1
|
Wang X, Bai H, Zhang J, Wang Z, Duan J, Cai H, Cao Z, Lin Q, Ding X, Sun Y, Zhang W, Xu X, Chen H, Zhang D, Feng X, Wan J, Zhang J, He J, Wang J. Genetic Intratumor Heterogeneity Remodels the Immune Microenvironment and Induces Immune Evasion in Brain Metastasis of Lung Cancer. J Thorac Oncol 2024; 19:252-272. [PMID: 37717855 DOI: 10.1016/j.jtho.2023.09.276] [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: 06/06/2023] [Revised: 08/18/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023]
Abstract
INTRODUCTION Brain metastasis, with the highest incidence in patients with lung cancer, significantly worsens prognosis and poses challenges to clinical management. To date, how brain metastasis evades immune elimination remains unknown. METHODS Whole-exome sequencing and RNA sequencing were performed on 30 matched brain metastasis, primary lung adenocarcinoma, and normal tissues. Data from The Cancer Genome Atlas primary lung adenocarcinoma cohort, including multiplex immunofluorescence, were used to support the findings of bioinformatics analysis. RESULTS Our study highlights the key role of intratumor heterogeneity of genomic alterations in the metastasis process, mainly caused by homologous recombination deficiency or other somatic copy number alteration-associated mutation mechanisms, leading to increased genomic instability and genomic complexity. We further proposed a selection model of brain metastatic evolution in which intratumor heterogeneity drives immune remodeling, leading to immune escape through different mechanisms under local immune pressure. CONCLUSIONS Our findings provide novel insights into the metastatic process and immune escape mechanisms of brain metastasis and pave the way for precise immunotherapeutic strategies for patients with lung cancer with brain metastasis.
Collapse
Affiliation(s)
- Xin Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiyang Zhang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianchun Duan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongqing Cai
- Department of Neurosurgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Cao
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qingtang Lin
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xiaosheng Ding
- Department of Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yiting Sun
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Zhang
- Department of Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Xiaoya Xu
- Department of Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Hao Chen
- Department of Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Dadong Zhang
- Department of Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Xiaoli Feng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinghai Wan
- Department of Neurosurgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianjun Zhang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| |
Collapse
|
2
|
Wei W, Shi F, Xu Y, Jiao Y, Zhang Y, Ou Q, Wu X, Yang L, Lai J. The enrichment of Fanconi anemia/homologous recombination pathway aberrations in ATM/ATR-mutated NSCLC was accompanied by unique molecular features and poor prognosis. J Transl Med 2023; 21:874. [PMID: 38041093 PMCID: PMC10690992 DOI: 10.1186/s12967-023-04634-1] [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: 06/19/2023] [Accepted: 10/14/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND ATM and ATR are two critical factors to regulate DNA damage response (DDR), and their mutations were frequently observed in different types of cancer, including non-small cell lung cancer (NSCLC). Given that the majority of identified ATM/ATR mutations were variants of uncertain significance, the clinical/molecular features of pathogenic ATM/ATR aberrations have not been comprehensively investigated in NSCLC. METHODS Next-generation sequencing (NGS) analyses were conducted to investigate the molecular features in 191 NSCLC patients who harbored pathogenic/likely pathogenic ATM/ATR mutations and 308 NSCLC patients who did not have any types of ATM/ATR variants. The results were validated using an external cohort of 2727 NSCLC patients (including 48 with ATM/ATR pathogenic mutations). RESULTS Most pathogenic ATM/ATR genetic alterations were frameshift and nonsense mutations that disrupt critical domains of the two proteins. ATM/ATR-mutated patients had significantly higher tumor mutational burdens (TMB; P < 0.001) and microsatellite instabilities (MSI; P = 0.023), but not chromosomal instabilities, than those without any ATM/ATR variations. In particular, KRAS mutations were significantly enriched in ATM-mutated patients (P = 0.014), whereas BRCA2 mutations (P = 0.014), TP53 mutations (P = 0.014), and ZNF703 amplification (P = 0.008) were enriched in ATR-mutated patients. Notably, patients with ATM/ATR pathogenic genetic alterations were likely to be accompanied by mutations in Fanconi anemia (FA) and homologous recombination (HR) pathways, which were confirmed using both the study (P < 0.001) and validation (P < 0.001) cohorts. Furthermore, the co-occurrence of FA/HR aberrations could contribute to increased TMB and MSI, and patients with both ATM/ATR and FA/HR mutations tended to have worse overall survival. CONCLUSIONS Our results demonstrated the unique clinical and molecular features of pathogenic ATM/ATR mutations in NSCLC, which helps better understand the cancerous involvement of these DDR regulators, as well as directing targeted therapies and/or immunotherapies to treat ATM/ATR-mutated NSCLC, especially those with co-existing FA/HR aberrations.
Collapse
Affiliation(s)
- Wei Wei
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Fangfang Shi
- Department of Oncology, Zhongda Hospital Southeast University, Nanjing, 210009, Jiangsu, China
| | - Yang Xu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, Jiangsu, China
| | - Yang Jiao
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Ying Zhang
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, Jiangsu, China
| | - Qiuxiang Ou
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, Jiangsu, China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, Jiangsu, China
| | - Lingyi Yang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu, China.
| | - Jinhuo Lai
- Department of Medical Oncology, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, 350025, Fujian, China.
| |
Collapse
|
3
|
Zhong X, Lin Y, Zhang W, Bi Q. Predicting diagnosis and survival of bone metastasis in breast cancer using machine learning. Sci Rep 2023; 13:18301. [PMID: 37880320 PMCID: PMC10600146 DOI: 10.1038/s41598-023-45438-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/19/2023] [Indexed: 10/27/2023] Open
Abstract
This study aimed at establishing more accurate predictive models based on novel machine learning algorithms, with the overarching goal of providing clinicians with effective decision-making assistance. We retrospectively analyzed the breast cancer patients recorded in the Surveillance, Epidemiology, and End Results (SEER) database from 2010 to 2016. Multivariable logistic regression analyses were used to identify risk factors for bone metastases in breast cancer, whereas Cox proportional hazards regression analyses were used to identify prognostic factors for breast cancer with bone metastasis (BCBM). Based on the identified risk and prognostic factors, we developed diagnostic and prognostic models that incorporate six machine learning classifiers. We then used the area under the receiver operating characteristic (ROC) curve (AUC), learning curve, precision curve, calibration plot, and decision curve analysis to evaluate performance of the machine learning models. Univariable and multivariable logistic regression analyses showed that bone metastases were significantly associated with age, race, sex, grade, T stage, N stage, surgery, radiotherapy, chemotherapy, tumor size, brain metastasis, liver metastasis, lung metastasis, breast subtype, and PR. Univariate and multivariate Cox regression analyses revealed that age, race, marital status, grade, surgery, radiotherapy, chemotherapy, brain metastasis, liver metastasis, lung metastasis, breast subtype, ER, and PR were closely associated with the prognosis of BCBM. Among the six machine learning models, the XGBoost algorithm predicted the most accurate results (Diagnostic model AUC = 0.98; Prognostic model AUC = 0.88). According to the Shapley additive explanations (SHAP), the most critical feature of the diagnostic model was surgery, followed by N stage. Interestingly, surgery was also the most critical feature of prognostic model, followed by liver metastasis. Based on the XGBoost algorithm, we could effectively predict the diagnosis and survival of bone metastasis in breast cancer and provide targeted references for the treatment of BCBM patients.
Collapse
Affiliation(s)
- Xugang Zhong
- Center for Rehabilitation Medicine, Cancer Center, Department of Orthopedics, Zhejiang Provincial People's Hospital Affiliated to Qingdao University, Qingdao, Shandong, People's Republic of China
- Center for Rehabilitation Medicine, Cancer Center, Department of Orthopedics, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Yanze Lin
- Center for Rehabilitation Medicine, Cancer Center, Department of Orthopedics, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Wei Zhang
- Center for Rehabilitation Medicine, Cancer Center, Department of Orthopedics, Zhejiang Provincial People's Hospital Affiliated to Qingdao University, Qingdao, Shandong, People's Republic of China.
- Department of Orthopedics, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, 317000, People's Republic of China.
| | - Qing Bi
- Center for Rehabilitation Medicine, Cancer Center, Department of Orthopedics, Zhejiang Provincial People's Hospital Affiliated to Qingdao University, Qingdao, Shandong, People's Republic of China.
- Center for Rehabilitation Medicine, Cancer Center, Department of Orthopedics, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, People's Republic of China.
| |
Collapse
|
4
|
Khan SU, Fatima K, Malik F, Kalkavan H, Wani A. Cancer metastasis: Molecular mechanisms and clinical perspectives. Pharmacol Ther 2023; 250:108522. [PMID: 37661054 DOI: 10.1016/j.pharmthera.2023.108522] [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: 05/03/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Metastatic progression combined with non-responsiveness towards systemic therapy often shapes the course of disease for cancer patients and commonly determines its lethal outcome. The complex molecular events that promote metastasis are a combination of both, the acquired pro-metastatic properties of cancer cells and a metastasis-permissive or -supportive tumor micro-environment (TME). Yet, dissemination is a challenging process for cancer cells that requires a series of events to enable cancer cell survival and growth. Metastatic cancer cells have to initially detach themselves from primary tumors, overcome the challenges of their intravasal journey and colonize distant sites that are suited for their metastases. The implicated obstacles including anoikis and immune surveillance, can be overcome by intricate intra- and extracellular signaling pathways, which we will summarize and discuss in this review. Further, emerging modulators of metastasis, like the immune-microenvironment, microbiome, sublethal cell death engagement, or the nervous system will be integrated into the existing working model of metastasis.
Collapse
Affiliation(s)
- Sameer Ullah Khan
- The University of Texas MD Anderson Cancer Center, Division of Genitourinary Medical Oncology, Holcombe Blvd, Houston, TX 77030, USA; Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Jammu and Kashmir, India
| | - Kaneez Fatima
- Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Jammu and Kashmir, India; Academy of Scientific and Innovative Research (ASIR), Ghaziabad 201002, India
| | - Fayaz Malik
- Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Jammu and Kashmir, India; Academy of Scientific and Innovative Research (ASIR), Ghaziabad 201002, India.
| | - Halime Kalkavan
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany.
| | - Abubakar Wani
- St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN 38105, United States.
| |
Collapse
|
5
|
Nathanson SD, Dieterich LC, Zhang XHF, Chitale DA, Pusztai L, Reynaud E, Wu YH, Ríos-Hoyo A. Associations amongst genes, molecules, cells, and organs in breast cancer metastasis. Clin Exp Metastasis 2023:10.1007/s10585-023-10230-w. [PMID: 37688650 DOI: 10.1007/s10585-023-10230-w] [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: 05/09/2023] [Accepted: 08/18/2023] [Indexed: 09/11/2023]
Abstract
This paper is a cross fertilization of ideas about the importance of molecular aspects of breast cancer metastasis by basic scientists, a pathologist, and clinical oncologists at the Henry Ford Health symposium. We address four major topics: (i) the complex roles of lymphatic endothelial cells and the molecules that stimulate them to enhance lymph node and systemic metastasis and influence the anti-tumor immunity that might inhibit metastasis; (ii) the interaction of molecules and cells when breast cancer spreads to bone, and how bone metastases may themselves spread to internal viscera; (iii) how molecular expression and morphologic subtypes of breast cancer assist clinicians in determining which patients to treat with more or less aggressive therapies; (iv) how the outcomes of patients with oligometastases in breast cancer are different from those with multiple metastases and how that could justify the aggressive treatment of these patients with the hope of cure.
Collapse
Affiliation(s)
- S David Nathanson
- Department of Surgery, Henry Ford Health, 2799 W. Grand Blvd, Detroit, MI, 48202, USA.
- Cancer Center, Henry Ford Health, Detroit, MI, USA.
| | - Lothar C Dieterich
- European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center, Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | | | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, USA
| | - Emma Reynaud
- European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Yi-Hsuan Wu
- Lester and Sue Smith Breast Center, Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | | |
Collapse
|
6
|
Martino F, Lupi M, Giraudo E, Lanzetti L. Breast cancers as ecosystems: a metabolic perspective. Cell Mol Life Sci 2023; 80:244. [PMID: 37561190 PMCID: PMC10415483 DOI: 10.1007/s00018-023-04902-9] [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: 06/01/2023] [Revised: 07/18/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023]
Abstract
Breast cancer (BC) is the most frequently diagnosed cancer and one of the major causes of cancer death. Despite enormous progress in its management, both from the therapeutic and early diagnosis viewpoints, still around 700,000 patients succumb to the disease each year, worldwide. Late recurrency is the major problem in BC, with many patients developing distant metastases several years after the successful eradication of the primary tumor. This is linked to the phenomenon of metastatic dormancy, a still mysterious trait of the natural history of BC, and of several other types of cancer, by which metastatic cells remain dormant for long periods of time before becoming reactivated to initiate the clinical metastatic disease. In recent years, it has become clear that cancers are best understood if studied as ecosystems in which the impact of non-cancer-cell-autonomous events-dependent on complex interaction between the cancer and its environment, both local and systemic-plays a paramount role, probably as significant as the cell-autonomous alterations occurring in the cancer cell. In adopting this perspective, a metabolic vision of the cancer ecosystem is bound to improve our understanding of the natural history of cancer, across space and time. In BC, many metabolic pathways are coopted into the cancer ecosystem, to serve the anabolic and energy demands of the cancer. Their study is shedding new light on the most critical aspect of BC management, of metastatic dissemination, and that of the related phenomenon of dormancy and fostering the application of the knowledge to the development of metabolic therapies.
Collapse
Affiliation(s)
- Flavia Martino
- Department of Oncology, University of Torino Medical School, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Mariadomenica Lupi
- Department of Oncology, University of Torino Medical School, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Enrico Giraudo
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
- Department of Science and Drug Technology, University of Torino, Turin, Italy
| | - Letizia Lanzetti
- Department of Oncology, University of Torino Medical School, Turin, Italy.
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Lučić I, Kurtović M, Mlinarić M, Piteša N, Čipak Gašparović A, Sabol M, Milković L. Deciphering Common Traits of Breast and Ovarian Cancer Stem Cells and Possible Therapeutic Approaches. Int J Mol Sci 2023; 24:10683. [PMID: 37445860 DOI: 10.3390/ijms241310683] [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: 05/06/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Breast cancer (BC) and ovarian cancer (OC) are among the most common and deadly cancers affecting women worldwide. Both are complex diseases with marked heterogeneity. Despite the induction of screening programs that increase the frequency of earlier diagnosis of BC, at a stage when the cancer is more likely to respond to therapy, which does not exist for OC, more than 50% of both cancers are diagnosed at an advanced stage. Initial therapy can put the cancer into remission. However, recurrences occur frequently in both BC and OC, which are highly cancer-subtype dependent. Therapy resistance is mainly attributed to a rare subpopulation of cells, named cancer stem cells (CSC) or tumor-initiating cells, as they are capable of self-renewal, tumor initiation, and regrowth of tumor bulk. In this review, we will discuss the distinctive markers and signaling pathways that characterize CSC, their interactions with the tumor microenvironment, and the strategies they employ to evade immune surveillance. Our focus will be on identifying the common features of breast cancer stem cells (BCSC) and ovarian cancer stem cells (OCSC) and suggesting potential therapeutic approaches.
Collapse
Affiliation(s)
- Ivan Lučić
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Matea Kurtović
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Monika Mlinarić
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Nikolina Piteša
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Ana Čipak Gašparović
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Maja Sabol
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Lidija Milković
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| |
Collapse
|
9
|
Zheng W, Pu M, Li X, Du Z, Jin S, Li X, Zhou J, Zhang Y. Deep learning model accurately classifies metastatic tumors from primary tumors based on mutational signatures. Sci Rep 2023; 13:8752. [PMID: 37253775 DOI: 10.1038/s41598-023-35842-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 05/24/2023] [Indexed: 06/01/2023] Open
Abstract
Metastatic propagation is the leading cause of death for most cancers. Prediction and elucidation of metastatic process is crucial for the treatment of cancer. Even though somatic mutations have been linked to tumorigenesis and metastasis, it is less explored whether metastatic events can be identified through genomic mutational signatures, which are concise descriptions of the mutational processes. Here, we developed MetaWise, a Deep Neural Network (DNN) model, by applying mutational signatures as input features calculated from Whole-Exome Sequencing (WES) data of TCGA and other metastatic cohorts. This model can accurately classify metastatic tumors from primary tumors and outperform traditional machine learning (ML) models and a deep learning (DL) model, DiaDeL. Signatures of non-coding mutations also have a major impact on the model's performance. SHapley Additive exPlanations (SHAP) and Local Surrogate (LIME) analyses identify several mutational signatures which are directly correlated to metastatic spread in cancers, including APOBEC-mutagenesis, UV-induced signatures, and DNA damage response deficiency signatures.
Collapse
Affiliation(s)
- Weisheng Zheng
- Beijing StoneWise Technology Co Ltd., Haidian District, Beijing, China
| | - Mengchen Pu
- Beijing StoneWise Technology Co Ltd., Haidian District, Beijing, China
| | - Xiaorong Li
- Beijing StoneWise Technology Co Ltd., Haidian District, Beijing, China
- Minzu University of China, Beijing, China
| | - Zhaolan Du
- Beijing StoneWise Technology Co Ltd., Haidian District, Beijing, China
- Beijing University of Technology, Beijing, China
| | - Sutong Jin
- Beijing StoneWise Technology Co Ltd., Haidian District, Beijing, China
- Harbin Institute of Technology, Weihai, Shandong, China
| | - Xingshuai Li
- Beijing StoneWise Technology Co Ltd., Haidian District, Beijing, China
| | - Jielong Zhou
- Beijing StoneWise Technology Co Ltd., Haidian District, Beijing, China
| | - Yingsheng Zhang
- Beijing StoneWise Technology Co Ltd., Haidian District, Beijing, China.
| |
Collapse
|
10
|
Rare mutation-dominant compound EGFR-positive NSCLC is associated with enriched kinase domain-resided variants of uncertain significance and poor clinical outcomes. BMC Med 2023; 21:73. [PMID: 36829178 PMCID: PMC9960474 DOI: 10.1186/s12916-023-02768-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 02/02/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Compound epidermal growth factor receptor (EGFR) mutations are less responsive to tyrosine kinase inhibitors (TKIs) than single EGFR mutations in non-small cell lung cancer (NSCLC). However, the detailed clinical characteristics and prognosis of various compound EGFR mutations remain to be elucidated. METHODS We retrospectively studied the next-generation sequencing (NGS) data of treatment-naïve tumors from 1025 NSCLC patients with compound EGFR mutations, which were sub-categorized into different combinations of common mutations (19-Del and EGFR exon 21 p.L858R), rare mutations, and variants of uncertain significance (VUSs). Prognosis and drug resistance to first-line TKIs were analyzed in 174 and 95 patients, respectively. RESULTS Compound EGFR mutations were enriched with EGFR exon 21 p.L858R and rare mutations, but not 19-Del (P < 0.001). The common + rare and rare + rare subtypes had fewer concurrent mutations in the PI3K pathway (P = 0.032), while the rare + rare and common + VUSs subtypes showed increased association with smoking- and temozolomide-related mutational signatures, respectively (P < 0.001). The rare mutation-dominant subtypes (rare + VUSs and rare + rare) had the worst clinical outcomes to first-line TKIs (P < 0.001), which was further confirmed using an external cohort (P = 0.0066). VUSs in the rare + VUSs subtype selectively reside in the EGFR kinase domain (P < 0.001), implying these tumors might select additional mutations to disrupt the regulation/function of the kinase domain. CONCLUSIONS Different subtypes of compound EGFR mutations displayed distinct clinical features and genetic architectures, and rare mutation-dominant compound EGFR mutations were associated with enriched kinase domain-resided VUSs and poor clinical outcomes. Our findings help better understand the oncogenesis of compound EGFR mutations and forecast prognostic outcomes of personalized treatments.
Collapse
|
11
|
Tu SM, Moran C, Norton W, Zacharias NM. Stem Cell Theory of Cancer: Origin of Metastasis and Sub-clonality. Semin Diagn Pathol 2023; 40:63-68. [PMID: 35729019 DOI: 10.1053/j.semdp.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/09/2022] [Indexed: 01/28/2023]
Abstract
Metastasis may be the secret weapon cancer uses to dominate and subjugate, to persist and prevail. However, it is no longer a secret when we realize that a stem cell has the same ways and means to fulfill its own omnipotence and accomplish its own omnipresence… and when we realize that a cancer cell has its own version of stem-ness origin and stem-like nature. In this perspective, we discuss whether stem-ness enables metastasis or mutations drive metastasis. We ponder about low-grade versus high-grade tumors and about primary versus metastatic tumors. We wonder about stochasticity and hierarchy in the genesis and evolution of cancer and of metastasis. We postulate that metastasis may hold the elusive code that makes or breaks a stem-cell versus a genetic theory of cancer. We speculate that the vaunted model of multistep carcinogenesis may be in error and needs some belated remodeling and a major overhaul. We propose that subsequent malignant neoplasms from germ cell tumors and donor-derived malignancies in organ transplants are quintessential experiments of nature and by man that may eventually empower us to elucidate a stem-cell origin of cancer and metastasis. Unfortunately, even the best experiments of cancer and of metastasis will be left unfinished, overlooked, or forgotten, when we do not formulate a proper cancer theory derived from pertinent and illuminating clinical observations. Ultimately, there should be no consternations when we realize that metastasis has a stem-cell rather than a genetic origin, and no reservations when we recognize that metastasis has been providing us some of the most enduring tests and endearing proofs to demonstrate that cancer is indeed a stem-cell rather than a genetic disease after all.
Collapse
Affiliation(s)
- Shi-Ming Tu
- Division of Hematology and Oncology, University of Arkansas for Medical Sciences.
| | - Cesar Moran
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center.
| | - William Norton
- Department of Veterinary Medicine & Surgery, The University of Texas MD Anderson Cancer Center.
| | - Niki M Zacharias
- Department of Urology - Research, The University of Texas MD Anderson Cancer Center.
| |
Collapse
|
12
|
Qian L, Liu YF, Lu SM, Yang JJ, Miao HJ, He X, Huang H, Zhang JG. Construction of a fatty acid metabolism-related gene signature for predicting prognosis and immune response in breast cancer. Front Genet 2023; 14:1002157. [PMID: 36936412 PMCID: PMC10014556 DOI: 10.3389/fgene.2023.1002157] [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: 07/24/2022] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Background: Breast cancer has the highest incidence among malignant tumors in women, and its prevalence ranks first in global cancer morbidity. Aim: This study aimed to explore the feasibility of a prognostic model for patients with breast cancer based on the differential expression of genes related to fatty acid metabolism. Methods: The mRNA expression matrix of breast cancer and paracancer tissues was downloaded from The Cancer Genome Atlas database. The differentially expressed genes related to fatty acid metabolism were screened in R language. The TRRUST database was used to predict transcriptional regulators related to hub genes and construct an mRNA-transcription factor interaction network. A consensus clustering approach was used to identify different fatty acid regulatory patterns. In combination with patient survival data, Lasso and multivariate Cox proportional risk regression models were used to establish polygenic prognostic models based on fatty acid metabolism. The median risk score was used to categorize patients into high- and low-risk groups. Kaplan-Meier survival curves were used to analyze the survival differences between both groups. The Cox regression analysis included risk score and clinicopathological factors to determine whether risk score was an independent risk factor. Models based on genes associated with fatty acid metabolism were evaluated using receiver operating characteristic curves. A comparison was made between risk score levels and the fatty acid metabolism-associated genes in different subtypes of breast cancer. The differential gene sets of the Kyoto Encyclopedia of Genes and Genomes for screening high- and low-risk populations were compared using a gene set enrichment analysis. Furthermore, we utilized CIBERSORT to examine the abundance of immune cells in breast cancer in different clustering models. Results: High expression levels of ALDH1A1 and UBE2L6 prevented breast cancer, whereas high RDH16 expression levels increased its risk. Our comprehensive assessment of the association between prognostic risk scoring models and tumor microenvironment characteristics showed significant differences in the abundance of various immune cells between high- and low-risk breast cancer patients. Conclusions: By assessing fatty acid metabolism patterns, we gained a better understanding of the infiltration characteristics of the tumor microenvironment. Our findings are valuable for prognosis prediction and treatment of patients with breast cancer based on their clinicopathological characteristics.
Collapse
Affiliation(s)
- Li Qian
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Yi-Fei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Shu-Min Lu
- Department of Oncology, Shanghai Jiaotong University School of Medicine Xinhua Hospital, Shanghai, China
| | - Juan-Juan Yang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Hua-Jie Miao
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xin He
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Hua Huang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Hua Huang, ; Jian-Guo Zhang,
| | - Jian-Guo Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Hua Huang, ; Jian-Guo Zhang,
| |
Collapse
|
13
|
McAnena P, Moloney BM, Browne R, O’Halloran N, Walsh L, Walsh S, Sheppard D, Sweeney KJ, Kerin MJ, Lowery AJ. A radiomic model to classify response to neoadjuvant chemotherapy in breast cancer. BMC Med Imaging 2022; 22:225. [PMID: 36564734 PMCID: PMC9789647 DOI: 10.1186/s12880-022-00956-6] [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: 10/13/2021] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Medical image analysis has evolved to facilitate the development of methods for high-throughput extraction of quantitative features that can potentially contribute to the diagnostic and treatment paradigm of cancer. There is a need for further improvement in the accuracy of predictive markers of response to neo-adjuvant chemotherapy (NAC). The aim of this study was to develop a radiomic classifier to enhance current approaches to predicting the response to NAC breast cancer. METHODS Data on patients treated for breast cancer with NAC prior to surgery who had a pre-NAC dynamic contrast enhanced breast MRI were included. Response to NAC was assessed using the Miller-Payne system on the excised tumor. Tumor segmentation was carried out manually under the supervision of a consultant breast radiologist. Features were selected using least absolute shrinkage selection operator regression. A support vector machine learning model was used to classify response to NAC. RESULTS 74 patients were included. Patients were classified as having a poor response to NAC (reduction in cellularity < 90%, n = 44) and an excellent response (> 90% reduction in cellularity, n = 30). 4 radiomics features (discretized kurtosis, NGDLM contrast, GLZLM_SZE and GLZLM_ZP) were identified as pertinent predictors of response to NAC. A SVM model using these features stratified patients into poor and excellent response groups producing an AUC of 0.75. Addition of estrogen receptor status improved the accuracy of the model with an AUC of 0.811. CONCLUSION This study identified a radiomic classifier incorporating 4 radiomics features to augment subtype based classification of response to NAC in breast cancer.
Collapse
Affiliation(s)
- Peter McAnena
- grid.412440.70000 0004 0617 9371Department of Surgery, Clinical Sciences Institute, University Hospital Galway, Galway, Ireland
| | - Brian M. Moloney
- grid.412440.70000 0004 0617 9371Department of Radiology, University Hospital Galway, Galway, Ireland
| | - Robert Browne
- grid.412440.70000 0004 0617 9371Department of Surgery, Clinical Sciences Institute, University Hospital Galway, Galway, Ireland
| | - Niamh O’Halloran
- grid.412440.70000 0004 0617 9371Department of Radiology, University Hospital Galway, Galway, Ireland
| | - Leon Walsh
- grid.412440.70000 0004 0617 9371Department of Radiology, University Hospital Galway, Galway, Ireland
| | - Sinead Walsh
- grid.412440.70000 0004 0617 9371Department of Radiology, University Hospital Galway, Galway, Ireland
| | - Declan Sheppard
- grid.412440.70000 0004 0617 9371Department of Radiology, University Hospital Galway, Galway, Ireland
| | - Karl J. Sweeney
- grid.412440.70000 0004 0617 9371Department of Surgery, Clinical Sciences Institute, University Hospital Galway, Galway, Ireland
| | - Michael J. Kerin
- grid.412440.70000 0004 0617 9371Department of Surgery, Clinical Sciences Institute, University Hospital Galway, Galway, Ireland ,grid.6142.10000 0004 0488 0789Discipline of Surgery, Lambe Institute for Translational Research, National University of Ireland, Galway, Ireland
| | - Aoife J. Lowery
- grid.412440.70000 0004 0617 9371Department of Surgery, Clinical Sciences Institute, University Hospital Galway, Galway, Ireland ,grid.6142.10000 0004 0488 0789Discipline of Surgery, Lambe Institute for Translational Research, National University of Ireland, Galway, Ireland
| |
Collapse
|
14
|
Mellouli M, Graja S, Kridis WB, Ayed HB, Makni S, Triki M, Charfi S, Khanfir A, Boudawara TS, Kallel R. Discordance in receptor status between primary and metastatic breast cancer and overall survival: A single-center analysis. Ann Diagn Pathol 2022; 61:152044. [PMID: 36099874 DOI: 10.1016/j.anndiagpath.2022.152044] [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: 08/11/2022] [Accepted: 09/03/2022] [Indexed: 11/01/2022]
Abstract
BACKGROUND The tumor phenotype may change between primary and metastatic breast cancer. We compared the expression of estrogen receptor (ER), progesterone receptor (PR), and HER2 in a series of primary breast carcinomas (PBC) with their metastatic relapses and analyzed the impact of any changes on survival. MATERIALS AND METHODS It was a single-center retrospective study, collecting consecutive cases of metastatic breast carcinoma diagnosed in the pathology and medical oncology departments at Habib Bourguiba University Hospital in Sfax, Tunisia. An immunohistochemical study was used to assess ER, PR, and HER2 expression. Overall survival (OS) and post-metastasis survival (PMS) were evaluated using multivariable Cox regression analysis. RESULTS Our study included 68 patients. ER and PR status changed in 29.4 % and 39.7 % of cases, respectively. Conversions were mainly from positive to negative status (22 % and 23.5 % for ER and PR, respectively). Differences in HER2 status were observed in 19.6 % of cases, with loss of overexpression in 6 patients (10.7 %). Adjuvant trastuzumab therapy and PBC molecular subtype (HR-, HER2+) were associated with HER2 status discordance (p = 0.02 and 0.03, respectively). On multivariable analysis, HR-negative conversion tumors were significantly associated with a worse OS (p = 0.042) and PMS (p < 0.001), compared to HR-concordant positive tumors. CONCLUSION This study establishes that HR and HER2 status discordance between primary and metastatic breast carcinoma has a prognostic impact on patient outcome. Analyzing these receptors' status in all newly diagnosed cases of metastatic breast carcinoma is strongly recommended and would provide information for changing treatment strategies.
Collapse
Affiliation(s)
- Manel Mellouli
- Department of Pathology and Research Laboratory LR18SP10, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia.
| | - Soumaya Graja
- Department of Pathology and Research Laboratory LR18SP10, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Wala Ben Kridis
- Department of Medical Oncology, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Houda Ben Ayed
- Department of Community Health and Epidemiology, Hedi Chaker University Hospital, University of Sfax, Sfax, Tunisia
| | - Saadia Makni
- Department of Pathology and Research Laboratory LR18SP10, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Meriam Triki
- Department of Pathology and Research Laboratory LR18SP10, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Slim Charfi
- Department of Pathology and Research Laboratory LR18SP10, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Afef Khanfir
- Department of Medical Oncology, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Tahya Sellami Boudawara
- Department of Pathology and Research Laboratory LR18SP10, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Rim Kallel
- Department of Pathology and Research Laboratory LR18SP10, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| |
Collapse
|
15
|
Yang G, Lu T, Weisenberger DJ, Liang G. The Multi-Omic Landscape of Primary Breast Tumors and Their Metastases: Expanding the Efficacy of Actionable Therapeutic Targets. Genes (Basel) 2022; 13:genes13091555. [PMID: 36140723 PMCID: PMC9498783 DOI: 10.3390/genes13091555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/08/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Breast cancer (BC) mortality is almost exclusively due to metastasis, which is the least understood aspect of cancer biology and represents a significant clinical challenge. Although we have witnessed tremendous advancements in the treatment for metastatic breast cancer (mBC), treatment resistance inevitably occurs in most patients. Recently, efforts in characterizing mBC revealed distinctive genomic, epigenomic and transcriptomic (multi-omic) landscapes to that of the primary tumor. Understanding of the molecular underpinnings of mBC is key to understanding resistance to therapy and the development of novel treatment options. This review summarizes the differential molecular landscapes of BC and mBC, provides insights into the genomic heterogeneity of mBC and highlights the therapeutically relevant, multi-omic features that may serve as novel therapeutic targets for mBC patients.
Collapse
Affiliation(s)
- Guang Yang
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- China Grand Enterprises, Beijing 100101, China
| | - Tao Lu
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211121, China
| | - Daniel J. Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Gangning Liang
- Department of Urology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
- Correspondence:
| |
Collapse
|
16
|
Yamada T, Nakanishi Y, Hayashi H, Tanishima S, Mori R, Fujii K, Okamura K, Tsuchikawa T, Nakamura T, Noji T, Asano T, Matsui A, Tanaka K, Watanabe Y, Kurashima Y, Ebihara Y, Murakami S, Shichinohe T, Mitsuhashi T, Hirano S. Targeted amplicon sequencing for primary tumors and matched lymph node metastases in patients with extrahepatic cholangiocarcinoma. HPB (Oxford) 2022; 24:1035-1043. [PMID: 34903468 DOI: 10.1016/j.hpb.2021.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/06/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Lymph node metastasis (LNM) is one of the most adverse prognostic factors in extrahepatic cholangiocarcinoma (EHCC) cases. As next-generation sequencing technology has become more widely available, the genomic profile of biliary tract carcinoma has been clarified. However, whether LNMs have additional genomic alterations in patients with EHCC has not been investigated. Here, we aimed to compare the genomic alterations between primary tumors and matched LNMs in patients with EHCC. METHODS Sixteen patients with node-positive EHCCs were included. Genomic DNA was extracted from tissue samples of primary tumors and matched LNMs. Targeted amplicon sequencing of 160 cancer-related genes was performed. RESULTS Among the 32 tumor samples from 16 patients, 91 genomic mutations were identified. Genomic mutations were noted in 31 genes, including TP53, MAP3K1, SMAD4, APC, and ARID1A. TP53 mutations were most frequently observed (12/32; 37.5%). Genomic mutation profiles were highly concordant between primary tumors and matched LNMs (13/16; 81.3%), and an additional genomic mutation of CDK12 was observed in only one patient. CONCLUSION Genomic mutations were highly concordant between primary tumors and matched LNMs, suggesting that genotyping of archived primary tumor samples may help predict genomic mutations of metastatic tumors in patients with EHCC.
Collapse
Affiliation(s)
- Toru Yamada
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan; Department of Surgical Pathology, Hokkaido University Hospital, Sapporo, Japan
| | - Yoshitsugu Nakanishi
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan.
| | - Hideyuki Hayashi
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan; Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | | | - Ryo Mori
- Mitsubishi Space Software, Tokyo, Japan
| | - Kyoko Fujii
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan; Department of Cancer Pathology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Keisuke Okamura
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Takahiro Tsuchikawa
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Toru Nakamura
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Takehiro Noji
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Toshimichi Asano
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Aya Matsui
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Kimitaka Tanaka
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Yusuke Watanabe
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Yo Kurashima
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Yuma Ebihara
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Soichi Murakami
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Toshiaki Shichinohe
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Tomoko Mitsuhashi
- Department of Surgical Pathology, Hokkaido University Hospital, Sapporo, Japan
| | - Satoshi Hirano
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| |
Collapse
|
17
|
Maddox AL, Brehove MS, Eliato KR, Saftics A, Romano E, Press MF, Mortimer J, Jones V, Schmolze D, Seewaldt VL, Jovanovic-Talisman T. Molecular Assessment of HER2 to Identify Signatures Associated with Therapy Response in HER2-Positive Breast Cancer. Cancers (Basel) 2022; 14:cancers14112795. [PMID: 35681773 PMCID: PMC9179327 DOI: 10.3390/cancers14112795] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The HER2 status of breast cancers is accurately determined by measuring HER2 protein overexpression and gene amplification. However, these clinical diagnostic tests cannot predict the response to therapy. Single molecule imaging approaches can quantify molecular features of HER2, such as receptor nano-organization, with exquisite spatial resolution and sensitivity. The aim of our study was to assess how the molecular features of HER2 varied with the therapy response. According to our results in cultured cell lines and six patient specimens, the therapy response was associated with high detected HER2 densities and clustering. This advanced imaging approach can thus provide key data to complement the current diagnostic standards. Abstract Trastuzumab, the prototype HER2-directed therapy, has markedly improved survival for women with HER2-positive breast cancers. However, only 40–60% of women with HER2-positive breast cancers achieve a complete pathological response to chemotherapy combined with HER2-directed therapy. The current diagnostic assays have poor positive-predictive accuracy in identifying therapy-responsive breast cancers. Here, we deployed quantitative single molecule localization microscopy to assess the molecular features of HER2 in a therapy-responsive setting. Using fluorescently labeled trastuzumab as a probe, we first compared the molecular features of HER2 in trastuzumab-sensitive (BT-474 and SK-BR-3) and trastuzumab-resistant (BT-474R and JIMT-1) cultured cell lines. Trastuzumab-sensitive cells had significantly higher detected HER2 densities and clustering. We then evaluated HER2 in pre-treatment core biopsies from women with breast cancer undergoing neoadjuvant therapy. A complete pathological response was associated with a high detected HER2 density and significant HER2 clustering. These results established the nano-organization of HER2 as a potential signature of therapy-responsive disease.
Collapse
Affiliation(s)
- Adam L. Maddox
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
| | - Matthew S. Brehove
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
| | - Kiarash R. Eliato
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
| | - Andras Saftics
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
| | - Eugenia Romano
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
| | - Michael F. Press
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA;
| | - Joanne Mortimer
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Veronica Jones
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Daniel Schmolze
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Victoria L. Seewaldt
- Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Tijana Jovanovic-Talisman
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; (A.L.M.); (M.S.B.); (K.R.E.); (A.S.); (E.R.)
- Correspondence:
| |
Collapse
|
18
|
Beyond Genetics: Metastasis as an Adaptive Response in Breast Cancer. Int J Mol Sci 2022; 23:ijms23116271. [PMID: 35682953 PMCID: PMC9181003 DOI: 10.3390/ijms23116271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 01/27/2023] Open
Abstract
Metastatic disease represents the primary cause of breast cancer (BC) mortality, yet it is still one of the most enigmatic processes in the biology of this tumor. Metastatic progression includes distinct phases: invasion, intravasation, hematogenous dissemination, extravasation and seeding at distant sites, micro-metastasis formation and metastatic outgrowth. Whole-genome sequencing analyses of primary BC and metastases revealed that BC metastatization is a non-genetically selected trait, rather the result of transcriptional and metabolic adaptation to the unfavorable microenvironmental conditions which cancer cells are exposed to (e.g., hypoxia, low nutrients, endoplasmic reticulum stress and chemotherapy administration). In this regard, the latest multi-omics analyses unveiled intra-tumor phenotypic heterogeneity, which determines the polyclonal nature of breast tumors and constitutes a challenge for clinicians, correlating with patient poor prognosis. The present work reviews BC classification and epidemiology, focusing on the impact of metastatic disease on patient prognosis and survival, while describing general principles and current in vitro/in vivo models of the BC metastatic cascade. The authors address here both genetic and phenotypic intrinsic heterogeneity of breast tumors, reporting the latest studies that support the role of the latter in metastatic spreading. Finally, the review illustrates the mechanisms underlying adaptive stress responses during BC metastatic progression.
Collapse
|
19
|
Yang Z, Cui W, Yu R, Dong X, Zhao J, Dai L, Ou Q, Bao H, Wu X, Wu C, Lai J. Altered Signaling Pathways Revealed by Comprehensive Genomic Profiling in Patients With Unknown Primary Tumors. Front Oncol 2022; 12:753311. [PMID: 35402276 PMCID: PMC8991684 DOI: 10.3389/fonc.2022.753311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/17/2022] [Indexed: 01/16/2023] Open
Abstract
Purpose Carcinoma of unknown primary (CUP) is a clinically aggressive disorder with early tumor dissemination. Identifying molecular traits of CUP can be not only beneficial for a better therapeutic approach but also potentially valuable for patients with general metastatic dissemination. Patients and Methods We retrospectively investigated a total of 35 unique CUP cases. Tumor tissue samples were available in 26 patients, and plasma samples were available in 22 patients. Targeted sequencing was performed with a panel of 416 pan cancer-related genes. Results A genomic landscape of the CUP cohort showed that TP53 mutation was the most frequently observed mutation while MYC amplification was the most common CNV. Aberrant TP53, RTK-RAS, and PI3K signaling pathways were also prevalent, identified in more than half of the cases with tumor tissue. Around 58% of the CUP cases harbored homologous recombinant repair (HRR) pathway gene alterations. The tumor mutational load of CUP patients with altered HRR pathway displayed a significant increase than that of patients with intact HRR. Clinically actionable mutations were identified in eight patients, which may benefit from targeted therapies. Eight patients were treated with platinum-based chemotherapy, showing different responses, HRR, and LOH status. Conclusion Collectively, our data have provided much-need insights into the treatment options for patients diagnosed with CUP in the era of precision medicine.
Collapse
Affiliation(s)
- Zhen Yang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Cui
- Department of Colorectal Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Ruoying Yu
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Canada
| | - Xinhua Dong
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jian Zhao
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Lu Dai
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Qiuxiang Ou
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Canada
| | - Hua Bao
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Canada
| | - Xue Wu
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Canada
| | - Chuanxin Wu
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jinhuo Lai
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, China
| |
Collapse
|
20
|
Kavan S, Kruse TA, Vogsen M, Hildebrandt MG, Thomassen M. Heterogeneity and tumor evolution reflected in liquid biopsy in metastatic breast cancer patients: a review. Cancer Metastasis Rev 2022; 41:433-446. [PMID: 35286542 DOI: 10.1007/s10555-022-10023-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/07/2022] [Indexed: 02/06/2023]
Abstract
Breast cancer is a spatially and temporally dynamic disease in which differently evolving genetic clones are responsible for progression and clinical outcome. We review tumor heterogeneity and clonal evolution from studies comparing primary tumors and metastasis and discuss plasma circulating tumor DNA as a powerful real-time approach for monitoring the clonal landscape of breast cancer during treatment and recurrence. We found only a few early studies exploring clonal evolution and heterogeneity through analysis of multiregional tissue biopsies of different progression steps in comparison with circulating tumor DNA (ctDNA) from blood plasma. The model of linear progression seemed to be more often reported than the model of parallel progression. The results show complex routes to metastasis, however, and plasma most often reflected metastasis more than primary tumor. The described patterns of evolution and the polyclonal nature of breast cancer have clinical consequences and should be considered during patient diagnosis and treatment selection. Current studies focusing on the relevance of clonal evolution in the clinical setting illustrate the role of liquid biopsy as a noninvasive biomarker for monitoring clonal progression and response to treatment. In the clinical setting, circulating tumor DNA may be an ideal support for tumor biopsies to characterize the genetic landscape of the metastatic disease and to improve longitudinal monitoring of disease dynamics and treatment effectiveness through detection of residual tumor after resection, relapse, or metastasis within a particular patient.
Collapse
Affiliation(s)
- Stephanie Kavan
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark. .,Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Marianne Vogsen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Malene G Hildebrandt
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Nuclear Medicine, Odense University Hospital, Odense, Denmark.,Centre for Personalized Response Monitoring in Oncology (PREMIO), Odense University Hospital, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Centre for Personalized Response Monitoring in Oncology (PREMIO), Odense University Hospital, Odense, Denmark
| |
Collapse
|
21
|
Di J, Chai Y, Yang X, Dong H, Jiang B, Ji F. ELP6 and PLIN5 Mutations Were Probably Prognostic Biomarkers for Patients With Gastric Cancer. Front Med (Lausanne) 2022; 9:803617. [PMID: 35223903 PMCID: PMC8864479 DOI: 10.3389/fmed.2022.803617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Purpose Gastric cancer (GC) is the fifth leading cancer around world. And prognosis of patients with GC is still undesirable. Our study aimed to explore potential prognostic biomarkers for patients with GC. Methods The clinical samples were collected from the Qinghai University Affiliated Hospital, which were subjected to the whole exome sequencing (WES). The other GC-related data were obtained from The Cancer Genome Atlas (TCGA) database. Cross analyses were done to determine the candidate genes. And the final mutated genes were determined by survival analyses, univariate and multivariate Cox regression analyses. CIBERSORT and GSEA were used for immune cell infiltration analysis and functional enrichment, respectively. Results After cross analyses, 160 candidate-mutated genes were identified. And mutated ELP6 and PLIN5 were significantly independently correlated with the overall survival (OS) of patients with GC. Patients with GC with ELP6 and PLIN5 mutations had worse and better prognosis, respectively. Totally 5 types of immune cells were significantly differentially infiltrated in wild-type and mutated ELP6 and PLIN5 GC samples. In mutated ELP6 and PLIN5 GC samples, totally 7 and 11 pathways were significantly enriched, respectively. Conclusions The ELP6 and PLIN5 mutations were probably prognostic biomarkers for patients with GC.
Collapse
Affiliation(s)
- Ji Di
- Department of Medical Oncology, Affiliated Hospital of Qinghai University, Xining, China.,School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Yan Chai
- School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Xin Yang
- Department of Medical Oncology, Affiliated Hospital of Qinghai University, Xining, China
| | - Haibin Dong
- Department of Gastroenterology, Tsinghua Changgeng Hospital, Tsinghua University, Beijing, China
| | - Bo Jiang
- Department of Gastroenterology, Tsinghua Changgeng Hospital, Tsinghua University, Beijing, China
| | - Faxiang Ji
- Department of Medical Oncology, Affiliated Hospital of Qinghai University, Xining, China
| |
Collapse
|
22
|
Abstract
Triple-negative breast cancer (TNBC) encompasses a heterogeneous group of fundamentally different diseases with different histologic, genomic, and immunologic profiles, which are aggregated under this term because of their lack of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 expression. Massively parallel sequencing and other omics technologies have demonstrated the level of heterogeneity in TNBCs and shed light into the pathogenesis of this therapeutically challenging entity in breast cancer. In this review, we discuss the histologic and molecular classifications of TNBC, the genomic alterations these different tumor types harbor, and the potential impact of these alterations on the pathogenesis of these tumors. We also explore the role of the tumor microenvironment in the biology of TNBCs and its potential impact on therapeutic response. Dissecting the biology and understanding the therapeutic dependencies of each TNBC subtype will be essential to delivering on the promise of precision medicine for patients with triple-negative disease.
Collapse
Affiliation(s)
- Fatemeh Derakhshan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA;
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA;
| |
Collapse
|
23
|
Fan B, Xu X, Wang X. Mutational landscape of paired primary and synchronous metastatic lymph node in chemotherapy naive gallbladder cancer. Mol Biol Rep 2022; 49:1295-1301. [PMID: 34988893 DOI: 10.1007/s11033-021-06957-y] [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: 08/15/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Comprehensive genomic analysis of paired primary tumors and their metastatic lesions may provide new insights into the biology of metastatic processes and therefore guide the development of novel strategies for intervention. To date, our knowledge of the genetic divergence and phylogenetic relationships in gallbladder cancer (GBC) is limited. METHODS We performed whole exome sequencing for 5 patients with primary tumor, metastatic lymph node (LNM) and corresponding normal tissue. Mutations, mutation signatures and copy number variations were analyzed with state-of-art bioinformatics methods. Phylogenetic tree was also generated to infer metastatic pattern. RESULTS Five driver mutations were detected in these patients. Among which, TP53 was the only shared mutation between primary tumor and LNM. Although tumor mutational burden was comparable between primary tumor and LNM, higher mutation burden was observed in LNM of one patient. Copy number variations (CNVs) burden was higher in LNM than their primary tumor. Phylogenetic analysis indicated both linear and parallel progression of metastasis exist in these patients. TP53 mutation and CNVs were homogenously between primary tumor and LNM. CONCLUSIONS High consistence of genetic landscape were shown between primary tumor and LNM in GBC. However, heterogenicity still exist between primary tumor and LNM in particular patients in term of driver mutation, TMB and CNV burden. Phylogenetic analysis indicated both Linear and parallel progression of metastasis were exist among these patients.
Collapse
Affiliation(s)
- Boqiang Fan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300, Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Xianfeng Xu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xuehao Wang
- Key Laboratory of Liver Transplantation, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Chinese Academy of Medical Sciences, Nanjing, Jiangsu Province, China.
| |
Collapse
|
24
|
Zong Y, Pegram M. Research advances and new challenges in overcoming triple-negative breast cancer. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2021; 4:517-542. [PMID: 34888495 PMCID: PMC8654168 DOI: 10.20517/cdr.2021.04] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Triple-negative breast cancer (TNBC) is a pathological term used to identify invasive breast cancers that lack expression of estrogen and progesterone receptors and do not have pathologic overexpression of the HER2 receptor or harbor ERBB2 gene amplification. TNBC includes a collection of multiple distinct disease entities based upon genomic, transcriptomic and phenotypic characterization. Despite improved clinical outcomes with the development of novel therapeutics, TNBC still yields the worst prognosis among all clinical subtypes of breast cancer. We will systematically review evidence of the genomic evolution of TNBC, as well as potential mechanisms of disease progression and treatment resistance, defined in part by advances in next-generation DNA sequencing technology (including single cell sequencing), providing a new perspective on treatment strategies, and promise to reveal new potential therapeutic targets. Moreover, we review novel therapies aimed at homologous recombination deficiency, PI3 kinase/AKT/PTEN pathway activation, androgen receptor blockade, immune checkpoint inhibition, as well as antibody-drug conjugates engaging novel cell surface targets, including recent progress in pre-clinical and clinical studies which further validate the role of targeted therapies in TNBC. Despite major advances in treatment for TNBC, including FDA approval of 2 PARP inhibitors for metastatic TNBC, the crossing of the superiority boundary in a phase 3, placebo-controlled study of adjuvant olaparib in early-stage patients with germline BRCA-mutated high-risk HER2-negative early breast cancer, the FDA approval of 2 PD-(L)1 checkpoint antibodies for metastatic TNBC, and the FDA approval of the first antibody drug conjugate for TNBC, significant challenges remain. For example, despite the dawn of immunotherapy in metastatic TNBC, durable responses are limited to a small subset of patients, definitive biomarkers for patient selection are lacking, and the Oncology Drug Advisory Committee to the FDA has recently voted against approval of an anti-PD-1 checkpoint antibody high risk early-stage TNBC in the neoadjuvant setting. Also, despite early positive randomized phase 2 studies of AKT inhibition in metastatic TNBC, a recent phase 3 registration trial failed to validate earlier phase 2 data. Finally, we note that level one evidence for clinical efficacy of androgen receptor blockade in TNBC is still lacking. To meet these and other challenges, we will catalogue the ongoing exponential increase in interest in basic, translational, and clinical research to develop new treatment paradigms for TNBC.
Collapse
Affiliation(s)
- Yu Zong
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark Pegram
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
25
|
Grote I, Bartels S, Kandt L, Bollmann L, Christgen H, Gronewold M, Raap M, Lehmann U, Gluz O, Nitz U, Kuemmel S, Zu Eulenburg C, Braun M, Aktas B, Grischke EM, Schumacher C, Luedtke-Heckenkamp K, Kates R, Wuerstlein R, Graeser M, Harbeck N, Christgen M, Kreipe H. TP53 mutations are associated with primary endocrine resistance in luminal early breast cancer. Cancer Med 2021; 10:8581-8594. [PMID: 34779146 PMCID: PMC8633262 DOI: 10.1002/cam4.4376] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/19/2022] Open
Abstract
Background Whereas the genomic landscape of endocrine‐resistant breast cancer has been intensely characterized in previously treated cases with local or distant recurrence, comparably little is known about genomic alterations conveying primary non‐responsiveness to endocrine treatment in luminal early breast cancer. Methods In this study, 622 estrogen receptor‐expressing breast cancer cases treated with short‐term preoperative endocrine therapy (pET) from the WSG‐ADAPT trial (NCT01779206) were analyzed for genetic alterations associated with impaired endocrine proliferative response (EPR) to 3‐week pET with tamoxifen or aromatase inhibitors. EPR was categorized as optimal (post‐pET Ki67 <10%) versus slightly, moderately, and severely impaired (post‐pET Ki67 10%–19%, 20%–34%, and ≥35%, respectively). Recently described gene mutations frequently found in previously treated advanced breast cancer were analyzed (ARID1A, BRAF, ERBB2, ESR1, GATA3, HRAS, KRAS, NRAS, PIK3CA, and TP53) by next‐generation sequencing. Amplifications of CCND1, FGFR1, ERBB2, and PAK1 were determined by digital PCR or fluorescence in situ hybridization. Results ERBB2 amplification (p = 0.0015) and mutations of TP53 (p < 0.0001) were significantly associated with impaired EPR. Impaired EPR in TP53‐mutated breast cancer cases was independent from the Oncotype DX Recurrence Score group and was seen both with tamoxifen‐ and aromatase inhibitor‐based pET (p = 0.0005 each). Conclusion We conclude that impaired EPR to pET is suitable to identify cases with primary endocrine resistance in early luminal breast cancer and that TP53‐mutated luminal cancers might not be sufficiently treated by endocrine therapy alone.
Collapse
Affiliation(s)
- Isabel Grote
- Hannover Medical School, Institute of Pathology, Hannover, Germany
| | - Stephan Bartels
- Hannover Medical School, Institute of Pathology, Hannover, Germany
| | - Leonie Kandt
- Hannover Medical School, Institute of Pathology, Hannover, Germany
| | - Laura Bollmann
- Hannover Medical School, Institute of Pathology, Hannover, Germany
| | | | - Malte Gronewold
- Hannover Medical School, Institute of Pathology, Hannover, Germany
| | - Mieke Raap
- Hannover Medical School, Institute of Pathology, Hannover, Germany
| | - Ulrich Lehmann
- Hannover Medical School, Institute of Pathology, Hannover, Germany
| | - Oleg Gluz
- West German Study Group, Moenchengladbach, Germany.,Ev. Bethesda Hospital, Moenchengladbach, Germany.,University Clinics Cologne, Women's Clinic and Breast Center, Cologne, Germany
| | - Ulrike Nitz
- West German Study Group, Moenchengladbach, Germany.,Ev. Bethesda Hospital, Moenchengladbach, Germany
| | - Sherko Kuemmel
- West German Study Group, Moenchengladbach, Germany.,Clinics Essen-Mitte, Breast Unit, Essen, Germany.,Charité, Women's Clinic, Berlin, Germany
| | | | | | - Bahriye Aktas
- University Clinics Essen, Women's Clinic, Essen, Germany.,University Clinics Leipzig, Women's Clinic, Leipzig, Germany
| | | | | | | | - Ronald Kates
- West German Study Group, Moenchengladbach, Germany
| | - Rachel Wuerstlein
- Department OB&GYN and CCC Munich, LMU University Hospital, Breast Center, Munich, Germany
| | - Monika Graeser
- West German Study Group, Moenchengladbach, Germany.,Ev. Bethesda Hospital, Moenchengladbach, Germany.,Department of Gynecology, University Medical Center Hamburg, Hamburg, Germany
| | - Nadia Harbeck
- West German Study Group, Moenchengladbach, Germany.,Department OB&GYN and CCC Munich, LMU University Hospital, Breast Center, Munich, Germany
| | | | - Hans Kreipe
- Hannover Medical School, Institute of Pathology, Hannover, Germany
| |
Collapse
|
26
|
Lacaze JL, Aziza R, Chira C, De Maio E, Izar F, Jouve E, Massabeau C, Pradines A, Selmes G, Ung M, Zerdoud S, Dalenc F. Diagnosis, biology and epidemiology of oligometastatic breast cancer. Breast 2021; 59:144-156. [PMID: 34252822 PMCID: PMC8441842 DOI: 10.1016/j.breast.2021.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 05/31/2021] [Accepted: 06/23/2021] [Indexed: 11/01/2022] Open
Abstract
Does oligometastatic breast cancer (OMBC) deserve a dedicated treatment? Although some authors recommend multidisciplinary management of OMBC with a curative intent, there is no evidence proving this strategy beneficial in the absence of a randomized trial. The existing literature sheds little light on OMBC. Incidence is unknown; data available are either obsolete or biased; there is no consensus on the definition of OMBC and metastatic sites, nor on necessary imaging techniques. However, certain proposals merit consideration. Knowledge of eventual specific OMBC biological characteristics is limited to circulating tumor cell (CTC) counts. Given the data available for other cancers, studies on microRNAs (miRNAs), circulating tumor DNA (ctDNA) and genomic alterations should be developed Finally, safe and effective therapies do exist, but results of randomized trials will not be available for many years. Prospective observational cohort studies need to be implemented.
Collapse
Affiliation(s)
- Jean-Louis Lacaze
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département d'Oncologie Médicale, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France.
| | - Richard Aziza
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département d'Imagerie Médicale, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Ciprian Chira
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Radiothérapie, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Eleonora De Maio
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département d'Oncologie Médicale, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Françoise Izar
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Radiothérapie, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Eva Jouve
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Chirurgie, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Carole Massabeau
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Radiothérapie, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Anne Pradines
- Institut Claudius Regaud (ICR), Département Biologie Médicale Oncologique, Centre de Recherche en Cancérologie de Toulouse, (CRCT), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), INSERM UMR-1037, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Gabrielle Selmes
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Chirurgie, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Mony Ung
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département d'Oncologie Médicale, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Slimane Zerdoud
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Médecine Nucléaire, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Florence Dalenc
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département d'Oncologie Médicale, Université de Toulouse, UPS, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| |
Collapse
|
27
|
Biomarkers of Targeted Therapy and Immuno-Oncology in Cancers Metastatic to the Breast. Appl Immunohistochem Mol Morphol 2021; 28:661-668. [PMID: 31517642 PMCID: PMC7664953 DOI: 10.1097/pai.0000000000000808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The breast is a rare site for metastases, and their molecular characteristics have not been studied yet. Intrinsic molecular genetics, cancer characteristics, and breast tissue immune responses in diverse metastases to the breast have not been previously studied. We identified 64 patients with cancers metastatic to the breast: 51 carcinomas and 13 melanomas. Programmed death ligand 1 (PD-L1), steroid receptors, and HER2/neu expressions were evaluated using immunohistochemistry. Gene sequencing, copy number alterations, microsatellite instability, and tumor mutational burden were performed using next-generation sequencing platforms. The 3 most common primary sites for metastatic carcinomas were lung (37%), ovary (29%), and fallopian tubes/peritoneum (14%). TP53 mutations were commonly (50%) observed among the carcinoma cases, while other mutations were characteristic for the primary cancers (VHL in renal, BRCA1 in the fallopian tube, and BRAF in melanomas). High tumor mutational burden was detected in 5/14 carcinomas and 3/7 melanomas. Tumor cell PD-L1 expression was detected in 6 carcinomas, but not in any of the melanomas, whereas immune cells' expression of PD-L1 was seen in 17 carcinomas and 6 melanomas. Estrogen receptor status was positive in 13/49 carcinomas including 12 adenocarcinomas originating from the ovary and fallopian tube or peritoneum and 1 duodenal neuroendocrine carcinoma. No carcinoma was HER2/neu positive. Intrinsic genetic characteristics of the metastases to the breast followed the pattern commonly seen in primary tumors. Biomarkers of potential benefit to immune checkpoint inhibition therapy were limited to PD-L1-positive non-small cell lung cancer. No common characteristics of the heterogeneous group of tumor metastases to this organ were identified.
Collapse
|
28
|
Harbers L, Agostini F, Nicos M, Poddighe D, Bienko M, Crosetto N. Somatic Copy Number Alterations in Human Cancers: An Analysis of Publicly Available Data From The Cancer Genome Atlas. Front Oncol 2021; 11:700568. [PMID: 34395272 PMCID: PMC8355892 DOI: 10.3389/fonc.2021.700568] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/06/2021] [Indexed: 12/24/2022] Open
Abstract
Somatic copy number alterations (SCNAs) are a pervasive trait of human cancers that contributes to tumorigenesis by affecting the dosage of multiple genes at the same time. In the past decade, The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) initiatives have generated and made publicly available SCNA genomic profiles from thousands of tumor samples across multiple cancer types. Here, we present a comprehensive analysis of 853,218 SCNAs across 10,729 tumor samples belonging to 32 cancer types using TCGA data. We then discuss current models for how SCNAs likely arise during carcinogenesis and how genomic SCNA profiles can inform clinical practice. Lastly, we highlight open questions in the field of cancer-associated SCNAs.
Collapse
Affiliation(s)
- Luuk Harbers
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Bienko-Crosetto Lab, Science for Life Laboratory, Stockholm, Sweden
| | - Federico Agostini
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Bienko-Crosetto Lab, Science for Life Laboratory, Stockholm, Sweden
| | - Marcin Nicos
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, Lublin, Poland
| | - Dimitri Poddighe
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan
- Clinical Academic Department of Pediatrics, National Research Center for Maternal and Child Health, University Medical Center, Nur-Sultan, Kazakhstan
| | - Magda Bienko
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Bienko-Crosetto Lab, Science for Life Laboratory, Stockholm, Sweden
| | - Nicola Crosetto
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Bienko-Crosetto Lab, Science for Life Laboratory, Stockholm, Sweden
| |
Collapse
|
29
|
Yu Z, Song M, Chouchane L, Ma X. Functional Genomic Analysis of Breast Cancer Metastasis: Implications for Diagnosis and Therapy. Cancers (Basel) 2021; 13:cancers13133276. [PMID: 34208889 PMCID: PMC8268362 DOI: 10.3390/cancers13133276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Metastasis remains the greatest cause of fatalities in breast cancer patients world-wide. The process of metastases is highly complex, and the current research efforts in this area are still rather fragmented. The revolution of genomic profiling methods to analyze samples from human and animal models dramatically improved our understanding of breast cancer metastasis. This article summarizes the recent breakthroughs in genomic analyses of breast cancer metastasis and discusses their implications for prognostic and therapeutic applications. Abstract Breast cancer (BC) is one of the most diagnosed cancers worldwide and is the second cause of cancer related death in women. The most frequent cause of BC-related deaths, like many cancers, is metastasis. However, metastasis is a complicated and poorly understood process for which there is a shortage of accurate prognostic indicators and effective treatments. With the rapid and ever-evolving development and application of genomic sequencing technologies, many novel molecules were identified that play previously unappreciated and important roles in the various stages of metastasis. In this review, we summarize current advancements in the functional genomic analysis of BC metastasis and discuss about the potential prognostic and therapeutic implications from the recent genomic findings.
Collapse
Affiliation(s)
- Ziqi Yu
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA;
- Correspondence: (Z.Y.); (X.M.)
| | - Mei Song
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA;
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Qatar Foundation, Doha P.O. Box 24144, Qatar;
| | - Xiaojing Ma
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA;
- Correspondence: (Z.Y.); (X.M.)
| |
Collapse
|
30
|
Turner KM, Yeo SK, Holm TM, Shaughnessy E, Guan JL. Heterogeneity within molecular subtypes of breast cancer. Am J Physiol Cell Physiol 2021; 321:C343-C354. [PMID: 34191627 DOI: 10.1152/ajpcell.00109.2021] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Breast cancer is the quintessential example of how molecular characterization of tumor biology guides therapeutic decisions. From the discovery of the estrogen receptor to current clinical molecular profiles to evolving single-cell analytics, the characterization and compartmentalization of breast cancer into divergent subtypes is clear. However, competing with this divergent model of breast cancer is the recognition of intratumoral heterogeneity, which acknowledges the possibility that multiple different subtypes exist within a single tumor. Intratumoral heterogeneity is driven by both intrinsic effects of the tumor cells themselves as well as extrinsic effects from the surrounding microenvironment. There is emerging evidence that these intratumoral molecular subtypes are not static; rather, plasticity between divergent subtypes is possible. Interconversion between seemingly different subtypes within a tumor drives tumor progression, metastases, and treatment resistance. Therapeutic strategies must, therefore, contend with changing phenotypes in an individual patient's tumor. Identifying targetable drivers of molecular heterogeneity may improve treatment durability and disease progression.
Collapse
Affiliation(s)
- Kevin M Turner
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio.,Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Syn Kok Yeo
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Tammy M Holm
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Elizabeth Shaughnessy
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| |
Collapse
|
31
|
Amplifications of Stemness Gene Loci-New Markers for the Determination of the Need for Neoadjuvant Chemotherapy for Patients with Breast Cancer. A Prospective Study. J Pers Med 2021; 11:jpm11050397. [PMID: 34064798 PMCID: PMC8151881 DOI: 10.3390/jpm11050397] [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: 03/29/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 11/24/2022] Open
Abstract
In this prospective study, a new strategy for the prescription of neoadjuvant chemotherapy (NAC) was prospectively tested and depended on the presence of stemness gene amplifications in the tumor before treatment, which in our early studies showed a connection with metastasis. The study included 92 patients with grade IIA–IIIB luminal B breast cancer. Patients underwent a biopsy before treatment, and with the use of a CytoScan HD Array microarray (Affymetrix, Santa Clara, CA, USA), the presence of stemness gene amplifications (3q, 5p, 6p, 7q, 8q, 13q, 9p, 9q, 10p, 10q21.1, 16p, 18chr, 19p) in the tumor was determined. In group 1 (n = 41), in the presence of two or more amplifications, patients were prescribed a personalized NAC regimen. In group 2 (n = 21), if there was no amplification of stemness genes in the tumor, then patients were not prescribed NAC, and treatment began with surgery. Group 3 (n = 30) served as a historical control. The frequency of an objective response to NAC in groups 1 and 3 was 79%. Nonmetastatic survival was found in 100% of patients in group 2, who did not undergo NAC. In patients in group 1, the frequency of metastasis was 10% (4/41). At the same time, in patients in group 3, who received NAC, the rate of metastasis was 47% (14/30). The differences between group 1 and group 3 and between group 2 and group 3 were statistically significant, both by Fisher’s criterion and a log-rank test. The appointment of NAC was most feasible in patients with clones with stemness gene amplifications in the primary tumor, while in the absence of amplifications, preoperative chemotherapy led to a sharp decrease in metastasis-free survival. This strategy of NAC prescription allowed us to achieve 93% metastatic survival in patients with breast cancer.
Collapse
|
32
|
Zhao W, Sun L, Dong G, Wang X, Jia Y, Tong Z. Receptor conversion impacts outcomes of different molecular subtypes of primary breast cancer. Ther Adv Med Oncol 2021; 13:17588359211012982. [PMID: 33995598 PMCID: PMC8111518 DOI: 10.1177/17588359211012982] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/01/2021] [Indexed: 11/16/2022] Open
Abstract
Background Although the conversion of clinically used breast cancer biomarkers such as estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) between primary tumors and metastatic lesions is well recognized, data on whether receptor conversion has an effect on therapy management and survival in patients with metastatic breast cancer is limited. This study aimed to investigate the clinical implications of receptor conversion throughout tumor progression. Methods In total, 2450 patients diagnosed with metastatic breast cancer in Tianjin Medical University Cancer Institute and Hospital were analyzed and 426 female patients with available biopsy results from both primary and metastatic sites were included in this study. We investigated the alteration of ER, PR and HER2 during breast cancer progression and evaluated the therapy management and prognostic value of receptor conversion. Results The conversion rates of ER, PR, and HER2 between primary tumors and metastasis were 21.1% (McNemar's test p < 0.001), 33.2% (p < 0.001), and 11.6% (p = 0.868), respectively. Evaluation of ER, PR, and HER2 status in multiple consecutive metastases revealed a change in 19.1% (p > 0.05), 23.5% (p = 0.021), and 9.8% (p > 0.05) of patients, respectively. Adjuvant therapy (chemotherapy/endocrine therapy) was related to hormone receptor conversion (p < 0.05). A statistically significant differential survival associated with hormone receptor (ER/PR) conversion (log-rank p < 0.05) was observed. In the multivariate analysis, ER conversion was an independent influence factor of survival (p < 0.05). Molecular typing conversion in primary and metastatic lesions also had a significant effect on survival (p < 0.05). We found that changing treatment based on the receptor conversion could affect clinical outcomes (p < 0.05). Conclusions Our findings indicated that receptor conversion during breast tumor progression had a significant effect on survival. Most importantly, our findings proved that patients with receptor conversion benefited from a change in therapy.
Collapse
Affiliation(s)
- Weipeng Zhao
- Department of Breast Oncology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Ti Yuan Bei, Hexi District, Tianjin, China
| | - Linlin Sun
- Department of Breast Oncology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Ti Yuan Bei, Hexi District, Tianjin, China
| | - Guolei Dong
- Department of Breast Oncology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Ti Yuan Bei, Hexi District, Tianjin, China
| | - Xiaorui Wang
- Department of Breast Oncology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Ti Yuan Bei, Hexi District, Tianjin, China
| | - Yan Jia
- Department of Breast Oncology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Ti Yuan Bei, Hexi District, Tianjin, China
| | - Zhongsheng Tong
- Department of Breast Oncology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, West Huan-Hu Road, Ti Yuan Bei, Hexi District, Tianjin, 300060, China
| |
Collapse
|
33
|
Kingston B, Cutts RJ, Bye H, Beaney M, Walsh-Crestani G, Hrebien S, Swift C, Kilburn LS, Kernaghan S, Moretti L, Wilkinson K, Wardley AM, Macpherson IR, Baird RD, Roylance R, Reis-Filho JS, Hubank M, Faull I, Banks KC, Lanman RB, Garcia-Murillas I, Bliss JM, Ring A, Turner NC. Genomic profile of advanced breast cancer in circulating tumour DNA. Nat Commun 2021; 12:2423. [PMID: 33893289 PMCID: PMC8065112 DOI: 10.1038/s41467-021-22605-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 03/16/2021] [Indexed: 12/31/2022] Open
Abstract
The genomics of advanced breast cancer (ABC) has been described through tumour tissue biopsy sequencing, although these approaches are limited by geographical and temporal heterogeneity. Here we use plasma circulating tumour DNA sequencing to interrogate the genomic profile of ABC in 800 patients in the plasmaMATCH trial. We demonstrate diverse subclonal resistance mutations, including enrichment of HER2 mutations in HER2 positive disease, co-occurring ESR1 and MAP kinase pathway mutations in HR + HER2- disease that associate with poor overall survival (p = 0.0092), and multiple PIK3CA mutations in HR + disease that associate with short progression free survival on fulvestrant (p = 0.0036). The fraction of cancer with a mutation, the clonal dominance of a mutation, varied between genes, and within hotspot mutations of ESR1 and PIK3CA. In ER-positive breast cancer subclonal mutations were enriched in an APOBEC mutational signature, with second hit PIK3CA mutations acquired subclonally and at sites characteristic of APOBEC mutagenesis. This study utilises circulating tumour DNA analysis in a large clinical trial to demonstrate the subclonal diversification of pre-treated advanced breast cancer, identifying distinct mutational processes in advanced ER-positive breast cancer, and novel therapeutic opportunities.
Collapse
Affiliation(s)
- Belinda Kingston
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rosalind J Cutts
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Hannah Bye
- Centre for Molecular Pathology, Royal Marsden Hospital, London, UK
| | - Matthew Beaney
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Giselle Walsh-Crestani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Sarah Hrebien
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Claire Swift
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | | | - Laura Moretti
- ICR-CTSU, The Institute of Cancer Research, London, UK
| | | | - Andrew M Wardley
- NIHR Manchester Clinical Research Facility at The Christie, Manchester Academic Health Science Centre & Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology Medicine & Health, University of Manchester, Manchester, UK
| | | | | | - Rebecca Roylance
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Michael Hubank
- Centre for Molecular Pathology, Royal Marsden Hospital, London, UK
| | - Iris Faull
- Guardant Health, Inc., Redwood City, CA, USA
| | | | | | - Isaac Garcia-Murillas
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Alistair Ring
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK.
| | - Nicholas C Turner
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK.
| |
Collapse
|
34
|
Hagio K, Amano T, Hayashi H, Takeshita T, Oshino T, Kikuchi J, Ohhara Y, Yabe I, Kinoshita I, Nishihara H, Yamashita H. Impact of clinical targeted sequencing on endocrine responsiveness in estrogen receptor-positive, HER2-negative metastatic breast cancer. Sci Rep 2021; 11:8109. [PMID: 33854152 PMCID: PMC8047009 DOI: 10.1038/s41598-021-87645-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/01/2021] [Indexed: 01/22/2023] Open
Abstract
Clinical targeted sequencing allows for the selection of patients expected to have a better treatment response, and reveals mechanisms of resistance to molecular targeted therapies based on actionable gene mutations. We underwent comprehensive genomic testing with either our original in-house CLHURC system or with OncoPrime. Samples from 24 patients with estrogen receptor-positive, human epidermal growth factor receptor 2-negative metastatic breast cancer underwent targeted sequencing between 2016 and 2018. Germline and somatic gene alterations and patients' prognosis were retrospectively analyzed according to the response to endocrine therapy. All of the patients had one or more germline and/or somatic gene alterations. Four patients with primary or secondary endocrine-resistant breast cancer harbored germline pathogenic variants of BRCA1, BRCA2, or PTEN. Among somatic gene alterations, TP53, PIK3CA, AKT1, ESR1, and MYC were the most frequently mutated genes. TP53 gene mutation was more frequently observed in patients with primary endocrine resistance compared to those with secondary endocrine resistance or endocrine-responsive breast cancer. Recurrent breast cancer patients carrying TP53-mutant tumors had significantly worse overall survival compared to those with TP53-wild type tumors. Our 160-gene cancer panel will be useful to identify clinically actionable gene alterations in breast cancer in clinical practice.
Collapse
Affiliation(s)
- Kanako Hagio
- Department of Breast Surgery, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, 060-8648, Japan
| | - Toraji Amano
- Clinical Research and Medical Innovation Center, Hokkaido University Hospital, Sapporo, Japan
| | - Hideyuki Hayashi
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjukuku, Tokyo, 160-8582, Japan
| | - Takashi Takeshita
- Department of Breast Surgery, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, 060-8648, Japan
| | - Tomohiro Oshino
- Department of Breast Surgery, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, 060-8648, Japan
| | - Junko Kikuchi
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
| | - Yoshihito Ohhara
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
| | - Ichiro Yabe
- Division of Clinical Genetics, Hokkaido University Hospital, Sapporo, Japan
| | - Ichiro Kinoshita
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
| | - Hiroshi Nishihara
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjukuku, Tokyo, 160-8582, Japan
| | - Hiroko Yamashita
- Department of Breast Surgery, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, 060-8648, Japan.
| |
Collapse
|
35
|
Evolutionary Trajectories and Genomic Divergence in Localized Breast Cancers after Ipsilateral Breast Tumor Recurrence. Cancers (Basel) 2021; 13:cancers13081821. [PMID: 33920370 PMCID: PMC8069481 DOI: 10.3390/cancers13081821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Ipsilateral breast tumor relapse (IBTR) occurs in 5–10% of localized breast cancers (BCs) within 10 years of incidence, despite proper treatment of the primary lesion. However, the clinical consequences of evolutionary trajectories of BC cells and their impact on IBTR remain poorly understood. Here, we conducted a longitudinal genomic analysis of 10 matched localized BC patients with IBTR. Overall, we identified the differences in homologous recombination deficiency, chromosomal instability, and somatic mutation drivers between primary and relapsed lesions. Our analyses highlighted three clonal architectures that shape by distinct mutagenic processes and subclonal diversification during relapse progression. Finally, this study provided a framework, which integrated actionable biomarkers with clonal architectures, towards improvement of future treatment decisions. Abstract The evolutionary trajectories that drive clinical and therapeutic consequences in localized breast cancers (BCs) with ipsilateral breast tumor relapse (IBTR) remain largely unknown. Analyses of longitudinal paired whole-exome sequencing data from 10 localized BC patients with IBTR reveal that, compared to primary breast tumors, homologous recombination (HR) deficiency, inactivation of the HR pathway, chromosomal instability, and somatic driver mutations are more frequent. Furthermore, three major models of evolution in IBTR are summarized, through which relative contributions of mutational signatures shift, and the subclonal diversity expansions are shown. Optimal treatment regimens are suggested by the clinically relevant molecular features, such as HR deficiency (20%) or specific alterations (30%) with sensitivity to available FDA-approved drugs. Finally, a rationale for the development of the therapeutic management framework is provided. This study sheds light on the complicated evolution patterns in IBTR and has significant clinical implications for future improvement of treatment decisions.
Collapse
|
36
|
Peng L, Zhang Z, Zhao D, Zhao J, Mao F, Sun Q. Discordance in ER, PR, HER2, and Ki-67 Expression Between Primary and Recurrent/Metastatic Lesions in Patients with Primary Early Stage Breast Cancer and the Clinical Significance: Retrospective Analysis of 75 Cases. Pathol Oncol Res 2021; 27:599894. [PMID: 34257555 PMCID: PMC8262146 DOI: 10.3389/pore.2021.599894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 03/02/2021] [Indexed: 12/23/2022]
Abstract
Background: The objective was to explore the discordance in the expression of the estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and Ki-67 between primary and recurrent/metastatic lesions in patients with early stage breast cancer as well as the prognostic impact. Method: Patients with early-stage primary breast cancer and confirmed recurrence/metastasis at Peking Union Medical College Hospital between January 2005 and August 2018 were screened. The details of discordance in each parameter between primary and recurrent/metastatic lesions and progression were recorded. Regression and survival analysis were applied to determine the association and clinical impact of the discordance. Results: We evaluated 75 patients. The discordance rate of ER, PR, HER2, and Ki-67 expression was 9.3, 14.7, 14.7, and 21.5%, respectively. Additionally, 66.7, 11.8, 14.3, and 0% of patients with Luminal A, Luminal B, HER2, and triple-negative primary tumors presented with a different subtype for the recurrent/metastatic tumors, respectively. No statistical difference in progression-free survival was observed according to the subtype of the recurrent or metastatic breast cancer (p > 0.05). Among 69 patients for whom treatment was adjusted after recurrence or metastasis, 66 patients remained recurrence-free during the follow-up period. Conclusion: For patients with early-stage breast cancer, the ER, PR, HER2, and Ki-67 expression profile for recurrent/metastatic tumors does not always match that of the primary tumor. After adjusting treatment according to the receptor expression in recurrent/metastatic lesions, most patients remained progression-free during the follow-up period.
Collapse
Affiliation(s)
- Li Peng
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Zhen Zhang
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Dachun Zhao
- Department of Pathology, Peking Union Medical College Hospital, Beijing, China
| | - Jialin Zhao
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Feng Mao
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Qiang Sun
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| |
Collapse
|
37
|
Krause A, Roma L, Lorber T, Dietsche T, Perrina V, Müller DC, Lardinois D, Ruiz C, Savic Prince S, Piscuoglio S, Ng CKY, Bubendorf L. Genomic evolutionary trajectory of metastatic squamous cell carcinoma of the lung. Transl Lung Cancer Res 2021; 10:1792-1803. [PMID: 34012793 PMCID: PMC8107762 DOI: 10.21037/tlcr-21-48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background The extent of inter- and intratumoral genomic heterogeneity and the clonal evolution of metastatic squamous cell carcinoma of the lung (LUSC) are poorly understood. Genomic studies of LUSC are challenged by their low tumor cell content. We sought to define the genomic landscape and evolutionary trajectories of metastatic LUSC combining nuclei-flow sorting and whole exome sequencing. Methods Five patients with primary LUSC and six matched metastases were investigated. Tumor nuclei were sorted based on ploidy and expression of cytokeratin to enrich for tumor cells for whole exome sequencing. Results Flow-sorting increased the mean tumor purity from 26% (range, 12–50%) to 73% (range, 42–93%). Overall, primary LUSCs and their matched metastases shared a median of 79% (range, 67–85%) of copy number aberrations (CNAs) and 74% (range, 65–94%) of non-synonymous mutations, including in tumor suppressor genes such as TP53. Furthermore, the ploidy of the tumors remained unchanged between primary and metastasis in 4/5 patients over time. We found differences in the mutational signatures of shared mutations compared to the private mutations in the primary or metastasis. Conclusions Our results demonstrate a close genomic relationship between primary LUSCs and their matched metastases, suggesting late dissemination of the metastases from the primary tumors during tumor evolution.
Collapse
Affiliation(s)
- Arthur Krause
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Luca Roma
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Thomas Lorber
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Tanja Dietsche
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Valeria Perrina
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - David C Müller
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Christian Ruiz
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Spasenija Savic Prince
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Salvatore Piscuoglio
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.,Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine; University of Basel, Basel, Switzerland
| | - Charlotte K Y Ng
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Lukas Bubendorf
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| |
Collapse
|
38
|
Callens C, Driouch K, Boulai A, Tariq Z, Comte A, Berger F, Belin L, Bièche I, Servois V, Legoix P, Bernard V, Baulande S, Chemlali W, Bidard FC, Fourchotte V, Salomon AV, Brain E, Lidereau R, Bachelot T, Saghatchian M, Campone M, Giacchetti S, Zafrani BS, Cottu P. Molecular features of untreated breast cancer and initial metastatic event inform clinical decision-making and predict outcome: long-term results of ESOPE, a single-arm prospective multicenter study. Genome Med 2021; 13:44. [PMID: 33722295 PMCID: PMC7962302 DOI: 10.1186/s13073-021-00862-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/25/2021] [Indexed: 12/04/2022] Open
Abstract
Background Prognosis evaluation of advanced breast cancer and therapeutic strategy are mostly based on clinical features of advanced disease and molecular profiling of the primary tumor. Very few studies have evaluated the impact of metastatic subtyping during the initial metastatic event in a prospective study. The genomic landscape of metastatic breast cancer has mostly been described in very advanced, pretreated disease, limiting the findings transferability to clinical use. Methods We developed a multicenter, single-arm, prospective clinical trial in order to address these issues. Between November 2010 and September 2013, 123 eligible patients were included. Patients at the first, untreated metastatic event were eligible. All matched primary tumors and metastatic samples were centrally reviewed for pathological typing. Targeted and whole-exome sequencing was applied to matched pairs of frozen tissue. A multivariate overall survival analysis was performed (median follow-up 64 months). Results Per central review in 84 patients (out of 130), we show that luminal A breast tumors are more prone to subtype switching. By combining targeted sequencing of a 91 gene panel (n = 67) and whole-exome sequencing (n = 30), a slight excess of mutations is observed in the metastases. Luminal A breast cancer has the most heterogeneous mutational profile and the highest number of mutational signatures, when comparing primary tumor and the matched metastatic tissue. Tumors with a subtype change have more mutations that are private. The metastasis-specific mutation load is significantly higher in late than in de novo metastases. The most frequently mutated genes were TP53 and PIK3CA. The most frequent metastasis-specific druggable genes were PIK3CA, PTEN, KDR, ALK, CDKN2A, NOTCH4, POLE, SETD2, SF3B1, and TSC2. Long-term outcome is driven by a combination of tumor load and metastasis biology. Conclusions Profiling of the first, untreated, metastatic event of breast cancer reveals a profound heterogeneity mostly in luminal A tumors and in late metastases. Based on this profiling, we can derive information relevant to prognosis and therapeutic intervention, which support current guidelines recommending a biopsy at the first metastatic relapse. Trial registration The trial was registered at ClinicalTrials.gov (NCT01956552). Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00862-6.
Collapse
Affiliation(s)
- Céline Callens
- Genetics Department, Institut Curie, PSL Research University, Paris, France
| | - Keltouma Driouch
- Genetics Department, Institut Curie, PSL Research University, Paris, France
| | - Anaïs Boulai
- Genetics Department, Institut Curie, PSL Research University, Paris, France
| | - Zakia Tariq
- Genetics Department, Institut Curie, PSL Research University, Paris, France
| | - Aurélie Comte
- Department of Medical Oncology, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | | | - Lisa Belin
- Department of Biostatistics, Institut Curie, Saint-Cloud, France
| | - Ivan Bièche
- Genetics Department, Institut Curie, PSL Research University, Paris, France
| | - Vincent Servois
- Imaging Department, Institut Curie, PSL Research University, Paris, France
| | - Patricia Legoix
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, PSL Research University, Paris, France
| | - Virginie Bernard
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, PSL Research University, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, PSL Research University, Paris, France
| | - Walid Chemlali
- Genetics Department, Institut Curie, PSL Research University, Paris, France
| | - François-Clément Bidard
- Department of Medical Oncology, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | | | - Anne Vincent- Salomon
- Pathology and Tumor Biology Department, Institut Curie, PSL Research University, Paris, France
| | - Etienne Brain
- Medical Oncology, Institut Curie, Saint-Cloud, France
| | - Rosette Lidereau
- Genetics Department, Institut Curie, PSL Research University, Paris, France
| | | | | | - Mario Campone
- Institut de Cancérologie de l'Ouest Nantes, Nantes, France
| | | | - Brigitte Sigal Zafrani
- Pathology and Tumor Biology Department, Institut Curie, PSL Research University, Paris, France
| | - Paul Cottu
- Department of Medical Oncology, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France.
| |
Collapse
|
39
|
Tian C, Liu S, Wang Y, Song X. Prognosis and Genomic Landscape of Liver Metastasis in Patients With Breast Cancer. Front Oncol 2021; 11:588136. [PMID: 33777740 PMCID: PMC7991092 DOI: 10.3389/fonc.2021.588136] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 02/01/2021] [Indexed: 12/20/2022] Open
Abstract
Objective The prognosis of breast cancer liver metastasis (BCLM) is poor, and its molecular mechanism is unclear. We aimed to determine the factors that affect the prognosis of patients with BCLM and investigate the genomic landscape of liver metastasis (LM). Methods We described the prognosis of patients with BCLM and focused on prognosis prediction for these patients based on clinicopathological factors. Nomogram models were constructed for progression-free survival (PFS) and overall survival (OS) by using a cohort of 231 patients with BCLM who underwent treatment at Shandong Cancer Hospital and Institute (SCHI). We explored the molecular mechanism of LM and constructed driver genes, mutation signatures by using a targeted sequencing dataset of 217 samples of LM and 479 unpaired samples of primary breast cancer (pBC) from Memorial Sloan Kettering Cancer Center (MSKCC). Results The median follow-up time for 231 patients with BCLM in the SCHI cohort was 46 months. The cumulative incidence of LM at 1, 2, and 5 years was 17.5%, 45.0%, and 86.8%, respectively. The median PFS and OS were 7 months (95% CI, 6-8) and 22 months (95% CI, 19-25), respectively. The independent factors that increased the progression risk of patients with LM were Karnofsky performance status (KPS) ≤ 80, TNBC subtype, grade III, increasing trend of CA153, and disease-free interval (DFS) ≤ 1 year. Simultaneously, the independent factors that increased the mortality risk of patients with LM were Ki-67 ≥ 30%, grade III, increasing trend of CA153, pain with initial LM, diabetes, and DFI ≤ 1 year. In the MSKCC dataset, the LM driver genes were ESR1, AKT1, ERBB2, and FGFR4, and LM matched three prominent mutation signatures: APOBEC cytidine deaminase, ultraviolet exposure, and defective DNA mismatch repair. Conclusion This study systematically describes the survival prognosis and characteristics of LM from the clinicopathological factors to the genetic level. These results not only enable clinicians to assess the risk of disease progression in patients with BCLM to optimize treatment options, but also help us better understand the underlying mechanisms of tumor metastasis and evolution and provide new therapeutic targets with potential benefits for drug-resistant patients.
Collapse
Affiliation(s)
- Chonglin Tian
- Graduate School, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.,Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Sujing Liu
- Department of Radiation Oncology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Yongsheng Wang
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xianrang Song
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| |
Collapse
|
40
|
Caswell-Jin JL, Lorenz C, Curtis C. Molecular Heterogeneity and Evolution in Breast Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2021. [DOI: 10.1146/annurev-cancerbio-060220-014137] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Breast cancer comprises a heterogeneous group of tumor subtypes, whether defined by immunohistochemistry of key proteins, RNA expression profiles, or genetic alterations, and each of these subtypes may benefit from a distinct treatment approach. However, there can be striking heterogeneity within tumors, which may pose challenges to the development of personalized approaches to therapy. Intratumor heterogeneity can be divided into three main categories: genetic, phenotypic, and microenvironmental. Here, we review technologies to interrogate these three categories of heterogeneity in patient samples, as well as the current state of understanding of these categories in breast cancer, from cell to cell, across different regions of the same tumor mass, across treatment, and across metastasis. Efforts to characterize tumor heterogeneity longitudinally will be crucial to the development of personalized oncology for breast cancer.
Collapse
Affiliation(s)
- Jennifer L. Caswell-Jin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Carina Lorenz
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Christina Curtis
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| |
Collapse
|
41
|
Rong G, Yi Z, Ma F, Guan Y, Xu Y, Li L, Xu B. DNA damage response as a prognostic indicator in metastatic breast cancer via mutational analysis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:220. [PMID: 33708847 PMCID: PMC7940884 DOI: 10.21037/atm-20-2137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background High tumor heterogeneity contributes to breast cancer recurrence and metastasis. However, the lack of indicators to serve as precise and reliable means of predicting breast cancer prognosis has yet to be addressed. This study aims to reveal the prognostic relevance of mutations in metastatic breast cancer (MBC) by large-scale circulating tumor DNA (ctDNA) analysis in China. Methods We performed ctDNA panel-captured sequencing of 958 blood samples from MBC patients including 494 hormone receptor (HR)-positive cases, 130 human epidermal growth factor receptor 2-positive cases, and 177 triple-negative breast cancer (TNBC) cases. The somatic mutations and potential targets were assessed. Progression-free survival (PFS) was analyzed using the Kaplan-Meier method. Results In 801 of the 958 MBC blood samples, 663 mutated genes and 5,829 nonsynonymous alterations were identified. Mutated genes of the highest frequency were tumor protein p53 (TP53, 54%), phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA, 41%), estrogen receptor 1 (ESR1, 12%), myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3, 11%), DNA (cytosine-5)-methyltransferase 3A (DNMT3A, 10%), erb-b2 receptor tyrosine kinase 2 (ERBB2, 10%), GATA binding protein 3 (GATA3, 8%), FAT atypical cadherin 1 (FAT1, 7%), phosphatase and tensin homolog (PTEN, 6%), and mitogen-activated protein kinase kinase kinase 1 (MAP3K1, 6%). Enriched mutations and driver genes in MBC varied across stages and in multiple subtypes. Moreover, TP53, ERBB2, or coexisting TP53/PIK3CA mutations in MBC were remarkably related with shorter PFS. Mutated DNA damage response (DDR) genes were significantly associated with tumor mutation burden and mutant-allele tumor heterogeneity score, as well as with worse clinical outcome. Conclusions Our findings indicate that the mutations of TP53, PIK3CA, ERBB2, and in particular, DDR genes, in MBC might be relevant indicators of unfavorable prognosis in MBC.
Collapse
Affiliation(s)
- Guohua Rong
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zongbi Yi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanfang Guan
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Yaping Xu
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Lifeng Li
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
42
|
Hernández-Lemus E, Martínez-García M. Pathway-Based Drug-Repurposing Schemes in Cancer: The Role of Translational Bioinformatics. Front Oncol 2021; 10:605680. [PMID: 33520715 PMCID: PMC7841291 DOI: 10.3389/fonc.2020.605680] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/24/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer is a set of complex pathologies that has been recognized as a major public health problem worldwide for decades. A myriad of therapeutic strategies is indeed available. However, the wide variability in tumor physiology, response to therapy, added to multi-drug resistance poses enormous challenges in clinical oncology. The last years have witnessed a fast-paced development of novel experimental and translational approaches to therapeutics, that supplemented with computational and theoretical advances are opening promising avenues to cope with cancer defiances. At the core of these advances, there is a strong conceptual shift from gene-centric emphasis on driver mutations in specific oncogenes and tumor suppressors-let us call that the silver bullet approach to cancer therapeutics-to a systemic, semi-mechanistic approach based on pathway perturbations and global molecular and physiological regulatory patterns-we will call this the shrapnel approach. The silver bullet approach is still the best one to follow when clonal mutations in driver genes are present in the patient, and when there are targeted therapies to tackle those. Unfortunately, due to the heterogeneous nature of tumors this is not the common case. The wide molecular variability in the mutational level often is reduced to a much smaller set of pathway-based dysfunctions as evidenced by the well-known hallmarks of cancer. In such cases "shrapnel gunshots" may become more effective than "silver bullets". Here, we will briefly present both approaches and will abound on the discussion on the state of the art of pathway-based therapeutic designs from a translational bioinformatics and computational oncology perspective. Further development of these approaches depends on building collaborative, multidisciplinary teams to resort to the expertise of clinical oncologists, oncological surgeons, and molecular oncologists, but also of cancer cell biologists and pharmacologists, as well as bioinformaticians, computational biologists and data scientists. These teams will be capable of engaging on a cycle of analyzing high-throughput experiments, mining databases, researching on clinical data, validating the findings, and improving clinical outcomes for the benefits of the oncological patients.
Collapse
Affiliation(s)
- Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mireya Martínez-García
- Sociomedical Research Unit, National Institute of Cardiology “Ignacio Chávez”, Mexico City, Mexico
| |
Collapse
|
43
|
Krause A, Roma L, Lorber T, Habicht J, Lardinois D, De Filippo MR, Prince SS, Piscuoglio S, Ng C, Bubendorf L. Deciphering the clonal relationship between glandular and squamous components in adenosquamous carcinoma of the lung using whole exome sequencing. Lung Cancer 2020; 150:132-138. [PMID: 33137577 DOI: 10.1016/j.lungcan.2020.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/17/2020] [Accepted: 10/17/2020] [Indexed: 02/07/2023]
Abstract
Adenosquamous carcinoma of the lung (ASC) is a rare subtype of non-small cell lung cancer, consisting of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) components. ASC shows morphological characteristics of classic LUAD and LUSC but behaves more aggressively. Although ASC can serve as a model of lung cancer heterogeneity and transdifferentiation, its genomic background remains poorly understood. In this study, we sought to explore the genomic landscape of macrodissected LUAD and LUSC components of three ASC using whole exome sequencing (WES). Identified truncal mutations included the pan-cancer tumor-suppressor gene TP53 but also EGFR, BRAF, and MET, which are characteristic for LUAD but uncommon in LUSC. No truncal mutation of classical LUSC driver mutations were found. Both components showed unique driver mutations that did not overlap between the three ASC. Mutational signatures of truncal mutations differed from those of the branch mutations in their descendants LUAD and LUSC. Most common signatures were related to aging (1, 5) and smoking (4). Truncal chromosomal copy number aberrations shared by all three ASC included losses of 3p, 15q and 19p, and an amplified region in 5p. Furthermore, we detected loss of STK11 and SOX2 amplification in ASC, which has previously been shown to drive transdifferentiation from LUAD to LUSC in preclinical mouse models. Conclusively, this is the first study using WES to elucidate the clonal evolution of ASC. It provides strong evidence that the LUAD and LUSC components of ASC share a common origin and that the LUAD component appears to transform to LUSC.
Collapse
Affiliation(s)
- Arthur Krause
- Institute of Molecular Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Luca Roma
- Institute of Molecular Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Thomas Lorber
- Institute of Molecular Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - James Habicht
- Thoracic Surgery, St. Clara Hospital, Basel, Switzerland
| | | | - Maria Rosaria De Filippo
- Institute of Molecular Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland; Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland
| | - Spasenija Savic Prince
- Institute of Molecular Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Salvatore Piscuoglio
- Institute of Molecular Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland; Visceral Surgery Research Laboratory, Clarunis, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - CharlotteKY Ng
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Lukas Bubendorf
- Institute of Molecular Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland.
| |
Collapse
|
44
|
Siraj S, Masoodi T, Siraj AK, Azam S, Qadri Z, Ahmed SO, AlBalawy WN, Al-Obaisi KA, Parvathareddy SK, AlManea HM, AlHussaini HF, Abduljabbar A, Alhomoud S, Al-Dayel FH, Alkuraya FS, Al-Kuraya KS. Clonal Evolution and Timing of Metastatic Colorectal Cancer. Cancers (Basel) 2020; 12:cancers12102938. [PMID: 33053768 PMCID: PMC7601934 DOI: 10.3390/cancers12102938] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is the third most frequently diagnosed cancer worldwide, where ~50% of patients develop metastasis, despite current improved management. Genomic characterisation of metastatic CRC, and elucidating the effects of therapy on the metastatic process, are essential to help guide precision medicine. Multi-region whole-exome sequencing was performed on 191 sampled tumour regions of patient-matched therapy-naïve and treated CRC primary tumours (n = 92 tumour regions) and metastases (n = 99 tumour regions), in 30 patients. Somatic variants were analysed to define the origin, composition, and timing of seeding in the metastatic progression of therapy-naïve and treated metastatic CRC. High concordance, with few genomic differences, was observed between primary CRC and metastases. Most cases supported a late dissemination model, via either monoclonal or polyclonal seeding. Polyclonal seeding appeared more common in therapy-naïve metastases than in treated metastases. Whereby, treatment prompted for the selection of distinct resistant clones, through monoclonal seeding to distant metastatic sites. Overall, this study reinforces the importance of early clinical detection and surgical excision of the CRC tumour, whilst further highlighting the clinical challenges for metastatic CRC with increased intratumour heterogeneity (either due to early dissemination or polyclonal metastatic spread) and the underlying risk of future therapeutic resistance in treated patients.
Collapse
Affiliation(s)
- Sarah Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Tariq Masoodi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Abdul K. Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Saud Azam
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Zeeshan Qadri
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Saeeda O. Ahmed
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Wafaa N. AlBalawy
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Khadija A. Al-Obaisi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Sandeep K. Parvathareddy
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Hadeel M. AlManea
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (H.M.A.); (H.F.A.); (F.H.A.-D.)
| | - Hussah F. AlHussaini
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (H.M.A.); (H.F.A.); (F.H.A.-D.)
| | - Alaa Abduljabbar
- Department of Surgery, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.)
| | - Samar Alhomoud
- Department of Surgery, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.)
| | - Fouad H. Al-Dayel
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (H.M.A.); (H.F.A.); (F.H.A.-D.)
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Khawla S. Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
- Correspondence: ; Tel.: +966-112-055-2167
| |
Collapse
|
45
|
Dessources K, Da Cruz Paula A, Pareja F, Stylianou A, Cybulska P, Farmanbar A, Chandarlapaty S, Abu-Rustum NR, Reis-Filho JS, Weigelt B, Mueller JJ. Acquisition of APOBEC Mutagenesis and Microsatellite Instability Signatures in the Development of Brain Metastases in Low-Grade, Early-Stage Endometrioid Endometrial Carcinoma. JCO Precis Oncol 2020; 4:PO.20.00044. [PMID: 33163849 PMCID: PMC7608574 DOI: 10.1200/po.20.00044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anthe Stylianou
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paulina Cybulska
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amir Farmanbar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | |
Collapse
|
46
|
Paul MR, Pan TC, Pant DK, Shih NN, Chen Y, Harvey KL, Solomon A, Lieberman D, Morrissette JJ, Soucier-Ernst D, Goodman NG, Stavropoulos SW, Maxwell KN, Clark C, Belka GK, Feldman M, DeMichele A, Chodosh LA. Genomic landscape of metastatic breast cancer identifies preferentially dysregulated pathways and targets. J Clin Invest 2020; 130:4252-4265. [PMID: 32657779 PMCID: PMC7410083 DOI: 10.1172/jci129941] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/05/2020] [Indexed: 12/21/2022] Open
Abstract
Nearly all breast cancer deaths result from metastatic disease. Despite this, the genomic events that drive metastatic recurrence are poorly understood. We performed whole-exome and shallow whole-genome sequencing to identify genes and pathways preferentially mutated or copy-number altered in metastases compared with the paired primary tumors from which they arose. Seven genes were preferentially mutated in metastases - MYLK, PEAK1, SLC2A4RG, EVC2, XIRP2, PALB2, and ESR1 - 5 of which are not significantly mutated in any type of human primary cancer. Four regions were preferentially copy-number altered: loss of STK11 and CDKN2A/B, as well as gain of PTK6 and the membrane-bound progesterone receptor, PAQR8. PAQR8 gain was mutually exclusive with mutations in the nuclear estrogen and progesterone receptors, suggesting a role in treatment resistance. Several pathways were preferentially mutated or altered in metastases, including mTOR, CDK/RB, cAMP/PKA, WNT, HKMT, and focal adhesion. Immunohistochemical analyses revealed that metastases preferentially inactivate pRB, upregulate the mTORC1 and WNT signaling pathways, and exhibit nuclear localization of activated PKA. Our findings identify multiple therapeutic targets in metastatic recurrence that are not significantly mutated in primary cancers, implicate membrane progesterone signaling and nuclear PKA in metastatic recurrence, and provide genomic bases for the efficacy of mTORC1, CDK4/6, and PARP inhibitors in metastatic breast cancer.
Collapse
Affiliation(s)
- Matt R. Paul
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Abramson Family Cancer Research Institute
- Department of Cancer Biology
| | - Tien-chi Pan
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Abramson Family Cancer Research Institute
- Department of Cancer Biology
| | - Dhruv K. Pant
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Abramson Family Cancer Research Institute
- Department of Cancer Biology
| | - Natalie N.C. Shih
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Department of Pathology and Laboratory Medicine
| | - Yan Chen
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Abramson Family Cancer Research Institute
- Department of Cancer Biology
| | - Kyra L. Harvey
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Abramson Family Cancer Research Institute
- Department of Cancer Biology
| | - Aaron Solomon
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Abramson Family Cancer Research Institute
- Department of Cancer Biology
| | | | | | - Danielle Soucier-Ernst
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Department of Medicine
| | - Noah G. Goodman
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Department of Medicine
| | - S. William Stavropoulos
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Department of Radiology, and
| | - Kara N. Maxwell
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Department of Medicine
| | - Candace Clark
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Department of Medicine
| | - George K. Belka
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Abramson Family Cancer Research Institute
- Department of Cancer Biology
| | - Michael Feldman
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Department of Pathology and Laboratory Medicine
| | - Angela DeMichele
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Department of Medicine
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lewis A. Chodosh
- Secondary Prevention through Surveillance and Intervention (2-PREVENT) Translational Center of Excellence
- Abramson Family Cancer Research Institute
- Department of Cancer Biology
- Department of Medicine
| |
Collapse
|
47
|
Da Cruz Paula A, da Silva EM, Segura SE, Pareja F, Bi R, Selenica P, Kim SH, Ferrando L, Vahdatinia M, Soslow RA, Vidal A, Gatius S, Przybycin CG, Abu-Rustum NR, Matias-Guiu X, Rubin BP, Reis-Filho JS, DeLair DF, Weigelt B. Genomic profiling of primary and recurrent adult granulosa cell tumors of the ovary. Mod Pathol 2020; 33:1606-1617. [PMID: 32203090 PMCID: PMC7390666 DOI: 10.1038/s41379-020-0514-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 02/06/2023]
Abstract
Adult-type granulosa cell tumor (aGCT) is a rare malignant ovarian sex cord-stromal tumor, harboring recurrent FOXL2 c.C402G/p.C134W hotspot mutations in 97% of cases. These tumors are considered to have a favorable prognosis, however aGCTs have a tendency for local spread and late recurrences, which are associated with poor survival rates. We sought to determine the genetic alterations associated with aGCT disease progression. We subjected primary non-recurrent aGCTs (n = 7), primary aGCTs that subsequently recurred (n = 9) and their matched recurrences (n = 9), and aGCT recurrences without matched primary tumors (n = 10) to targeted massively parallel sequencing of ≥410 cancer-related genes. In addition, three primary non-recurrent aGCTs and nine aGCT recurrences were subjected to FOXL2 and TERT promoter Sanger sequencing analysis. All aGCTs harbored the FOXL2 C134W hotspot mutation. TERT promoter mutations were found to be significantly more frequent in recurrent (18/28, 64%) than primary aGCTs (5/19, 26%, p = 0.017). In addition, mutations affecting TP53, MED12, and TET2 were restricted to aGCT recurrences. Pathway annotation of altered genes demonstrated that aGCT recurrences displayed an enrichment for genetic alterations affecting cell cycle pathway-related genes. Analysis of paired primary and recurrent aGCTs revealed that TERT promoter mutations were either present in both primary tumors and matched recurrences or were restricted to the recurrence and absent in the respective primary aGCT. Clonal composition analysis of these paired samples further revealed that aGCTs display intra-tumor genetic heterogeneity and harbor multiple clones at diagnosis and relapse. We observed that in a subset of cases, recurrences acquired additional genetic alterations not present in primary aGCTs, including TERT, MED12, and TP53 mutations and CDKN2A/B homozygous deletions. Albeit harboring relatively simple genomes, our data provide evidence to suggest that aGCTs are genetically heterogeneous tumors and that TERT promoter mutations and/or genetic alterations affecting other cell cycle-related genes may be associated with disease progression and recurrences.
Collapse
Affiliation(s)
- Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sheila E Segura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rui Bi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Fudan University Shanghai Cancer Center, Shanghai, PR China
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah H Kim
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenzo Ferrando
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Internal Medicine, University of Genoa, Genova, Italy
| | - Mahsa Vahdatinia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - August Vidal
- Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, University of Barcelona, CIBERONC, Barcelona, Spain
| | - Sonia Gatius
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, University of Lleida, CIBERONC, Lleida, Spain
| | - Christopher G Przybycin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nadeem R Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xavier Matias-Guiu
- Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, University of Barcelona, CIBERONC, Barcelona, Spain
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, University of Lleida, CIBERONC, Lleida, Spain
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Deborah F DeLair
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pathology, NYU Langone Health, New York, NY, USA.
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
48
|
Menck K, Sivaloganathan S, Bleckmann A, Binder C. Microvesicles in Cancer: Small Size, Large Potential. Int J Mol Sci 2020; 21:E5373. [PMID: 32731639 PMCID: PMC7432491 DOI: 10.3390/ijms21155373] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EV) are secreted by all cell types in a tumor and its microenvironment (TME), playing an essential role in intercellular communication and the establishment of a TME favorable for tumor invasion and metastasis. They encompass a variety of vesicle populations, among them the well-known endosomal-derived small exosomes (Exo), but also larger vesicles (diameter > 100 nm) that are shed directly from the plasma membrane, the so-called microvesicles (MV). Increasing evidence suggests that MV, although biologically different, share the tumor-promoting features of Exo in the TME. Due to their larger size, they can be readily harvested from patients' blood and characterized by routine methods such as conventional flow cytometry, exploiting the plethora of molecules expressed on their surface. In this review, we summarize the current knowledge about the biology and the composition of MV, as well as their role within the TME. We highlight not only the challenges and potential of MV as novel biomarkers for cancer, but also discuss their possible use for therapeutic intervention.
Collapse
Affiliation(s)
- Kerstin Menck
- Department of Medicine A, Hematology, Oncology, and Pneumology, University Hospital Münster, 48149 Münster, Germany; (K.M.); (S.S.); (A.B.)
| | - Suganja Sivaloganathan
- Department of Medicine A, Hematology, Oncology, and Pneumology, University Hospital Münster, 48149 Münster, Germany; (K.M.); (S.S.); (A.B.)
| | - Annalen Bleckmann
- Department of Medicine A, Hematology, Oncology, and Pneumology, University Hospital Münster, 48149 Münster, Germany; (K.M.); (S.S.); (A.B.)
- Department of Hematology/Medical Oncology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Claudia Binder
- Department of Hematology/Medical Oncology, University Medical Center Göttingen, 37075 Göttingen, Germany
| |
Collapse
|
49
|
Sutton EJ, Onishi N, Fehr DA, Dashevsky BZ, Sadinski M, Pinker K, Martinez DF, Brogi E, Braunstein L, Razavi P, El-Tamer M, Sacchini V, Deasy JO, Morris EA, Veeraraghavan H. A machine learning model that classifies breast cancer pathologic complete response on MRI post-neoadjuvant chemotherapy. Breast Cancer Res 2020; 22:57. [PMID: 32466777 PMCID: PMC7254668 DOI: 10.1186/s13058-020-01291-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/10/2020] [Indexed: 12/13/2022] Open
Abstract
Background For breast cancer patients undergoing neoadjuvant chemotherapy (NAC), pathologic complete response (pCR; no invasive or in situ) cannot be assessed non-invasively so all patients undergo surgery. The aim of our study was to develop and validate a radiomics classifier that classifies breast cancer pCR post-NAC on MRI prior to surgery. Methods This retrospective study included women treated with NAC for breast cancer from 2014 to 2016 with (1) pre- and post-NAC breast MRI and (2) post-NAC surgical pathology report assessing response. Automated radiomics analysis of pre- and post-NAC breast MRI involved image segmentation, radiomics feature extraction, feature pre-filtering, and classifier building through recursive feature elimination random forest (RFE-RF) machine learning. The RFE-RF classifier was trained with nested five-fold cross-validation using (a) radiomics only (model 1) and (b) radiomics and molecular subtype (model 2). Class imbalance was addressed using the synthetic minority oversampling technique. Results Two hundred seventy-three women with 278 invasive breast cancers were included; the training set consisted of 222 cancers (61 pCR, 161 no-pCR; mean age 51.8 years, SD 11.8), and the independent test set consisted of 56 cancers (13 pCR, 43 no-pCR; mean age 51.3 years, SD 11.8). There was no significant difference in pCR or molecular subtype between the training and test sets. Model 1 achieved a cross-validation AUROC of 0.72 (95% CI 0.64, 0.79) and a similarly accurate (P = 0.1) AUROC of 0.83 (95% CI 0.71, 0.94) in both the training and test sets. Model 2 achieved a cross-validation AUROC of 0.80 (95% CI 0.72, 0.87) and a similar (P = 0.9) AUROC of 0.78 (95% CI 0.62, 0.94) in both the training and test sets. Conclusions This study validated a radiomics classifier combining radiomics with molecular subtypes that accurately classifies pCR on MRI post-NAC.
Collapse
Affiliation(s)
- Elizabeth J Sutton
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Natsuko Onishi
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Duc A Fehr
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brittany Z Dashevsky
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meredith Sadinski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katja Pinker
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Danny F Martinez
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lior Braunstein
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mahmoud El-Tamer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Virgilio Sacchini
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph O Deasy
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth A Morris
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Harini Veeraraghavan
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
50
|
Freitag CE, Mei P, Wei L, Parwani AV, Li Z. Genetic alterations and their association with clinicopathologic characteristics in advanced breast carcinomas: focusing on clinically actionable genetic alterations. Hum Pathol 2020; 102:94-103. [PMID: 32445652 DOI: 10.1016/j.humpath.2020.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/17/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023]
Abstract
Breast carcinomas (BCs) are genetically heterogeneous and associated with numerous mutations which can be used to predict outcomes and initiate targeted therapies. We investigated clinicopathologic characteristics associated with gene mutations detected using the FoundationOne CDx assay in a cohort of 223 clinically advanced BCs (66 locally recurrent and 157 metastatic) from our institution. One hundred fifty unique mutations were identified (total 1008) in the cohort, with the most prevalent (>10%) including TP53 (53.8%), PIK3CA (35%), MYC (22%), CCND1 (19.7%), FGF19 (19.7%), FGF4 (16.6%), FGF3 (16.1%), ZNF703 (14.8%), ESR1 (13.9%), FGFR1 (13.5%), PTEN (12.1%), and CDH1 (10.8%). ERBB2 genetic alteration was most common in human epidermal growth factor receptor 2 (HER2)-positive BCs, and GATA3 and ESR1 mutations were only identified in hormone receptor-positive BC. Mutations enriched in triple-negative BCs (TNBCs) included TP53, PTEN, RB1, and CDKN2A/B. CDH1 mutation was predominantly found in lobular carcinomas, and PIK3CA mutation was also enriched. Mutations enriched in metaplastic carcinomas with heterologous mesenchymal differentiation included TP53, PTEN, MCL1, CDKN2A/B, and NOTCH2. An increase in mutations of CCND1, FGF19, FGF4, FGF3, ESR1, and EMSY was identified in metastatic BCs compared with locally recurrent BCs. Overall, PIK3CA was the most frequent clinically actionable genetic alteration (35%), followed by MYC (22%), CCND1 (19.7%), and FGF3/FGF4/FGFR1 (16%). In conclusion, our study provides genetic insight into the biology of advanced BCs and summarizes their most frequent clinically actionable genetic alterations, generating useful genomic information for potential improvement of patient management.
Collapse
Affiliation(s)
- Cody Eric Freitag
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Ping Mei
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Lai Wei
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Anil V Parwani
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Zaibo Li
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA.
| |
Collapse
|