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Xu Y, Qi Y, Lu Z, Tan Y, Chen D, Luo H. Navigating precision: the crucial role of next-generation sequencing recurrence risk assessment in tailoring adjuvant therapy for hormone receptor-positive, human epidermal growth factor Receptor2-negative early breast cancer. Cancer Biol Ther 2024; 25:2405060. [PMID: 39304993 PMCID: PMC11418226 DOI: 10.1080/15384047.2024.2405060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/02/2024] [Accepted: 09/12/2024] [Indexed: 09/25/2024] Open
Abstract
Hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2-) breast cancer is the most common subtype, representing over two-thirds of new diagnoses. Adjuvant therapy, which encompasses various medications and treatment durations, is the standard approach for managing early stage HR+ HER2- breast cancer. Optimizing treatment is essential to minimize unnecessary side effects while addressing the biological variability inherent in HR+/HER2- breast cancers. Incorporating biological biomarkers into treatment decisions, alongside traditional clinical factors, is vital. Gene expression assays can identify patients unlikely to benefit from adjuvant chemotherapy, thereby refining treatment strategies and improving risk assessment. This paper reviews evidence for several genomic tests, including Oncotype DX, MammaPrint, Breast Cancer Index, RucurIndex, and EndoPredict, which assist in tailoring adjuvant therapy. Additionally, we explore the role of liquid biopsies in personalizing treatment, emphasizing the importance of considering late relapse risks and potential benefits of extended systemic therapy for HR+/HER2- breast cancer patients.
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MESH Headings
- Humans
- Breast Neoplasms/genetics
- Breast Neoplasms/drug therapy
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Female
- Chemotherapy, Adjuvant/methods
- Receptor, ErbB-2/metabolism
- Receptor, ErbB-2/genetics
- Risk Assessment/methods
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Neoplasm Recurrence, Local/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- High-Throughput Nucleotide Sequencing/methods
- Precision Medicine/methods
- Receptors, Estrogen/metabolism
- Receptors, Progesterone/metabolism
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Affiliation(s)
- Ying Xu
- Department of Obestetrics and Gynecology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Yingxue Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd. Nanjing Simcere Medical Laboratory Science Co. Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Zhongyu Lu
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd. Nanjing Simcere Medical Laboratory Science Co. Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Yuan Tan
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd. Nanjing Simcere Medical Laboratory Science Co. Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Dongsheng Chen
- The Medical Department, Jiangsu Simcere Diagnostics Co. Ltd. Nanjing Simcere Medical Laboratory Science Co. Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
- Cancer Center, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
- Center of Translational Medicine, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Haijun Luo
- Department of Pathology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
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2
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Lee JJ, Yeh JJ. Updates in Molecular Profiling of Pancreatic Ductal Adenocarcinoma. Surg Clin North Am 2024; 104:939-950. [PMID: 39237169 PMCID: PMC11377860 DOI: 10.1016/j.suc.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
Outcomes from pancreatic ductal adenocarcinoma (PDAC) remain poor and better methods of prognostication and therapeutic approaches are needed. Recent advances in cancer genomics have led to the development of molecular subtypes of PDAC associated with clinical outcomes. Current evidence also suggests that the subtypes have differential response to first-line chemotherapy regimens. PDAC is also characterized by different stroma and immune environments. Further work is needed to confirm the utility of these subtypes to predicting response to different systemic therapies.
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Affiliation(s)
- Jaewon James Lee
- Department of Surgery, University of North Carolina at Chapel Hill, 170 Manning Dr, CB7213, Chapel Hill, NC 27599-7213, USA
| | - Jen Jen Yeh
- Department of Surgery, University of North Carolina at Chapel Hill, 170 Manning Dr, CB7213, Chapel Hill, NC 27599-7213, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB7295, Chapel Hill, NC 27599-7295, USA.
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3
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Xie Y, Yang J, Ouyang JF, Petretto E. scPanel: a tool for automatic identification of sparse gene panels for generalizable patient classification using scRNA-seq datasets. Brief Bioinform 2024; 25:bbae482. [PMID: 39350339 PMCID: PMC11442147 DOI: 10.1093/bib/bbae482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/30/2024] [Accepted: 09/12/2024] [Indexed: 10/04/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies can generate transcriptomic profiles at a single-cell resolution in large patient cohorts, facilitating discovery of gene and cellular biomarkers for disease. Yet, when the number of biomarker genes is large, the translation to clinical applications is challenging due to prohibitive sequencing costs. Here, we introduce scPanel, a computational framework designed to bridge the gap between biomarker discovery and clinical application by identifying a sparse gene panel for patient classification from the cell population(s) most responsive to perturbations (e.g. diseases/drugs). scPanel incorporates a data-driven way to automatically determine a minimal number of informative biomarker genes. Patient-level classification is achieved by aggregating the prediction probabilities of cells associated with a patient using the area under the curve score. Application of scPanel to scleroderma, colorectal cancer, and COVID-19 datasets resulted in high patient classification accuracy using only a small number of genes (<20), automatically selected from the entire transcriptome. In the COVID-19 case study, we demonstrated cross-dataset generalizability in predicting disease state in an external patient cohort. scPanel outperforms other state-of-the-art gene selection methods for patient classification and can be used to identify parsimonious sets of reliable biomarker candidates for clinical translation.
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Affiliation(s)
- Yi Xie
- Programme in Cardiovascular and Metabolic Disorders, Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jianfei Yang
- The School of Mechanical and Aerospace Engineering and the School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore 639798, Singapore
| | - John F Ouyang
- Programme in Cardiovascular and Metabolic Disorders, Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
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4
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Esin E, Yildirim HC, Oksuzoglu B, Markoc F, Guntekin S, Bilgetekin I, Yildiz F, Yukruk F, Demirci U, Cetin-Atalay R. Prosigna Assay for Treatment Decisions in Early Breast Cancer: A Decision Impact Study. J Clin Med 2024; 13:5328. [PMID: 39274541 PMCID: PMC11396381 DOI: 10.3390/jcm13175328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/03/2024] [Accepted: 09/05/2024] [Indexed: 09/16/2024] Open
Abstract
Introduction: Therapeutic decisions in early breast cancer are based on clinico-pathological features which are subject to intra- and inter-observer variability. This single-center decision impact study aimed to evaluate the effects of the Prosigna assay on physicians' adjuvant treatment choices. Methods: Between 09/2017 and 02/2018, formalin-fixed tumor samples from 52 newly diagnosed, postmenopausal, hormone receptor-positive, HER2-negative breast cancer (T1-T2; pN0-N1a) patients were analyzed. Pre-test clinical judgements and Prosigna test results were compared. Results: The mean age was 59 (42-77). Invasive ductal carcinoma (79.2%), grade 2 (52.8%) and T1c-N0 tumors (43.4%) were represented. There was 40.4% discordance between the pre- and post-test risk of recurrences. No significant change was observed in the clinical intermediate risk category, while there was a net reclassification of low-risk patients into a high Prosigna recurrence risk group. In addition, clinically determined intrinsic subtypes were 34.6% discordant with the Prosigna results, which is largely driven by the reclassification of the luminal A tumors into the Prosigna-assessed luminal B group. Before the Prosigna test, endocrine treatment was the primary choice in 20 patients (39.2%), and chemotherapy was recommended to 31 patients (60.8%). Overall, the Prosigna assay led to a change in treatment choice for one patient. Conclusions: Although conventional risk assessment methods are relatively inexpensive with shorter turnaround times, their accuracy and value for risk reduction are suboptimal. According to our results, the Prosigna assay was found to be a relevant tool for the clinical decision making process. Long-term follow-up of these patients will elucidate the potential benefits of using multigene molecular tests as biomarkers for treatment.
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Affiliation(s)
- Ece Esin
- Department of Medical Oncology, Dr. A.Y. Ankara Oncology Education and Research Hospital, University of Health Sciences, Ankara 06540, Turkey
| | - Hasan Cagri Yildirim
- Department of Medical Oncology, Nigde Education and Research Hospital, Niğde 51100, Turkey
| | - Berna Oksuzoglu
- Department of Medical Oncology, Dr. A.Y. Ankara Oncology Education and Research Hospital, University of Health Sciences, Ankara 06540, Turkey
| | - Fatma Markoc
- Department of Pathology, Dr. A.Y. Ankara Oncology Education and Research Hospital, University of Health Sciences, Ankara 06540, Turkey
| | - Sezen Guntekin
- CanSyL, Graduate School of Informatics, Middle East Technical University, Ankara 06800, Turkey
| | - Irem Bilgetekin
- Department of Medical Oncology, Dr. A.Y. Ankara Oncology Education and Research Hospital, University of Health Sciences, Ankara 06540, Turkey
| | - Fatih Yildiz
- Department of Medical Oncology, Dr. A.Y. Ankara Oncology Education and Research Hospital, University of Health Sciences, Ankara 06540, Turkey
| | - Fisun Yukruk
- Department of Pathology, Dr. A.Y. Ankara Oncology Education and Research Hospital, University of Health Sciences, Ankara 06540, Turkey
| | - Umut Demirci
- Department of Medical Oncology, Dr. A.Y. Ankara Oncology Education and Research Hospital, University of Health Sciences, Ankara 06540, Turkey
| | - Rengul Cetin-Atalay
- CanSyL, Graduate School of Informatics, Middle East Technical University, Ankara 06800, Turkey
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5
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Ingebriktsen LM, Humlevik ROC, Svanøe AA, Sæle AKM, Winge I, Toska K, Kalvenes MB, Davidsen B, Heie A, Knutsvik G, Askeland C, Stefansson IM, Hoivik EA, Akslen LA, Wik E. Elevated expression of Aurora-A/AURKA in breast cancer associates with younger age and aggressive features. Breast Cancer Res 2024; 26:126. [PMID: 39198859 PMCID: PMC11360479 DOI: 10.1186/s13058-024-01882-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 08/16/2024] [Indexed: 09/01/2024] Open
Abstract
BACKGROUND AND OBJECTIVE Aurora kinase A (AURKA) is reported to be overexpressed in breast cancer. In addition to its role in regulating cell cycle and mitosis, studies have reported AURKA involvements in oncogenic signaling in suppressing BRCA1 and BRCA2. We aimed to characterize AURKA protein and mRNA expression in a breast cancer cohort of the young, investigating its relation to clinico-pathologic features and survival, and exploring age-related AURKA-associated biological processes. METHODS Aurora kinase A immunohistochemical staining was performed on tissue microarrays of primary tumors from an in-house breast cancer cohort (n = 355) with information on clinico-pathologic data, molecular markers, and long and complete follow-up. A subset of the in-house cohort (n = 127) was studied by the NanoString Breast Cancer 360 expression panel for exploration of mRNA expression. METABRIC cohorts < 50 years at breast cancer diagnosis (n = 368) were investigated for differentially expressed genes and enriched gene sets in AURKA mRNA high tumors stratified by age. Differentially expressed genes and gene sets were investigated using network analyses and g:Profiler. RESULTS High Aurora kinase A protein expression associated with aggressive clinico-pathologic features, a basal-like subtype, and high risk of recurrence score. These patterns were confirmed using mRNA data. High AURKA gene expression demonstrated independent prognostic value when adjusted for traditional clinico-pathologic features and molecular subtypes. Notably, high AURKA expression significantly associated with reduced disease-specific survival within patients below 50 years, also within the luminal A subtype. Tumors of high AURKA expression showed gene expression patterns reflecting increased DNA damage activation and higher BRCAness score. CONCLUSIONS Our findings indicate higher AURKA expression in young breast cancer, and associations between high Aurora-A/AURKA and aggressive tumor features, including higher tumor cell proliferation, and shorter survival, in the young. Our findings point to AURKA as a marker for increased DNA damage and DNA repair deficiency and suggest AURKA as a biomarker of clinical relevance in young breast cancer.
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Grants
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- F-12143 Helse Vest Research Fund
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- 223250 University of Bergen, Research Council of Norway, Center of Excellence funding scheme
- University of Bergen (incl Haukeland University Hospital)
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Affiliation(s)
- L M Ingebriktsen
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
| | - R O C Humlevik
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
| | - A A Svanøe
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
| | - A K M Sæle
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
| | - I Winge
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
| | - K Toska
- Section for Cancer Genomics, Haukeland University Hospital, Bergen, Norway
| | - M B Kalvenes
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
| | - B Davidsen
- Department of Surgery, Section for Breast and Endocrine Surgery, Haukeland University Hospital, Bergen, Norway
| | - A Heie
- Department of Surgery, Section for Breast and Endocrine Surgery, Haukeland University Hospital, Bergen, Norway
| | - G Knutsvik
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - C Askeland
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - I M Stefansson
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - E A Hoivik
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - L A Akslen
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - E Wik
- Department of Clinical Medicine, Section for Pathology, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway.
- Department of Pathology, Haukeland University Hospital, Bergen, Norway.
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Stephenson-Gussinye A, Rendón-Bautista LA, Ruiz-Medina BE, Blanco-Olais E, Pérez-Molina R, Marcial-Medina C, Chavarri-Guerra Y, Soto-Pérez-de-Celis E, Morales-Alfaro A, Esquivel-López A, Candanedo-González F, Gamboa-Domínguez A, Cortes-González R, Alfaro-Goldaracena A, Vázquez-Manjarrez SE, Grajales-Figueroa G, Astudillo-Romero B, Ruiz-Manriquez J, Poot-Hernández AC, Licona-Limón P, Furlan-Magaril M. Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single-cell transcriptome analysis. Front Mol Biosci 2024; 11:1420308. [PMID: 39239354 PMCID: PMC11375512 DOI: 10.3389/fmolb.2024.1420308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/16/2024] [Indexed: 09/07/2024] Open
Abstract
Molecular and cellular characterization of tumors is essential due to the complex and heterogeneous nature of cancer. In recent decades, many bioinformatic tools and experimental techniques have been developed to achieve personalized characterization of tumors. However, sample handling continues to be a major challenge as limitations such as prior treatments before sample acquisition, the amount of tissue obtained, transportation, or the inability to process fresh samples pose a hurdle for experimental strategies that require viable cell suspensions. Here, we present an optimized protocol that allows the recovery of highly viable cell suspensions from breast cancer primary tumor biopsies. Using these cell suspensions we have successfully characterized genome architecture through Hi-C. Also, we have evaluated single-cell gene expression and the tumor cellular microenvironment through single-cell RNAseq. Both technologies are key in the detailed and personalized molecular characterization of tumor samples. The protocol described here is a cost-effective alternative to obtain viable cell suspensions from biopsies simply and efficiently.
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Affiliation(s)
- Aura Stephenson-Gussinye
- Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Luis A Rendón-Bautista
- Department of Cellular and Developmental Biology, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Blanca E Ruiz-Medina
- Department of Cellular and Developmental Biology, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Eduardo Blanco-Olais
- Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Rosario Pérez-Molina
- Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Cleofas Marcial-Medina
- Department of Cellular and Developmental Biology, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Yanin Chavarri-Guerra
- Department of Hemato-Oncology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Enrique Soto-Pérez-de-Celis
- Department of Geriatrics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Department of Medicine, Division of Medical Oncology, University of Colorado Cancer Center, Denver, CO, United States
| | - Andrea Morales-Alfaro
- Department of Medicine, Division of Medical Oncology, University of Colorado Cancer Center, Denver, CO, United States
| | - Ayerim Esquivel-López
- Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Fernando Candanedo-González
- Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Armando Gamboa-Domínguez
- Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Rubén Cortes-González
- Surgical Oncology Service, Department of Surgery, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Alejandro Alfaro-Goldaracena
- Surgical Oncology Service, Department of Surgery, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Sara E Vázquez-Manjarrez
- Department of Radiology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Guido Grajales-Figueroa
- Department of Gastrointestinal Endoscopy, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Beatriz Astudillo-Romero
- Department of Gastrointestinal Endoscopy, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Jesús Ruiz-Manriquez
- Department of Gastrointestinal Endoscopy, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - A César Poot-Hernández
- Unidad de Bioinformática y Manejo de Información, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Paula Licona-Limón
- Department of Cellular and Developmental Biology, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Mayra Furlan-Magaril
- Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
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7
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Sharma A, Lövgren SK, Eriksson KL, Wang Y, Robertson S, Hartman J, Rantalainen M. Validation of an AI-based solution for breast cancer risk stratification using routine digital histopathology images. Breast Cancer Res 2024; 26:123. [PMID: 39143539 PMCID: PMC11323658 DOI: 10.1186/s13058-024-01879-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 08/06/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Stratipath Breast is a CE-IVD marked artificial intelligence-based solution for prognostic risk stratification of breast cancer patients into high- and low-risk groups, using haematoxylin and eosin (H&E)-stained histopathology whole slide images (WSIs). In this validation study, we assessed the prognostic performance of Stratipath Breast in two independent breast cancer cohorts. METHODS This retrospective multi-site validation study included 2719 patients with primary breast cancer from two Swedish hospitals. The Stratipath Breast tool was applied to stratify patients based on digitised WSIs of the diagnostic H&E-stained tissue sections from surgically resected tumours. The prognostic performance was evaluated using time-to-event analysis by multivariable Cox Proportional Hazards analysis with progression-free survival (PFS) as the primary endpoint. RESULTS In the clinically relevant oestrogen receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative patient subgroup, the estimated hazard ratio (HR) associated with PFS between low- and high-risk groups was 2.76 (95% CI: 1.63-4.66, p-value < 0.001) after adjusting for established risk factors. In the ER+/HER2- Nottingham histological grade (NHG) 2 subgroup, the HR was 2.20 (95% CI: 1.22-3.98, p-value = 0.009) between low- and high-risk groups. CONCLUSION The results indicate an independent prognostic value of Stratipath Breast among all breast cancer patients, as well as in the clinically relevant ER+/HER2- subgroup and the NHG2/ER+/HER2- subgroup. Improved risk stratification of intermediate-risk ER+/HER2- breast cancers provides information relevant for treatment decisions of adjuvant chemotherapy and has the potential to reduce both under- and overtreatment. Image-based risk stratification provides the added benefit of short lead times and substantially lower cost compared to molecular diagnostics and therefore has the potential to reach broader patient groups.
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Affiliation(s)
- Abhinav Sharma
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sandy Kang Lövgren
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Stratipath AB, Solna, Sweden
| | - Kajsa Ledesma Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Stratipath AB, Solna, Sweden
| | - Yinxi Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Stratipath AB, Solna, Sweden
| | - Stephanie Robertson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Stratipath AB, Solna, Sweden
| | - Johan Hartman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- MedTechLabs, BioClinicum, Karolinska University Hospital, Solna, Sweden
| | - Mattias Rantalainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- MedTechLabs, BioClinicum, Karolinska University Hospital, Solna, Sweden.
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8
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Hassing CMS, Tvedskov THF, Kroman N, Knoop AS, Lænkholm AV. Evaluating the Prognostic Role of the PAM50 Signature and Selected Immune-Related Signatures for Recurrence in Patients With T1abN0 Breast Cancer. Clin Breast Cancer 2024:S1526-8209(24)00215-5. [PMID: 39209597 DOI: 10.1016/j.clbc.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/15/2024] [Accepted: 08/03/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND De-escalation of adjuvant treatment in patients with T1abN0 breast cancer is discussed internationally. Identification of new prognostic factors in these patients may assist this de-escalation. The PAM50 signature and tumor inflammation signature (TIS), Programmed Cell Death Protein 1 (PD-1) and Programmed Cell Death Ligand 1 (PD-L1) signatures are possible prognostic factors for recurrence. MATERIALS AND METHODS Danish patients with T1abN0 breast cancer diagnosed between 2007-2016 were identified, the NanoString Breast Cancer 360 Panel was performed on tissue samples from cases with recurrence matched 1:1 with controls without recurrence (n = 234). The association between gene signatures and recurrence was analyzed with conditional logistic regression. RESULTS Patients with the basal-like subtype had higher values of TIS, PD-1 and PD-L1 scores compared with other subtypes. Patients with higher PD-L1 score had significantly lower odds of recurrence (odds ratio [OR] 0.61, P = .01). Likewise, an increased TIS score was associated to lower, but nonsignificant odds of recurrence (OR 0.76, P = .07). Patients with human epidermal growth factor receptor 2 (HER2)-enriched subtype had significantly higher odds of recurrence compared with patients with luminal A subtype (OR 4.8, P = .03). DISCUSSION PAM50 and immune-related signatures provide important prognostic information in patients with T1abN0 breast cancer, which may refine the risk assessment in these patients.
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Affiliation(s)
- Christina M S Hassing
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Gentofte Hospitalsvej 1, 2900 Hellerup, Denmark.
| | - Tove Holst Filtenborg Tvedskov
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Gentofte Hospitalsvej 1, 2900 Hellerup, Denmark
| | - Niels Kroman
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Gentofte Hospitalsvej 1, 2900 Hellerup, Denmark; Danish Cancer Society, Strandboulevarden 49, 2100 Copenhagen Ø, Denmark
| | - Ann Søegaard Knoop
- Department of Oncology, Section 4262, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen Ø, Denmark
| | - Anne-Vibeke Lænkholm
- Department of Surgical Pathology, Zealand University Hospital, Sygehusvej 9 (postal: Sygehusvej 10), 4000 Roskilde, Denmark
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9
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Ingebriktsen LM, Svanøe AA, Myrmel Sæle AK, Humlevik ROC, Toska K, Kalvenes MB, Aas T, Heie A, Askeland C, Knutsvik G, Stefansson IM, Akslen LA, Hoivik EA, Wik E. Age-Related Clusters and Favorable Immune Phenotypes in Young Breast Cancer Patients. Mod Pathol 2024; 37:100529. [PMID: 38810731 DOI: 10.1016/j.modpat.2024.100529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024]
Abstract
Breast cancer (BC) patients aged <40 years at diagnosis experience aggressive disease and poorer survival compared with women diagnosed with BC at 40 to 49 years, but the age-related biology is described to little extent. Here, we explored transcriptional alterations in BC to gain better understanding of age-related tumor biology. We studied a subset of the Bergen in-house cohort (n = 127; age range, 26-49 years) and used the NanoString Breast Cancer 360 expression panel on formalin-fixed paraffin-embedded BC tissue, and publicly available global BC messenger RNA expression data (n = 204; age range, 22-49 years), to explore differentially expressed genes between the young (age <40 years) and older (age 40-49 years) patients. Unsupervised hierarchical clustering was applied to identify gene expression-based patient clusters. We applied established computational approaches to define the PAM50 subtypes, risk of recurrence scores (ROR), and risk groups and to infer the proportions of 22 immune cell types from bulk gene expression profiles of patients aged <50 years at BC diagnosis. Differentially expressed genes and gene sets were investigated using OncoEnrichR and g:Profiler to describe functional profiles and pathway enrichment. We identified 4 age-related patient clusters presenting distinct characteristics of PAM50 subtypes and ROR profiles, which demonstrated independent prognostic value when adjusted for traditional clinicopathologic variables and the known molecular subtypes. Our findings showed better survival than expected in the basal-enriched cluster 2 and in triple-negative and basal-like BC. Deconvolution analyses of immunophenotypes indicated higher levels of M0 and M1 macrophages than M2 macrophages in subsets of young BC. Our approach identifies age-based patient clusters with distinct clinicopathologic profiles, to a large extent overlapping with the PAM50 subtypes, although with independent prognostic values in multivariate survival analyses. The patient clusters provided new insight in the immune cell distribution across tumor subtypes, potentially contributing to survival differences between the clusters and the molecular subtypes and indicating age-related mechanisms improving outcome. Our study confirms the applicability of ROR as a valid prognosticator also in a young BC cohort.
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Affiliation(s)
- Lise Martine Ingebriktsen
- Centre for Cancer Biomarkers CCBIO, Section for Pathology, Department of Clinical Medicine, University of Bergen, Norway
| | - Amalie Abrahamsen Svanøe
- Centre for Cancer Biomarkers CCBIO, Section for Pathology, Department of Clinical Medicine, University of Bergen, Norway
| | - Anna Kristine Myrmel Sæle
- Centre for Cancer Biomarkers CCBIO, Section for Pathology, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Rasmus Olai Collett Humlevik
- Centre for Cancer Biomarkers CCBIO, Section for Pathology, Department of Clinical Medicine, University of Bergen, Norway
| | - Karen Toska
- Section for Cancer Genomics, Haukeland University Hospital, Bergen, Norway
| | - May Britt Kalvenes
- Centre for Cancer Biomarkers CCBIO, Section for Pathology, Department of Clinical Medicine, University of Bergen, Norway
| | - Turid Aas
- Department of Surgery, Section for Breast and Endocrine Surgery, Haukeland University Hospital, Bergen, Norway
| | - Anette Heie
- Department of Surgery, Section for Breast and Endocrine Surgery, Haukeland University Hospital, Bergen, Norway
| | - Cecilie Askeland
- Centre for Cancer Biomarkers CCBIO, Section for Pathology, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Gøril Knutsvik
- Centre for Cancer Biomarkers CCBIO, Section for Pathology, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Ingunn Marie Stefansson
- Centre for Cancer Biomarkers CCBIO, Section for Pathology, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Lars Andreas Akslen
- Centre for Cancer Biomarkers CCBIO, Section for Pathology, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Erling Andre Hoivik
- Centre for Cancer Biomarkers CCBIO, Section for Pathology, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Elisabeth Wik
- Centre for Cancer Biomarkers CCBIO, Section for Pathology, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway.
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10
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González-Woge M, Contreras-Espinosa L, García-Gordillo JA, Aguilar-Villanueva S, Bargallo-Rocha E, Cabrera-Galeana P, Vasquez-Mata T, Cervantes-López X, Vargas-Lías DS, Montiel-Manríquez R, Bautista-Hinojosa L, Rebollar-Vega R, Castro-Hernández C, Álvarez-Gómez RM, De La Rosa-Velázquez IA, Díaz-Chávez J, Jiménez-Trejo F, Arriaga-Canon C, Herrera LA. The Expression Profiles of lncRNAs Are Associated with Neoadjuvant Chemotherapy Resistance in Locally Advanced, Luminal B-Type Breast Cancer. Int J Mol Sci 2024; 25:8077. [PMID: 39125649 PMCID: PMC11311431 DOI: 10.3390/ijms25158077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/06/2024] [Accepted: 07/16/2024] [Indexed: 08/12/2024] Open
Abstract
lncRNAs are noncoding transcripts with tissue and cancer specificity. Particularly, in breast cancer, lncRNAs exhibit subtype-specific expression; they are particularly upregulated in luminal tumors. However, no gene signature-based laboratory tests have been developed for luminal breast cancer identification or the differential diagnosis of luminal tumors, since no luminal A- or B-specific genes have been identified. Particularly, luminal B patients are of clinical interest, since they have the most variable response to neoadjuvant treatment; thus, it is necessary to develop diagnostic and predictive biomarkers for these patients to optimize treatment decision-making and improve treatment quality. In this study, we analyzed the lncRNA expression profiles of breast cancer cell lines and patient tumor samples from RNA-Seq data to identify an lncRNA signature specific for luminal phenotypes. We identified an lncRNA signature consisting of LINC01016, GATA3-AS1, MAPT-IT1, and DSCAM-AS1 that exhibits luminal subtype-specific expression; among these lncRNAs, GATA3-AS1 is associated with the presence of residual disease (Wilcoxon test, p < 0.05), which is related to neoadjuvant chemotherapy resistance in luminal B breast cancer patients. Furthermore, analysis of GATA3-AS1 expression using RNA in situ hybridization (RNA ISH) demonstrated that this lncRNA is detectable in histological slides. Similar to estrogen receptors and Ki67, both commonly detected biomarkers, GATA3-AS1 proves to be a suitable predictive biomarker for clinical application in breast cancer laboratory tests.
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Affiliation(s)
- Miguel González-Woge
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (M.G.-W.); (L.C.-E.); (T.V.-M.); (X.C.-L.); (R.M.-M.); (C.C.-H.); (J.D.-C.)
| | - Laura Contreras-Espinosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (M.G.-W.); (L.C.-E.); (T.V.-M.); (X.C.-L.); (R.M.-M.); (C.C.-H.); (J.D.-C.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Mexico City C. P. 04510, Mexico;
| | - José Antonio García-Gordillo
- Departamento de Oncología Médica de Mama, Instituto Nacional de Cancerología, Tlalpan, Mexico City C. P. 14080, Mexico; (J.A.G.-G.); (P.C.-G.)
| | - Sergio Aguilar-Villanueva
- Departamento de Tumores Mamarios, Instituto Nacional de Cancerología, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (S.A.-V.); (E.B.-R.); (D.S.V.-L.)
| | - Enrique Bargallo-Rocha
- Departamento de Tumores Mamarios, Instituto Nacional de Cancerología, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (S.A.-V.); (E.B.-R.); (D.S.V.-L.)
| | - Paula Cabrera-Galeana
- Departamento de Oncología Médica de Mama, Instituto Nacional de Cancerología, Tlalpan, Mexico City C. P. 14080, Mexico; (J.A.G.-G.); (P.C.-G.)
| | - Tania Vasquez-Mata
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (M.G.-W.); (L.C.-E.); (T.V.-M.); (X.C.-L.); (R.M.-M.); (C.C.-H.); (J.D.-C.)
| | - Ximena Cervantes-López
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (M.G.-W.); (L.C.-E.); (T.V.-M.); (X.C.-L.); (R.M.-M.); (C.C.-H.); (J.D.-C.)
| | - Diana Sofía Vargas-Lías
- Departamento de Tumores Mamarios, Instituto Nacional de Cancerología, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (S.A.-V.); (E.B.-R.); (D.S.V.-L.)
| | - Rogelio Montiel-Manríquez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (M.G.-W.); (L.C.-E.); (T.V.-M.); (X.C.-L.); (R.M.-M.); (C.C.-H.); (J.D.-C.)
| | - Luis Bautista-Hinojosa
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Mexico City C. P. 04510, Mexico;
| | - Rosa Rebollar-Vega
- Genomics Laboratory, Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México, Tlalpan, Mexico City C. P. 14080, Mexico;
| | - Clementina Castro-Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (M.G.-W.); (L.C.-E.); (T.V.-M.); (X.C.-L.); (R.M.-M.); (C.C.-H.); (J.D.-C.)
| | - Rosa María Álvarez-Gómez
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico;
| | | | - José Díaz-Chávez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (M.G.-W.); (L.C.-E.); (T.V.-M.); (X.C.-L.); (R.M.-M.); (C.C.-H.); (J.D.-C.)
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey C. P. 64710, Mexico
| | - Francisco Jiménez-Trejo
- Instituto Nacional de Pediatría, Insurgentes Sur No. 3700-C, Coyoacán, Mexico City C. P. 04530, Mexico;
| | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (M.G.-W.); (L.C.-E.); (T.V.-M.); (X.C.-L.); (R.M.-M.); (C.C.-H.); (J.D.-C.)
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey C. P. 64710, Mexico
| | - Luis Alonso Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C. P. 14080, Mexico; (M.G.-W.); (L.C.-E.); (T.V.-M.); (X.C.-L.); (R.M.-M.); (C.C.-H.); (J.D.-C.)
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey C. P. 64710, Mexico
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11
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Enoma D. Genomics in Clinical trials for Breast Cancer. Brief Funct Genomics 2024; 23:325-334. [PMID: 38146120 DOI: 10.1093/bfgp/elad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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12
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Godina C, Khazaei S, Belting M, Vallon-Christersson J, Nodin B, Jirström K, Isaksson K, Bosch A, Jernström H. High Caveolin-1 mRNA expression in triple-negative breast cancer is associated with an aggressive tumor microenvironment, chemoresistance, and poor clinical outcome. PLoS One 2024; 19:e0305222. [PMID: 38959243 PMCID: PMC11221642 DOI: 10.1371/journal.pone.0305222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/28/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Currently, there are few treatment-predictive and prognostic biomarkers in triple-negative breast cancer (TNBC). Caveolin-1 (CAV1) is linked to chemoresistance and several important processes involved in tumor progression and metastasis, such as epithelial-mesenchymal transition (EMT). Herein, we report that high CAV1 gene expression is an independent factor of poor prognosis in TNBC. METHODS CAV1 gene expression was compared across different molecular features (e.g., PAM50 subtypes). CAV1 expression was assessed in relation to clinical outcomes using Cox regression adjusted for clinicopathological predictors. Differential gene expression and gene set enrichment analyses were applied to compare high- and low-expressing CAV1 tumors. Tumor microenvironment composition of high- and low-expressing CAV1 tumors was estimated using ECOTYPER. Tumor tissue microarrays were used to evaluate CAV1 protein levels in stromal and malignant cells. RESULTS In the SCAN-B (n = 525) and GSE31519 (n = 327) cohorts, patients with CAV1-high tumors had an increased incidence of early recurrence adjusted HR 1.78 (95% CI 1.12-2.81) and 2.20 (95% CI 1.39-3.47), respectively. In further analysis, high CAV1 gene expression was associated with a molecular profile indicating altered metabolism, neovascularization, chemoresistance, EMT, suppressed immune response, and active tumor microenvironment. Protein levels of CAV1 in malignant and stromal cells were not correlated with CAV1 gene expression. CONCLUSION CAV1 gene expression in TNBC is a biomarker that merits further investigation in clinical trials and as a therapeutic target.
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Affiliation(s)
- Christopher Godina
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Somayeh Khazaei
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Mattias Belting
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, 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, Lund, Sweden
| | - Björn Nodin
- Department of Clinical Sciences Lund, Oncology and Therapeutic Pathology, Lund University, Lund, Sweden
| | - Karin Jirström
- Department of Clinical Sciences Lund, Oncology and Therapeutic Pathology, Lund University, 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, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Sweden
| | - Helena Jernström
- Department of Clinical Sciences Lund, Oncology, Lund University and Skåne University Hospital, Lund, Sweden
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13
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Van Alsten SC, Vohra SN, Ivory JM, Hamilton AM, Gao X, Kirk EL, Butler EN, Earp HS, Reeder-Hayes KE, Hoadley KA, Carey LA, Troester MA. Differences in 21-Gene and PAM50 Recurrence Scores in Younger and Black Women With Breast Cancer. JCO Precis Oncol 2024; 8:e2400137. [PMID: 39013134 DOI: 10.1200/po.24.00137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/08/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
PURPOSE Genomic tests, such as the Oncotype Dx 21-gene and Prosigna risk of recurrence (ROR-P) assay, are commonly used for breast cancer prognostication. Emerging data suggest variability between assays, but this has not been compared in diverse populations. MATERIALS AND METHODS RNA sequencing was performed on 647 previously untreated stage I-III estrogen receptor-positive/human epidermal growth factor receptor 2-negative tumors in the Carolina Breast Cancer Study, which oversampled Black and younger women (age <50 years at diagnosis), using research versions of two common RNA-based prognostic assays: ROR-PR and the 21-gene recurrence score (RSR). Relative frequency differences and 95% CIs were estimated for associations with race and age, and hazards of 5-year local or distant recurrence were modeled with Cox regression. Proliferation and estrogen module scores from each assay, representing broad activity of genes in those pathways, were examined to guide interpretation of differences between tests. RESULTS Among both younger and older individuals, Black women had higher frequency of intermediate and high ROR-PR scores than non-Black women. Race was not significantly associated with RSR in either age group. High (hazard ratio [HR], 4.67 [95% CI, 1.73 to 12.70]) and intermediate (HR, 2.12 [95% CI, 0.98 to 4.62]) ROR-PR scores were associated with greater risk of recurrence, but RSR did not predict recurrence. RSR emphasized estrogen over proliferation modules, whereas ROR-PR emphasized proliferation. Higher proliferation scores were associated with younger age and Black race in both assays. Modifications to the RSR algorithm that increased emphasis on proliferation improved prognostication in this diverse population. CONCLUSION ROR-PR and the 21-gene RSR differentially emphasize estrogen-related and proliferative biology. The emphasis of 21-gene RS on estrogen-related biology and lower endocrine therapy initiation among Black women may contribute to poorer prognostic ability in heterogeneously treated populations.
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Affiliation(s)
- Sarah C Van Alsten
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sanah N Vohra
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Joannie M Ivory
- Division of Oncology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alina M Hamilton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Xiaohua Gao
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Erin L Kirk
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Eboneé N Butler
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - H Shelton Earp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Katherine E Reeder-Hayes
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Division of Oncology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Lisa A Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Melissa A Troester
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
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14
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Cheang MCU, Rimawi M, Johnston S, Jacobs SA, Bliss J, Pogue-Geile K, Kilburn L, Zhu Z, Schuster EF, Xiao H, Swaim L, Deng S, Lu DR, Gauthier E, Tursi J, Slamon DJ, Rugo HS, Finn RS, Liu Y. Effect of cross-platform gene-expression, computational methods on breast cancer subtyping in PALOMA-2 and PALLET studies. NPJ Breast Cancer 2024; 10:54. [PMID: 38951507 PMCID: PMC11217366 DOI: 10.1038/s41523-024-00658-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
Intrinsic breast cancer molecular subtyping (IBCMS) provides significant prognostic information for patients with breast cancer and helps determine treatment. This study compared IBCMS methods on various gene-expression platforms in PALOMA-2 and PALLET trials. PALOMA-2 tumor samples were profiled using EdgeSeq and nanostring and subtyped with AIMS, PAM50, and research-use-only (ruo)Prosigna. PALLET tumor biopsies were profiled using mRNA sequencing and subtyped with AIMS and PAM50. In PALOMA-2 (n = 222), a 54% agreement was observed between results from AIMS and gold-standard ruoProsigna, with AIMS assigning 67% basal-like to HER2-enriched. In PALLET (n = 224), a 69% agreement was observed between results from PAM50 and AIMS. Different IBCMS methods may lead to different results and could misguide treatment selection; hence, a standardized clinical PAM50 assay and computational approach should be used.Trial number: NCT01740427.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Hui Xiao
- The Institute of Cancer Research, London, UK
| | | | | | | | | | | | - Dennis J Slamon
- David Geffen School of Medicine, University of California Los Angeles, Santa Monica, CA, USA
| | - Hope S Rugo
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Richard S Finn
- David Geffen School of Medicine, University of California Los Angeles, Santa Monica, CA, USA
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15
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Harris AR, Wang T, Heng YJ, Baker GM, Le PA, Wang J, Ambrosone C, Brufsky A, Couch FJ, Modugno F, Scott CG, Vachon CM, Hankinson SE, Rosner BA, Tamimi RM, Peng C, Eliassen AH. Association of early menarche with breast tumor molecular features and recurrence. Breast Cancer Res 2024; 26:102. [PMID: 38886818 PMCID: PMC11181557 DOI: 10.1186/s13058-024-01839-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Early menarche is an established risk factor for breast cancer but its molecular contribution to tumor biology and prognosis remains unclear. METHODS We profiled transcriptome-wide gene expression in breast tumors (N = 846) and tumor-adjacent normal tissues (N = 666) from women in the Nurses' Health Studies (NHS) to investigate whether early menarche (age < 12) is associated with tumor molecular and prognostic features in women with breast cancer. Multivariable linear regression and pathway analyses using competitive gene set enrichment analysis were conducted in both tumor and adjacent-normal tissue and externally validated in TCGA (N = 116). Subgroup analyses stratified on ER-status based on the tumor were also performed. PAM50 signatures were used for tumor molecular subtyping and to generate proliferation and risk of recurrence scores. We created a gene expression score using LASSO regression to capture early menarche based on 28 genes from FDR-significant pathways in breast tumor tissue in NHS and tested its association with 10-year disease-free survival in both NHS (N = 836) and METABRIC (N = 952). RESULTS Early menarche was significantly associated with 369 individual genes in adjacent-normal tissues implicated in extracellular matrix, cell adhesion, and invasion (FDR ≤ 0.1). Early menarche was associated with upregulation of cancer hallmark pathways (18 significant pathways in tumor, 23 in tumor-adjacent normal, FDR ≤ 0.1) related to proliferation (e.g. Myc, PI3K/AKT/mTOR, cell cycle), oxidative stress (e.g. oxidative phosphorylation, unfolded protein response), and inflammation (e.g. pro-inflammatory cytokines IFN α and IFN γ ). Replication in TCGA confirmed these trends. Early menarche was associated with significantly higher PAM50 proliferation scores (β = 0.082 [0.02-0.14]), odds of aggressive molecular tumor subtypes (basal-like, OR = 1.84 [1.18-2.85] and HER2-enriched, OR = 2.32 [1.46-3.69]), and PAM50 risk of recurrence score (β = 4.81 [1.71-7.92]). Our NHS-derived early menarche gene expression signature was significantly associated with worse 10-year disease-free survival in METABRIC (N = 952, HR = 1.58 [1.10-2.25]). CONCLUSIONS Early menarche is associated with more aggressive molecular tumor characteristics and its gene expression signature within tumors is associated with worse 10-year disease-free survival among women with breast cancer. As the age of onset of menarche continues to decline, understanding its relationship to breast tumor characteristics and prognosis may lead to novel secondary prevention strategies.
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Grants
- R01 CA050385 NCI NIH HHS
- R01 CA067262 NCI NIH HHS
- U01 CA176726 NCI NIH HHS
- K01AG080030 NIA NIH HHS
- SAC110014 Susan G. Komen
- P50 CA116201 NCI NIH HHS
- UM1 CA186107 NCI NIH HHS
- U19 CA148065 NCI NIH HHS
- R01 CA049449 NCI NIH HHS
- P30 CA016056 NCI NIH HHS
- R01 CA166666 NCI NIH HHS
- P01 CA087969 NCI NIH HHS
- UM1 CA186107, P01 CA87969, R01 CA49449, U01 CA176726, R01 CA67262, R01 CA50385, T32 CA009001, U19 CA148065, R01 CA166666, P30 CA016056, R35 CA253187, P50 CA116201 NIH HHS
- R35 CA253187 NCI NIH HHS
- K01 AG080030 NIA NIH HHS
- T32 CA009001 NCI NIH HHS
- National Cancer Institute Cancer Prevention Fellowship Program
- Breast Cancer Research Foundation,United States
- National Institutes of Health
- National Institute on Aging
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Affiliation(s)
- Alexandra R Harris
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, MD, 20892, USA.
| | - Tengteng Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Yujing J Heng
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Gabrielle M Baker
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Phuong Anh Le
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jun Wang
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christine Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Adam Brufsky
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PN, USA
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Francesmary Modugno
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Women's Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, PA, USA
| | | | - Celine M Vachon
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Susan E Hankinson
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Bernard A Rosner
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rulla M Tamimi
- Department of Population Health Sciences, Weill Cornell Medical College, New York, NY, USA
| | - Cheng Peng
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - A Heather Eliassen
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Han YJ, Liu S, Hardeman A, Rajagopal PS, Mueller J, Khramtsova G, Sanni A, Ajani M, Clayton W, Hurley IW, Yoshimatsu TF, Zheng Y, Parker J, Perou CM, Olopade OI. The VEGF-Hypoxia Signature Is Upregulated in Basal-like Breast Tumors from Women of African Ancestry and Associated with Poor Outcomes in Breast Cancer. Clin Cancer Res 2024; 30:2609-2618. [PMID: 38564595 DOI: 10.1158/1078-0432.ccr-23-1526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 11/21/2023] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
PURPOSE Black women experience the highest breast cancer mortality rate compared with women of other racial/ethnic groups. To gain a deeper understanding of breast cancer heterogeneity across diverse populations, we examined a VEGF-hypoxia gene expression signature in breast tumors from women of diverse ancestry. EXPERIMENTAL DESIGN We developed a NanoString nCounter gene expression panel and applied it to breast tumors from Nigeria (n = 182) and the University of Chicago (Chicago, IL; n = 161). We also analyzed RNA sequencing data from Nigeria (n = 84) and The Cancer Genome Atlas (TCGA) datasets (n = 863). Patient prognosis was analyzed using multiple datasets. RESULTS The VEGF-hypoxia signature was highest in the basal-like subtype compared with other subtypes, with greater expression in Black women compared with White women. In TCGA dataset, necrotic breast tumors had higher scores for the VEGF-hypoxia signature compared with non-necrosis tumors (P < 0.001), with the highest proportion in the basal-like subtype. Furthermore, necrotic breast tumors have higher scores for the proliferation signature, suggesting an interaction between the VEGF-hypoxia signature, proliferation, and necrosis. T-cell gene expression signatures also correlated with the VEGF-hypoxia signature when testing all tumors in TCGA dataset. Finally, we found a significant association of the VEGF-hypoxia profile with poor outcomes when using all patients in the METABRIC (P < 0.0001) and SCAN-B datasets (P = 0.002). CONCLUSIONS These data provide further evidence for breast cancer heterogeneity across diverse populations and molecular subtypes. Interventions selectively targeting VEGF-hypoxia and the immune microenvironment have the potential to improve overall survival in aggressive breast cancers that disproportionately impact Black women in the African Diaspora.
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Affiliation(s)
- Yoo Jane Han
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Siyao Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Ashley Hardeman
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Padma Sheila Rajagopal
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Jeffrey Mueller
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Galina Khramtsova
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Ayodele Sanni
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Mustapha Ajani
- Department of Pathology, College of Medicine, University of Ibadan/University College Hospital, Ibadan, Oyo, Nigeria
| | - Wendy Clayton
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Ian W Hurley
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Joel Parker
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
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17
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Kos Z, Nielsen TO, Laenkholm AV. Breast Cancer Histopathology in the Age of Molecular Oncology. Cold Spring Harb Perspect Med 2024; 14:a041647. [PMID: 38151327 PMCID: PMC11146312 DOI: 10.1101/cshperspect.a041647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
For more than a century, microscopic histology has been the cornerstone for cancer diagnosis, and breast carcinoma is no exception. In recent years, clinical biomarkers, gene expression profiles, and other molecular tests have shown increasing utility for identifying the key biological features that guide prognosis and treatment of breast cancer. Indeed, the most common histologic pattern-invasive ductal carcinoma of no special type-provides relatively little guidance to management beyond triggering grading, biomarker testing, and clinical staging. However, many less common histologic patterns can be recognized by trained pathologists, which in many cases can be linked to characteristic biomarker and gene expression patterns, underlying mutations, prognosis, and therapy. Herein we describe more than a dozen such histomorphologic subtypes (including lobular, metaplastic, salivary analog, and several good prognosis special types of breast cancer) in the context of their molecular and clinical features.
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Affiliation(s)
- Zuzana Kos
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- BC Cancer Vancouver Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Torsten O Nielsen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Molecular and Advanced Pathology Core, Vancouver, British Columbia V6H 3Z6, Canada
| | - Anne-Vibeke Laenkholm
- Department of Surgical Pathology, Zealand University Hospital, 4000 Roskilde, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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18
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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; 205:227-239. [PMID: 38273214 PMCID: PMC11101536 DOI: 10.1007/s10549-023-07186-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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19
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Ohnstad HO, Blix ES, Akslen LA, Gilje B, Raj SX, Skjerven H, Borgen E, Janssen EAM, Mortensen E, Brekke MB, Falk RS, Schlichting E, Boge B, Songe-Møller S, Olsson P, Heie A, Mannsåker B, Vestlid MA, Kursetgjerde T, Gravdehaug B, Suhrke P, Sanchez E, Bublevic J, Røe OD, Geitvik GA, Halset EH, Rypdal MC, Langerød A, Lømo J, Garred Ø, Porojnicu A, Engebraaten O, Geisler J, Lyngra M, Hansen MH, Søiland H, Nakken T, Asphaug L, Kristensen V, Sørlie T, Nygård JF, Kiserud CE, Reinertsen KV, Russnes HG, Naume B. Impact of Prosigna test on adjuvant treatment decision in lymph node-negative early breast cancer-a prospective national multicentre study (EMIT-1). ESMO Open 2024; 9:103475. [PMID: 38838499 PMCID: PMC11190479 DOI: 10.1016/j.esmoop.2024.103475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND EMIT-1 is a national, observational, single-arm trial designed to assess the value of the Prosigna, Prediction Analysis of Microarray using the 50 gene classifier (PAM50)/Risk of Recurrence (ROR), test as a routine diagnostic tool, examining its impact on adjuvant treatment decisions, clinical outcomes, side-effects and cost-effectiveness. Here we present the impact on treatment decisions. PATIENTS AND METHODS Patients with hormone receptor-positive, human epidermal growth factor receptor 2-negative pT1-pT2 lymph node-negative early breast cancer (EBC) were included. The Prosigna test and standard histopathology assessments were carried out. Clinicians' treatment decisions were recorded before (pre-Prosigna) and after (post-Prosigna) the Prosigna test results were disclosed. RESULTS Of 2217 patients included, 2178 had conclusive Prosigna results. The pre-Prosigna treatment decisions were: no systemic treatment (NT) in 27% of patients, endocrine treatment alone (ET) in 38% and chemotherapy (CT) followed by ET (CT + ET) in 35%. Post-Prosigna treatment decisions were 25% NT, 51% ET and 24% CT + ET, respectively. Adjuvant treatment changed in 28% of patients, including 21% change in CT use. Among patients assigned to CT + ET pre-Prosigna, 45% were de-escalated to ET post-Prosigna. Of patients assigned to ET, 12% were escalated to CT + ET and 8% were de-escalated to NT; of those assigned to NT, 18% were escalated to ET/CT + ET. CT was more frequently recommended for patients aged ≤50 years. In the subgroup with pT1c-pT2 G2 and intermediate Ki67 (0.5-1.5× local laboratory median Ki67 score), the pre-Prosigna CT treatment decision varied widely across hospitals (3%-51%). Post-Prosigna, the variability of CT use was markedly reduced (8%-24%). The correlation between Ki67 and ROR score within this subgroup was poor (r = 0.25-0.39). The median ROR score increased by increasing histological grade, but the ROR score ranges were wide (for G1 0-79, G2 0-90, G3 16-94). CONCLUSION The Prosigna test result changed adjuvant treatment decisions in all EBC clinical risk groups, markedly decreased the CT use for patients categorized as higher clinical risk pre-Prosigna and reduced treatment decision discrepancies between hospitals.
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Affiliation(s)
- H O Ohnstad
- Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo
| | - E S Blix
- Department of Oncology, University of North Norway, Tromsø; Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø
| | - L A Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, Bergen; Department of Pathology Haukeland University Hospital, Bergen
| | - B Gilje
- Department of Haematology and Oncology, Stavanger University Hospital, Stavanger
| | - S X Raj
- Department of Oncology, St Olavs Hospital, Trondheim
| | - H Skjerven
- Department of Breast Surgery, Vestre Viken Hospital Trust, Drammen
| | - E Borgen
- Department of Pathology, Division of Laboratory Medicine, Oslo University Hospital, Oslo
| | - E A M Janssen
- Department of Pathology, Stavanger University Hospital, Stavanger; Department of Chemistry, Bioscience and Environmental Engineering, Stavanger University, Stavanger, Norway; Menzies Health Institute Queensland and Griffith University, Southport, Australia
| | - E Mortensen
- Department of Pathology, University of North Norway, Tromsø
| | - M B Brekke
- Department of Pathology, St Olavs Hospital, Trondheim
| | - R S Falk
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo
| | - E Schlichting
- Department of Oncology, Breast and Endocrine Surgery Unit, Division of Cancer Medicine, Oslo University Hospital, Oslo
| | - B Boge
- Department of Oncology, Hospital of Southern Norway, Kristiansand
| | | | - P Olsson
- Department of Breast Surgery, Innlandet Hospital Trust, Hamar
| | - A Heie
- Department of Breast Surgery, Haukeland University Hospital, Bergen
| | - B Mannsåker
- Department of Oncology, Nordland Hospital, Bodø
| | - M A Vestlid
- Department of Breast Surgery, Telemark Hospital Trust, Skien
| | - T Kursetgjerde
- Department of Oncology, Møre og Romsdal Hospital Trust, Ålesund
| | - B Gravdehaug
- Department of Breast Surgery, Akershus University Hospital, Lørenskog
| | - P Suhrke
- Department of Pathology, Vestfold Hospital Trust, Tønsberg
| | - E Sanchez
- Department of Oncology, Haugesund Hospital, Haugesund
| | - J Bublevic
- Department of Oncology, Førde Central Hospital, Førde
| | - O D Røe
- Department of Oncology, Levanger Hospital, Levanger
| | - G A Geitvik
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo
| | - E H Halset
- Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo
| | - M C Rypdal
- Department of Pathology, Division of Laboratory Medicine, Oslo University Hospital, Oslo
| | - A Langerød
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo
| | - J Lømo
- Department of Pathology, Division of Laboratory Medicine, Oslo University Hospital, Oslo
| | - Ø Garred
- Department of Pathology, Division of Laboratory Medicine, Oslo University Hospital, Oslo
| | - A Porojnicu
- Department of Oncology, Vestre Viken Hospital Trust, Drammen
| | - O Engebraaten
- Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo; Institute of Clinical Medicine, University of Oslo, Oslo
| | - J Geisler
- Institute of Clinical Medicine, University of Oslo, Oslo; Department of Oncology, Akershus University Hospital, Lørenskog
| | - M Lyngra
- Department of Pathology, Akershus University Hospital, Lørenskog
| | - M H Hansen
- Department of Breast Surgery, University of North Norway, Tromsø
| | - H Søiland
- Department of Research, Stavanger University Hospital, Stavanger; Department of Clinical Science, University of Bergen, Bergen
| | - T Nakken
- User representative, Oslo University Hospital, Oslo
| | - L Asphaug
- Clinical Trials Unit, Oslo University Hospital, Oslo; Institute of Health and Society, Faculty of Medicine, University of Oslo, Oslo
| | - V Kristensen
- Institute of Clinical Medicine, University of Oslo, Oslo
| | - T Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo; Institute of Clinical Medicine, University of Oslo, Oslo
| | | | - C E Kiserud
- National Advisory Unit for Late Effects after Cancer Treatment, Oslo University Hospital, Oslo, Norway
| | - K V Reinertsen
- Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo; National Advisory Unit for Late Effects after Cancer Treatment, Oslo University Hospital, Oslo, Norway
| | - H G Russnes
- Department of Pathology, Division of Laboratory Medicine, Oslo University Hospital, Oslo; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo; Institute of Clinical Medicine, University of Oslo, Oslo
| | - B Naume
- Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo; Institute of Clinical Medicine, University of Oslo, Oslo.
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20
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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] [Abstract] [Key Words] [MESH Headings] [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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21
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Venetis K, Pescia C, Cursano G, Frascarelli C, Mane E, De Camilli E, Munzone E, Dellapasqua S, Criscitiello C, Curigliano G, Guerini Rocco E, Fusco N. The Evolving Role of Genomic Testing in Early Breast Cancer: Implications for Diagnosis, Prognosis, and Therapy. Int J Mol Sci 2024; 25:5717. [PMID: 38891906 PMCID: PMC11172282 DOI: 10.3390/ijms25115717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Multigene prognostic genomic assays have become indispensable in managing early breast cancer (EBC), offering crucial information for risk stratification and guiding adjuvant treatment strategies in conjunction with traditional clinicopathological parameters. The American Society of Clinical Oncology (ASCO) guidelines endorse these assays, though some clinical contexts still lack definitive recommendations. The dynamic landscape of EBC management demands further refinement and optimization of genomic assays to streamline their incorporation into clinical practice. The breast cancer community is poised at the brink of transformative advances in enhancing the clinical utility of genomic assays, aiming to significantly improve the precision and effectiveness of both diagnosis and treatment for women with EBC. This article methodically examines the testing methodologies, clinical validity and utility, costs, diagnostic frameworks, and methodologies of the established genomic tests, including the Oncotype Dx Breast Recurrence Score®, MammaPrint, Prosigna®, EndoPredict®, and Breast Cancer Index (BCI). Among these tests, Prosigna and EndoPredict® have at present been validated only on a prognostic level, while Oncotype Dx, MammaPrint, and BCI hold both a prognostic and predictive role. Oncologists and pathologists engaged in the management of EBC will find in this review a thorough comparison of available genomic assays, as well as strategies to optimize the utilization of the information derived from them.
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Affiliation(s)
- Konstantinos Venetis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (K.V.); (C.P.); (G.C.); (C.F.); (E.M.); (E.D.C.); (E.G.R.)
| | - Carlo Pescia
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (K.V.); (C.P.); (G.C.); (C.F.); (E.M.); (E.D.C.); (E.G.R.)
- School of Pathology, University of Milan, 20122 Milan, Italy
| | - Giulia Cursano
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (K.V.); (C.P.); (G.C.); (C.F.); (E.M.); (E.D.C.); (E.G.R.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (C.C.); (G.C.)
| | - Chiara Frascarelli
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (K.V.); (C.P.); (G.C.); (C.F.); (E.M.); (E.D.C.); (E.G.R.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (C.C.); (G.C.)
| | - Eltjona Mane
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (K.V.); (C.P.); (G.C.); (C.F.); (E.M.); (E.D.C.); (E.G.R.)
| | - Elisa De Camilli
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (K.V.); (C.P.); (G.C.); (C.F.); (E.M.); (E.D.C.); (E.G.R.)
| | - Elisabetta Munzone
- Division of Medical Senology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (E.M.); (S.D.)
| | - Silvia Dellapasqua
- Division of Medical Senology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (E.M.); (S.D.)
| | - Carmen Criscitiello
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (C.C.); (G.C.)
- Division of New Drugs and Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (C.C.); (G.C.)
- Division of New Drugs and Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Elena Guerini Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (K.V.); (C.P.); (G.C.); (C.F.); (E.M.); (E.D.C.); (E.G.R.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (C.C.); (G.C.)
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (K.V.); (C.P.); (G.C.); (C.F.); (E.M.); (E.D.C.); (E.G.R.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (C.C.); (G.C.)
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Bleaney CW, Abdelaal H, Reardon M, Anandadas C, Hoskin P, Choudhury A, Forker L. Clinical Biomarkers of Tumour Radiosensitivity and Predicting Benefit from Radiotherapy: A Systematic Review. Cancers (Basel) 2024; 16:1942. [PMID: 38792019 PMCID: PMC11119069 DOI: 10.3390/cancers16101942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/18/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Modern advanced radiotherapy techniques have improved the precision and accuracy of radiotherapy delivery, with resulting plans being highly personalised based on individual anatomy. Adaptation for individual tumour biology remains elusive. There is an unmet need for biomarkers of intrinsic radiosensitivity that can predict tumour response to radiation to facilitate individualised decision-making, dosing and treatment planning. Over the last few decades, the use of high throughput molecular biology technologies has led to an explosion of newly discovered cancer biomarkers. Gene expression signatures are now used routinely in clinic to aid decision-making regarding adjuvant systemic therapy. They have great potential as radiotherapy biomarkers. A previous systematic review published in 2015 reported only five studies of signatures evaluated for their ability to predict radiotherapy benefits in clinical cohorts. This updated systematic review encompasses the expanded number of studies reported in the last decade. An additional 27 studies were identified. In total, 22 distinct signatures were recognised (5 pre-2015, 17 post-2015). Seventeen signatures were 'radiosensitivity' signatures and five were breast cancer prognostic signatures aiming to identify patients at an increased risk of local recurrence and therefore were more likely to benefit from adjuvant radiation. Most signatures (15/22) had not progressed beyond the discovery phase of development, with no suitable validated clinical-grade assay for application. Very few signatures (4/17 'radiosensitivity' signatures) had undergone any laboratory-based biological validation of their ability to predict tumour radiosensitivity. No signatures have been assessed prospectively in a phase III biomarker-led trial to date and none are recommended for routine use in clinical guidelines. A phase III prospective evaluation is ongoing for two breast cancer prognostic signatures. The most promising radiosensitivity signature remains the radiosensitivity index (RSI), which is used to calculate a genomic adjusted radiation dose (GARD). There is an ongoing phase II prospective biomarker-led study of RSI/GARD in triple negative breast cancer. The results of these trials are eagerly anticipated over the coming years. Future work in this area should focus on (1) robust biological validation; (2) building biobanks alongside large radiotherapy randomised controlled trials with dose variance (to demonstrate an interaction between radiosensitivity signature and dose); (3) a validation of clinical-grade cost-effective assays that are deliverable within current healthcare infrastructure; and (4) an integration with biomarkers of other determinants of radiation response.
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Affiliation(s)
- Christopher W. Bleaney
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK (L.F.)
- Department of Clinical Oncology, The Christie NHS Foundation Trust, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Hebatalla Abdelaal
- Department of Clinical Oncology, The Christie NHS Foundation Trust, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Mark Reardon
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK (L.F.)
| | - Carmel Anandadas
- Department of Clinical Oncology, The Christie NHS Foundation Trust, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Peter Hoskin
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK (L.F.)
- Department of Clinical Oncology, The Christie NHS Foundation Trust, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Ananya Choudhury
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK (L.F.)
- Department of Clinical Oncology, The Christie NHS Foundation Trust, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Laura Forker
- Translational Radiobiology Group, Division of Cancer Sciences, The Oglesby Cancer Research Building, The University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK (L.F.)
- Department of Clinical Oncology, The Christie NHS Foundation Trust, 550 Wilmslow Road, Manchester M20 4BX, UK
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23
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Aupperle-Lellbach H, Kehl A, de Brot S, van der Weyden L. Clinical Use of Molecular Biomarkers in Canine and Feline Oncology: Current and Future. Vet Sci 2024; 11:199. [PMID: 38787171 PMCID: PMC11126050 DOI: 10.3390/vetsci11050199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Molecular biomarkers are central to personalised medicine for human cancer patients. It is gaining traction as part of standard veterinary clinical practice for dogs and cats with cancer. Molecular biomarkers can be somatic or germline genomic alterations and can be ascertained from tissues or body fluids using various techniques. This review discusses how these genomic alterations can be determined and the findings used in clinical settings as diagnostic, prognostic, predictive, and screening biomarkers. We showcase the somatic and germline genomic alterations currently available to date for testing dogs and cats in a clinical setting, discussing their utility in each biomarker class. We also look at some emerging molecular biomarkers that are promising for clinical use. Finally, we discuss the hurdles that need to be overcome in going 'bench to bedside', i.e., the translation from discovery of genomic alterations to adoption by veterinary clinicians. As we understand more of the genomics underlying canine and feline tumours, molecular biomarkers will undoubtedly become a mainstay in delivering precision veterinary care to dogs and cats with cancer.
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Affiliation(s)
- Heike Aupperle-Lellbach
- Laboklin GmbH&Co.KG, Steubenstr. 4, 97688 Bad Kissingen, Germany; (H.A.-L.); (A.K.)
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 80333 München, Germany
| | - Alexandra Kehl
- Laboklin GmbH&Co.KG, Steubenstr. 4, 97688 Bad Kissingen, Germany; (H.A.-L.); (A.K.)
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 80333 München, Germany
| | - Simone de Brot
- Institute of Animal Pathology, COMPATH, University of Bern, 3012 Bern, Switzerland;
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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] [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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25
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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] [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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26
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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] [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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27
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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] [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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28
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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] [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] [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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30
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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] [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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31
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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] [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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32
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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] [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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Paiva CE, Silva ATF, Oliveira IDS, Guimarães VS, Lacerda DC, Teixeira GR, Watanabe AHU, Onari N, Paiva BSR, Oliveira-Junior ID, Marques MMC, Maia YCDP. A Research Protocol for a Phase II Single-Arm Clinical Trial Assessing the Feasibility and Efficacy of Neoadjuvant Anastrozole in Patients With Luminal Breast Cancer and Low Proliferative Index: The ANNE Trial. Cancer Control 2024; 31:10732748241272463. [PMID: 39140157 PMCID: PMC11325316 DOI: 10.1177/10732748241272463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024] Open
Abstract
INTRODUCTION Neoadjuvant endocrine therapy (NET) is recommended for the treatment of invasive breast cancer (BC), particularly luminal subtypes, in locally advanced stages. Previous randomized studies have demonstrated the benefits of aromatase inhibitors in this context. However, NET is typically reserved for elderly or frail patients who may not tolerate neoadjuvant chemotherapy. Identifying non-responsive patients early and extending treatment for responsive ones would be ideal, yet optimal strategies are awaited. AIMS This non-randomized phase 2 clinical trial aims to assess NET feasibility and efficacy in postmenopausal stage II and III luminal BC patients, identifying predictive therapeutic response biomarkers. Efficacy will be gauged by patients with Ki67 ≤ 10% after 4 weeks and Preoperative Endocrine Prognostic Index (PEPI) scores 0 post-surgery. Study feasibility will be determined by participation acceptance rate (recruitment rate ≥50%) and inclusion rate (>2 patients/month). METHODS Postmenopausal women with luminal, HER2-tumors in stages II and III undergo neoadjuvant anastrozole treatment, evaluating continuing NET or receiving chemotherapy through early Ki67 analysis after 2 to 4 weeks. The study assesses NET extension for up to 10 months, using serial follow-ups with standardized breast ultrasound and clinical criteria-based NET suspension. Clinical and pathological responses will be measured overall and in the luminal tumor A subgroup. Toxicity, health-related quality of life, and circulating biomarkers predicting early NET response will also be evaluated.
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Affiliation(s)
- Carlos Eduardo Paiva
- Deparment of Clinical Oncology, Barretos Cancer Hospital, Barretos-SP, Brazil
- Palliative Care and Quality of Life Research Group (GPQual), Barretos Cancer Hospital, Barretos-SP, Brazil
| | - Alinne Tatiane Faria Silva
- Nutrition and Molecular Biology Research Group, School of Medicine, Federal University of Uberlandia, Uberlandia, Brazil
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, Brazil
| | - Izabella da Silva Oliveira
- Palliative Care and Quality of Life Research Group (GPQual), Barretos Cancer Hospital, Barretos-SP, Brazil
| | - Vitor Souza Guimarães
- Palliative Care and Quality of Life Research Group (GPQual), Barretos Cancer Hospital, Barretos-SP, Brazil
| | | | - Gustavo Ramos Teixeira
- Department of Pathology, Barretos Cancer Hospital, Barretos-SP, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata - FACISB, Barretos-SP, Brazil
| | | | - Nilton Onari
- Department of Breast Radiology, Barretos Cancer Hospital, Barretos-SP, Brazil
| | | | | | | | - Yara Cristina de Paiva Maia
- Nutrition and Molecular Biology Research Group, School of Medicine, Federal University of Uberlandia, Uberlandia, Brazil
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, Brazil
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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] [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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Das S, Dey MK, Devireddy R, Gartia MR. Biomarkers in Cancer Detection, Diagnosis, and Prognosis. SENSORS (BASEL, SWITZERLAND) 2023; 24:37. [PMID: 38202898 PMCID: PMC10780704 DOI: 10.3390/s24010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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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] [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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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] [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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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] [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] [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] [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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Roper B, Mathews JC, Nadeem S, Park JH. Vis-SPLIT: Interactive Hierarchical Modeling for mRNA Expression Classification. IEEE VISUALIZATION CONFERENCE : VIS. IEEE CONFERENCE ON VISUALIZATION 2023; 2023:106-110. [PMID: 38881685 PMCID: PMC11179685 DOI: 10.1109/vis54172.2023.00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
We propose an interactive visual analytics tool, Vis-SPLIT, for partitioning a population of individuals into groups with similar gene signatures. Vis-SPLIT allows users to interactively explore a dataset and exploit visual separations to build a classification model for specific cancers. The visualization components reveal gene expression and correlation to assist specific partitioning decisions, while also providing overviews for the decision model and clustered genetic signatures. We demonstrate the effectiveness of our framework through a case study and evaluate its usability with domain experts. Our results show that Vis-SPLIT can classify patients based on their genetic signatures to effectively gain insights into RNA sequencing data, as compared to an existing classification system.
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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] [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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45
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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] [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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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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48
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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] [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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49
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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: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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 MEDICAL 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] [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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