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Peters AL, Hall PS, Jordan LB, Soh FY, Hannington L, Makaranka S, Urquhart G, Vallet M, Cartwright D, Marashi H, Elsberger B. Enhancing clinical decision support with genomic tools in breast cancer: A Scottish perspective. Breast 2024; 75:103728. [PMID: 38657322 PMCID: PMC11061332 DOI: 10.1016/j.breast.2024.103728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 03/12/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
INTRODUCTION The Oncotype DX Breast RS test has been adopted in Scotland and has been the subject of a large population-based study by a Scottish Consensus Group to assess the uptake of the recurrence score (RS), evaluate co-variates associated with the RS and to analyse the effect it may have had on clinical practice. MATERIALS & METHODS Pan-Scotland study between August 2018-August 2021 evaluating 833 patients who had a RS test performed as part of their diagnostic pathway. Data was extracted retrospectively from electronic records and analysis conducted to describe change in chemotherapy administration (by direct comparison with conventional risk assessment tools), and univariate/multivariate analysis to assess relationship between covariates and the RS. RESULTS Chemotherapy treatment was strongly influenced by the RS (p < 0.001). Only 30 % of patients received chemotherapy treatment in the intermediate and high risk PREDICT groups, where chemotherapy is considered. Additionally, 55.5 % of patients with a high risk PREDICT had a low RS and did not receive chemotherapy. There were 17 % of patients with a low risk PREDICT but high RS who received chemotherapy. Multivariate regression analysis showed the progesterone receptor Allred score (PR score) to be a strong independent predictor of the RS, with a negative PR score being associated with high RS (OR 4.49, p < 0.001). Increasing grade was also associated with high RS (OR 3.81, p < 0.001). Classic lobular pathology was associated with a low RS in comparison to other tumour pathology (p < 0.01). Nodal disease was associated with a lower RS (p = 0.012) on univariate analysis, with menopausal status (p = 0.43) not influencing the RS on univariate or multivariate analysis. CONCLUSIONS Genomic assays offer the potential for risk-stratified decision making regarding the use of chemotherapy. They can help reduce unnecessary chemotherapy treatment and identify a subgroup of patients with more adverse genomic tumour biology. A recent publication by Health Improvement Scotland (HIS) has updated guidance on use of the RS test for NHS Scotland. It suggests to limit its use to the intermediate risk PREDICT group. Our study shows the impact of the RS test in the low and high risk PREDICT groups. The implementation across Scotland has resulted in a notable shift in practice, leading to a significant reduction in chemotherapy administration in the setting of high risk PREDICT scores returning low risk RS. There has also been utility for the test in the low risk PREDICT group to detect a small subgroup with a high RS. We have found the PR score to have a strong independent association with high risk RS. This finding was not evaluated by the key RS test papers, and the potential prognostic information provided by the PR score as a surrogate biomarker is an outstanding question that requires more research to validate.
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Affiliation(s)
- A L Peters
- Beatson West of Scotland Cancer Centre, Gartnavel Hospital, NHS Greater Glasgow & Clyde, 1053 Great Western Rd, Glasgow G12 0YN, UK; Cancer Research UK (CRUK) Scotland Institute, Switchback Road, Bearsden, Glasgow G61 1BD, UK.
| | - P S Hall
- Edinburgh Cancer Research Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, UK
| | - L B Jordan
- Ninewells Hospital & Medical School, NHS Tayside, Department of Pathology, Dundee, DD1 9SY, UK
| | - F Y Soh
- Raigmore Hospital, NHS Highland, Department of Oncology, Inverness IV2 3UJ, UK
| | - L Hannington
- Beatson West of Scotland Cancer Centre, Gartnavel Hospital, NHS Greater Glasgow & Clyde, 1053 Great Western Rd, Glasgow G12 0YN, UK
| | - S Makaranka
- Aberdeen Royal Infirmary, NHS Grampian, Department of Breast Surgery, Aberdeen AB25 2ZN, UK
| | - G Urquhart
- Aberdeen Royal Infirmary, NHS Grampian, Department of Oncology, Aberdeen AB25 2ZN, UK
| | - M Vallet
- Edinburgh Cancer Research Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, UK
| | - D Cartwright
- Beatson West of Scotland Cancer Centre, Gartnavel Hospital, NHS Greater Glasgow & Clyde, 1053 Great Western Rd, Glasgow G12 0YN, UK; Cancer Research UK (CRUK) Scotland Institute, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - H Marashi
- Beatson West of Scotland Cancer Centre, Gartnavel Hospital, NHS Greater Glasgow & Clyde, 1053 Great Western Rd, Glasgow G12 0YN, UK
| | - B Elsberger
- Aberdeen Royal Infirmary, NHS Grampian, Department of Breast Surgery, Aberdeen AB25 2ZN, UK
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Hamilton AM, Walens A, Van Alsten SC, Olsson LT, Nsonwu-Farley J, Gao X, Kirk EL, Perou CM, Carey LA, Troester MA, Abdou Y. BIRC5 expression by race, age and clinical factors in breast cancer patients. Breast Cancer Res 2024; 26:50. [PMID: 38515208 PMCID: PMC10956264 DOI: 10.1186/s13058-024-01792-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024] Open
Abstract
PURPOSE Survivin/BIRC5 is a proliferation marker that is associated with poor prognosis in breast cancer and an attractive therapeutic target. However, BIRC5 has not been well studied among racially diverse populations where aggressive breast cancers are prevalent. EXPERIMENTAL DESIGN We studied BIRC5 expression in association with clinical and demographic variables and as a predictor of recurrence in 2174 participants in the Carolina Breast Cancer Study (CBCS), a population-based study that oversampled Black (n = 1113) and younger (< 50 years; n = 1137) participants with breast cancer. For comparison, similar analyses were conducted in The Cancer Genome Atlas [TCGA N = 1094, Black (n = 183), younger (n = 295)]. BIRC5 was evaluated as a continuous and categorical variable (highest quartile vs. lower three quartiles). RESULTS Univariate, continuous BIRC5 expression was higher in breast tumors from Black women relative to non-Black women in both estrogen receptor (ER)-positive and ER-negative tumors and in analyses stratified by stage (i.e., within Stage I, Stage II, and Stage III/IV tumors). Within CBCS and TCGA, BIRC5-high was associated with young age (< 50 years) and Black race, as well as hormone receptor-negative tumors, non-Luminal A PAM50 subtypes, advanced stage, and larger tumors (> 2 cm). Relative to BIRC5-low, BIRC5-high tumors were associated with poor 5-year recurrence-free survival (RFS) among ER-positive tumors, both in unadjusted models [HR (95% CI): 2.7 (1.6, 4.6)] and after adjustment for age and stage [Adjusted HR (95% CI): 1.87 (1.07, 3.25)]. However, this relationship was not observed among ER-negative tumors [Crude HR (95% CI): 0.7 (0.39, 1.2); Adjusted HR (95% CI): 0.67 (0.37, 1.2)]. CONCLUSION Black and younger women with breast cancer have a higher burden of BIRC5-high tumors than older and non-Black women. Emerging anti-survivin treatment strategies may be an important future direction for equitable breast cancer outcomes.
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Affiliation(s)
- Alina M Hamilton
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Andrea Walens
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sarah C Van Alsten
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Linnea T Olsson
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joseph Nsonwu-Farley
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Xiaohua Gao
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Erin L Kirk
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Charles M Perou
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Lisa A Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Melissa A Troester
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yara Abdou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Department of Medicine, Division of Oncology, University of North Carolina at Chapel Hill, 101 Manning Drive, CB# 7305, Chapel Hill, NC, 27514, USA.
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Godina C, Belting M, Vallon-Christersson J, Isaksson K, Bosch A, Jernström H. Caveolin-1 gene expression provides additional prognostic information combined with PAM50 risk of recurrence (ROR) score in breast cancer. Sci Rep 2024; 14:6675. [PMID: 38509243 PMCID: PMC10954762 DOI: 10.1038/s41598-024-57365-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
Combining information from the tumor microenvironment (TME) with PAM50 Risk of Recurrence (ROR) score could improve breast cancer prognostication. Caveolin-1 (CAV1) is a marker of an active TME. CAV1 is a membrane protein involved in cell signaling, extracellular matrix organization, and tumor-stroma interactions. We sought to investigate CAV1 gene expression in relation to PAM50 subtypes, ROR score, and their joint prognostic impact. CAV1 expression was compared between PAM50 subtypes and ROR categories in two cohorts (SCAN-B, n = 5326 and METABRIC, n = 1980). CAV1 expression was assessed in relation to clinical outcomes using Cox regression and adjusted for clinicopathological predictors. Effect modifications between CAV1 expression and ROR categories on clinical outcome were investigated using multiplicative and additive two-way interaction analyses. Differential gene expression and gene set enrichment analyses were applied to compare high and low expressing CAV1 tumors. All samples expressed CAV1 with the highest expression in the Normal-like subtype. Gene modules consistent with epithelial-mesenchymal transition (EMT), hypoxia, and stromal activation were associated with high CAV1 expression. CAV1 expression was inversely associated with ROR category. Interactions between CAV1 expression and ROR categories were observed in both cohorts. High expressing CAV1 tumors conferred worse prognosis only within the group classified as ROR high. ROR gave markedly different prognostic information depending on the underlying CAV1 expression. CAV1, a potential mediator between the malignant cells and TME, could be a useful biomarker that enhances and further refines PAM50 ROR risk stratification in patients with ROR high tumors and a potential therapeutic target.
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Affiliation(s)
- Christopher Godina
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden.
| | - Mattias Belting
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Skåne, Sweden
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Vallon-Christersson
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden
| | - Karolin Isaksson
- Department of Clinical Sciences Lund, Surgery, Lund University and Kristianstad Hospital, Kristianstad, Sweden
| | - Ana Bosch
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Skåne, Sweden
| | - Helena Jernström
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden.
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Tsang HF, Pei XM, Wong YKE, Wong SCC. Plasma Circulating mRNA Profile for the Non-Invasive Diagnosis of Colorectal Cancer Using NanoString Technologies. Int J Mol Sci 2024; 25:3012. [PMID: 38474258 DOI: 10.3390/ijms25053012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/26/2024] [Accepted: 03/02/2024] [Indexed: 03/14/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers and the second leading cause of cancer deaths in developed countries. Early CRC may have no symptoms and symptoms usually appear with more advanced diseases. Regular screening can identify people who are at increased risk of CRC in order to offer earlier treatment. A cost-effective non-invasive platform for the screening and monitoring of CRC patients allows early detection and appropriate treatment of the disease, and the timely application of adjuvant therapy after surgical operation is needed. In this study, a cohort of 71 plasma samples that include 48 colonoscopy- and histopathology-confirmed CRC patients with TNM stages I to IV were recruited between 2017 and 2019. Plasma mRNA profiling was performed in CRC patients using NanoString nCounter. Normalized data were analyzed using a Mann-Whitney U test to determine statistically significant differences between samples from CRC patients and healthy subjects. A multiple-group comparison of clinical phenotypes was performed using the Kruskal-Wallis H test for statistically significant differences between multiple groups. Among the 27 selected circulating mRNA markers, all of them were found to be overexpressed (gene expression fold change > 2) in the plasma of patients from two or more CRC stages. In conclusion, NanoString-based targeted plasma CRC-associated mRNAs circulating the marker panel that can significantly distinguish CRC patients from a healthy population were developed for the non-invasive diagnosis of CRC using peripheral blood samples.
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Affiliation(s)
- Hin Fung Tsang
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong SAR, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Yin Kwan Evelyn Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
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5
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Okimoto LYS, Mendonca-Neto R, Nakamura FG, Nakamura EF, Fenyö D, Silva CT. Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification. BMC Bioinformatics 2024; 25:92. [PMID: 38429657 PMCID: PMC10908178 DOI: 10.1186/s12859-024-05715-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/21/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND In recent years, researchers have made significant strides in understanding the heterogeneity of breast cancer and its various subtypes. However, the wealth of genomic and proteomic data available today necessitates efficient frameworks, instruments, and computational tools for meaningful analysis. Despite its success as a prognostic tool, the PAM50 gene signature's reliance on many genes presents challenges in terms of cost and complexity. Consequently, there is a need for more efficient methods to classify breast cancer subtypes using a reduced gene set accurately. RESULTS This study explores the potential of achieving precise breast cancer subtype categorization using a reduced gene set derived from the PAM50 gene signature. By employing a "Few-Shot Genes Selection" method, we randomly select smaller subsets from PAM50 and evaluate their performance using metrics and a linear model, specifically the Support Vector Machine (SVM) classifier. In addition, we aim to assess whether a more compact gene set can maintain performance while simplifying the classification process. Our findings demonstrate that certain reduced gene subsets can perform comparable or superior to the full PAM50 gene signature. CONCLUSIONS The identified gene subsets, with 36 genes, have the potential to contribute to the development of more cost-effective and streamlined diagnostic tools in breast cancer research and clinical settings.
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Affiliation(s)
- Leandro Y S Okimoto
- Institute of Computing, Universidade Federal do Amazonas, Manaus, BR, Brazil.
| | - Rayol Mendonca-Neto
- Institute of Computing, Universidade Federal do Amazonas, Manaus, BR, Brazil
| | - Fabíola G Nakamura
- Institute of Computing, Universidade Federal do Amazonas, Manaus, BR, Brazil
| | - Eduardo F Nakamura
- Institute of Computing, Universidade Federal do Amazonas, Manaus, BR, Brazil
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Lee S, Kang BH, Lee HB, Jang BS, Han W, Kim IA. B-Cell-Mediated Immunity Predicts Survival of Patients With Estrogen Receptor-Positive Breast Cancer. JCO Precis Oncol 2024; 8:e2300263. [PMID: 38452311 DOI: 10.1200/po.23.00263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 03/09/2024] Open
Abstract
PURPOSE The estrogen receptor-positive (ER+) breast cancer (BC), which constitutes the majority of BC cases, exhibits highly heterogeneous clinical behavior. To aid precision treatments, we aimed to find molecular subtypes of ER+ BC representing the tumor microenvironment and prognosis. METHODS We analyzed RNA-seq data of 113 patients with BC and classified them according to the PAM50 intrinsic subtypes using gene expression profiles. Among them, we further focused on 44 patients with luminal-type (ER+) BC for subclassification. The Cancer Genome Atlas (TCGA) data of patients with BC were used as a validation data set to verify the new classification. We estimated the immune cell composition using CIBERSORT and further analyzed its association with clinical or molecular parameters. RESULTS Principal component analysis clearly divided the patients into two subgroups separately from the luminal A and B classification. The top differentially expressed genes between the subgroups were distinctly characterized by immunoglobulin and B-cell-related genes. We could also cluster a separate cohort of patients with luminal-type BC from TCGA into two subgroups on the basis of the expression of a B-cell-specific gene set, and patients who were predicted to have high B-cell immune activity had better prognoses than other patients. CONCLUSION Our transcriptomic approach emphasize a molecular phenotype of B-cell immunity in ER+ BC that may help to predict disease prognosis. Although further researches are required, B-cell immunity for patients with ER+ BC may be helpful for identifying patients who are good responders to chemotherapy or immunotherapy.
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Affiliation(s)
- Seungbok Lee
- Department of Genomic Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Byung-Hee Kang
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Radiation Oncology, Ewha Womans University Seoul Hospital, Seoul, Republic of Korea
| | - Han-Byoel Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Bum-Sup Jang
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Wonshik Han
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - In Ah Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Radiation Oncology and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
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Hummelink K, Tissier R, Bosch LJ, Krijgsman O, van den Heuvel MM, Theelen WS, Damotte D, Goldwasser F, Leroy K, Smit EF, Meijer GA, Thommen DS, Monkhorst K. A Dysfunctional T-cell Gene Signature for Predicting Nonresponse to PD-1 Blockade in Non-small Cell Lung Cancer That Is Suitable for Routine Clinical Diagnostics. Clin Cancer Res 2024; 30:814-823. [PMID: 38088895 PMCID: PMC10870113 DOI: 10.1158/1078-0432.ccr-23-1061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/25/2023] [Accepted: 12/07/2023] [Indexed: 02/17/2024]
Abstract
PURPOSE Because PD-1 blockade is only effective in a minority of patients with advanced-stage non-small cell lung cancer (NSCLC), biomarkers are needed to guide treatment decisions. Tumor infiltration by PD-1T tumor-infiltrating lymphocytes (TIL), a dysfunctional TIL pool with tumor-reactive capacity, can be detected by digital quantitative IHC and has been established as a novel predictive biomarker in NSCLC. To facilitate translation of this biomarker to the clinic, we aimed to develop a robust RNA signature reflecting a tumor's PD-1T TIL status. EXPERIMENTAL DESIGN mRNA expression analysis using the NanoString nCounter platform was performed in baseline tumor samples from 41 patients with advanced-stage NSCLC treated with nivolumab that were selected on the basis of PD-1T TIL infiltration by IHC. Samples were included as a training cohort (n = 41) to develop a predictive gene signature. This signature was independently validated in a second cohort (n = 42). Primary outcome was disease control at 12 months (DC 12 m), and secondary outcome was progression-free and overall survival. RESULTS Regularized regression analysis yielded a signature using 12 out of 56 differentially expressed genes between PD-1T IHC-high tumors from patients with DC 12 m and PD-1T IHC-low tumors from patients with progressive disease (PD). In the validation cohort, 6/6 (100%) patients with DC 12 m and 23/36 (64%) with PD were correctly classified with a negative predictive value (NPV) of 100% and a positive predictive value of 32%. CONCLUSIONS The PD-1T mRNA signature showed a similar high sensitivity and high NPV as the digital IHC quantification of PD-1T TIL. This finding provides a straightforward approach allowing for easy implementation in a routine diagnostic clinical setting.
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Affiliation(s)
- Karlijn Hummelink
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Renaud Tissier
- Biostatistics Unit, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Linda J.W. Bosch
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Michel M. van den Heuvel
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Willemijn S.M.E. Theelen
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Diane Damotte
- Team Cancer, Immune Control and Escape, Cordeliers Research Center, UMRS 1138, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- University Paris Cité, Paris, France
- CERTIM, Medical Oncology, Hôpital Cochin, APHP, Paris, France
| | - François Goldwasser
- University Paris Cité, Paris, France
- CERTIM, Medical Oncology, Hôpital Cochin, APHP, Paris, France
| | - Karen Leroy
- Team Cancer, Immune Control and Escape, Cordeliers Research Center, UMRS 1138, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- University Paris Cité, Paris, France
- CERTIM, Medical Oncology, Hôpital Cochin, APHP, Paris, France
- Department of Biochemistry, Hôpital Cochin, Européen Georges Pompidou, APHP Centre, Paris, France
| | - Egbert F. Smit
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daniela S. Thommen
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kim Monkhorst
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
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Kalaba P, Sanchez de la Rosa C, Möller A, Alewood PF, Muttenthaler M. Targeting the Oxytocin Receptor for Breast Cancer Management: A Niche for Peptide Tracers. J Med Chem 2024; 67:1625-1640. [PMID: 38235665 PMCID: PMC10859963 DOI: 10.1021/acs.jmedchem.3c01089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Abstract
Breast cancer is a leading cause of death in women, and its management highly depends on early disease diagnosis and monitoring. This remains challenging due to breast cancer's heterogeneity and a scarcity of specific biomarkers that could predict responses to therapy and enable personalized treatment. This Perspective describes the diagnostic landscape for breast cancer management, molecular strategies targeting receptors overexpressed in tumors, the theranostic potential of the oxytocin receptor (OTR) as an emerging breast cancer target, and the development of OTR-specific optical and nuclear tracers to study, visualize, and treat tumors. A special focus is on the chemistry and pharmacology underpinning OTR tracer development, preclinical in vitro and in vivo studies, challenges, and future directions. The use of peptide-based tracers targeting upregulated receptors in cancer is a highly promising strategy complementing current diagnostics and therapies and providing new opportunities to improve cancer management and patient survival.
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Affiliation(s)
- Predrag Kalaba
- Institute
of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | | | - Andreas Möller
- QIMR
Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
- The
Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Paul F. Alewood
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
| | - Markus Muttenthaler
- Institute
of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
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Wei L, Xin Y, Pu M, Zhang Y. Patient-specific analysis of co-expression to measure biological network rewiring in individuals. Life Sci Alliance 2024; 7:e202302253. [PMID: 37977656 PMCID: PMC10656351 DOI: 10.26508/lsa.202302253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
To effectively understand the underlying mechanisms of disease and inform the development of personalized therapies, it is critical to harness the power of differential co-expression (DCE) network analysis. Despite the promise of DCE network analysis in precision medicine, current approaches have a major limitation: they measure an average differential network across multiple samples, which means the specific etiology of individual patients is often overlooked. To address this, we present Cosinet, a DCE-based single-sample network rewiring degree quantification tool. By analyzing two breast cancer datasets, we demonstrate that Cosinet can identify important differences in gene co-expression patterns between individual patients and generate scores for each individual that are significantly associated with overall survival, recurrence-free interval, and other clinical outcomes, even after adjusting for risk factors such as age, tumor size, HER2 status, and PAM50 subtypes. Cosinet represents a remarkable development toward unlocking the potential of DCE analysis in the context of precision medicine.
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Affiliation(s)
- Lanying Wei
- Beijing StoneWise Technology Co Ltd, Danling SOHO, Beijing, China
| | - Yucui Xin
- Beijing StoneWise Technology Co Ltd, Danling SOHO, Beijing, China
| | - Mengchen Pu
- Beijing StoneWise Technology Co Ltd, Danling SOHO, Beijing, China
| | - Yingsheng Zhang
- Beijing StoneWise Technology Co Ltd, Danling SOHO, Beijing, China
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10
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Gherman LM, Chiroi P, Nuţu A, Bica C, Berindan-Neagoe I. Profiling canine mammary tumors: A potential model for studying human breast cancer. Vet J 2024; 303:106055. [PMID: 38097103 DOI: 10.1016/j.tvjl.2023.106055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
Despite all clinical progress recorded in the last decades, human breast cancer (HBC) remains a major challenge worldwide both in terms of its incidence and its management. Canine mammary tumors (CMTs) share similarities with HBC and represent an alternative model for HBC. The utility of the canine model in studying HBC relies on their common features, include spontaneous development, subtype classification, mutational profile, alterations in gene expression profile, and incidence/prevalence. This review describes the similarities between CMTs and HBC regarding genomic landscape, microRNA expression alteration, methylation, and metabolomic changes occurring during mammary gland carcinogenesis. The primary purpose of this review is to highlight the advantages of using the canine model as a translational animal model for HBC research and to investigate the challenges and limitations of this approach.
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Affiliation(s)
- Luciana-Madalina Gherman
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; Experimental Center of Iuliu Hatieganu University of Medicine and Pharmacy Cluj-Napoca, 400349 Cluj-Napoca, Romania
| | - Paul Chiroi
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania
| | - Andreea Nuţu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania
| | - Cecilia Bica
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania
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11
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Wimmer K, Hlauschek D, Balic M, Pfeiler G, Greil R, Singer CF, Halper S, Steger G, Suppan C, Gampenrieder SP, Helfgott R, Egle D, Filipits M, Jakesz R, Sölkner L, Fesl C, Gnant M, Fitzal F. Is the CTS5 a helpful decision-making tool in the extended adjuvant therapy setting? Breast Cancer Res Treat 2024:10.1007/s10549-023-07186-6. [PMID: 38273214 DOI: 10.1007/s10549-023-07186-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 11/06/2023] [Indexed: 01/27/2024]
Abstract
PURPOSE The Clinical Treatment Score post-5 years (CTS5) is an easy-to-use tool estimating the late distant recurrence (LDR) risk in patients with hormone receptor-positive breast cancer after 5 years of endocrine therapy (ET). Apart from evaluating the prognostic value and calibration accuracy of CTS5, the aim of this study is to clarify if this score is able to identify patients at higher risk for LDR who will benefit from extended ET. METHODS Prognostic power, calibration, and predictive value of the CTS5 was tested in patients of the prospective ABCSG-06 and -06a trials (n = 1254 and 860 patients, respectively). Time to LDR was analyzed with Cox regression models. RESULTS Higher rates of LDR in the years five to ten were observed in high- and intermediate-risk patients compared to low-risk patients (HR 4.02, 95%CI 2.26-7.15, p < 0.001 and HR 1.93, 95%CI 1.05-3.56, p = 0.035). An increasing continuous CTS5 was associated with increasing LDR risk (HR 2.23, 95% CI 1.74-2.85, p < 0.001). Miscalibration of CTS5 in high-risk patients could be observed. Although not reaching significance, high-risk patients benefitted the most from prolonged ET with an absolute reduction of the estimated 5-year LDR of - 6.1% (95%CI - 14.4 to 2.3). CONCLUSION The CTS5 is a reliable prognostic tool that is well calibrated in the lower and intermediate risk groups with a substantial difference of expected versus observed LDR rates in high-risk patients. While a numerical trend in favoring prolonged ET for patients with a higher CTS5 was found, a significantly predictive value for the score could not be confirmed. CLINICAL TRIAL REGISTRATION ABCSG-06 trial (NCT00309491), ABCSG-06A7 1033AU/0001 (NCT00300508).
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Affiliation(s)
- Kerstin Wimmer
- Department of General Surgery, Division of Visceral Surgery, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
| | | | - Marija Balic
- Department of Oncology, Medical University of Graz, Graz, Austria
| | - Georg Pfeiler
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Gynecology and Obstetrics, Medical University of Vienna, Vienna, Austria
| | - Richard Greil
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University Salzburg, Salzburg, Austria
- Salzburg Cancer Research Institute-CCCIT, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | - Christian F Singer
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Gynecology and Obstetrics, Medical University of Vienna, Vienna, Austria
| | - Stefan Halper
- Department of Surgery, Regional Hospital Wiener Neustadt, Wiener Neustadt, Austria
| | - Günther Steger
- Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Christoph Suppan
- Department of Oncology, Medical University of Graz, Graz, Austria
| | - Simon P Gampenrieder
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University Salzburg, Salzburg, Austria
- Salzburg Cancer Research Institute-CCCIT, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | - Ruth Helfgott
- Department of Surgery, Ordensklinikum Linz - Sisters of Charity, Linz, Austria
| | - Daniel Egle
- Department of Gynaecology, Medical University Innsbruck, Innsbruck, Austria
| | - Martin Filipits
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Raimund Jakesz
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Lidija Sölkner
- Austrian Breast & Colorectal Cancer Study Group, Vienna, Austria
| | - Christian Fesl
- Austrian Breast & Colorectal Cancer Study Group, Vienna, Austria
| | - Michael Gnant
- Austrian Breast & Colorectal Cancer Study Group, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Florian Fitzal
- Department of General Surgery, Division of Visceral Surgery, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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12
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Lopez-Tarruella S, Del Monte-Millán M, Roche-Molina M, Jerez Y, Echavarria Diaz-Guardamino I, Herrero López B, Gamez Casado S, Marquez-Rodas I, Alvarez E, Cebollero M, Massarrah T, Ocaña I, Arias A, García-Sáenz JÁ, Moreno Anton F, Olier Garate C, Moreno Muñoz D, Marrupe D, Lara Álvarez MÁ, Enrech S, Bueno Muiño C, Martín M. Correlation between breast cancer subtypes determined by immunohistochemistry and n-COUNTER PAM50 assay: a real-world study. Breast Cancer Res Treat 2024; 203:163-172. [PMID: 37773555 PMCID: PMC10771357 DOI: 10.1007/s10549-023-07094-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 08/13/2023] [Indexed: 10/01/2023]
Abstract
PURPOSE Molecular subtyping based on gene expression profiling (i.e., PAM50 assay) aids in determining the prognosis and treatment of breast cancer (BC), particularly in hormone receptor (HR)-positive/human epidermal growth factor receptor 2 (HER2)-negative tumors, where luminal A and B subtypes have different prognoses and treatments. Several surrogate classifications have been proposed for distinguishing between the luminal A and B subtypes. This study determines the accuracy of local immunohistochemistry (IHC) techniques for classifying HR-positive/HER2-negative (HR+/HER2-) tumors according to intrinsic subtypes using the nCOUNTER PAM50 assay as reference and the HR status definition according the ASCO/CAP recommendations. METHODS Molecular subtypes resulting from nCOUNTER PAM50 performed in our laboratory between 2014 and 2020 were correlated with three different proxy surrogates proposed in the literature based on ER, PR, HER2, and Ki67 expression with different cut-off values. Concordance was measured using the level of agreement and kappa statistics. RESULTS From 1049 samples with the nCOUNTER test, 679 and 350 were luminal A and B subtypes, respectively. Only a poor-to-fair correlation was observed between the three proxy surrogates and real genomic subtypes as determined by nCOUNTER PAM50. Moreover, 5-11% and 18-36% of the nCOUNTER PAM50 luminal B and A tumors were classified as luminal A and B, respectively, by these surrogates. CONCLUSION The concordance between luminal subtypes determined by three different IHC-based classifiers and the nCOUNTER PAM50 assay was suboptimal. Thus, a significant proportion of luminal A and B tumors as determined by the surrogate classifiers could be undertreated or over-treated.
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Affiliation(s)
- Sara Lopez-Tarruella
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañon (IiSGM), CIBERONC, Geicam, Universidad Complutense, 28007, Madrid, Spain
| | - María Del Monte-Millán
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), CiberOnc, Madrid, Spain
| | - Marta Roche-Molina
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Yolanda Jerez
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), CiberOnc, Madrid, Spain
| | - Isabel Echavarria Diaz-Guardamino
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), CiberOnc, Madrid, Spain
| | - Blanca Herrero López
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Salvador Gamez Casado
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Iván Marquez-Rodas
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), CiberOnc, Madrid, Spain
| | - Enrique Alvarez
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - María Cebollero
- Pathology Service, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Tatiana Massarrah
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), CiberOnc, Madrid, Spain
| | - Inmaculada Ocaña
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Ainhoa Arias
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - José Ángel García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), CIBERONC, Madrid, Spain
| | - Fernando Moreno Anton
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), CIBERONC, Madrid, Spain
| | - Clara Olier Garate
- Medical Oncology Department, Hospital Universitario Fundación Alcorcón, Alcorcon, Spain
| | - Diana Moreno Muñoz
- Medical Oncology Department, Hospital Universitario Fundación Alcorcón, Alcorcon, Spain
| | - David Marrupe
- Department of Oncologia, Hospital Universitario de Móstoles, Mostoles, Spain
| | - Miguel Ángel Lara Álvarez
- Medical Oncology Department, Hospital Universitario Infanta Leonor, Universidad Complutense, Madrid, Spain
| | - Santos Enrech
- Medical Oncology Department, Hospital Universitario de Getafe, Madrid, Spain
| | - Coralia Bueno Muiño
- Medical Oncology Department, Hospital Infanta Cristina (Parla), Fundación de Investigación Biomédica del H.U. Puerta de Hierro, Majadahonda, 28009, Madrid, Spain
| | - Miguel Martín
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañon (IiSGM), CIBERONC, Geicam, Universidad Complutense, 28007, Madrid, Spain.
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13
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Enoma D. Genomics in Clinical trials for Breast Cancer. Brief Funct Genomics 2023:elad054. [PMID: 38146120 DOI: 10.1093/bfgp/elad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023] Open
Abstract
Breast cancer (B.C.) still has increasing incidences and mortality rates globally. It is known that B.C. and other cancers have a very high rate of genetic heterogeneity and genomic mutations. Traditional oncology approaches have not been able to provide a lasting solution. Targeted therapeutics have been instrumental in handling the complexity and resistance associated with B.C. However, the progress of genomic technology has transformed our understanding of the genetic landscape of breast cancer, opening new avenues for improved anti-cancer therapeutics. Genomics is critical in developing tailored therapeutics and identifying patients most benefit from these treatments. The next generation of breast cancer clinical trials has incorporated next-generation sequencing technologies into the process, and we have seen benefits. These innovations have led to the approval of better-targeted therapies for patients with breast cancer. Genomics has a role to play in clinical trials, including genomic tests that have been approved, patient selection and prediction of therapeutic response. Multiple clinical trials in breast cancer have been done and are still ongoing, which have applied genomics technology. Precision medicine can be achieved in breast cancer therapy with increased efforts and advanced genomic studies in this domain. Genomics studies assist with patient outcomes improvement and oncology advancement by providing a deeper understanding of the biology behind breast cancer. This article will examine the present state of genomics in breast cancer clinical trials.
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Affiliation(s)
- David Enoma
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 2500 University Dr NW, Calgary, Alberta, T2N 1N4, Canada
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14
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Das S, Dey MK, Devireddy R, Gartia MR. Biomarkers in Cancer Detection, Diagnosis, and Prognosis. Sensors (Basel) 2023; 24:37. [PMID: 38202898 PMCID: PMC10780704 DOI: 10.3390/s24010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/27/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024]
Abstract
Biomarkers are vital in healthcare as they provide valuable insights into disease diagnosis, prognosis, treatment response, and personalized medicine. They serve as objective indicators, enabling early detection and intervention, leading to improved patient outcomes and reduced costs. Biomarkers also guide treatment decisions by predicting disease outcomes and facilitating individualized treatment plans. They play a role in monitoring disease progression, adjusting treatments, and detecting early signs of recurrence. Furthermore, biomarkers enhance drug development and clinical trials by identifying suitable patients and accelerating the approval process. In this review paper, we described a variety of biomarkers applicable for cancer detection and diagnosis, such as imaging-based diagnosis (CT, SPECT, MRI, and PET), blood-based biomarkers (proteins, genes, mRNA, and peptides), cell imaging-based diagnosis (needle biopsy and CTC), tissue imaging-based diagnosis (IHC), and genetic-based biomarkers (RNAseq, scRNAseq, and spatial transcriptomics).
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Affiliation(s)
| | | | | | - Manas Ranjan Gartia
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA; (S.D.); (M.K.D.); (R.D.)
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15
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Shi Y, Olsson LT, Hoadley KA, Calhoun BC, Marron JS, Geradts J, Niethammer M, Troester MA. Predicting early breast cancer recurrence from histopathological images in the Carolina Breast Cancer Study. NPJ Breast Cancer 2023; 9:92. [PMID: 37952058 PMCID: PMC10640636 DOI: 10.1038/s41523-023-00597-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Approaches for rapidly identifying patients at high risk of early breast cancer recurrence are needed. Image-based methods for prescreening hematoxylin and eosin (H&E) stained tumor slides could offer temporal and financial efficiency. We evaluated a data set of 704 1-mm tumor core H&E images (2-4 cores per case), corresponding to 202 participants (101 who recurred; 101 non-recurrent matched on age and follow-up time) from breast cancers diagnosed between 2008-2012 in the Carolina Breast Cancer Study. We leveraged deep learning to extract image information and trained a model to identify recurrence. Cross-validation accuracy for predicting recurrence was 62.4% [95% CI: 55.7, 69.1], similar to grade (65.8% [95% CI: 59.3, 72.3]) and ER status (66.3% [95% CI: 59.8, 72.8]). Interestingly, 70% (19/27) of early-recurrent low-intermediate grade tumors were identified by our image model. Relative to existing markers, image-based analyses provide complementary information for predicting early recurrence.
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Affiliation(s)
- Yifeng Shi
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Linnea T Olsson
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin C Calhoun
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J S Marron
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joseph Geradts
- Department of Pathology, East Carolina University, Greenville, NC, USA
| | - Marc Niethammer
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa A Troester
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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16
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Futamura M, Nakayama T, Yoshinami T, Oshiro C, Ishihara M, Morita M, Watanabe A, Tanigichi A, Tsukabe M, Shimoda M, Nitta K, Chihara Y, Yasojima H, Ouchi Y, Tokumaru Y, Masuda N. Detection of high-risk patients resistant to CDK4/6 inhibitors with hormone receptor-positive HER2-negative advanced and metastatic breast cancer in Japan (KBCSG-TR-1316). Breast Cancer 2023; 30:943-951. [PMID: 37486454 PMCID: PMC10587336 DOI: 10.1007/s12282-023-01485-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) improve the prognosis of hormone receptor-positive HER2-negative advanced/metastatic breast cancer (HR+/HER2- mBC). However, some cancers show resistance to CDK4/6i and have a poor prognosis. The non-luminal disease score (NOLUS) was developed to predict non-luminal disease using immunohistochemical analysis. METHODS The association between the efficacy of CDK4/6i and NOLUS was investigated by evaluating pathological and clinical data, including real-world progression-free survival (rw-PFS) and overall survival (OS). Real-world data of patients with HR+/HER2- mBC who received CDK4/6i therapy [palbociclib or abemaciclib] as first- or second-line endocrine treatments was obtained. NOLUS was calculated using the formula: NOLUS (0-100) = - 0.45 × estrogen receptor (ER) (%) - 0.28 × progesterone receptor (PR) (%) + 0.27 × Ki67(%) + 73, and the patients were divided into two groups: NOLUS-positive (≥ 51.38) and NOLUS-negative (< 51.38). RESULTS Of the 300 patients, 28 (9.3%) were NOLUS-positive, and 272 (90.7%) were NOLUS-negative. The expression rates (%) of ER and PgR in NOLUS-positive patients were lower than those in NOLUS-negative patients (p < 0.001). Ki67 expression was higher in NOLUS-positive patients. There were statistically significant differences in prognosis (rw-PFS and OS) between the two groups. Moreover, NOLUS-negative patients showed statistically better rw-PFS with first-line therapy than second-line therapy. However, NOLUS-positive patients showed poor prognoses with both the first and second therapeutic lines, suggesting CDK4/6i inefficacy for NOLUS-positive patients. CONCLUSIONS The efficacy and prognosis of CDK4/6i significantly differed between the NOLUS-positive and NOLUS-negative patients. This feasible method can predict patients with HR+/HER2- mBC resistant to CDK4/6i and help select a better therapeutic approach to overcome resistance.
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Affiliation(s)
- Manabu Futamura
- Department of Breast Surgery, Gifu University Hospital, 1-1 Yanagido, Gifu, 501-1194, Japan.
| | - Takahiro Nakayama
- Department of Breast and Endocrine Surgery, Osaka International Cancer Institute, Osaka, Japan
| | - Tetsuhiro Yoshinami
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Chiya Oshiro
- Department of Breast Surgery, Kaizuka City Hospital, Kaizuka, Japan
| | | | - Midori Morita
- Division of Endocrine and Breast Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Akira Watanabe
- Division of Endocrine and Breast Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Azusa Tanigichi
- Department of Breast and Endocrine Surgery, Osaka International Cancer Institute, Osaka, Japan
| | - Masami Tsukabe
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Breast and Endocrine Surgery, Osaka Police Hospital, Osaka, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kanae Nitta
- Breast and Endocrine Surgery, Otemae Hospital, Osaka, Japan
| | - Yoko Chihara
- Department of Breast Surgery, Itami City Hospital, Itami, Japan
| | - Hiroyuki Yasojima
- Department of Surgery Breast Oncology, NHO Osaka National Hospital, Osaka, Japan
| | - Yoshimi Ouchi
- Department of Breast Surgery, Saiseikai Shiga Hospital, Ritto, Japan
| | - Yoshihisa Tokumaru
- Department of Breast Surgery, Gifu University Hospital, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Norikazu Masuda
- Department of Surgery Breast Oncology, NHO Osaka National Hospital, Osaka, Japan
- Department of Breast and Endocrine Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
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17
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Tesch ME. Precision medicine in extended adjuvant endocrine therapy for breast cancer. Curr Opin Oncol 2023; 35:453-460. [PMID: 37621168 DOI: 10.1097/cco.0000000000000985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
PURPOSE OF REVIEW In this review, the evolving role of currently available genomic assays for hormone receptor-positive, early-stage breast cancer in the selection of patients for extended adjuvant endocrine therapy will be discussed. RECENT FINDINGS Several studies have investigated the prognostic performance of the Oncotype DX, Breast Cancer Index (BCI), Prosigna, and EndoPredict genomic assays in the late recurrence setting (>5 years after diagnosis), beyond standardly used clinicopathologic parameters, with mixed results. Recently, BCI has also been validated to predict the likelihood of benefit from extended endocrine therapy, though certain data limitations may need to be addressed to justify routine use in clinical practice. SUMMARY Even after 5 years of adjuvant endocrine therapy, patients with hormone receptor-positive breast cancer have a significant risk for late recurrence, including distant metastases, that might be prevented with longer durations of endocrine therapy. However, the added toxicity and variable benefit derived from extended endocrine therapy make optimal patient selection crucial. Genomic assays are in development to risk-stratify patients for late recurrence and determine efficacy of extended endocrine therapy, with the aim to help guide extended endocrine therapy decisions for clinicians and individualize treatment strategies for patients.
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Affiliation(s)
- Megan E Tesch
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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18
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Lautert-Dutra W, Melo CM, Chaves LP, Souza FC, Crozier C, Sundby AE, Woroszchuk E, Saggioro FP, Avante FS, dos Reis RB, Squire JA, Bayani J. Identification of tumor-agnostic biomarkers for predicting prostate cancer progression and biochemical recurrence. Front Oncol 2023; 13:1280943. [PMID: 37965470 PMCID: PMC10641020 DOI: 10.3389/fonc.2023.1280943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023] Open
Abstract
The diverse clinical outcomes of prostate cancer have led to the development of gene signature assays predicting disease progression. Improved prostate cancer progression biomarkers are needed as current RNA biomarker tests have varying success for intermediate prostate cancer. Interest grows in universal gene signatures for invasive carcinoma progression. Early breast and prostate cancers share characteristics, including hormone dependence and BRCA1/2 mutations. Given the similarities in the pathobiology of breast and prostate cancer, we utilized the NanoString BC360 panel, comprising the validated PAM50 classifier and pathway-specific signatures associated with general tumor progression as well as breast cancer-specific classifiers. This retrospective cohort of primary prostate cancers (n=53) was stratified according to biochemical recurrence (BCR) status and the CAPRA-S to identify genes related to high-risk disease. Two public cohort (TCGA-PRAD and GSE54460) were used to validate the results. Expression profiling of our cohort uncovered associations between PIP and INHBA with BCR and high CAPRA-S score, as well as associations between VCAN, SFRP2, and THBS4 and BCR. Despite low levels of the ESR1 gene compared to AR, we found strong expression of the ER signaling signature, suggesting that BCR may be driven by ER-mediated pathways. Kaplan-Meier and univariate Cox proportional hazards regression analysis indicated the expression of ESR1, PGR, VCAN, and SFRP2 could predict the occurrence of relapse events. This is in keeping with the pathways represented by these genes which contribute to angiogenesis and the epithelial-mesenchymal transition. It is likely that VCAN works by activating the stroma and remodeling the tumor microenvironment. Additionally, SFRP2 overexpression has been associated with increased tumor size and reduced survival rates in breast cancer and among prostate cancer patients who experienced BCR. ESR1 influences disease progression by activating stroma, stimulating stem/progenitor prostate cancer, and inducing TGF-β. Estrogen signaling may therefore serve as a surrogate to AR signaling during progression and in hormone-refractory disease, particularly in prostate cancer patients with stromal-rich tumors. Collectively, the use of agnostic biomarkers developed for breast cancer stratification has facilitated a precise clinical classification of patients undergoing radical prostatectomy and highlighted the therapeutic potential of targeting estrogen signaling in prostate cancer.
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Affiliation(s)
- William Lautert-Dutra
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Camila M. Melo
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Luiz P. Chaves
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Francisco C. Souza
- Division of Urology, Department of Surgery and Anatomy, Medical School of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Cheryl Crozier
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Adam E. Sundby
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Elizabeth Woroszchuk
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Fabiano P. Saggioro
- Department of Pathology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Filipe S. Avante
- Division of Urology, Department of Surgery and Anatomy, Medical School of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Rodolfo B. dos Reis
- Division of Urology, Department of Surgery and Anatomy, Medical School of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Jeremy A. Squire
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - Jane Bayani
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, Canada
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Veerla S, Hohmann L, Nacer DF, Vallon-Christersson J, Staaf J. Perturbation and stability of PAM50 subtyping in population-based primary invasive breast cancer. NPJ Breast Cancer 2023; 9:83. [PMID: 37857634 PMCID: PMC10587090 DOI: 10.1038/s41523-023-00589-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
PAM50 gene expression subtypes represent a cornerstone in the molecular classification of breast cancer and are included in risk prediction models to guide therapy. We aimed to illustrate the impact of included genes and biological processes on subtyping while considering a tumor's underlying clinical subgroup defined by ER, PR, and HER2 status. To do this we used a population-representative and clinically annotated early-stage breast tumor cohort of 6233 samples profiled by RNA sequencing and applied a perturbation strategy of excluding co-expressed genes (gene sets). We demonstrate how PAM50 nearest-centroid classification depends on biological processes present across, but also within, ER/PR/HER2 subgroups and PAM50 subtypes themselves. Our analysis highlights several key aspects of PAM50 classification. Firstly, we demonstrate the tight connection between a tumor's nearest and second-nearest PAM50 centroid. Additionally, we show that the second-best subtype is associated with overall survival in ER-positive, HER2-negative, and node-negative disease. We also note that ERBB2 expression has little impact on PAM50 classification in HER2-positive disease regardless of ER status and that the Basal subtype is highly stable in contrast to the Normal subtype. Improved consciousness of the commonly used PAM50 subtyping scheme will aid in our understanding and interpretation of breast tumors that have seemingly conflicting PAM50 classification when compared to clinical biomarkers. Finally, our study adds further support in challenging the common misconception that PAM50 subtypes are distinct classes by illustrating that PAM50 subtypes in tumors represent a continuum with prognostic implications.
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Affiliation(s)
- Srinivas Veerla
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Lennart Hohmann
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Deborah F Nacer
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden.
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Kay C, Martinez-Perez C, Dixon JM, Turnbull AK. The Role of Nodes and Nodal Assessment in Diagnosis, Treatment and Prediction in ER+, Node-Positive Breast Cancer. J Pers Med 2023; 13:1476. [PMID: 37888087 PMCID: PMC10608445 DOI: 10.3390/jpm13101476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Abstract
The majority of breast cancers are oestrogen receptor-positive (ER+). In ER+ cancers, oestrogen acts as a disease driver, so these tumours are likely to be susceptible to endocrine therapy (ET). ET works by blocking the hormone's synthesis or effect. A significant number of patients diagnosed with breast cancer will have the spread of tumour cells into regional lymph nodes either at the time of diagnosis, or as a recurrence some years later. Patients with node-positive disease have a poorer prognosis and can respond less well to ET. The nodal metastases may be genomically similar or, as is becoming more evident, may differ from the primary tumour. However, nodal metastatic disease is often not assessed, and treatment decisions are almost always based on biomarkers evaluated in the primary tumour. This review will summarise the evidence in the field on ER+, node-positive breast cancer, including diagnosis, treatment, prognosis and predictive tools.
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Affiliation(s)
- Charlene Kay
- Translational Oncology Research Group, MRC Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Carlos Martinez-Perez
- Translational Oncology Research Group, MRC Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - J Michael Dixon
- Edinburgh Breast Unit, Western General Hospital, NHS Lothian, Edinburgh Eh4 2XU, UK
| | - Arran K Turnbull
- Translational Oncology Research Group, MRC Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
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Abstract
Breast carcinomas classified based on traditional morphologic assessment provide useful prognostic information. Although morphology is still the gold standard of classification, recent advances in molecular technologies have enabled the classification of these tumors into four distinct subtypes based on its intrinsic molecular profile that provide both predictive and prognostic information. This article describes the association between the different molecular subtypes with the histologic subtypes of breast cancer and illustrates how these subtypes may affect the appearance of tumors on imaging studies.
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Affiliation(s)
- Madhuchhanda Roy
- Department of Pathology and Laboratory Medicine, University of Wisconsin - Madison, B1761 WIMR, 1111 Highland Avenue, Madison, WI 53705, USA.
| | - Amy M Fowler
- Department of Radiology, Section of Breast Imaging and Intervention, University of Wisconsin - Madison, 600 Highland Avenue, Madison, WI 53792-3252, USA; Department of Medical Physics, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792-3252, USA
| | - Gary A Ulaner
- Hoag Family Cancer Institute, 16105 Sand Canyon Avenue, Ste 215, Irvine, CA 92618, USA; Department of Radiology, Department of Translational Genomics, University of Southern California, Los Angeles, CA 90007, USA
| | - Aparna Mahajan
- Department of Pathology and Laboratory Medicine, University of Wisconsin - Madison, B1781 WIMR, 1111 Highland Avenue, Madison, WI 53705, USA
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Jeong H, Kim SB. Neoadjuvant endocrine therapy in ER-positive breast cancer: evolution, indication, and tailored treatment strategy. Ther Adv Med Oncol 2023; 15:17588359231200457. [PMID: 37786536 PMCID: PMC10541763 DOI: 10.1177/17588359231200457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 08/25/2023] [Indexed: 10/04/2023] Open
Abstract
In recent years, endocrine therapy (ET), an effective systemic treatment for the management of estrogen receptor (ER)-positive breast cancers, has regained interest as a neoadjuvant therapy based on evidence that ET can fulfill the aim of neoadjuvant systemic treatment for tumor shrinkage as well as elucidate important clinical information on endocrine sensitivity that enables the prognostication of patients. Moreover, neoadjuvant endocrine therapy (NET) potentially provides an opportunity for early assessment of the clinical efficacy of novel agents. Furthermore, recently reported trials have generated evidence for a more tailored approach for perioperative management of ER-positive breast cancer using clinical and molecular biomarkers, and this has provided a rationale that enables the broadening of clinical indications for NET. This review discusses the current evidence for NET, the evolution of NET trials, clinical indications, and NET-based treatment strategies.
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Affiliation(s)
- Hyehyun Jeong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sung-Bae Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea
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Lundgren C, Tutzauer J, Church SE, Stål O, Ekholm M, Forsare C, Nordenskjöld B, Fernö M, Bendahl PO, Rydén L. Tamoxifen-predictive value of gene expression signatures in premenopausal breast cancer: data from the randomized SBII:2 trial. Breast Cancer Res 2023; 25:110. [PMID: 37773134 PMCID: PMC10540453 DOI: 10.1186/s13058-023-01719-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Gene expression (GEX) signatures in breast cancer provide prognostic information, but little is known about their predictive value for tamoxifen treatment. We examined the tamoxifen-predictive value and prognostic effects of different GEX signatures in premenopausal women with early breast cancer. METHODS RNA from formalin-fixed paraffin-embedded tumor tissue from premenopausal women randomized between two years of tamoxifen treatment and no systemic treatment was extracted and successfully subjected to GEX profiling (n = 437, NanoString Breast Cancer 360™ panel). The median follow-up periods for a recurrence-free interval (RFi) and overall survival (OS) were 28 and 33 years, respectively. Associations between GEX signatures and tamoxifen effect were assessed in patients with estrogen receptor-positive/human epidermal growth factor receptor 2-negative (ER+ /HER2-) tumors using Kaplan-Meier estimates and Cox regression. The prognostic effects of GEX signatures were studied in the entire cohort. False discovery rate adjustments (q-values) were applied to account for multiple hypothesis testing. RESULTS In patients with ER+/HER2- tumors, FOXA1 expression below the median was associated with an improved effect of tamoxifen after 10 years with regard to RFi (hazard ratio [HR]FOXA1(high) = 1.04, 95% CI = 0.61-1.76, HRFOXA1(low) = 0.30, 95% CI = 0.14-0.67, qinteraction = 0.0013), and a resembling trend was observed for AR (HRAR(high) = 1.15, 95% CI = 0.60-2.20, HRAR(low) = 0.42, 95% CI = 0.24-0.75, qinteraction = 0.87). Similar patterns were observed for OS. Tamoxifen was in the same subgroup most beneficial for RFi in patients with low ESR1 expression (HRRFi ESR1(high) = 0.76, 95% CI = 0.43-1.35, HRRFi, ESR1(low) = 0.56, 95% CI = 0.29-1.06, qinteraction = 0.37). Irrespective of molecular subtype, higher levels of ESR1, Mast cells, and PGR on a continuous scale were correlated with improved 10 years RFi (HRESR1 = 0.80, 95% CI = 0.69-0.92, q = 0.005; HRMast cells = 0.74, 95% CI = 0.65-0.85, q < 0.0001; and HRPGR = 0.78, 95% CI = 0.68-0.89, q = 0.002). For BC proliferation and Hypoxia, higher scores associated with worse outcomes (HRBCproliferation = 1.54, 95% CI = 1.33-1.79, q < 0.0001; HRHypoxia = 1.38, 95% CI = 1.20-1.58, q < 0.0001). The results were similar for OS. CONCLUSIONS Expression of FOXA1 is a promising predictive biomarker for tamoxifen effect in ER+/HER2- premenopausal breast cancer. In addition, each of the signatures BC proliferation, Hypoxia, Mast cells, and the GEX of AR, ESR1, and PGR had prognostic value, also after adjusting for established prognostic factors. Trial registration This trial was retrospectively registered in the ISRCTN database the 6th of December 2019, trial ID: https://clinicaltrials.gov/ct2/show/ISRCTN12474687 .
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Affiliation(s)
- Christine Lundgren
- Department of Oncology, Region Jönköping County, Jönköping, Sweden.
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Building 404, 223 81, Lund, Sweden.
| | - Julia Tutzauer
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Building 404, 223 81, Lund, Sweden
| | | | - Olle Stål
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Maria Ekholm
- Department of Oncology, Region Jönköping County, Jönköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Carina Forsare
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Building 404, 223 81, Lund, Sweden
| | - Bo Nordenskjöld
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Mårten Fernö
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Building 404, 223 81, Lund, Sweden
| | - Pär-Ola Bendahl
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Building 404, 223 81, Lund, Sweden
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Surgery, Skåne University Hospital, Malmö, Sweden
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Gygi JP, Konstorum A, Pawar S, Aron E, Kleinstein SH, Guan L. A supervised Bayesian factor model for the identification of multi-omics signatures. bioRxiv 2023:2023.01.25.525545. [PMID: 36747790 PMCID: PMC9900835 DOI: 10.1101/2023.01.25.525545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
MOTIVATION Predictive biological signatures provide utility as biomarkers for disease diagnosis and prognosis, as well as prediction of responses to vaccination or therapy. These signatures are iden-tified from high-throughput profiling assays through a combination of dimensionality reduction and machine learning techniques. The genes, proteins, metabolites, and other biological analytes that compose signatures also generate hypotheses on the underlying mechanisms driving biological responses, thus improving biological understanding. Dimensionality reduction is a critical step in signature discovery to address the large number of analytes in omics datasets, especially for multi-omics profiling studies with tens of thousands of measurements. Latent factor models, which can account for the structural heterogeneity across diverse assays, effectively integrate multi-omics data and reduce dimensionality to a small number of factors that capture correlations and associations among measurements. These factors provide biologically interpretable features for predictive model-ing. However, multi-omics integration and predictive modeling are generally performed independent-ly in sequential steps, leading to suboptimal factor construction. Combining these steps can yield better multi-omics signatures that are more predictive while still being biologically meaningful. RESULTS We developed a supervised variational Bayesian factor model that extracts multi-omics signatures from high-throughput profiling datasets that can span multiple data types. Signature-based multiPle-omics intEgration via lAtent factoRs (SPEAR) adaptively determines factor rank, emphasis on factor structure, data relevance and feature sparsity. The method improves the recon-struction of underlying factors in synthetic examples and prediction accuracy of COVID-19 severity and breast cancer tumor subtypes. AVAILABILITY SPEAR is a publicly available R-package hosted at https://bitbucket.org/kleinstein/SPEAR.
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Hamid R, Alaziz M, Mahal AS, Ashton AW, Halama N, Jaeger D, Jiao X, Pestell RG. The Role and Therapeutic Targeting of CCR5 in Breast Cancer. Cells 2023; 12:2237. [PMID: 37759462 PMCID: PMC10526962 DOI: 10.3390/cells12182237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
The G-protein-coupled receptor C-C chemokine receptor 5 (CCR5) functions as a co-receptor for the entry of HIV into immune cells. CCR5 binds promiscuously to a diverse array of ligands initiating cell signaling that includes guided migration. Although well known to be expressed on immune cells, recent studies have shown the induction of CCR5 on the surface of breast cancer epithelial cells. The function of CCR5 on breast cancer epithelial cells includes the induction of aberrant cell survival signaling and tropism towards chemo attractants. As CCR5 is not expressed on normal epithelium, the receptor provides a potential useful target for therapy. Inhibitors of CCR5 (CCR5i), either small molecules (maraviroc, vicriviroc) or humanized monoclonal antibodies (leronlimab) have shown anti-tumor and anti-metastatic properties in preclinical studies. In early clinical studies, reviewed herein, CCR5i have shown promising results and evidence for effects on both the tumor and the anti-tumor immune response. Current clinical studies have therefore included combination therapy approaches with checkpoint inhibitors.
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Affiliation(s)
- Rasha Hamid
- Xavier University School of Medicine, Oranjestad, Aruba (A.S.M.)
| | - Mustafa Alaziz
- Xavier University School of Medicine, Oranjestad, Aruba (A.S.M.)
| | | | - Anthony W. Ashton
- Xavier University School of Medicine, Oranjestad, Aruba (A.S.M.)
- Lightseed Inc., Wynnewood, PA 19096, USA
- Lankenau Institute for Medical Research Philadelphia, Wynnewood, PA 19096, USA
| | - Niels Halama
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, 69120 Heidelberg, Germany; (N.H.); (D.J.)
- Department of Translational Immunotherapy, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Dirk Jaeger
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, 69120 Heidelberg, Germany; (N.H.); (D.J.)
- Clinical Cooperation Unit Applied Tumor-Immunity, 69120 Heidelberg, Germany
| | - Xuanmao Jiao
- Xavier University School of Medicine, Oranjestad, Aruba (A.S.M.)
- Lightseed Inc., Wynnewood, PA 19096, USA
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA 19096, USA
| | - Richard G. Pestell
- Xavier University School of Medicine, Oranjestad, Aruba (A.S.M.)
- Lightseed Inc., Wynnewood, PA 19096, USA
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA 19096, USA
- The Wistar Cancer Center, Philadelphia, PA 19107, USA
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26
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Dank M, Mühl D, Pölhös A, Csanda R, Herold M, Kovacs AK, Madaras L, Kulka J, Palhazy T, Tokes AM, Toth M, Ujhelyi M, Szasz AM, Herold Z. The Prediction Analysis of Microarray 50 (PAM50) Gene Expression Classifier Utilized in Indeterminate-Risk Breast Cancer Patients in Hungary: A Consecutive 5-Year Experience. Genes (Basel) 2023; 14:1708. [PMID: 37761848 PMCID: PMC10530528 DOI: 10.3390/genes14091708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Breast cancer has been categorized into molecular subtypes using immunohistochemical staining (IHC) and fluorescence in situ hybridization (FISH) since the early 2000s. However, recent research suggests that gene expression testing, specifically Prosigna® Prediction Analysis of Microarray 50 (PAM50), provides more accurate classification methods. In this retrospective study, we compared the results of IHC/FISH and PAM50 testing. We also examined the impact of various PAM50 parameters on overall survival (OS) and progression-free survival (PFS). RESULTS We analyzed 42 unilateral breast cancer samples, with 18 classified as luminal A, 10 as luminal B, 8 as Human epidermal growth factor receptor 2 (HER2)-positive, and 6 as basal-like using PAM50. Interestingly, 17 out of the 42 samples (40.47%) showed discordant results between histopathological assessment and the PAM50 classifier. While routine IHC/FISH resulted in classification differences for a quarter to a third of samples within each subtype, all basal-like tumors were misclassified. Hormone receptor-positive tumors (hazard rate: 8.7803; p = 0.0085) and patients who had higher 10-year recurrence risk scores (hazard rate: 1.0539; p = 0.0201) had shorter OS and PFS. CONCLUSIONS Our study supports the existing understanding of molecular subtypes in breast cancer and emphasizes the overlap between clinical characteristics and molecular subtyping. These findings underscore the value of gene expression profiling, such as PAM50, in improving treatment decisions for breast cancer patients.
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Affiliation(s)
- Magdolna Dank
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, H-1083 Budapest, Hungary
| | - Dorottya Mühl
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, H-1083 Budapest, Hungary
| | - Annamária Pölhös
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, H-1083 Budapest, Hungary
| | - Renata Csanda
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, H-1083 Budapest, Hungary
| | - Magdolna Herold
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, H-1083 Budapest, Hungary
- Department of Internal Medicine and Hematology, Semmelweis University, H-1088 Budapest, Hungary
| | - Attila Kristof Kovacs
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, H-1091 Budapest, Hungary
| | - Lilla Madaras
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, H-1091 Budapest, Hungary
| | - Janina Kulka
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, H-1091 Budapest, Hungary
| | - Timea Palhazy
- Department of Surgery, Transplantation and Gastroenterology, Semmelweis University, H-1082 Budapest, Hungary
| | - Anna-Maria Tokes
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, H-1091 Budapest, Hungary
| | - Monika Toth
- Department of Radiology, Semmelweis University, H-1082 Budapest, Hungary
| | | | - Attila Marcell Szasz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, H-1083 Budapest, Hungary
| | - Zoltan Herold
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, H-1083 Budapest, Hungary
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Xulu KR, Nweke EE, Augustine TN. Delineating intra-tumoral heterogeneity and tumor evolution in breast cancer using precision-based approaches. Front Genet 2023; 14:1087432. [PMID: 37662839 PMCID: PMC10469897 DOI: 10.3389/fgene.2023.1087432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
The burden of breast cancer continues to increase worldwide as it remains the most diagnosed tumor in females and the second leading cause of cancer-related deaths. Breast cancer is a heterogeneous disease characterized by different subtypes which are driven by aberrations in key genes such as BRCA1 and BRCA2, and hormone receptors. However, even within each subtype, heterogeneity that is driven by underlying evolutionary mechanisms is suggested to underlie poor response to therapy, variance in disease progression, recurrence, and relapse. Intratumoral heterogeneity highlights that the evolvability of tumor cells depends on interactions with cells of the tumor microenvironment. The complexity of the tumor microenvironment is being unraveled by recent advances in screening technologies such as high throughput sequencing; however, there remain challenges that impede the practical use of these approaches, considering the underlying biology of the tumor microenvironment and the impact of selective pressures on the evolvability of tumor cells. In this review, we will highlight the advances made thus far in defining the molecular heterogeneity in breast cancer and the implications thereof in diagnosis, the design and application of targeted therapies for improved clinical outcomes. We describe the different precision-based approaches to diagnosis and treatment and their prospects. We further propose that effective cancer diagnosis and treatment are dependent on unpacking the tumor microenvironment and its role in driving intratumoral heterogeneity. Underwriting such heterogeneity are Darwinian concepts of natural selection that we suggest need to be taken into account to ensure evolutionarily informed therapeutic decisions.
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Affiliation(s)
- Kutlwano Rekgopetswe Xulu
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ekene Emmanuel Nweke
- Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tanya Nadine Augustine
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Shirman Y, Lubovsky S, Shai A. HER2-Low Breast Cancer: Current Landscape and Future Prospects. Breast Cancer (Dove Med Press) 2023; 15:605-616. [PMID: 37600670 PMCID: PMC10439285 DOI: 10.2147/bctt.s366122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023]
Abstract
More than 50% of breast cancers are currently defined as "Human epidermal growth factor receptor 2 (HER2) low breast cancer (BC)", with HER2 immunohistochemistry (IHC) scores of +1 or +2 with a negative fluorescence in situ hybridization (FISH) test. In most studies that compared the clinical and biological characteristics of HER2-low BC with HER2-negative BC, HER2-low was not associated with unique clinical and molecular characteristics, and it seems that the importance of HER2 in these tumors is being a docking site for the antibody portion of antibody drug conjugates (ADCs). Current pathological methods may underestimate the proportion of BCs that express low levels of HER2 due to analytical limitations and tumor heterogeneity. In this review we summarize and contextualize the most recent literature on HER2-low breast cancers, including clinical and translational studies We also review the challenges of assessing low HER2 expression in BC and discuss the current and future therapeutic landscape for these tumors.
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Affiliation(s)
- Yelena Shirman
- Division of Oncology, Rambam Health Care Campus, Haifa, Israel
| | | | - Ayelet Shai
- Division of Oncology, Rambam Health Care Campus, Haifa, Israel
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Bhargava R, Dabbs DJ. The Story of the Magee Equations: The Ultimate in Applied Immunohistochemistry. Appl Immunohistochem Mol Morphol 2023; 31:490-499. [PMID: 36165933 PMCID: PMC10396078 DOI: 10.1097/pai.0000000000001065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022]
Abstract
Magee equations (MEs) are a set of multivariable models that were developed to estimate the actual Onco type DX (ODX) recurrence score in invasive breast cancer. The equations were derived from standard histopathologic factors and semiquantitative immunohistochemical scores of routinely used biomarkers. The 3 equations use slightly different parameters but provide similar results. ME1 uses Nottingham score, tumor size, and semiquantitative results for estrogen receptor (ER), progesterone receptor, HER2, and Ki-67. ME2 is similar to ME1 but does not require Ki-67. ME3 includes only semiquantitative immunohistochemical expression levels for ER, progesterone receptor, HER2, and Ki-67. Several studies have validated the clinical usefulness of MEs in routine clinical practice. The new cut-off for ODX recurrence score, as reported in the Trial Assigning IndividuaLized Options for Treatment trial, necessitated the development of Magee Decision Algorithm (MDA). MEs, along with mitotic activity score can now be used algorithmically to safely forgo ODX testing. MDA can be used to triage cases for molecular testing and has the potential to save an estimated $300,000 per 100 clinical requests. Another potential use of MEs is in the neoadjuvant setting to appropriately select patients for chemotherapy. Both single and multi-institutional studies have shown that the rate of pathologic complete response (pCR) to neoadjuvant chemotherapy in ER+/HER2-negative patients can be predicted by ME3 scores. The estimated pCR rates are 0%, <5%, 14%, and 35 to 40% for ME3 score <18, 18 to 25, >25 to <31, and 31 or higher, respectively. This information is similar to or better than currently available molecular tests. MEs and MDA provide valuable information in a time-efficient manner and are available free of cost for anyone to use. The latter is certainly important for institutions in resource-poor settings but is also valuable for large institutions and integrated health systems.
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Affiliation(s)
- Rohit Bhargava
- Department of Pathology, UPMC Magee-Womens Hospital, Pittsburgh, PA
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Reynisdottir I, Arason A, Freysteinsdottir ES, Kristjansdottir SB, Hilmarsdottir B, Traustadottir GA, Johannsson OT, Agnarsson BA, Barkardottir RB. High Atlastin 2-2 (ATL2-2) Expression Associates with Worse Prognosis in Estrogen-Receptor-Positive Breast Cancer. Genes (Basel) 2023; 14:1559. [PMID: 37628611 PMCID: PMC10454310 DOI: 10.3390/genes14081559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
The disruption of endoplasmic reticulum (ER) homeostasis occurs in many human diseases. Atlastins (ATLs) maintain the branched network of the ER. The dysregulation of ATL2, located at ER network junctions, has been associated with cancer. ATL2 is necessary for lipid droplet formation in murine breast tissue. Thus, we analyzed whether ATL2 has a role in human breast cancer (BC) pathology. The expression of ATL2 variant ATL2-2 was analyzed in breast tumors from the BC cohorts of the TCGA, METABRIC, and two independent Icelandic cohorts, Cohort 1 and 2; its association with clinical, pathological, survival, and cellular pathways was explored. ATL2-2 mRNA and protein expression were higher in breast tumors than in normal tissue. ATL2-2 mRNA associated with tumor characteristics that indicate a worse prognosis. In METABRIC, high ATL2-2 mRNA levels were associated with shorter BC-specific survival (BCSS) in patients with estrogen-receptor-positive luminal breast tumors, which remained significant after correction for grade and tumor size (HR 1.334, CI 1.063-1.673). Tumors with high ATL2 mRNA showed an upregulation of hallmark pathways MYC targets v1, E2F targets, and G2M checkpoint genes. Taken together, the results suggest that high levels of ATL2-2 may support BC progression through key cancer driver pathways.
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Affiliation(s)
- Inga Reynisdottir
- Cell Biology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; (A.A.); (B.H.); (G.A.T.); (R.B.B.)
| | - Adalgeir Arason
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; (A.A.); (B.H.); (G.A.T.); (R.B.B.)
- Molecular Pathology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
| | - Edda S. Freysteinsdottir
- Molecular Pathology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
| | - Sigrun B. Kristjansdottir
- Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland; (S.B.K.); (B.A.A.)
| | - Bylgja Hilmarsdottir
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; (A.A.); (B.H.); (G.A.T.); (R.B.B.)
- Molecular Pathology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
| | - Gunnhildur A. Traustadottir
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; (A.A.); (B.H.); (G.A.T.); (R.B.B.)
- Molecular Pathology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
| | - Oskar T. Johannsson
- Department of Oncology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
| | - Bjarni A. Agnarsson
- Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland; (S.B.K.); (B.A.A.)
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Rosa B. Barkardottir
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; (A.A.); (B.H.); (G.A.T.); (R.B.B.)
- Molecular Pathology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
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van Amerongen R, Bentires-Alj M, van Boxtel AL, Clarke RB, Fre S, Suarez EG, Iggo R, Jechlinger M, Jonkers J, Mikkola ML, Koledova ZS, Sørlie T, Vivanco MDM. Imagine beyond: recent breakthroughs and next challenges in mammary gland biology and breast cancer research. J Mammary Gland Biol Neoplasia 2023; 28:17. [PMID: 37450065 PMCID: PMC10349020 DOI: 10.1007/s10911-023-09544-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
On 8 December 2022 the organizing committee of the European Network for Breast Development and Cancer labs (ENBDC) held its fifth annual Think Tank meeting in Amsterdam, the Netherlands. Here, we embraced the opportunity to look back to identify the most prominent breakthroughs of the past ten years and to reflect on the main challenges that lie ahead for our field in the years to come. The outcomes of these discussions are presented in this position paper, in the hope that it will serve as a summary of the current state of affairs in mammary gland biology and breast cancer research for early career researchers and other newcomers in the field, and as inspiration for scientists and clinicians to move the field forward.
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Affiliation(s)
- Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands.
| | - Mohamed Bentires-Alj
- Laboratory of Tumor Heterogeneity, Metastasis and Resistance, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Antonius L van Boxtel
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Robert B Clarke
- Manchester Breast Centre, Division of Cancer Sciences, School of Medical Sciences, University of Manchester, Manchester, UK
| | - Silvia Fre
- Institut Curie, Genetics and Developmental Biology Department, PSL Research University, CNRS UMR3215, U93475248, InsermParis, France
| | - Eva Gonzalez Suarez
- Transformation and Metastasis Laboratory, Molecular Oncology, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Richard Iggo
- INSERM U1312, University of Bordeaux, 33076, Bordeaux, France
| | - Martin Jechlinger
- Cell Biology and Biophysics Department, EMBL, Heidelberg, Germany
- Molit Institute of Personalized Medicine, Heilbronn, Germany
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Marja L Mikkola
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, P.O.B. 56, 00014, Helsinki, Finland
| | - Zuzana Sumbalova Koledova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Maria dM Vivanco
- Cancer Heterogeneity Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Technological Park Bizkaia, 48160, Derio, Spain
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Sutera P, Skinner H, Witek M, Mishra M, Kwok Y, Davicioni E, Feng F, Song D, Nichols E, Tran PT, Bergom C. Histology Specific Molecular Biomarkers: Ushering in a New Era of Precision Radiation Oncology. Semin Radiat Oncol 2023; 33:232-242. [PMID: 37331778 PMCID: PMC10446901 DOI: 10.1016/j.semradonc.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Histopathology and clinical staging have historically formed the backbone for allocation of treatment decisions in oncology. Although this has provided an extremely practical and fruitful approach for decades, it has long been evident that these data alone do not adequately capture the heterogeneity and breadth of disease trajectories experienced by patients. As efficient and affordable DNA and RNA sequencing have become available, the ability to provide precision therapy has become within grasp. This has been realized with systemic oncologic therapy, as targeted therapies have demonstrated immense promise for subsets of patients with oncogene-driver mutations. Further, several studies have evaluated predictive biomarkers for response to systemic therapy within a variety of malignancies. Within radiation oncology, the use of genomics/transcriptomics to guide the use, dose, and fractionation of radiation therapy is rapidly evolving but still in its infancy. The genomic adjusted radiation dose/radiation sensitivity index is one such early and exciting effort to provide genomically guided radiation dosing with a pan-cancer approach. In addition to this broad method, a histology specific approach to precision radiation therapy is also underway. Herein we review select literature surrounding the use of histology specific, molecular biomarkers to allow for precision radiotherapy with the greatest emphasis on commercially available and prospectively validated biomarkers.
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Affiliation(s)
- Philip Sutera
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Heath Skinner
- Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew Witek
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark Mishra
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Young Kwok
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Felix Feng
- Departments of Radiation Oncology, Medicine and Urology, UCSF, San Francisco, CA, USA
| | - Daniel Song
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Nichols
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Phuoc T. Tran
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carmen Bergom
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
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Curigliano G, Dent R, Llombart-Cussac A, Pegram M, Pusztai L, Turner N, Viale G. Incorporating clinicopathological and molecular risk prediction tools to improve outcomes in early HR+/HER2- breast cancer. NPJ Breast Cancer 2023; 9:56. [PMID: 37380659 PMCID: PMC10307886 DOI: 10.1038/s41523-023-00560-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/06/2023] [Indexed: 06/30/2023] Open
Abstract
Stratification of recurrence risk is a cornerstone of early breast cancer diagnosis that informs a patient's optimal treatment pathway. Several tools exist that combine clinicopathological and molecular information, including multigene assays, which can estimate risk of recurrence and quantify the potential benefit of different adjuvant treatment modalities. While the tools endorsed by treatment guidelines are supported by level I and II evidence and provide similar prognostic accuracy at the population level, they can yield discordant risk prediction at the individual patient level. This review examines the evidence for these tools in clinical practice and offers a perspective of potential future risk stratification strategies. Experience from clinical trials with cyclin D kinase 4/6 (CDK4/6) inhibitors in the setting of hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2-) early breast cancer is provided as an illustrative example of risk stratification.
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Affiliation(s)
- Giuseppe Curigliano
- European Institute of Oncology, IRCCS, Milan, Italy.
- Department of Oncology and Hemato-Oncology, University of Milano, Milan, Italy.
| | | | | | | | | | | | - Giuseppe Viale
- European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milano, Milan, Italy
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Phakathi B, Dix-Peek T, Van Den Berg E, Dickens C, Nietz S, Cubasch H, Joffe M, Neugut AI, Jacobson JS, Ruff P, Duarte R. PAM50 intrinsic subtypes, risk of recurrence score and breast cancer survival in HIV-positive and HIV-negative patients-a South African cohort study. Breast Cancer Res Treat 2023:10.1007/s10549-023-06969-1. [PMID: 37266756 DOI: 10.1007/s10549-023-06969-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/03/2023] [Indexed: 06/03/2023]
Abstract
PURPOSE Treatment decision making for patients with breast cancer increasingly depends on analysis of markers or systems for estimating risk of breast cancer recurrence. Breast cancer intrinsic subtypes and risk of recurrence (ROR) scores have been found to be valuable in predicting survival and determining optimal treatment for individual patients. We studied the association of breast cancer survival with the PAM50 gene expression assay in HIV-positive and HIV-negative patients. METHOD RNA was extracted from formalin-fixed paraffin-embedded specimens of histologically confirmed invasive carcinoma and was purified using the AllPrep® DNA/RNA FFPE kit, Qiagen (Hilden, Germany). The NanoString RUO PAM50 algorithm was used to determine the molecular subtype and the risk of recurrence score of each sample. The overall and disease-free survival were determined with comparison made among HIV-positive and -negative patients. We then generated Kaplan-Meier survival curves, calculated p-values and estimated hazard ratios and their 95% confidence intervals using Cox regression models. RESULTS Of the 384 RNA samples analysed, 98.4% met the required RNA quality standard and the specified QC threshold for the test. Luminal B was the most common PAM50 intrinsic subtype and 82.1% of patients were at high risk for disease recurrence based on ROR score. HIV infection, PAM50-based HER2-enriched and basal-like intrinsic subtypes, and high ROR were associated with poor overall and disease-free survival. HIV-positive patients with luminal A & B subtypes had significantly worse survival outcomes than HIV-negative luminal patents. CONCLUSION Aggressive tumour biology was common in our cohort. HIV infection, PAM50 HER2-enriched,basal-like intrinsic subtypes and high ROR score were associated with poor overall and disease-free survival. HIV infection impacted survival in patients with luminal subtypes only.
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Affiliation(s)
- Boitumelo Phakathi
- Department of Surgery, Nelson R Mandela School of Medicine, University of Kwa-Zulu Natal, 719 Umbilo Road, Durban, 4001, South Africa.
| | - Therese Dix-Peek
- Department of Internal Medicine, University of Witwatersrand Faculty of Health Sciences, 7 York Road, Parktown, Johannesburg, South Africa
| | - Eunice Van Den Berg
- Department of Anatomical Pathology, University of Witwatersrand Faculty of Health Sciences, 7 York Road, Parktown, Johannesburg, South Africa
| | - Caroline Dickens
- Department of Internal Medicine, University of Witwatersrand Faculty of Health Sciences, 7 York Road, Parktown, Johannesburg, South Africa
| | - Sarah Nietz
- Department of Surgery, University of the Witwatersrand Faculty of Health Sciences, 7 York Road, Parktown, Johannesburg, 2193, South Africa
- Strengthening Oncology Services Research Unit, University of the Witwatersrand Faculty of Health Sciences, Johannesburg, South Africa
| | - Herbert Cubasch
- Department of Surgery, University of the Witwatersrand Faculty of Health Sciences, 7 York Road, Parktown, Johannesburg, 2193, South Africa
- Strengthening Oncology Services Research Unit, University of the Witwatersrand Faculty of Health Sciences, Johannesburg, South Africa
- Batho Pele Breast Unit, Chris Hani Baragwanath Academic Hospital, 26 Chris Hani Road, Diepkloof, Soweto, 1860, South Africa
- WITS/SAMRC Common Epithelial Cancers Research Centre (CECRC, Cape Town, South Africa
| | - Maureen Joffe
- Strengthening Oncology Services Research Unit, University of the Witwatersrand Faculty of Health Sciences, Johannesburg, South Africa
- WITS/SAMRC Common Epithelial Cancers Research Centre (CECRC, Cape Town, South Africa
| | - Alfred I Neugut
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA
| | - Judith S Jacobson
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA
| | - Paul Ruff
- Department of Internal Medicine, University of Witwatersrand Faculty of Health Sciences, 7 York Road, Parktown, Johannesburg, South Africa
- Strengthening Oncology Services Research Unit, University of the Witwatersrand Faculty of Health Sciences, Johannesburg, South Africa
- WITS/SAMRC Common Epithelial Cancers Research Centre (CECRC, Cape Town, South Africa
- Division of Medical Oncology, University of the Witwatersrand Faculty of Health Sciences, 7 York Road, Parktown, Johannesburg, South Africa
| | - Raquel Duarte
- Department of Internal Medicine, University of Witwatersrand Faculty of Health Sciences, 7 York Road, Parktown, Johannesburg, South Africa
- WITS/SAMRC Common Epithelial Cancers Research Centre (CECRC, Cape Town, South Africa
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Chen Z, Yang Z, Zhu L, Gao P, Matsubara T, Kanaya S, Altaf-Ul-Amin M. Learning vector quantized representation for cancer subtypes identification. Comput Methods Programs Biomed 2023; 236:107543. [PMID: 37100024 DOI: 10.1016/j.cmpb.2023.107543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/13/2023] [Accepted: 04/07/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND OBJECTIVE Defining and separating cancer subtypes is essential for facilitating personalized therapy modality and prognosis of patients. The definition of subtypes has been constantly recalibrated as a result of our deepened understanding. During this recalibration, researchers often rely on clustering of cancer data to provide an intuitive visual reference that could reveal the intrinsic characteristics of subtypes. The data being clustered are often omics data such as transcriptomics that have strong correlations to the underlying biological mechanism. However, while existing studies have shown promising results, they suffer from issues associated with omics data: sample scarcity and high dimensionality while they impose unrealistic assumptions to extract useful features from the data while avoiding overfitting to spurious correlations. METHODS This paper proposes to leverage a recent strong generative model, Vector-Quantized Variational AutoEncoder, to tackle the data issues and extract discrete representations that are crucial to the quality of subsequent clustering by retaining only information relevant to reconstructing the input. RESULTS Extensive experiments and medical analysis on multiple datasets comprising 10 distinct cancers demonstrate the proposed clustering results can significantly and robustly improve prognosis over prevalent subtyping systems. CONCLUSION Our proposal does not impose strict assumptions on data distribution; while, its latent features are better representations of the transcriptomic data in different cancer subtypes, capable of yielding superior clustering performance with any mainstream clustering method.
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Affiliation(s)
- Zheng Chen
- Graduate School of Engineering Science, Osaka University, Japan.
| | - Ziwei Yang
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Japan
| | - Lingwei Zhu
- Department of Computing Science, University of Alberta, Canada
| | - Peng Gao
- Institute for Quantitative Biosciences, University of Tokyo, Japan
| | | | - Shigehiko Kanaya
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Japan; Data Science Center, Nara Insitute of Science and Technology, Japan
| | - Md Altaf-Ul-Amin
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Japan
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36
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Voorwerk L, Sanders J, Keusters MS, Balduzzi S, Cornelissen S, Duijst M, Lips EH, Sonke GS, Linn SC, Horlings HM, Kok M. Immune landscape of breast tumors with low and intermediate estrogen receptor expression. NPJ Breast Cancer 2023; 9:39. [PMID: 37179445 PMCID: PMC10182974 DOI: 10.1038/s41523-023-00543-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Immune checkpoint blockade (ICB) is currently approved for patients with triple-negative breast cancer (TNBC), whereas responses to ICB are also observed in a small subgroup of Estrogen Receptor (ER)-positive breast cancer. The cut-off for ER-positivity (≥1%) is based on likelihood of endocrine treatment response, but ER-positive breast cancer represents a very heterogeneous group. This raises the question whether selection based on ER-negativity should be revisited to select patients for ICB treatment in the context of clinical trials. Stromal tumor-infiltrating lymphocytes (sTILs) and other immune parameters are higher in TNBC compared to ER-positive breast cancer, but it is unknown whether lower ER levels are associated with more inflamed tumor microenvironments (TME). We collected a consecutive series of primary tumors from 173 HER2-negative breast cancer patients, enriched for tumors with ER expression between 1 and 99% and found levels of stromal TILs, CD8 + T cells, and PD-L1 positivity in breast tumors with ER 1-9% and ER 10-50% to be comparable to tumors with ER 0%. Expression of immune-related gene signatures in tumors with ER 1-9% and ER 10-50% was comparable to ER 0%, and higher than in tumors with ER 51-99% and ER 100%. Our results suggest that the immune landscape of ER low tumors (1-9%) and ER intermediate tumors (10-50%) mimic that of primary TNBC.
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Affiliation(s)
- Leonie Voorwerk
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joyce Sanders
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Milou S Keusters
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sara Balduzzi
- Department of Biometrics, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sten Cornelissen
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maxime Duijst
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Gabe S Sonke
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sabine C Linn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hugo M Horlings
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marleen Kok
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
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Tada H, Gonda K, Kitamura N, Ishida T. Clinical Significance of ABCG2/BCRP Quantified by Fluorescent Nanoparticles in Breast Cancer Patients Undergoing Neoadjuvant Chemotherapy. Cancers (Basel) 2023; 15:cancers15082365. [PMID: 37190293 DOI: 10.3390/cancers15082365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Breast cancer resistance protein (BCRP), also known as ATP-binding cassette transporter G2 (ABCG2), is associated with chemotherapy resistance. BCRP is also implicated in breast cancer stem cells, and is reported as a poor prognostic factor. However, the relationship of BCRP levels in breast cancer tissues with chemotherapy resistance and prognosis has not been clarified. We aimed to evaluate the correlation between BCRP expression and prognosis in breast cancer using immunohistochemistry with fluorescent phosphor-integrated dots (IHC-PIDs). A total of 37 breast cancer patients with residual cancer in the primary tumor and axillary lymph nodes were evaluated. BCRP levels in breast cancer tissue and metastatic lymph nodes were quantitatively detected after neoadjuvant chemotherapy (NAC). Among these 37 patients, 24 had corresponding core needle biopsies obtained before NAC. Biomarker assay with IHC-PIDs showed high accuracy for the quantitative assessment of BCRP with low expression. High BCRP expression in the primary tumor and metastatic lymph nodes after preoperative chemotherapy was associated with worse overall survival. In conclusion, high BCRP levels may be associated with poor prognosis in patients with breast cancer, having residual tumors within the primary tumor and lymph nodes after preoperative chemotherapy. These findings provide a basis for further appropriate adjuvant therapy in these patients.
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Affiliation(s)
- Hiroshi Tada
- Division of Breast and Endocrine Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Miyagi, Japan
| | - Kohsuke Gonda
- Department of Medical Physics, Tohoku University Graduate School of Medicine, Sendai 980-8575, Miyagi, Japan
| | - Narufumi Kitamura
- Department of Medical Physics, Tohoku University Graduate School of Medicine, Sendai 980-8575, Miyagi, Japan
| | - Takanori Ishida
- Division of Breast and Endocrine Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Miyagi, Japan
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38
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Bergom HE, Shabaneh A, Day A, Ali A, Boytim E, Tape S, Lozada JR, Shi X, Kerkvliet CP, McSweeney S, Pitzen SP, Ludwig M, Antonarakis ES, Drake JM, Dehm SM, Ryan CJ, Wang J, Hwang J. ALAN is a computational approach that interprets genomic findings in the context of tumor ecosystems. Commun Biol 2023; 6:417. [PMID: 37059746 PMCID: PMC10104859 DOI: 10.1038/s42003-023-04795-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 04/03/2023] [Indexed: 04/16/2023] Open
Abstract
Gene behavior is governed by activity of other genes in an ecosystem as well as context-specific cues including cell type, microenvironment, and prior exposure to therapy. Here, we developed the Algorithm for Linking Activity Networks (ALAN) to compare gene behavior purely based on patient -omic data. The types of gene behaviors identifiable by ALAN include co-regulators of a signaling pathway, protein-protein interactions, or any set of genes that function similarly. ALAN identified direct protein-protein interactions in prostate cancer (AR, HOXB13, and FOXA1). We found differential and complex ALAN networks associated with the proto-oncogene MYC as prostate tumors develop and become metastatic, between different cancer types, and within cancer subtypes. We discovered that resistant genes in prostate cancer shared an ALAN ecosystem and activated similar oncogenic signaling pathways. Altogether, ALAN represents an informatics approach for developing gene signatures, identifying gene targets, and interpreting mechanisms of progression or therapy resistance.
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Affiliation(s)
- Hannah E Bergom
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Ashraf Shabaneh
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
| | - Abderrahman Day
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
| | - Atef Ali
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Ella Boytim
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Sydney Tape
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - John R Lozada
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
| | - Xiaolei Shi
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
| | - Carlos Perez Kerkvliet
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
| | - Sean McSweeney
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
| | - Samuel P Pitzen
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Graduate Program in Molecular, Cellular, and Developmental Biology and Genetics, University of Minnesota, Minneapolis, MN, USA
| | - Megan Ludwig
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Emmanuel S Antonarakis
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Justin M Drake
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Department of Urology, University of Minnesota, Minneapolis, MN, USA
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Urology, University of Minnesota, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Charles J Ryan
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Prostate Cancer Foundation, Santa Monica, CA, USA
| | - Jinhua Wang
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Justin Hwang
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, MN, USA.
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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39
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Blanca A, Lopez-Beltran A, Lopez-Porcheron K, Gomez-Gomez E, Cimadamore A, Bilé-Silva A, Gogna R, Montironi R, Cheng L. Risk Classification of Bladder Cancer by Gene Expression and Molecular Subtype. Cancers (Basel) 2023; 15:cancers15072149. [PMID: 37046810 PMCID: PMC10093178 DOI: 10.3390/cancers15072149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/31/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023] Open
Abstract
This study evaluated a panel including the molecular taxonomy subtype and the expression of 27 genes as a diagnostic tool to stratify bladder cancer patients at risk of aggressive behavior, using a well-characterized series of non-muscle invasive bladder cancer (NMIBC) as well as muscle-invasive bladder cancer (MIBC). The study was conducted using the novel NanoString nCounter gene expression analysis. This technology allowed us to identify the molecular subtype and to analyze the gene expression of 27 bladder-cancer-related genes selected through a recent literature search. The differential gene expression was correlated with clinicopathological variables, such as the molecular subtypes (luminal, basal, null/double negative), histological subtype (conventional urothelial carcinoma, or carcinoma with variant histology), clinical subtype (NMIBC and MIBC), tumor stage category (Ta, T1, and T2–4), tumor grade, PD-L1 expression (high vs. low expression), and clinical risk categories (low, intermediate, high and very high). The multivariate analysis of the 19 genes significant for cancer-specific survival in our cohort study series identified TP53 (p = 0.0001), CCND1 (p = 0.0001), MKI67 (p < 0.0001), and molecular subtype (p = 0.005) as independent predictors. A scoring system based on the molecular subtype and the gene expression signature of TP53, CCND1, or MKI67 was used for risk assessment. A score ranging from 0 (best prognosis) to 7 (worst prognosis) was obtained and used to stratify our patients into two (low [score 0–2] vs. high [score 3–7], model A) or three (low [score 0–2] vs. intermediate [score 3–4] vs. high [score 5–7], model B) risk categories with different survival characteristics. Mean cancer-specific survival was longer (122 + 2.7 months) in low-risk than intermediate-risk (79.4 + 9.4 months) or high-risk (6.2 + 0.9 months) categories (p < 0.0001; model A); and was longer (122 + 2.7 months) in low-risk than high-risk (58 + 8.3 months) (p < 0.0001; model B). In conclusion, the molecular risk assessment model, as reported here, might be used better to select the appropriate management for patients with bladder cancer.
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Affiliation(s)
- Ana Blanca
- Department of Urology, Maimonides Biomedical Research Institute of Cordoba, University Hospital of Reina Sofia, UCO, 14004 Cordoba, Spain
| | - Antonio Lopez-Beltran
- Department of Morphological Sciences, University of Cordoba Medical School, 14004 Cordoba, Spain
| | - Kevin Lopez-Porcheron
- Department of Morphological Sciences, University of Cordoba Medical School, 14004 Cordoba, Spain
| | - Enrique Gomez-Gomez
- Department of Urology, Maimonides Biomedical Research Institute of Cordoba, University Hospital of Reina Sofia, UCO, 14004 Cordoba, Spain
| | - Alessia Cimadamore
- Department of Medical Area (DAME), Institute of Pathological Anatomy, University of Udine, 33100 Udine, Italy
| | - Andreia Bilé-Silva
- Urology Department, Egas Moniz Hospital, Centro Hospitalar de Lisboa Occidental, 1349-019 Lisbon, Portugal
| | - Rajan Gogna
- Department of Human & Molecular Genetics, VCU Institute of Molecular Medicine (VIMM), VCU Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
- BRIC-Biotech Research & Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Copenhagen, Denmark
- Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal
| | - Rodolfo Montironi
- Molecular Medicine and Cell Therapy Foundation, Polytechnic University of Marche, 60121 Ancona, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Brown University Warren Alpert Medical School, Lifespan Academic Medical Center, and the Legorreta Cancer Center at Brown University, Providence, RI 02903, USA
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40
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Faria RA, Leal LB, Thebit MM, Pereira SWA, Serafim NR, Barauna VG, da Chagas E Silva Carvalho LF, Sartório CL, Gouvea SA. Potential Role of Fourier Transform Infrared Spectroscopy as a Screening Approach for Breast Cancer. Appl Spectrosc 2023; 77:405-417. [PMID: 36703259 DOI: 10.1177/00037028231156194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Breast cancer is a heterogeneous disease, and its spread involves a succession of clinical and pathological stages. Screening is predominantly based on mammography, which has critical limitations related to the effectiveness and production of false-positive or false-negative results, generating discomfort and low adherence. In this context, infrared with attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopy emerges as a non-destructive sample tool, which is non-invasive, label-free, has a low operating-cost, and requires only a small amount of sample, including liquid plasma samples. We sought to evaluate the clinical applicability of ATR FT-IR in breast cancer screening. ATR FT-IR spectroscopy through its highest potential spectral biomarker could distinguish, by liquid plasma biopsy, breast cancer patients and healthy controls, obtaining a sensitivity of 97%, specificity of 93%, a receiver operating characteristic ROC curve of 97%, and a prediction accuracy of 94%. The main variance between the groups was mainly in the band 1511 cm-1 of the control group, 1502 and 1515 cm-1 of the cancer group, which are the peaks of the bands referring to proteins and amide II. ATR FT-IR spectroscopy has demonstrated to be a promising tool for breast cancer screening, given its time efficiency, cost of approach, and its high ability to distinguish between the liquid plasma samples of breast cancer patients and healthy controls.
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Affiliation(s)
- Rodrigo A Faria
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | - Leonardo B Leal
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | - Marcela M Thebit
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | - Sergio W A Pereira
- Mastology Service Evangelical Hospital of Vila Velha, Vila Velha, Brazil
| | - Neuzimar R Serafim
- Mastology Service Evangelical Hospital of Vila Velha, Vila Velha, Brazil
| | - Valerio G Barauna
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | | | - Carmem L Sartório
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | - Sonia A Gouvea
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
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41
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Romagnoli D, Nardone A, Galardi F, Paoli M, De Luca F, Biagioni C, Franceschini GM, Pestrin M, Sanna G, Moretti E, Demichelis F, Migliaccio I, Biganzoli L, Malorni L, Benelli M. MIMESIS: minimal DNA-methylation signatures to quantify and classify tumor signals in tissue and cell-free DNA samples. Brief Bioinform 2023; 24:6991124. [PMID: 36653909 DOI: 10.1093/bib/bbad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/17/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
DNA-methylation alterations are common in cancer and display unique characteristics that make them ideal markers for tumor quantification and classification. Here we present MIMESIS, a computational framework exploiting minimal DNA-methylation signatures composed by a few dozen informative DNA-methylation sites to quantify and classify tumor signals in tissue and cell-free DNA samples. Extensive analyses of multiple independent and heterogenous datasets including >7200 samples demonstrate the capability of MIMESIS to provide precise estimations of tumor content and to enable accurate classification of tumor type and molecular subtype. To assess our framework for clinical applications, we designed a MIMESIS-informed assay incorporating the minimal signatures for breast cancer. Using both artificial samples and clinical serial cell-free DNA samples from patients with metastatic breast cancer, we show that our approach provides accurate estimations of tumor content, sensitive detection of tumor signal and the ability to capture clinically relevant molecular subtype in patients' circulation. This study provides evidence that our extremely parsimonious approach can be used to develop cost-effective and highly scalable DNA-methylation assays that could support and facilitate the implementation of precision oncology in clinical practice.
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Affiliation(s)
| | - Agostina Nardone
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Francesca Galardi
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Marta Paoli
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesca De Luca
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Chiara Biagioni
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Gian Marco Franceschini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Marta Pestrin
- Medical Oncology Unit, Azienda Sanitaria Universitaria Giuliano Isontina, 34170 Gorizia, Italy
| | - Giuseppina Sanna
- Medical Oncology, Ospedale Civile SS Annunziata, 07100 Sassari, Italy
| | - Erica Moretti
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Ilenia Migliaccio
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Laura Biganzoli
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Luca Malorni
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Matteo Benelli
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
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42
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Marcinak CT, Murtaza M, Wilke LG. Genomic Profiling and Liquid Biopsies for Breast Cancer. Surg Clin North Am 2023; 103:49-61. [DOI: 10.1016/j.suc.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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43
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Pruneri G, Lorenzini D, Mastropasqua MG, Perrone G, Rizzo A, Santini D, Volpi CC, Cinieri S, Zambelli A, Sapino A, Castellano I. The central role of pathology labs in breast cancer precision oncology: a call for action. NPJ Breast Cancer 2023; 9:3. [PMID: 36697419 DOI: 10.1038/s41523-023-00506-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
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Chen X, Sifakis EG, Robertson S, Neo SY, Jun SH, Tong L, Hui Min AT, Lövrot J, Hellgren R, Margolin S, Bergh J, Foukakis T, Lagergren J, Lundqvist A, Ma R, Hartman J. Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction. Proc Natl Acad Sci U S A 2023; 120:e2209856120. [PMID: 36574653 DOI: 10.1073/pnas.2209856120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Breast cancer (BC) is a complex disease comprising multiple distinct subtypes with different genetic features and pathological characteristics. Although a large number of antineoplastic compounds have been approved for clinical use, patient-to-patient variability in drug response is frequently observed, highlighting the need for efficient treatment prediction for individualized therapy. Several patient-derived models have been established lately for the prediction of drug response. However, each of these models has its limitations that impede their clinical application. Here, we report that the whole-tumor cell culture (WTC) ex vivo model could be stably established from all breast tumors with a high success rate (98 out of 116), and it could reassemble the parental tumors with the endogenous microenvironment. We observed strong clinical associations and predictive values from the investigation of a broad range of BC therapies with WTCs derived from a patient cohort. The accuracy was further supported by the correlation between WTC-based test results and patients' clinical responses in a separate validation study, where the neoadjuvant treatment regimens of 15 BC patients were mimicked. Collectively, the WTC model allows us to accomplish personalized drug testing within 10 d, even for small-sized tumors, highlighting its potential for individualized BC therapy. Furthermore, coupled with genomic and transcriptomic analyses, WTC-based testing can also help to stratify specific patient groups for assignment into appropriate clinical trials, as well as validate potential biomarkers during drug development.
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Bueno-Fortes S, Berral-Gonzalez A, Sánchez-Santos JM, Martin-Merino M, De Las Rivas J. Identification of a gene expression signature associated with breast cancer survival and risk that improves clinical genomic platforms. Bioinform Adv 2023; 3:vbad037. [PMID: 37096121 PMCID: PMC10122606 DOI: 10.1093/bioadv/vbad037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/21/2023] [Indexed: 04/26/2023]
Abstract
Motivation Modern genomic technologies allow us to perform genome-wide analysis to find gene markers associated with the risk and survival in cancer patients. Accurate risk prediction and patient stratification based on robust gene signatures is a key path forward in personalized treatment and precision medicine. Several authors have proposed the identification of gene signatures to assign risk in patients with breast cancer (BRCA), and some of these signatures have been implemented within commercial platforms in the clinic, such as Oncotype and Prosigna. However, these platforms are black boxes in which the influence of selected genes as survival markers is unclear and where the risk scores provided cannot be clearly related to the standard clinicopathological tumor markers obtained by immunohistochemistry (IHC), which guide clinical and therapeutic decisions in breast cancer. Results Here, we present a framework to discover a robust list of gene expression markers associated with survival that can be biologically interpreted in terms of the three main biomolecular factors (IHC clinical markers: ER, PR and HER2) that define clinical outcome in BRCA. To test and ensure the reproducibility of the results, we compiled and analyzed two independent datasets with a large number of tumor samples (1024 and 879) that include full genome-wide expression profiles and survival data. Using these two cohorts, we obtained a robust subset of gene survival markers that correlate well with the major IHC clinical markers used in breast cancer. The geneset of survival markers that we identify (which includes 34 genes) significantly improves the risk prediction provided by the genesets included in the commercial platforms: Oncotype (16 genes) and Prosigna (50 genes, i.e. PAM50). Furthermore, some of the genes identified have recently been proposed in the literature as new prognostic markers and may deserve more attention in current clinical trials to improve breast cancer risk prediction. Availability and implementation All data integrated and analyzed in this research will be available on GitHub (https://github.com/jdelasrivas-lab/breastcancersurvsign), including the R scripts and protocols used for the analyses. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Santiago Bueno-Fortes
- Cancer Research Center (CiC-IMBCC, CSIC/USAL and IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), Salamanca 37007, Spain
| | - Alberto Berral-Gonzalez
- Cancer Research Center (CiC-IMBCC, CSIC/USAL and IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), Salamanca 37007, Spain
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Lien HC, Hsu CL, Lu YS, Chen TW, Chen IC, Li YC, Huang CS, Cheng AL, Lin CH. Transcriptomic alterations underlying metaplasia into specific metaplastic components in metaplastic breast carcinoma. Breast Cancer Res 2023; 25:11. [PMID: 36707876 DOI: 10.1186/s13058-023-01608-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/19/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Metaplastic breast carcinoma (MpBC) typically consists of carcinoma of no special type (NST) with various metaplastic components. Although previous transcriptomic and proteomic studies have reported subtype-related heterogeneity, the intracase transcriptomic alterations between metaplastic components and paired NST components, which are critical for understanding the pathogenesis underlying the metaplastic processes, remain unclear. METHODS Fifty-nine NST components and paired metaplastic components (spindle carcinomatous [SPS], matrix-producing, rhabdoid [RHA], and squamous carcinomatous [SQC] components) were microdissected from specimens obtained from 27 patients with MpBC for gene expression profiling using the NanoString Breast Cancer 360 Panel on a NanoString nCounter FLEX platform. BC360-defined signatures were scored using nSolver software. RESULTS Hierarchical clustering and principal component analysis revealed a heterogeneous gene expression profile (GEP) corresponding to the NST components, but the GEP of metaplastic components exhibited subtype dependence. Compared with the paired NST components, the SPS components demonstrated the upregulation of genes related to stem cells and epithelial-mesenchymal transition and displayed enrichment in claudin-low and macrophage signatures. Despite certain overlaps in the enriched functions and signatures between the RHA and SPS components, the specific differentially expressed genes differed. We observed the RHA-specific upregulation of genes associated with vascular endothelial growth factor signaling. The chondroid matrix-producing components demonstrated the upregulation of hypoxia-related genes and the downregulation of the immune-related MHC2 signature and the TIGIT gene. In the SQC components, TGF-β and genes associated with cell adhesion were upregulated. The differentially expressed genes among metaplastic components in the 22 MpBC cases with one or predominantly one metaplastic component clustered paired NST samples into clusters with correlation with their associated metaplastic types. These genes could be used to separate the 31 metaplastic components according to respective metaplastic types with an accuracy of 74.2%, suggesting that intrinsic signatures of NST may determine paired metaplastic type. Finally, the EMT activity and stem cell traits in the NST components were correlated with specimens displaying lymph node metastasis. CONCLUSIONS We presented the distinct transcriptomic alterations underlying metaplasia into specific metaplastic components in MpBCs, which contributes to the understanding of the pathogenesis underlying morphologically distinct metaplasia in MpBCs.
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Abstract
CONTEXT.— Appropriate patient management requires precise and meaningful tumor classification. Breast cancer classification continues to evolve from traditional morphologic evaluation to more sophisticated systems with the integration of new knowledge from research being translated into practice. Breast cancer is heterogeneous at the molecular level, with diversified patterns of gene expression, which is presumably responsible for the difference in tumor behavior and prognosis. Since the beginning of this century, new molecular technology has been gradually applied to breast cancer research on issues pertinent to prognosis (prognostic signature) and therapeutic prediction (predictive signature), and much progress has been made. OBJECTIVE.— To summarize the current state and the prospective future of molecular classification of breast cancer. DATA SOURCES.— Sources include recent medical literature on molecular classification of breast cancer. CONCLUSIONS.— Identification of intrinsic tumor subtypes has set a foundation for refining the breast cancer molecular classification. Studies have explored the genetic features within the intrinsic cancer subtypes and have identified novel molecular targets that led to the innovation of clinical assays to predict a patient's prognosis and to provide specific guidelines for therapeutic decisions. With the development and implication of these molecular tools, we have remarkably advanced our knowledge and enhanced our power to provide optimal management to patients. However, challenges still exist. Besides accurate prediction of prognosis, we are still in urgent need of more molecular predictors for tumor response to therapeutic regimes. Further exploration along this path will be critical for improving a patient's prognosis.
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Affiliation(s)
- Xinmin Zhang
- From the Department of Pathology, Cooper University Hospital, Cooper Medical School of Rowan University, Camden, New Jersey
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48
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Falato C, Schettini F, Pascual T, Brasó-Maristany F, Prat A. Clinical implications of the intrinsic molecular subtypes in hormone receptor-positive and HER2-negative metastatic breast cancer. Cancer Treat Rev 2023; 112:102496. [PMID: 36563600 DOI: 10.1016/j.ctrv.2022.102496] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Traditionally, the classification of breast cancer relies on the expression of immunohistochemical (IHC) biomarkers readily available in clinical practice. Using highly standardized and reproducible assays across patient cohorts, intrinsic molecular subtypes of breast cancer - also called "intrinsic subtypes" (IS) - have been identified based on the expression of 50 genes. Although IHC-based subgroups and IS moderately correlate to each other, they are not superimposable. In fact, non-luminal biology has been detected in a substantial proportion (5-20%) of hormone receptor-positive (HoR+) tumors, has prognostic value, and identifies reduced and increased sensitivity to endocrine therapy and chemotherapy, respectively. During tumor progression, a shift toward a non-luminal estrogen-independent and more aggressive phenotype has been demonstrated. Intrinsic genomic instability and cell plasticity, alone or combined with external constraints deriving from treatment selective pressure or interplay with the tumor microenvironment, may represent the determinants of such biological diversity between primary and metastatic disease, and during metastatic tumor evolution. In this review, we describe the distribution and the clinical behavior of IS as the disease progresses, focusing on HoR+/HER2-negative advanced breast cancer. In addition, we provide an overview of the ongoing clinical trials aiming to validate the predictive and prognostic value of IS towards their incorporation into routine care.
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Affiliation(s)
- Claudette Falato
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; SOLTI Cancer Research Group, Barcelona, Spain; Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden.
| | - Francesco Schettini
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain.
| | - Tomás Pascual
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; SOLTI Cancer Research Group, Barcelona, Spain; Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain.
| | - Fara Brasó-Maristany
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.
| | - Aleix Prat
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain; Reveal Genomics, Barcelona, Spain.
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Beyer SJ, Tallman M, Jhawar SR, White JR, Bazan JG. The Prognostic and Predictive Value of Genomic Assays in Guiding Adjuvant Breast Radiation Therapy. Biomedicines 2022; 11:biomedicines11010098. [PMID: 36672606 PMCID: PMC9855532 DOI: 10.3390/biomedicines11010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/01/2023] Open
Abstract
Many patients with non-metastatic breast cancer benefit from adjuvant radiation therapy after lumpectomy or mastectomy on the basis of many randomized trials. However, there are many patients that have such low risks of recurrence after surgery that de-intensification of therapy by either reducing the treatment volume or omitting radiation altogether may be appropriate options. On the other hand, dose intensification may be necessary for more aggressive breast cancers. Until recently, these treatment decisions were based solely on clinicopathologic factors. Here, we review the current literature on the role of genomic assays as prognostic and/or predictive biomarkers to help guide adjuvant radiation therapy decision-making.
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Affiliation(s)
- Sasha J. Beyer
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Miranda Tallman
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Sachin R. Jhawar
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Julia R. White
- Department of Radiation Oncology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jose G. Bazan
- Department of Radiation Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
- Correspondence:
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Zhou Q, Galindo-González L, Hwang SF, Strelkov SE. Application of the NanoString nCounter System as an Alternative Method to Investigate Molecular Mechanisms Involved in Host Plant Responses to Plasmodiophora brassicae. Int J Mol Sci 2022; 23. [PMID: 36555223 DOI: 10.3390/ijms232415581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Clubroot, caused by the soilborne pathogen Plasmodiophora brassicae, is an important disease of canola (Brassica napus) and other crucifers. The recent application of RNA sequencing (RNA-seq) technologies to study P. brassicae−host interactions has generated large amounts of gene expression data, improving knowledge of the molecular mechanisms of pathogenesis and host resistance. Quantitative PCR (qPCR) analysis has been widely applied to examine the expression of a limited number of genes and to validate the results of RNA-seq studies, but may not be ideal for analyzing larger suites of target genes or increased sample numbers. Moreover, the need for intermediate steps such as cDNA synthesis may introduce variability that could affect the accuracy of the data generated by qPCR. Here, we report the validation of gene expression data from a previous RNA-seq study of clubroot using the NanoString nCounter System, which achieves efficient gene expression quantification in a fast and simple manner. We first confirm the robustness of the NanoString system by comparing the results with those generated by qPCR and RNA-seq and then discuss the importance of some candidate genes for resistance or susceptibility to P. brassicae in the host. The results show that the expression of genes measured using NanoString have a high correlation with the values obtained using the other two technologies, with R > 0.90 and p < 0.01, and the same expression patterns for most genes. The three methods (qPCR, RNA-seq, and NanoString) were also compared in terms of laboratory procedures, time, and cost. We propose that the NanoString nCounter System is a robust, sensitive, highly reproducible, and simple technology for gene expression analysis. NanoString could become a common alternative to qPCR to validate RNA-seq data or to create panels of genes for use as markers of resistance/susceptibility when plants are challenged with different P. brassicae pathotypes.
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