications of BAX expression, highlighting a consistent association between up-regulated BAX and poor overall survival (OS) in Liver Hepatocellular Carcinoma (LIHC) and Skin Cutaneous Melanoma (SKCM). These results suggest that BAX may serve as an adverse prognostic indicator in these malignancies, emphasizing the importance of personalized treatment strategies. Epigenetic and genetic analyses of BAX provided valuable insights. Hypomethylation of the BAX promoter region was evident in LIHC and SKCM, which likely contributes to the up-regulation of BAX, while genetic mutations in the BAX gene itself were infrequent in these cancers. Our exploration of BAX-associated signaling pathways and the correlation between BAX expression and CD8+ T cell infiltration shed light on the intricate molecular landscape of cancer. BAX's interaction with key apoptotic and immune-related pathways reinforces its role as a central player in tumor development and the immune microenvironment. Moreover, our drug prediction analysis identified potential therapeutic agents for modulating BAX expression in the context of LIHC and SKCM, bridging the gap between research and clinical application. CONCLUSION In sum, our comprehensive BAX study not only enhances our understanding of its significance as a biomarker gene but also offers novel avenues for therapeutic interventions, contributing to the ongoing quest for more effective cancer treatments and improved patient care.
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Affiliation(s)
- Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Amun Nadeem
- Department of Pathology, Gujranwala Medical College Teaching Hospital GujranwalaPakistan
| | | | - Muhammad Khurram Zia
- Department of Surgery, Liaquat College of Medicine and Dentistry and Darul Sehat HospitalKarachi, Pakistan
| | - Adel M Zakri
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversityRiyadh 11451, Saudi Arabia
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Akram A Alfuraydi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Yasir Hameed
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of BahawalpurBahawalpur 63100, Pakistan
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Zaikova E, Cheng BYC, Cerda V, Kong E, Lai D, Lum A, Bates C, den Brok W, Kono T, Bourque S, Chan A, Feng X, Fenton D, Gurjal A, Levasseur N, Lohrisch C, Roberts S, Shenkier T, Simmons C, Taylor S, Villa D, Miller R, Aguirre-Hernandez R, Aparicio S, Gelmon K. Circulating tumour mutation detection in triple-negative breast cancer as an adjunct to tissue response assessment. NPJ Breast Cancer 2024; 10:3. [PMID: 38182588 PMCID: PMC10770342 DOI: 10.1038/s41523-023-00607-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/02/2023] [Indexed: 01/07/2024] Open
Abstract
Circulating tumour DNA (ctDNA) detection via liquid biopsy is an emerging alternative to tissue biopsy, but its potential in treatment response monitoring and prognosis in triple negative breast cancer (TNBC) is not yet well understood. Here we determined the prevalence of actionable mutations detectable in ctDNA using a clinically validated cancer gene panel assay in patients with TNBC, without recurrence at the time of study entry. Sequencing of plasma DNA and validation of variants from 130 TNBC patients collected within 7 months of primary treatment completion revealed that 7.7% had detectable residual disease with a hotspot panel. Among neoadjuvant treated patients, we observed a trend where patients with incomplete pathologic response and positive ctDNA within 7 months of treatment completion were at much higher risk of reduced progression free survival. We propose that a high risk subset of early TNBC patients treated in neoadjuvant therapy protocols may be identifiable by combining tissue response and sensitive ctDNA detection.
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Affiliation(s)
- Elena Zaikova
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Brian Y C Cheng
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Viviana Cerda
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Esther Kong
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Daniel Lai
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Amy Lum
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Cherie Bates
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Wendie den Brok
- Medical Oncology, BC Cancer, 600 W10th Avenue, Vancouver, Canada
| | - Takako Kono
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Sylvie Bourque
- Medical Oncology, BC Cancer, 13750 96 Ave, Surrey, Canada
| | - Angela Chan
- Medical Oncology, BC Cancer, 13750 96 Ave, Surrey, Canada
| | - Xioalan Feng
- Medical Oncology, BC Cancer, 2410 Lee Ave, Victoria, Canada
| | - David Fenton
- Medical Oncology, BC Cancer, 2410 Lee Ave, Victoria, Canada
| | - Anagha Gurjal
- Medical Oncology, BC Cancer, 32900 Marshall Rd, Abbotsford, Canada
| | | | | | - Sarah Roberts
- Medical Oncology, BC Cancer, 1215 Lethbridge St, Prince George, Canada
| | - Tamara Shenkier
- Medical Oncology, BC Cancer, 600 W10th Avenue, Vancouver, Canada
| | | | - Sara Taylor
- Medical Oncology, BC Cancer, 399 Royal Ave, Kelowna, Canada
| | - Diego Villa
- Medical Oncology, BC Cancer, 600 W10th Avenue, Vancouver, Canada
| | - Ruth Miller
- Imagia Canexia Health, 204-2389 Health Sciences Mall, Vancouver, Canada
| | | | - Samuel Aparicio
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada.
| | - Karen Gelmon
- Medical Oncology, BC Cancer, 600 W10th Avenue, Vancouver, Canada.
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Zhao D, Li W, Wang Y, Zhang G, Bai X, Yu H. HTRA1 expression is associated with immune-cell infiltration and survival in breast cancer. Transl Cancer Res 2023; 12:3503-3521. [PMID: 38197075 PMCID: PMC10774071 DOI: 10.21037/tcr-23-773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/18/2023] [Indexed: 01/11/2024]
Abstract
Background High temperature requirement A1 (HTRA1), a member of the HTRA family, is a serine peptidase involved in many crucial bioprocesses such as proliferation, mitochondrial homeostasis, apoptosis, and protein quality control. It also plays an important role in the development of various tumors. However, the potential role and mechanisms of action of HTRA1 in breast cancer (BRCA) remain unclear. We conducted a bioinformatics-based study to investigate HTRA1 expression in BRCA alongside its associations with immune-cell infiltrates and survival outcomes. Methods The expression of HTRA1 in BRCA samples was analyzed using RNAseq datasets from The Cancer Genome Atlas and Gene Expression Omnibus. R software was employed to assess the relationship between HTRA1 expression and clinicopathological characteristics, tumor-infiltrating immune cells, and immunity-associated biomarkers in BRCA. MethSurv and cBioPortal database were utilized to evaluate DNA methylation and genovariation within the HTRA1 DNA. Receiver operating characteristic curves, Kaplan-Meier analysis, and Cox regression were performed to estimate the impact of HTRA1 on diagnosis, prognosis, and response to chemotherapy in BRCA. Results HTRA1 expression was significantly downregulated in BRCA tissues compared to adjacent normal breast tissue controls. Differentially expressed genes associated with HTRA1 expression primarily enriched in cell proliferation pathways. Furthermore, altered HTRA1 expression significantly correlated with patient age, tumor histological type, T stage, progesterone receptor/estrogen receptor status, and PAM50 subtype of BRCA. Both positive and negative associations were observed between HTRA1 levels and the abundance of different types of immune cells, as well as immune biomarkers, including resting mast cells, follicular helper T cells, PD-L1, p53, and Ki67. Low HTRA1 expression was related with pathological complete response in luminal B BRCA patients undergoing chemotherapy. Additionally, lower HTRA1 expression in BRCA was associated with inferior overall survival and relapse-free survival. Conclusions HTRA1 expression is associated with immune-cell infiltration, response to chemotherapy, and survival outcomes in BRCA. HTRA1 has the potential to serve as a promising biomarker and therapeutic target moving forward.
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Affiliation(s)
- Dawei Zhao
- Department of Breast Cancer, Jilin Cancer Hospital, Changchun, China
| | - Wanfeng Li
- Department of Breast Cancer, Jilin Cancer Hospital, Changchun, China
| | - Yan Wang
- Department of Breast Cancer, Jilin Cancer Hospital, Changchun, China
| | - Gengyue Zhang
- Jilin Province Institute of Cancer Prevention and Treatment, Jilin Cancer Hospital, Changchun, China
| | - Xinhua Bai
- Department of Pathology, Jilin Cancer Hospital, Changchun, China
| | - Hong Yu
- Jilin Province Institute of Cancer Prevention and Treatment, Jilin Cancer Hospital, Changchun, China
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Kim HS, Noh YK, Min KW, Kim DH. Low CDKN1B Expression Associated with Reduced CD8+ T Lymphocytes Predicts Poor Outcome in Breast Cancer in a Machine Learning Analysis. J Pers Med 2023; 14:30. [PMID: 38248731 PMCID: PMC10817603 DOI: 10.3390/jpm14010030] [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: 11/24/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
The cyclin-dependent kinase inhibitor 1B (CDKN1B) gene, which encodes the p27Kip1 protein, is important in regulating the cell cycle process and cell proliferation. Its role in breast cancer prognosis is controversial. We evaluated the significance and predictive role of CDKN1B expression in breast cancer prognosis. We investigated the clinicopathologic factors, survival rates, immune cells, gene sets, and prognostic models according to CDKN1B expression in 3794 breast cancer patients. We performed gene set enrichment analysis (GSEA), in silico cytometry, pathway network analyses, gradient boosting machine (GBM) learning, and in vitro drug screening. High CDKN1B expression levels in breast cancer correlated with high lymphocyte infiltration signature scores and increased CD8+ T cells, both of which were associated with improved prognosis in breast cancer. which were associated with a better prognosis. CDKN1B expression was associated with gene sets for the upregulation of T-cell receptor signaling pathways and downregulation of CD8+ T cells. Pathway network analysis revealed a direct link between CDKN1B and the pathway involved in the positive regulation of the protein catabolic process pathway. In addition, an indirect link was identified between CDKN1B and the T-cell receptor signaling pathway. In in vitro drug screening, BMS-345541 demonstrated efficacy as a therapeutic targeting of CDKN1B, effectively impeding the growth of breast cancer cells characterized by low CDKN1B expression. The inclusion of CDKN1B expression in GBM models increased the accuracy of survival predictions. CDKN1B expression plays a significant role in breast cancer progression, implying that targeting CDKN1B might be a promising strategy for treating breast cancer.
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Affiliation(s)
- Hyung-Suk Kim
- Division of Breast Surgery, Department of Surgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 15588, Republic of Korea;
| | - Yung-Kyun Noh
- Department of Computer Science, Hanyang University, 222 Wangsimni-ro, Seoul 04763, Republic of Korea;
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Kyueng-Whan Min
- Department of Pathology, Uijeongbu Eulji Medical Center, School of Medicine, Eulji University, Uijeongbu 11759, Republic of Korea
| | - Dong-Hoon Kim
- Department of Pathology, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, 29 Saemunanro, Seoul 03181, Republic of Korea
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26
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Hu H, Yan T, Zhu H, Zhan W, Zhang J, Wang S, Jiang L, Escobar D, Zhang T. A novel immune checkpoint-related signature for prognosis and immune analysis in breast cancer. Clin Exp Med 2023; 23:5139-5159. [PMID: 37930605 DOI: 10.1007/s10238-023-01247-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
Breast cancer is one of the most prevailing forms of cancer globally. Immunotherapy has demonstrated efficacy in improving the overall survival of breast cancer. The aim of us was to formulate a novel signature predicated on immune checkpoint-related genes (ICGs) that could anticipate the prognosis and further analyze the immune status of patients with breast cancer. After acquiring data, we pinpointed the definitive ICGs for constructing the prognostic model of breast cancer. We constructed a novel prognostic model and created a fresh risk score called Immune Checkpoint-related Risk Score in breast cancer (ICRSBC). The nomogram was constructed to evaluate the accuracy of the model, and the new web-based tool was created to be more intuitive for predicting prognosis. We also investigated immunotherapy responsiveness and analyzed the tumor mutational burden (TMB) in ICRSBC subgroups. The ICRSBC was found to have significant correlations with the immune environment, immunotherapy responsiveness, and TMB. The expression levels of the 9 ICGs that construct the prognostic model and their promoter methylation levels are significantly different between breast cancer and normal tissues. Furthermore, the mutation profiles, the copy number alterations, and the levels of protein expression also exhibit marked disparities among the 9 ICGs. We have identified and validated a novel signature related to ICGs that is strongly associated with breast cancer progression. This signature enables us to create a risk score for prognosticating the survival and assessing the immune status of individuals affected by breast cancer.
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Affiliation(s)
- Haihong Hu
- Department of Pharmacy, The First Affiliated Hospital, Hengyang Medical School, University of South China, 69 Chuanshan Road, Hengyang, 421001, Hunan, People's Republic of China
- School of Pharmacy, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Ting Yan
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, People's Republic of China
| | - Hongxia Zhu
- Department of Pharmacy, The First Affiliated Hospital, Hengyang Medical School, University of South China, 69 Chuanshan Road, Hengyang, 421001, Hunan, People's Republic of China
- School of Pharmacy, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Wendi Zhan
- Department of Pharmacy, The First Affiliated Hospital, Hengyang Medical School, University of South China, 69 Chuanshan Road, Hengyang, 421001, Hunan, People's Republic of China
- School of Pharmacy, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Jingdi Zhang
- Department of Pharmacy, The First Affiliated Hospital, Hengyang Medical School, University of South China, 69 Chuanshan Road, Hengyang, 421001, Hunan, People's Republic of China
- School of Pharmacy, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Siyu Wang
- Department of Pharmacy, The First Affiliated Hospital, Hengyang Medical School, University of South China, 69 Chuanshan Road, Hengyang, 421001, Hunan, People's Republic of China
- School of Pharmacy, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Lingxiang Jiang
- Department of Radiation Oncology, Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - David Escobar
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH, 43606, USA
| | - Taolan Zhang
- Department of Pharmacy, The First Affiliated Hospital, Hengyang Medical School, University of South China, 69 Chuanshan Road, Hengyang, 421001, Hunan, People's Republic of China.
- School of Pharmacy, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China.
- Phase I Clinical Trial Center, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, People's Republic of China.
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27
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Srikanthan A, Awan AA, McGee S, Rushton M. Young Women with Breast Cancer: The Current Role of Precision Oncology. J Pers Med 2023; 13:1620. [PMID: 38003935 PMCID: PMC10672565 DOI: 10.3390/jpm13111620] [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: 10/08/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Young adults aged 40 years and younger with breast cancer represent less than 5% of all breast cancer cases, yet it is the leading cause of death among young women with cancer worldwide. Breast cancer that develops at a young age is more aggressive and has biological features that carry an increased risk of relapse and death. Young adults are more likely to have a genetic predisposition and key biomarkers, including endocrine receptors, the HER2 receptor, and proliferation biomarkers, that appear different compared to older adults. Despite being more aggressive, management strategies are largely the same irrespective of age. Given the higher rates of genetic predisposition, fast access to genetic counselling and testing is a necessity. In this review, the biological differences in young adult breast cancer and the current role precision medicine holds in the treatment of young adults with breast cancer are explored. Given the relatively high risk of relapse, developing novel genomic tools to refine the treatment options beyond the current standard is critical. Existing predictive genomic tests require careful interpretation with consideration of the patient's clinical and pathological features in the young patient cohort. Careful evaluation is also required when considering extended endocrine therapy options. Improved characterization of mutations occurring in tumors using next-generation sequencing could identify important driver mutations that arise in young women. Applying the advances of precision medicine equitably to patients in resource-rich and low- and middle-income countries will be critical to impacting the survival of young adults with breast cancer worldwide.
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Affiliation(s)
- Amirrtha Srikanthan
- Division of Medical Oncology, The Ottawa Hospital, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; (A.A.A.); (S.M.); (M.R.)
- Department of Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Arif Ali Awan
- Division of Medical Oncology, The Ottawa Hospital, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; (A.A.A.); (S.M.); (M.R.)
- Department of Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Sharon McGee
- Division of Medical Oncology, The Ottawa Hospital, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; (A.A.A.); (S.M.); (M.R.)
- Department of Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Moira Rushton
- Division of Medical Oncology, The Ottawa Hospital, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; (A.A.A.); (S.M.); (M.R.)
- Department of Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
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28
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Madan V, Shyamsunder P, Dakle P, Woon TW, Han L, Cao Z, Nordin HBM, Jizhong S, Shuizhou Y, Hossain MZ, Koeffler HP. Dissecting the role of SWI/SNF component ARID1B in steady-state hematopoiesis. Blood Adv 2023; 7:6553-6566. [PMID: 37611161 PMCID: PMC10632677 DOI: 10.1182/bloodadvances.2023009946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
The adenosine triphosphate (ATP)-dependent chromatin remodeling complex, SWItch/Sucrose Non-Fermentable (SWI/SNF), has been implicated in normal hematopoiesis. The AT-rich interaction domain 1B (ARID1B) and its paralog, ARID1A, are mutually exclusive, DNA-interacting subunits of the BRG1/BRM-associated factor (BAF) subclass of SWI/SNF complex. Although the role of several SWI/SNF components in hematopoietic differentiation and stem cell maintenance has been reported, the function of ARID1B in hematopoietic development has not been defined. To this end, we generated a mouse model of Arid1b deficiency specifically in the hematopoietic compartment. Unlike the extensive phenotype observed in mice deficient in its paralog, ARID1A, Arid1b knockout (KO) mice exhibited a modest effect on steady-state hematopoiesis. Nonetheless, transplantation experiments showed that the reconstitution of myeloid cells in irradiated recipient mice was dependent on ARID1B. Furthermore, to assess the effect of the complete loss of ARID1 proteins in the BAF complex, we generated mice lacking both ARID1A and ARID1B in the hematopoietic compartment. The double-KO mice succumbed to acute bone marrow failure resulting from complete loss of BAF-mediated chromatin remodeling activity. Our Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) analyses revealed that >80% of loci regulated by ARID1B were distinct from those regulated by ARID1A; and ARID1B controlled expression of genes crucial in myelopoiesis. Overall, loss of ARID1B affected chromatin dynamics in murine hematopoietic stem and progenitor cells, albeit to a lesser extent than cells lacking ARID1A.
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Affiliation(s)
- Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Teoh Weoi Woon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Lin Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Zeya Cao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Shi Jizhong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yu Shuizhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Md Zakir Hossain
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - H. Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA
- Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Hospital, Singapore
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29
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Morales-Pison S, Tapia JC, Morales-González S, Maldonado E, Acuña M, Calaf GM, Jara L. Association of Germline Variation in Driver Genes with Breast Cancer Risk in Chilean Population. Int J Mol Sci 2023; 24:16076. [PMID: 38003265 PMCID: PMC10671568 DOI: 10.3390/ijms242216076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Cancer is a genomic disease, with driver mutations contributing to tumorigenesis. These potentially heritable variants influence risk and underlie familial breast cancer (BC). This study evaluated associations between BC risk and 13 SNPs in driver genes MAP3K1, SF3B1, SMAD4, ARID2, ATR, KMT2C, MAP3K13, NCOR1, and TBX3, in BRCA1/2-negative Chilean families. SNPs were genotyped using TaqMan Assay in 492 cases and 1285 controls. There were no associations between rs75704921:C>T (ARID2); rs2229032:A>C (ATR); rs3735156:C>G (KMT2C); rs2276738:G>C, rs2293906:C>T, rs4075943T:>A, rs13091808:C>T (MAP3K13); rs178831:G>A (NCOR1); or rs3759173:C>A (TBX3) and risk. The MAP3K1 rs832583 A allele (C/A+A/A) showed a protective effect in families with moderate BC history (OR = 0.7 [95% CI 0.5-0.9] p = 0.01). SF3B1 rs16865677-T (G/T+T/T) increased risk in sporadic early-onset BC (OR = 1.4 [95% CI 1.0-2.0] p = 0.01). SMAD4 rs3819122-C (A/C+C/C) increased risk in cases with moderate family history (OR = 2.0 [95% CI 1.3-2.9] p ≤ 0.0001) and sporadic cases diagnosed ≤50 years (OR = 1.6 [95% CI 1.1-2.2] p = 0.006). SMAD4 rs12456284:A>G increased BC risk in G-allele carriers (A/G + G/G) in cases with ≥2 BC/OC cases and early-onset cases (OR = 1.2 [95% CI 1.0-1.6] p = 0.04 and OR = 1.4 [95% CI 1.0-1.9] p = 0.03, respectively). Our study suggests that specific germline variants in driver genes MAP3K1, SF3B1, and SMAD4 contribute to BC risk in Chilean population.
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Affiliation(s)
- Sebastián Morales-Pison
- Centro de Oncología de Precisión (COP), Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Las Condes, Santiago 7560908, Chile;
| | - Julio C. Tapia
- Laboratorio de Transformación Celular, Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile;
| | - Sarai Morales-González
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
| | - Edio Maldonado
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile;
| | - Mónica Acuña
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
| | - Gloria M. Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1010069, Chile;
| | - Lilian Jara
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
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30
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Tang W, Zhang F, Byun JS, Dorsey TH, Yfantis HG, Ajao A, Liu H, Pichardo MS, Pichardo CM, Harris AR, Yang XR, Figueroa JD, Sayed S, Makokha FW, Ambs S. Population-specific Mutation Patterns in Breast Tumors from African American, European American, and Kenyan Patients. CANCER RESEARCH COMMUNICATIONS 2023; 3:2244-2255. [PMID: 37902422 PMCID: PMC10629394 DOI: 10.1158/2767-9764.crc-23-0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 10/31/2023]
Abstract
Women of African descent have the highest breast cancer mortality in the United States and are more likely than women from other population groups to develop an aggressive disease. It remains uncertain to what extent breast cancer in Africa is reminiscent of breast cancer in African American or European American patients. Here, we performed whole-exome sequencing of genomic DNA from 191 breast tumor and non-cancerous adjacent tissue pairs obtained from 97 African American, 69 European American, 2 Asian American, and 23 Kenyan patients. Our analysis of the sequencing data revealed an elevated tumor mutational burden in both Kenyan and African American patients, when compared with European American patients. TP53 mutations were most prevalent, particularly in African American patients, followed by PIK3CA mutations, which showed similar frequencies in European American, African American, and the Kenyan patients. Mutations targeting TBX3 were confined to European Americans and those targeting the FBXW7 tumor suppressor to African American patients whereas mutations in the ARID1A gene that are known to confer resistance to endocrine therapy were distinctively enriched among Kenyan patients. A Kyoto Encyclopedia of Genes and Genomes pathway analysis could link FBXW7 mutations to an increased mitochondrial oxidative phosphorylation capacity in tumors carrying these mutations. Finally, Catalogue of Somatic Mutations in Cancer (COSMIC) mutational signatures in tumors correlated with the occurrence of driver mutations, immune cell profiles, and neighborhood deprivation with associations ranging from being mostly modest to occasionally robust. To conclude, we found mutational profiles that were different between these patient groups. The differences concentrated among genes with low mutation frequencies in breast cancer. SIGNIFICANCE The study describes differences in tumor mutational profiles between African American, European American, and Kenyan breast cancer patients. It also investigates how these profiles may relate to the tumor immune environment and the neighborhood environment in which the patients had residence. Finally, it describes an overrepresentation of ARID1A gene mutations in breast tumors of the Kenyan patients.
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Affiliation(s)
- Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, Maryland
| | - Flora Zhang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Colgate University, Hamilton, New York
| | - Jung S. Byun
- Division of Intramural Research, National Institute of Minority Health and Health Disparities, NIH, Bethesda, Maryland
| | - Tiffany H. Dorsey
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Harris G. Yfantis
- Department of Pathology, University of Maryland Medical Center and Veterans Affairs, Maryland Care System, Baltimore, Maryland
| | - Anuoluwapo Ajao
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Huaitian Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Margaret S. Pichardo
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Department of Surgery, Hospital of the University of Pennsylvania, Penn Medicine, Philadelphia, Pennsylvania
| | - Catherine M. Pichardo
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Division of Cancer Control and Population Sciences, NCI, NIH, Rockville, Maryland
| | - Alexandra R. Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Xiaohong R. Yang
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Jonine D. Figueroa
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | | | | | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
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31
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Nishimura Y, Ryo E, Inoue S, Kawazu M, Ueno T, Namikawa K, Takahashi A, Ogata D, Yoshida A, Yamazaki N, Mano H, Yatabe Y, Mori T. Strategic Approach to Heterogeneity Analysis of Cutaneous Adnexal Carcinomas Using Computational Pathology and Genomics. JID INNOVATIONS 2023; 3:100229. [PMID: 37965425 PMCID: PMC10641284 DOI: 10.1016/j.xjidi.2023.100229] [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: 12/01/2022] [Revised: 07/30/2023] [Accepted: 08/07/2023] [Indexed: 11/16/2023] Open
Abstract
Cutaneous adnexal tumors are neoplasms that arise from skin appendages. Their morphologic diversity and phenotypic variability with rare progression to malignancy make them difficult to diagnose and classify, and there is currently no established treatment strategy. To overcome these difficulties, this study investigated the transcription factor SOX9 expression, morphology, and genetics of skin adnexal tumors for understanding their biology, especially their histogenesis. We showed that cutaneous adnexal tumors and their nontumor counterparts of skin and appendages exhibit expression patterns similar to that of SOX9. Its expression intensity and pattern, as well as histopathologic evaluation of tumors, were analyzed using digital images of 69 normal skin adnexal 9-type organs and 185 skin adnexal 29-type tumors as references. It was possible to distinguish basal cell carcinoma from squamous cell carcinoma, sebaceous carcinoma, and pilomatrixoma with significant differences, along with porocarcinoma from squamous cell carcinoma. Furthermore, unsupervised machine learning "computational pathology" was used to derive a multiregion whole-exome sequencing fusion method termed "genocomputed pathology." The genocomputed pathology of three representable adnexal carcinomas (porocarcinoma, hidradenocarcinoma, and spiradenocarcinoma) was evaluated for total nine cases. We showed that there was more heterogeneity than expected within the tumors as well as the coexistence of components lacking driver fusion genes. The presence or absence of potential driver genes, such as PIK3CA, YAP1, and PTEN, in each region was identified, highlighting a therapeutic strategy for cutaneous adnexal carcinoma encompassing heterogeneous tumors.
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Affiliation(s)
- Yuuki Nishimura
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
- Course of Advanced Clinical Research of Cancer, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Eijitsu Ryo
- Division of Molecular Pathology, National Cancer Center Reserch Institute, Tokyo, Japan
| | - Satoshi Inoue
- Division of Cellular Signaling, National Cancer Center Reserch Institute, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Reserch Institute, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Reserch Institute, Tokyo, Japan
| | - Kenjiro Namikawa
- Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Akira Takahashi
- Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Dai Ogata
- Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Naoya Yamazaki
- Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Reserch Institute, Tokyo, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
- Course of Advanced Clinical Research of Cancer, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Division of Molecular Pathology, National Cancer Center Reserch Institute, Tokyo, Japan
| | - Taisuke Mori
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
- Division of Molecular Pathology, National Cancer Center Reserch Institute, Tokyo, Japan
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Thang NX, Han DW, Park C, Lee H, La H, Yoo S, Lee H, Uhm SJ, Song H, Do JT, Park KS, Choi Y, Hong K. INO80 function is required for mouse mammary gland development, but mutation alone may be insufficient for breast cancer. Front Cell Dev Biol 2023; 11:1253274. [PMID: 38020889 PMCID: PMC10646318 DOI: 10.3389/fcell.2023.1253274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
The aberrant function of ATP-dependent chromatin remodeler INO80 has been implicated in multiple types of cancers by altering chromatin architecture and gene expression; however, the underlying mechanism of the functional involvement of INO80 mutation in cancer etiology, especially in breast cancer, remains unclear. In the present study, we have performed a weighted gene co-expression network analysis (WCGNA) to investigate links between INO80 expression and breast cancer sub-classification and progression. Our analysis revealed that INO80 repression is associated with differential responsiveness of estrogen receptors (ERs) depending upon breast cancer subtype, ER networks, and increased risk of breast carcinogenesis. To determine whether INO80 loss induces breast tumors, a conditional INO80-knockout (INO80 cKO) mouse model was generated using the Cre-loxP system. Phenotypic characterization revealed that INO80 cKO led to reduced branching and length of the mammary ducts at all stages. However, the INO80 cKO mouse model had unaltered lumen morphology and failed to spontaneously induce tumorigenesis in mammary gland tissue. Therefore, our study suggests that the aberrant function of INO80 is potentially associated with breast cancer by modulating gene expression. INO80 mutation alone is insufficient for breast tumorigenesis.
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Affiliation(s)
- Nguyen Xuan Thang
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul, Republic of Korea
| | - Dong Wook Han
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul, Republic of Korea
| | - Hyeonji Lee
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul, Republic of Korea
| | - Hyeonwoo La
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul, Republic of Korea
| | - Seonho Yoo
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul, Republic of Korea
| | - Heeji Lee
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul, Republic of Korea
| | - Sang Jun Uhm
- Department of Animal Science, Sangji University, Wonju, Republic of Korea
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul, Republic of Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul, Republic of Korea
| | - Kyoung Sik Park
- Department of Surgery, School of Medicine, Konkuk University, Seoul, Republic of Korea
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul, Republic of Korea
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Angarola BL, Sharma S, Katiyar N, Gu Kang H, Nehar-Belaid D, Park S, Gott R, Eryilmaz GN, LaBarge MA, Palucka K, Chuang JH, Korstanje R, Ucar D, Anczukow O. Comprehensive single cell aging atlas of mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563147. [PMID: 37961129 PMCID: PMC10634680 DOI: 10.1101/2023.10.20.563147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Aging is the greatest risk factor for breast cancer; however, how age-related cellular and molecular events impact cancer initiation is unknown. We investigate how aging rewires transcriptomic and epigenomic programs of mouse mammary glands at single cell resolution, yielding a comprehensive resource for aging and cancer biology. Aged epithelial cells exhibit epigenetic and transcriptional changes in metabolic, pro-inflammatory, or cancer-associated genes. Aged stromal cells downregulate fibroblast marker genes and upregulate markers of senescence and cancer-associated fibroblasts. Among immune cells, distinct T cell subsets (Gzmk+, memory CD4+, γδ) and M2-like macrophages expand with age. Spatial transcriptomics reveal co-localization of aged immune and epithelial cells in situ. Lastly, transcriptional signatures of aging mammary cells are found in human breast tumors, suggesting mechanistic links between aging and cancer. Together, these data uncover that epithelial, immune, and stromal cells shift in proportions and cell identity, potentially impacting cell plasticity, aged microenvironment, and neoplasia risk.
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Affiliation(s)
| | | | - Neerja Katiyar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hyeon Gu Kang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Giray N Eryilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mark A LaBarge
- Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
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Karihtala P, Kilpivaara O, Porvari K. Mutational signatures and their association with survival and gene expression in urological carcinomas. Neoplasia 2023; 44:100933. [PMID: 37678146 PMCID: PMC10495641 DOI: 10.1016/j.neo.2023.100933] [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: 06/09/2023] [Accepted: 08/31/2023] [Indexed: 09/09/2023]
Abstract
Different sources of mutagenesis cause consistently identifiable patterns of mutations and mutational signatures that mirror the various carcinogenetic processes. We used publicly available data from the Cancer Genome Atlas to evaluate the associations between the activity of the mutational signatures and various survival endpoints in six types of urological cancers after adjusting for established prognostic factors. The predictive power of the signatures was evaluated with dynamic area under curve models. In addition, links between mutational signature activities and differences in gene expression patterns were analysed. APOBEC-related signature SBS2 was associated with improved overall survival (OS) and disease-specific survival (DSS) in bladder carcinomas in the multivariate analysis, while clock-like signature SBS1 predicted shortened DSS and progression-free interval (PFI) in clear cell renal cell carcinomas (ccRCC). In papillary renal cell carcinomas (pRCC), SBS45 was a predictor of improved outcomes, and APOBEC-related SBS13 was a predictor of worse outcomes. Gene expression analyses revealed various enriched pathways between the low- and high-signature groups. Interestingly, in both the ccRCC and pRCC cohorts, the genes of several members of the melanoma antigen (MAGE) family were highly upregulated in the signatures, which predicted poor outcomes, and downregulated in signatures, which were associated with improved survival. To summarize, SBS signatures provide substantial prognostic value compared with just the traditional prognostic factors in certain cancer types. APOBEC-related SBS2 and SBS13 seem to provide robust prognostic information for particular urological cancers, maybe driven by the expression of specific groups of genes, including the MAGE gene family.
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Affiliation(s)
- Peeter Karihtala
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center and University of Helsinki, Helsinki FI-00290, Finland.
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki FI-00014, Finland; Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland; HUSLAB Laboratory of Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki FI-00014, Finland
| | - Katja Porvari
- Department of Pathology, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu FI-90220, Finland
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Yang L, Zhang S, Pu P. Comprehensive analysis of ACKR family members in breast cancer using prognostic values. Oncol Lett 2023; 26:425. [PMID: 37664667 PMCID: PMC10472033 DOI: 10.3892/ol.2023.14011] [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: 05/12/2023] [Accepted: 07/25/2023] [Indexed: 09/05/2023] Open
Abstract
Breast cancer (BC) is by far the most prevalent malignancy found in the female population. Atypical chemokine receptors (ACKRs) are a subclass of G-protein-coupled receptors, which are characterized by disrupted ligand binding and a breakdown of signaling following ligand binding. The evolution and function of multiple ACKRs in BC have yet to be fully elucidated, although certain findings on this family have been reported in several studies in Homo sapiens and other species. The present study identified that the expression level of ACKRs was significantly lower in breast carcinoma (BRCA) tissues compared with normal breast tissues through searches of the Tumor Immune Estimation Resource, UALCAN and Gene Expression Profiling Interactive Analysis databases. Additionally, when comparing BRCA tissues with normal breast tissues, it was found that there was obvious hypomethylation in the promoters of ACKR1, ACKR3 and ACKR5, as well as a marked hypermethylation in the promoters of ACKR2 and ACKR6. In determining the prognosis of patients with BRCA, the expression levels of ACKR1, ACKR2, ACKR3, ACKR4 and ACKR6 were all found to be important factors. The values for distant metastasis-free survival (DMFS), overall survival (OS) and recurrence-free survival (RFS) were all found to be lower in patients with BRCA who had a low expression level of ACKR1. In addition, the RFS rates for patients with BRCA were lower when the expression of ACKR2 was low, and worse values for DMFS, OS and RFS were found to be highly correlated with higher expression levels of ACKR3. Moreover, the DMFS, OS, RFS and predictive power score values were worse in those patients with low ACKR4 expression, and the RFS values for patients with BRCA were also found to be lower when the expression level of ACKR6 was low. Additionally, dendritic cells, macrophages, neutrophils, T cells with CD4+ status, T cells with CD8+ status and B cells were all substantially linked with ACKR expression, as well as immune cell infiltration. Taken together, the findings of the present study may offer a theoretical foundation for the creation of novel targets and prognostic indicators for BRCA therapy.
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Affiliation(s)
- Lixian Yang
- Department of Breast Surgery, Xingtai People's Hospital, Xingtai, Hebei 054000, P.R. China
| | - Shiyu Zhang
- Department of Breast Surgery, Xingtai People's Hospital, Xingtai, Hebei 054000, P.R. China
| | - Pengpeng Pu
- Department of Breast Surgery, Xingtai People's Hospital, Xingtai, Hebei 054000, P.R. China
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Liu Q, Huang J, Yan W, Liu Z, Liu S, Fang W. FGFR families: biological functions and therapeutic interventions in tumors. MedComm (Beijing) 2023; 4:e367. [PMID: 37750089 PMCID: PMC10518040 DOI: 10.1002/mco2.367] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/28/2023] [Accepted: 08/11/2023] [Indexed: 09/27/2023] Open
Abstract
There are five fibroblast growth factor receptors (FGFRs), namely, FGFR1-FGFR5. When FGFR binds to its ligand, namely, fibroblast growth factor (FGF), it dimerizes and autophosphorylates, thereby activating several key downstream pathways that play an important role in normal physiology, such as the Ras/Raf/mitogen-activated protein kinase kinase/extracellular signal-regulated kinase, phosphoinositide 3-kinase (PI3K)/AKT, phospholipase C gamma/diacylglycerol/protein kinase c, and signal transducer and activator of transcription pathways. Furthermore, as an oncogene, FGFR genetic alterations were found in 7.1% of tumors, and these alterations include gene amplification, gene mutations, gene fusions or rearrangements. Therefore, FGFR amplification, mutations, rearrangements, or fusions are considered as potential biomarkers of FGFR therapeutic response for tyrosine kinase inhibitors (TKIs). However, it is worth noting that with increased use, resistance to TKIs inevitably develops, such as the well-known gatekeeper mutations. Thus, overcoming the development of drug resistance becomes a serious problem. This review mainly outlines the FGFR family functions, related pathways, and therapeutic agents in tumors with the aim of obtaining better outcomes for cancer patients with FGFR changes. The information provided in this review may provide additional therapeutic ideas for tumor patients with FGFR abnormalities.
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Affiliation(s)
- Qing Liu
- Cancer CenterIntegrated Hospital of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Jiyu Huang
- Cancer CenterIntegrated Hospital of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Weiwei Yan
- Cancer CenterIntegrated Hospital of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Zhen Liu
- Cancer CenterIntegrated Hospital of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdongChina
- Key Laboratory of Protein Modification and DegradationBasic School of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Shu Liu
- Department of Breast SurgeryThe Affiliated Hospital of Guizhou Medical UniversityGuiyangGuizhouChina
| | - Weiyi Fang
- Cancer CenterIntegrated Hospital of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdongChina
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37
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Miller GM, Brant TS, Goodrich JA, Kugel JF. Short-term exposure to ethanol induces transcriptional changes in nontumorigenic breast cells. FEBS Open Bio 2023; 13:1941-1952. [PMID: 37572351 PMCID: PMC10549231 DOI: 10.1002/2211-5463.13693] [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: 01/20/2023] [Revised: 06/15/2023] [Accepted: 08/11/2023] [Indexed: 08/14/2023] Open
Abstract
Breast cancer is a leading cause of cancer-related deaths in women. Many genetic and behavioral risk factors can contribute to the initiation and progression of breast cancer, one being alcohol consumption. Numerous epidemiological studies have established a positive correlation between alcohol consumption and breast cancer; however, the molecular basis for this link remains ill defined. Elucidating ethanol-induced changes to global transcriptional programming in breast cells is important to ultimately understand how alcohol and breast cancer are connected mechanistically. We investigated induced transcriptional changes in response to a short cellular exposure to moderate levels of alcohol. We treated the nontumorigenic breast cell line MCF10A and the tumorigenic breast cell lines MDA-MB-231 and MCF7, with ethanol for 6 h, and then captured the changes to ongoing transcription using 4-thiouridine metabolic labeling followed by deep sequencing. Only the MCF10A cell line exhibited statistically significant changes in newly transcribed RNA in response to ethanol treatment. Further experiments revealed that some ethanol-upregulated genes are sensitive to the dose of alcohol treatment, while others are not. Gene Ontology and biochemical pathway analyses revealed that ethanol-upregulated genes in MCF10A cells are enriched in biological functions that could contribute to cancer development.
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Affiliation(s)
| | - Tyler S. Brant
- Department of BiochemistryUniversity of Colorado BoulderCOUSA
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38
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López-Mejía JA, Mantilla-Ollarves JC, Rocha-Zavaleta L. Modulation of JAK-STAT Signaling by LNK: A Forgotten Oncogenic Pathway in Hormone Receptor-Positive Breast Cancer. Int J Mol Sci 2023; 24:14777. [PMID: 37834225 PMCID: PMC10573125 DOI: 10.3390/ijms241914777] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Breast cancer remains the most frequently diagnosed cancer in women worldwide. Tumors that express hormone receptors account for 75% of all cases. Understanding alternative signaling cascades is important for finding new therapeutic targets for hormone receptor-positive breast cancer patients. JAK-STAT signaling is commonly activated in hormone receptor-positive breast tumors, inducing inflammation, proliferation, migration, and treatment resistance in cancer cells. In hormone receptor-positive breast cancer, the JAK-STAT cascade is stimulated by hormones and cytokines, such as prolactin and IL-6. In normal cells, JAK-STAT is inhibited by the action of the adaptor protein, LNK. However, the role of LNK in breast tumors is not fully understood. This review compiles published reports on the expression and activation of the JAK-STAT pathway by IL-6 and prolactin and potential inhibition of the cascade by LNK in hormone receptor-positive breast cancer. Additionally, it includes analyses of available datasets to determine the level of expression of LNK and various members of the JAK-STAT family for the purpose of establishing associations between expression and clinical outcomes. Together, experimental evidence and in silico studies provide a better understanding of the potential implications of the JAK-STAT-LNK loop in hormone receptor-positive breast cancer progression.
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Affiliation(s)
- José A. López-Mejía
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 03100, Mexico; (J.A.L.-M.); (J.C.M.-O.)
| | - Jessica C. Mantilla-Ollarves
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 03100, Mexico; (J.A.L.-M.); (J.C.M.-O.)
| | - Leticia Rocha-Zavaleta
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 03100, Mexico; (J.A.L.-M.); (J.C.M.-O.)
- Programa Institucional de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 03100, Mexico
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Sigdel I, Ofori-Kwafo A, Heizelman RJ, Nestor-Kalinoski A, Prabhakarpandian B, Tiwari AK, Tang Y. Biomimetic on-chip assay reveals the anti-metastatic potential of a novel thienopyrimidine compound in triple-negative breast cancer cell lines. Front Bioeng Biotechnol 2023; 11:1227119. [PMID: 37840664 PMCID: PMC10569307 DOI: 10.3389/fbioe.2023.1227119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: This study presents a microfluidic tumor microenvironment (TME) model for evaluating the anti-metastatic efficacy of a novel thienopyrimidines analog with anti-cancer properties utilizing an existing commercial platform. The microfluidic device consists of a tissue compartment flanked by vascular channels, allowing for the co-culture of multiple cell types and providing a wide range of culturing conditions in one device. Methods: Human metastatic, drug-resistant triple-negative breast cancer (TNBC) cells (SUM159PTX) and primary human umbilical vein endothelial cells (HUVEC) were used to model the TME. A dynamic perfusion scheme was employed to facilitate EC physiological function and lumen formation. Results: The measured permeability of the EC barrier was comparable to observed microvessels permeability in vivo. The TNBC cells formed a 3D tumor, and co-culture with HUVEC negatively impacted EC barrier integrity. The microfluidic TME was then used to model the intravenous route of drug delivery. Paclitaxel (PTX) and a novel non-apoptotic agent TPH104c were introduced via the vascular channels and successfully reached the TNBC tumor, resulting in both time and concentration-dependent tumor growth inhibition. PTX treatment significantly reduced EC barrier integrity, highlighting the adverse effects of PTX on vascular ECs. TPH104c preserved EC barrier integrity and prevented TNBC intravasation. Discussion: In conclusion, this study demonstrates the potential of microfluidics for studying complex biological processes in a controlled environment and evaluating the efficacy and toxicity of chemotherapeutic agents in more physiologically relevant conditions. This model can be a valuable tool for screening potential anticancer drugs and developing personalized cancer treatment strategies.
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Affiliation(s)
- Indira Sigdel
- Biofluidics Laboratory, Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH, United States
| | - Awurama Ofori-Kwafo
- Biofluidics Laboratory, Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH, United States
| | - Robert J. Heizelman
- Department of Biomedical Engineering, College of Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Andrea Nestor-Kalinoski
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH, United States
| | | | - Amit K. Tiwari
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Yuan Tang
- Biofluidics Laboratory, Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH, United States
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Duan C, Zhang Y, Li L, Liu K, Yao X, Wu X, Li B, Mao X, Wu H, Liu H, Zeng J, Li S, Gong Y, Hu Z, Xu H. Identification of alternative splicing associated with clinical features: from pan-cancers to genitourinary tumors. Front Oncol 2023; 13:1249932. [PMID: 37810965 PMCID: PMC10557043 DOI: 10.3389/fonc.2023.1249932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/17/2023] [Indexed: 10/10/2023] Open
Abstract
Background Alternative splicing events (ASEs) are vital causes of tumor heterogeneity in genitourinary tumors and many other cancers. However, the clinicopathological relevance of ASEs in cancers has not yet been comprehensively characterized. Methods By analyzing splicing data from the TCGA SpliceSeq database and phenotype data for all TCGA samples from the UCSC Xena database, we identified differential clinical feature-related ASEs in 33 tumors. CIBERSORT immune cell infiltration data from the TIMER2.0 database were used for differential clinical feature-related immune cell infiltration analysis. Gene function enrichment analysis was used to analyze the gene function of ASEs related to different clinical features in tumors. To reveal the regulatory mechanisms of ASEs, we integrated race-related ASEs and splicing quantitative trait loci (sQTLs) data in kidney renal clear cell carcinoma (KIRC) to comprehensively assess the impact of SNPs on ASEs. In addition, we predicted regulatory RNA binding proteins in bladder urothelial carcinoma (BLCA) based on the enrichment of motifs around alternative exons for ASEs. Results Alternative splicing differences were systematically analyzed between different groups of 58 clinical features in 33 cancers, and 30 clinical features in 24 cancer types were identified to be associated with more than 50 ASEs individually. The types of immune cell infiltration were found to be significantly different between subgroups of primary diagnosis and disease type. After integrating ASEs with sQTLs data, we found that 63 (58.9%) of the race-related ASEs were significantly SNP-correlated ASEs in KIRC. Gene function enrichment analyses showed that metastasis-related ASEs in KIRC mainly enriched Rho GTPase signaling pathways. Among those ASEs associated with metastasis, alternative splicing of GIT2 and TUBB3 might play key roles in tumor metastasis in KIRC patients. Finally, we identified several RNA binding proteins such as PCBP2, SNRNP70, and HuR, which might contribute to splicing differences between different groups of neoplasm grade in BLCA. Conclusion We demonstrated the significant clinical relevance of ASEs in multiple cancer types. Furthermore, we identified and validated alternative splicing of TUBB3 and RNA binding proteins such as PCBP2 as critical regulators in the progression of urogenital cancers.
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Affiliation(s)
- Chen Duan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yangjun Zhang
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Lu Li
- Department of Radiation Oncology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Kai Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiangyang Yao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaoliang Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bo Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiongmin Mao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Huahui Wu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haoran Liu
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Jin Zeng
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Sheng Li
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yan Gong
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhiquan Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hua Xu
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
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Kaur J, Chandrashekar DS, Varga Z, Sobottka B, Janssen E, Gandhi K, Kowalski J, Kiraz U, Varambally S, Aneja R. Whole-Exome Sequencing Reveals High Mutational Concordance between Primary and Matched Recurrent Triple-Negative Breast Cancers. Genes (Basel) 2023; 14:1690. [PMID: 37761830 PMCID: PMC10531222 DOI: 10.3390/genes14091690] [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: 07/09/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
PURPOSE Triple-negative breast cancer (TNBC) is a molecularly complex and heterogeneous breast cancer subtype with distinct biological features and clinical behavior. Although TNBC is associated with an increased risk of metastasis and recurrence, the molecular mechanisms underlying TNBC metastasis remain unclear. We performed whole-exome sequencing (WES) analysis of primary TNBC and paired recurrent tumors to investigate the genetic profile of TNBC. METHODS Genomic DNA extracted from 35 formalin-fixed paraffin-embedded tissue samples from 26 TNBC patients was subjected to WES. Of these, 15 were primary tumors that did not have recurrence, and 11 were primary tumors that had recurrence (nine paired primary and recurrent tumors). Tumors were analyzed for single-nucleotide variants and insertions/deletions. RESULTS The tumor mutational burden (TMB) was 7.6 variants/megabase in primary tumors that recurred (n = 9); 8.2 variants/megabase in corresponding recurrent tumors (n = 9); and 7.3 variants/megabase in primary tumors that did not recur (n = 15). MUC3A was the most frequently mutated gene in all groups. Mutations in MAP3K1 and MUC16 were more common in our dataset. No alterations in PI3KCA were detected in our dataset. CONCLUSIONS We found similar mutational profiles between primary and paired recurrent tumors, suggesting that genomic features may be retained during local recurrence.
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Affiliation(s)
- Jaspreet Kaur
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA;
| | - Darshan S. Chandrashekar
- Department of Pathology—Molecular and Cellular, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (D.S.C.); (S.V.)
| | - Zsuzsanna Varga
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland; (Z.V.); (B.S.)
| | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland; (Z.V.); (B.S.)
| | - Emiel Janssen
- Department of Pathology, Stavanger University Hospital, Health Stavanger HF, 4068 Stavanger, Norway; (E.J.); (U.K.)
| | - Khanjan Gandhi
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA;
| | - Jeanne Kowalski
- Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Umay Kiraz
- Department of Pathology, Stavanger University Hospital, Health Stavanger HF, 4068 Stavanger, Norway; (E.J.); (U.K.)
| | - Sooryanarayana Varambally
- Department of Pathology—Molecular and Cellular, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (D.S.C.); (S.V.)
| | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA;
- Department of Clinical and Diagnostic Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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42
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Glaviano A, Foo ASC, Lam HY, Yap KCH, Jacot W, Jones RH, Eng H, Nair MG, Makvandi P, Geoerger B, Kulke MH, Baird RD, Prabhu JS, Carbone D, Pecoraro C, Teh DBL, Sethi G, Cavalieri V, Lin KH, Javidi-Sharifi NR, Toska E, Davids MS, Brown JR, Diana P, Stebbing J, Fruman DA, Kumar AP. PI3K/AKT/mTOR signaling transduction pathway and targeted therapies in cancer. Mol Cancer 2023; 22:138. [PMID: 37596643 PMCID: PMC10436543 DOI: 10.1186/s12943-023-01827-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023] Open
Abstract
The PI3K/AKT/mTOR (PAM) signaling pathway is a highly conserved signal transduction network in eukaryotic cells that promotes cell survival, cell growth, and cell cycle progression. Growth factor signalling to transcription factors in the PAM axis is highly regulated by multiple cross-interactions with several other signaling pathways, and dysregulation of signal transduction can predispose to cancer development. The PAM axis is the most frequently activated signaling pathway in human cancer and is often implicated in resistance to anticancer therapies. Dysfunction of components of this pathway such as hyperactivity of PI3K, loss of function of PTEN, and gain-of-function of AKT, are notorious drivers of treatment resistance and disease progression in cancer. In this review we highlight the major dysregulations in the PAM signaling pathway in cancer, and discuss the results of PI3K, AKT and mTOR inhibitors as monotherapy and in co-administation with other antineoplastic agents in clinical trials as a strategy for overcoming treatment resistance. Finally, the major mechanisms of resistance to PAM signaling targeted therapies, including PAM signaling in immunology and immunotherapies are also discussed.
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Affiliation(s)
- Antonino Glaviano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90123, Palermo, Italy
| | - Aaron S C Foo
- Department of Surgery, National University Hospital Singapore, National University of Singapore, Singapore, Singapore
| | - Hiu Y Lam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | - Kenneth C H Yap
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | - William Jacot
- Department of Medical Oncology, Institut du Cancer de Montpellier, Inserm U1194, Montpellier University, Montpellier, France
| | - Robert H Jones
- Cardiff University and Velindre Cancer Centre, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Huiyan Eng
- Department of Surgery, National University Hospital Singapore, National University of Singapore, Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Madhumathy G Nair
- Division of Molecular Medicine, St. John's Research Institute, St. John's Medical College, Bangalore, 560034, India
| | - Pooyan Makvandi
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Center, Inserm U1015, Université Paris-Saclay, Paris, France
| | - Matthew H Kulke
- Section of Hematology and Medical Oncology, Boston University and Boston Medical Center, Boston, MA, USA
| | - Richard D Baird
- Cancer Research UK Cambridge Centre, Hills Road, Cambridge, CB2 0QQ, UK
| | - Jyothi S Prabhu
- Division of Molecular Medicine, St. John's Research Institute, St. John's Medical College, Bangalore, 560034, India
| | - Daniela Carbone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90123, Palermo, Italy
| | - Camilla Pecoraro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90123, Palermo, Italy
| | - Daniel B L Teh
- Departments of Ophthalmology and Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, and Neurobiology Programme, National University of Singapore, Singapore, Singapore
| | - Gautam Sethi
- Department of Surgery, National University Hospital Singapore, National University of Singapore, Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90123, Palermo, Italy
| | - Kevin H Lin
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Eneda Toska
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Matthew S Davids
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jennifer R Brown
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Patrizia Diana
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90123, Palermo, Italy
| | - Justin Stebbing
- Division of Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - David A Fruman
- Department of Molecular Biology and Biochemistry, University of California, 216 Sprague Hall, Irvine, CA, USA
| | - Alan P Kumar
- Department of Surgery, National University Hospital Singapore, National University of Singapore, Singapore, Singapore.
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.
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43
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John L, Poos AM, Brobeil A, Schinke C, Huhn S, Prokoph N, Lutz R, Wagner B, Zangari M, Tirier SM, Mallm JP, Schumacher S, Vonficht D, Solé-Boldo L, Quick S, Steiger S, Przybilla MJ, Bauer K, Baumann A, Hemmer S, Rehnitz C, Lückerath C, Sachpekidis C, Mechtersheimer G, Haberkorn U, Dimitrakopoulou-Strauss A, Reichert P, Barlogie B, Müller-Tidow C, Goldschmidt H, Hillengass J, Rasche L, Haas SF, van Rhee F, Rippe K, Raab MS, Sauer S, Weinhold N. Resolving the spatial architecture of myeloma and its microenvironment at the single-cell level. Nat Commun 2023; 14:5011. [PMID: 37591845 PMCID: PMC10435504 DOI: 10.1038/s41467-023-40584-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
In multiple myeloma spatial differences in the subclonal architecture, molecular signatures and composition of the microenvironment remain poorly characterized. To address this shortcoming, we perform multi-region sequencing on paired random bone marrow and focal lesion samples from 17 newly diagnosed patients. Using single-cell RNA- and ATAC-seq we find a median of 6 tumor subclones per patient and unique subclones in focal lesions. Genetically identical subclones display different levels of spatial transcriptional plasticity, including nearly identical profiles and pronounced heterogeneity at different sites, which can include differential expression of immunotherapy targets, such as CD20 and CD38. Macrophages are significantly depleted in the microenvironment of focal lesions. We observe proportional changes in the T-cell repertoire but no site-specific expansion of T-cell clones in intramedullary lesions. In conclusion, our results demonstrate the relevance of considering spatial heterogeneity in multiple myeloma with potential implications for models of cell-cell interactions and disease progression.
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Affiliation(s)
- Lukas John
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexandra M Poos
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander Brobeil
- Department of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stefanie Huhn
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Nina Prokoph
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raphael Lutz
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Barbara Wagner
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephan M Tirier
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single Cell Open Lab, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Sabrina Schumacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Dominik Vonficht
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Llorenç Solé-Boldo
- Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - Sabine Quick
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Simon Steiger
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Moritz J Przybilla
- Division Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Katharina Bauer
- Single Cell Open Lab, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Anja Baumann
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Hemmer
- Department of Orthopedic Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Christoph Rehnitz
- Department of Radiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Lückerath
- Department of Radiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christos Sachpekidis
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Uwe Haberkorn
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Antonia Dimitrakopoulou-Strauss
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Reichert
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Bart Barlogie
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Jens Hillengass
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Leo Rasche
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center (MSNZ), University Hospital of Würzburg, Würzburg, Germany
| | - Simon F Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Marc S Raab
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra Sauer
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Niels Weinhold
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany.
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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44
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Thakur S, Haider S, Natrajan R. Implications of tumour heterogeneity on cancer evolution and therapy resistance: lessons from breast cancer. J Pathol 2023; 260:621-636. [PMID: 37587096 DOI: 10.1002/path.6158] [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: 05/22/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 08/18/2023]
Abstract
Tumour heterogeneity is pervasive amongst many cancers and leads to disease progression, and therapy resistance. In this review, using breast cancer as an exemplar, we focus on the recent advances in understanding the interplay between tumour cells and their microenvironment using single cell sequencing and digital spatial profiling technologies. Further, we discuss the utility of lineage tracing methodologies in pre-clinical models of breast cancer, and how these are being used to unravel new therapeutic vulnerabilities and reveal biomarkers of breast cancer progression. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Shefali Thakur
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
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45
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Wang B, Lei X, Tian W, Perez-Rathke A, Tseng YY, Liang J. Structure-based pathogenicity relationship identifier for predicting effects of single missense variants and discovery of higher-order cancer susceptibility clusters of mutations. Brief Bioinform 2023; 24:bbad206. [PMID: 37332013 PMCID: PMC10359089 DOI: 10.1093/bib/bbad206] [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: 02/01/2023] [Revised: 04/19/2023] [Accepted: 05/13/2023] [Indexed: 06/20/2023] Open
Abstract
We report the structure-based pathogenicity relationship identifier (SPRI), a novel computational tool for accurate evaluation of pathological effects of missense single mutations and prediction of higher-order spatially organized units of mutational clusters. SPRI can effectively extract properties determining pathogenicity encoded in protein structures, and can identify deleterious missense mutations of germ line origin associated with Mendelian diseases, as well as mutations of somatic origin associated with cancer drivers. It compares favorably to other methods in predicting deleterious mutations. Furthermore, SPRI can discover spatially organized pathogenic higher-order spatial clusters (patHOS) of deleterious mutations, including those of low recurrence, and can be used for discovery of candidate cancer driver genes and driver mutations. We further demonstrate that SPRI can take advantage of AlphaFold2 predicted structures and can be deployed for saturation mutation analysis of the whole human proteome.
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Affiliation(s)
- Boshen Wang
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill, Department of Biomedical Engineering, University of Illinois at Chicago, W103 Suite, 820 S Wood St, 60612 IL, USA
| | - Xue Lei
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill, Department of Biomedical Engineering, University of Illinois at Chicago, W103 Suite, 820 S Wood St, 60612 IL, USA
| | - Wei Tian
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill, Department of Biomedical Engineering, University of Illinois at Chicago, W103 Suite, 820 S Wood St, 60612 IL, USA
| | - Alan Perez-Rathke
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill, Department of Biomedical Engineering, University of Illinois at Chicago, W103 Suite, 820 S Wood St, 60612 IL, USA
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Biochemistry and Molecular Biology Department, School of Medicine, Wayne State University, 540 E. Canfield Avenue, 48201MI, USA
| | - Jie Liang
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill, Department of Biomedical Engineering, University of Illinois at Chicago, W103 Suite, 820 S Wood St, 60612 IL, USA
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46
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de Oliveira RC, Dos Reis SP, Cavalcante GC. Mutations in Structural Genes of the Mitochondrial Complex IV May Influence Breast Cancer. Genes (Basel) 2023; 14:1465. [PMID: 37510369 PMCID: PMC10379055 DOI: 10.3390/genes14071465] [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: 06/14/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Although it has gained more attention in recent years, the relationship between breast cancer (BC) and mitochondrial oxidative phosphorylation (OXPHOS) is still not well understood. Importantly, Complex IV or Cytochrome C Oxidase (COX) of OXPHOS is one of the key players in mitochondrial balance. An in silico investigation of mutations in structural genes of Complex IV was conducted in BC, comprising 2107 samples. Our findings show four variants (rs267606614, rs753969142, rs199476128 and rs267606884) with significant pathogenic potential. Moreover, we highlight nine genes (MT-CO1, MT-CO2, MT-CO3, CO4I2, COX5A, COX5B, COX6A2, COX6C and COX7B2) with a potential impact on BC.
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Affiliation(s)
- Ricardo Cunha de Oliveira
- Laboratory of Human and Medical Genetics, Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Belém 66075-110, Brazil
| | - Sávio Pinho Dos Reis
- Center for Biological and Health Sciences, State University of Pará, Belém 66087-662, Brazil
| | - Giovanna C Cavalcante
- Laboratory of Human and Medical Genetics, Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Belém 66075-110, Brazil
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47
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Jiang Z, Ju Y, Ali A, Chung PED, Skowron P, Wang DY, Shrestha M, Li H, Liu JC, Vorobieva I, Ghanbari-Azarnier R, Mwewa E, Koritzinsky M, Ben-David Y, Woodgett JR, Perou CM, Dupuy A, Bader GD, Egan SE, Taylor MD, Zacksenhaus E. Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer. Nat Commun 2023; 14:4313. [PMID: 37463901 PMCID: PMC10354065 DOI: 10.1038/s41467-023-39935-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Metastatic breast-cancer is a major cause of death in women worldwide, yet the relationship between oncogenic drivers that promote metastatic versus primary cancer is still contentious. To elucidate this relationship in treatment-naive animals, we hereby describe mammary-specific transposon-mutagenesis screens in female mice together with loss-of-function Rb, which is frequently inactivated in breast-cancer. We report gene-centric common insertion-sites (gCIS) that are enriched in primary-tumors, in metastases or shared by both compartments. Shared-gCIS comprise a major MET-RAS network, whereas metastasis-gCIS form three additional hubs: Rho-signaling, Ubiquitination and RNA-processing. Pathway analysis of four clinical cohorts with paired primary-tumors and metastases reveals similar organization in human breast-cancer with subtype-specific shared-drivers (e.g. RB1-loss, TP53-loss, high MET, RAS, ER), primary-enriched (EGFR, TGFβ and STAT3) and metastasis-enriched (RHO, PI3K) oncogenic signaling. Inhibitors of RB1-deficiency or MET plus RHO-signaling cooperate to block cell migration and drive tumor cell-death. Thus, targeting shared- and metastasis- but not primary-enriched derivers offers a rational avenue to prevent metastatic breast-cancer.
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Affiliation(s)
- Zhe Jiang
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - YoungJun Ju
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Amjad Ali
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Philip E D Chung
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Patryk Skowron
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
- Program in Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Dong-Yu Wang
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Mariusz Shrestha
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Huiqin Li
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Jeff C Liu
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Ioulia Vorobieva
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ronak Ghanbari-Azarnier
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ethel Mwewa
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | | | - Yaacov Ben-David
- The Key laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, Guizhou, 550014, China
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550025, China
| | - James R Woodgett
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON, Canada
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, Departments of Genetics and Pathology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Adam Dupuy
- Department of Pathology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, 52242, USA
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sean E Egan
- Program in Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael D Taylor
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
- Program in Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Eldad Zacksenhaus
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada.
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.
- Department of Medicine, University of Toronto, Toronto, ON, Canada.
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48
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van Amerongen R, Bentires-Alj M, van Boxtel AL, Clarke RB, Fre S, Suarez EG, Iggo R, Jechlinger M, Jonkers J, Mikkola ML, Koledova ZS, Sørlie T, Vivanco MDM. Imagine beyond: recent breakthroughs and next challenges in mammary gland biology and breast cancer research. J Mammary Gland Biol Neoplasia 2023; 28:17. [PMID: 37450065 PMCID: PMC10349020 DOI: 10.1007/s10911-023-09544-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
On 8 December 2022 the organizing committee of the European Network for Breast Development and Cancer labs (ENBDC) held its fifth annual Think Tank meeting in Amsterdam, the Netherlands. Here, we embraced the opportunity to look back to identify the most prominent breakthroughs of the past ten years and to reflect on the main challenges that lie ahead for our field in the years to come. The outcomes of these discussions are presented in this position paper, in the hope that it will serve as a summary of the current state of affairs in mammary gland biology and breast cancer research for early career researchers and other newcomers in the field, and as inspiration for scientists and clinicians to move the field forward.
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Affiliation(s)
- Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands.
| | - Mohamed Bentires-Alj
- Laboratory of Tumor Heterogeneity, Metastasis and Resistance, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Antonius L van Boxtel
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Robert B Clarke
- Manchester Breast Centre, Division of Cancer Sciences, School of Medical Sciences, University of Manchester, Manchester, UK
| | - Silvia Fre
- Institut Curie, Genetics and Developmental Biology Department, PSL Research University, CNRS UMR3215, U93475248, InsermParis, France
| | - Eva Gonzalez Suarez
- Transformation and Metastasis Laboratory, Molecular Oncology, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Richard Iggo
- INSERM U1312, University of Bordeaux, 33076, Bordeaux, France
| | - Martin Jechlinger
- Cell Biology and Biophysics Department, EMBL, Heidelberg, Germany
- Molit Institute of Personalized Medicine, Heilbronn, Germany
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Marja L Mikkola
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, P.O.B. 56, 00014, Helsinki, Finland
| | - Zuzana Sumbalova Koledova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Maria dM Vivanco
- Cancer Heterogeneity Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Technological Park Bizkaia, 48160, Derio, Spain
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49
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Carbajal-Ochoa WH, Johnson D, Alvarez A, Bernal AM, Anampa JD. Racial disparities in treatment and outcomes between non-Hispanic Black and non-Hispanic White women with nonmetastatic inflammatory breast cancer. Breast Cancer Res Treat 2023:10.1007/s10549-023-07018-7. [PMID: 37442877 DOI: 10.1007/s10549-023-07018-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
PURPOSE The incidence rate of inflammatory breast cancer (IBC) is higher among non-Hispanic Black (NHB) than non-Hispanic White (NHW) women. We examined the differences in treatment and outcomes between NHB and NHW women with IBC, accounting for demographic, clinicopathological, and socioeconomic factors. METHODS We collected data from the Surveillance, Epidemiology, and End Results database for NHB and NHW women with IBC diagnosed between 2010-2016. We analyzed the odds of receiving chemotherapy, radiation, and surgery between NHB and NHW women. We evaluated overall survival (OS) with Kaplan-Meier methods and Cox proportional hazards methods. Competing risk analysis was used to compare the risk of breast cancer death between NHB and NHW women. We also evaluated the magnitude of survival disparities within the strata of demographic, socioeconomic, and treatment factors. RESULTS Among 1,652 NHW and 371 NHB women with IBC, the odds of receiving chemotherapy, surgery, and radiation were similar for NHB and NHW. After 39-month follow-up, the median OS was 40 and 81 months for NHB and NHW, respectively (p < 0.0001). The risk of breast cancer death was higher for NHB than NHW women (5-year risk of breast cancer death, 51% vs. 35%, p < 0.0001). CONCLUSION After adjustment for demographic, clinicopathological, and socioeconomic factors; NHB women with IBC had similar odds of receiving surgery, chemotherapy, and radiation therapy, but were more likely to die of the disease compared to their NHW counterparts. Our findings suggest the presence of masked tumor biology, treatment, or socioeconomic factors associated with race that can lead to worse IBC outcomes.
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Affiliation(s)
- Walter H Carbajal-Ochoa
- Department of Medical Oncology, Catalan Institute of Oncology/Josep Trueta Hospital, Girona, Spain
| | - Devin Johnson
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alvaro Alvarez
- Department of Medicine, Hematology/Oncology, Carole and Ray Neag Comprehensive Cancer Center, UCONN Health, Farmington, CT, USA
| | - Ana M Bernal
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, 1695 Eastchester Rd, Bronx, NY, 10461, USA
| | - Jesus D Anampa
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, 1695 Eastchester Rd, Bronx, NY, 10461, USA.
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50
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Alvarez-Rivera E, Ortiz-Hernández EJ, Lugo E, Lozada-Reyes LM, Boukli NM. Oncogenic Proteomics Approaches for Translational Research and HIV-Associated Malignancy Mechanisms. Proteomes 2023; 11:22. [PMID: 37489388 PMCID: PMC10366845 DOI: 10.3390/proteomes11030022] [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: 03/30/2023] [Revised: 06/09/2023] [Accepted: 06/29/2023] [Indexed: 07/26/2023] Open
Abstract
Recent advances in the field of proteomics have allowed extensive insights into the molecular regulations of the cell proteome. Specifically, this allows researchers to dissect a multitude of signaling arrays while targeting for the discovery of novel protein signatures. These approaches based on data mining are becoming increasingly powerful for identifying both potential disease mechanisms as well as indicators for disease progression and overall survival predictive and prognostic molecular markers for cancer. Furthermore, mass spectrometry (MS) integrations satisfy the ongoing demand for in-depth biomarker validation. For the purpose of this review, we will highlight the current developments based on MS sensitivity, to place quantitative proteomics into clinical settings and provide a perspective to integrate proteomics data for future applications in cancer precision medicine. We will also discuss malignancies associated with oncogenic viruses such as Acquire Immunodeficiency Syndrome (AIDS) and suggest novel mechanisms behind this phenomenon. Human Immunodeficiency Virus type-1 (HIV-1) proteins are known to be oncogenic per se, to induce oxidative and endoplasmic reticulum stresses, and to be released from the infected or expressing cells. HIV-1 proteins can act alone or in collaboration with other known oncoproteins, which cause the bulk of malignancies in people living with HIV-1 on ART.
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Affiliation(s)
- Eduardo Alvarez-Rivera
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | - Emanuel J. Ortiz-Hernández
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | - Elyette Lugo
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
| | | | - Nawal M. Boukli
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR 00960, USA
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