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Lim B, Seth S, Yam C, Huo L, Fujii T, Lee J, Bassett R, Nasser S, Ravenberg L, White J, Clayborn A, Guerra G, Litton JK, Damodaran S, Layman R, Valero V, Tripathy D, Lewis M, Dobrolecki LE, Lei J, Candelaria R, Arun B, Rauch G, Zhao L, Zhang J, Ding Q, Symmans WF, Chang JT, Thompson AM, Moulder SL, Ueno NT. Phase 2 study of neoadjuvant enzalutamide and paclitaxel for luminal androgen receptor-enriched TNBC: Trial results and insights into "ARness". Cell Rep Med 2024; 5:101595. [PMID: 38838676 DOI: 10.1016/j.xcrm.2024.101595] [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: 06/09/2023] [Revised: 09/29/2023] [Accepted: 05/14/2024] [Indexed: 06/07/2024]
Abstract
Luminal androgen receptor (LAR)-enriched triple-negative breast cancer (TNBC) is a distinct subtype. The efficacy of AR inhibitors and the relevant biomarkers in neoadjuvant therapy (NAT) are yet to be determined. We tested the combination of the AR inhibitor enzalutamide (120 mg daily by mouth) and paclitaxel (80 mg/m2 weekly intravenously) (ZT) for 12 weeks as NAT for LAR-enriched TNBC. Eligibility criteria included a percentage of cells expressing nuclear AR by immunohistochemistry (iAR) of at least 10% and a reduction in sonographic volume of less than 70% after four cycles of doxorubicin and cyclophosphamide. Twenty-four patients were enrolled. Ten achieved a pathologic complete response or residual cancer burden-I. ZT was safe, with no unexpected side effects. An iAR of at least 70% had a positive predictive value of 0.92 and a negative predictive value of 0.97 in predicting LAR-enriched TNBC according to RNA-based assays. Our data support future trials of AR blockade in early-stage LAR-enriched TNBC.
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Affiliation(s)
- Bora Lim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Sahil Seth
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Clinton Yam
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lei Huo
- Department of Breast Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Takeo Fujii
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Cold Spring Harbor Laboratory-Northwell Health Cancer Institute, Riverhead, NY, USA
| | - Jangsoon Lee
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Roland Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara Nasser
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lisa Ravenberg
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason White
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alyson Clayborn
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gil Guerra
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer K Litton
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Senthil Damodaran
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rachel Layman
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vicente Valero
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Debasish Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Lewis
- Lester Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Lacey E Dobrolecki
- Lester Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Jonathan Lei
- Lester Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Rosalind Candelaria
- Department of Breast Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Banu Arun
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gaiane Rauch
- Department of Breast Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qingqing Ding
- Department of Breast Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - W Fraser Symmans
- Department of Breast Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Alastair M Thompson
- Department of Surgical Oncology, Baylor College of Medicine, Houston, TX, USA; Lester Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Stacy L Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; University of Hawaii Cancer Center, Honolulu, HI, USA.
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Guo Z, Luo J, Mashl RJ, Hoog J, Maiti P, Fettig N, Davies SR, Aft R, Held JM, Govindan R, Ding L, Li S, von Morze C, Wulf GM, Shoghi KI, Ma CX. Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models. CANCER RESEARCH COMMUNICATIONS 2024; 4:1430-1440. [PMID: 38717161 PMCID: PMC11152037 DOI: 10.1158/2767-9764.crc-24-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024]
Abstract
The PI3K pathway regulates essential cellular functions and promotes chemotherapy resistance. Activation of PI3K pathway signaling is commonly observed in triple-negative breast cancer (TNBC). However previous studies that combined PI3K pathway inhibitors with taxane regimens have yielded inconsistent results. We therefore set out to examine whether the combination of copanlisib, a clinical grade pan-PI3K inhibitor, and eribulin, an antimitotic chemotherapy approved for taxane-resistant metastatic breast cancer, improves the antitumor effect in TNBC. A panel of eight TNBC patient-derived xenograft (PDX) models was tested for tumor growth response to copanlisib and eribulin, alone or in combination. Treatment-induced signaling changes were examined by reverse phase protein array, immunohistochemistry (IHC) and 18F-fluorodeoxyglucose PET (18F-FDG PET). Compared with each drug alone, the combination of eribulin and copanlisib led to enhanced tumor growth inhibition, which was observed in both eribulin-sensitive and -resistant TNBC PDX models, regardless of PI3K pathway alterations or PTEN status. Copanlisib reduced PI3K signaling and enhanced eribulin-induced mitotic arrest. The combination enhanced induction of apoptosis compared with each drug alone. Interestingly, eribulin upregulated PI3K pathway signaling in PDX tumors, as demonstrated by increased tracer uptake by 18F-FDG PET scan and AKT phosphorylation by IHC. These changes were inhibited by the addition of copanlisib. These data support further clinical development for the combination of copanlisib and eribulin and led to a phase I/II trial of copanlisib and eribulin in patients with metastatic TNBC. SIGNIFICANCE In this research, we demonstrated that the pan-PI3K inhibitor copanlisib enhanced the cytotoxicity of eribulin in a panel of TNBC PDX models. The improved tumor growth inhibition was irrespective of PI3K pathway alteration and was corroborated by the enhanced mitotic arrest and apoptotic induction observed in PDX tumors after combination therapy compared with each drug alone. These data provide the preclinical rationale for the clinical testing in TNBC.
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Affiliation(s)
- Zhanfang Guo
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jingqin Luo
- Division of Public Health Science, Siteman Cancer Center Biostatistics Core, Washington University School of Medicine, St. Louis, Missouri
| | - R. Jay Mashl
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Jeremy Hoog
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Piyush Maiti
- Mallinckrodt Institute of Radiology, St. Louis, Missouri
| | - Nikki Fettig
- Mallinckrodt Institute of Radiology, St. Louis, Missouri
| | - Sherri R. Davies
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Rebecca Aft
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Jason M. Held
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Ramaswamy Govindan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Shunqiang Li
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | | | - Gerburg M. Wulf
- Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Cynthia X. Ma
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
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Lu M, Yin R, Chen XS. Ensemble methods of rank-based trees for single sample classification with gene expression profiles. J Transl Med 2024; 22:140. [PMID: 38321494 PMCID: PMC10848444 DOI: 10.1186/s12967-024-04940-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/27/2024] [Indexed: 02/08/2024] Open
Abstract
Building Single Sample Predictors (SSPs) from gene expression profiles presents challenges, notably due to the lack of calibration across diverse gene expression measurement technologies. However, recent research indicates the viability of classifying phenotypes based on the order of expression of multiple genes. Existing SSP methods often rely on Top Scoring Pairs (TSP), which are platform-independent and easy to interpret through the concept of "relative expression reversals". Nevertheless, TSP methods face limitations in classifying complex patterns involving comparisons of more than two gene expressions. To overcome these constraints, we introduce a novel approach that extends TSP rules by constructing rank-based trees capable of encompassing extensive gene-gene comparisons. This method is bolstered by incorporating two ensemble strategies, boosting and random forest, to mitigate the risk of overfitting. Our implementation of ensemble rank-based trees employs boosting with LogitBoost cost and random forests, addressing both binary and multi-class classification problems. In a comparative analysis across 12 cancer gene expression datasets, our proposed methods demonstrate superior performance over both the k-TSP classifier and nearest template prediction methods. We have further refined our approach to facilitate variable selection and the generation of clear, precise decision rules from rank-based trees, enhancing interpretability. The cumulative evidence from our research underscores the significant potential of ensemble rank-based trees in advancing disease classification via gene expression data, offering a robust, interpretable, and scalable solution. Our software is available at https://CRAN.R-project.org/package=ranktreeEnsemble .
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Affiliation(s)
- Min Lu
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, 1120 NW 14th Street, Miami, FL, 33136, USA.
| | - Ruijie Yin
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, 1120 NW 14th Street, Miami, FL, 33136, USA
| | - X Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, 1120 NW 14th Street, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, 1475 NW 12th Ave, Miami, FL, 33136, USA.
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4
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Atallah NM, Haque M, Quinn C, Toss MS, Makhlouf S, Ibrahim A, Green AR, Alsaleem M, Rutland CS, Allegrucci C, Mongan NP, Rakha E. Characterisation of luminal and triple-negative breast cancer with HER2 Low protein expression. Eur J Cancer 2023; 195:113371. [PMID: 37897865 DOI: 10.1016/j.ejca.2023.113371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023]
Abstract
BACKGROUND Breast cancer (BC) expressing low levels of human epidermal growth factor receptor 2 (HER2 Low) is an emerging category that needs further refining. This study aims to provide a comprehensive clinico-pathological and molecular profile of HER2 Low BC including response to therapy and patient outcome in the adjuvant and neoadjuvant settings. METHODS Two different independent and well-characterised BC cohorts were included. Nottingham cohort (A) (n = 5744) and The Cancer Genome Atlas (TCGA) BC cohort (B) (n = 854). The clinical, molecular, biological and immunological profile of HER2 Low BC was investigated. Transcriptomic and pathway enrichment analyses were performed on the TCGA BC cohort and validated through next-generation sequencing in a subset of Nottingham cases. RESULTS Ninety percent of HER2 Low tumours were hormone receptor (HR) positive (HR+), enriched with luminal intrinsic molecular subtype, lacking significant expression of HER2 oncogenic signalling genes and of favourable clinical behaviour compared to HER2 negative (HER2-) BC. In HR+ BC, no significant prognostic differences were detected between HER2 Low and HER2- tumours. However, in HR- BC, HER2 Low tumours were less aggressive with longer patient survival. Transcriptomic data showed that the majority of HR- /HER2 Low tumours were of luminal androgen receptor (LAR) intrinsic subtype, enriched with T-helper lymphocytes, activated dendritic cells and tumour associated neutrophils, while most HR-/HER2- tumours were basal-like, enriched with tumour associated macrophages. CONCLUSION HER2 Low BC is mainly driven by HR signalling in HR+ tumours. HR-/HER2 Low tumours tend to be enriched with LAR genes with a unique immune profile.
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Affiliation(s)
- Nehal M Atallah
- Translational Medical Science, School of Medicine, the University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, UK; Department of Pathology, Faculty of Medicine, Menoufia University, Egypt
| | - Maria Haque
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington, UK
| | - Cecily Quinn
- University College Dublin, School of Medicine, St Vincent's Hospital, Elm Park, Dublin, Ireland
| | - Michael S Toss
- Translational Medical Science, School of Medicine, the University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, UK; Histopathology Department, Royal Hallamshire Hospital, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Shorouk Makhlouf
- Translational Medical Science, School of Medicine, the University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, UK; Department of Pathology, Faculty of Medicine, Assiut University, Egypt
| | - Asmaa Ibrahim
- Translational Medical Science, School of Medicine, the University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, UK; Department of Pathology, Suez Canal University, Egypt
| | - Andrew R Green
- Translational Medical Science, School of Medicine, the University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Mansour Alsaleem
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington, UK; Unit of Scientific Research, Applied College, Qassim University, Saudi Arabia
| | - Catrin S Rutland
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington, UK
| | - Cinzia Allegrucci
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington, UK; Nottingham Breast Cancer Research Centre, Biodiscovery Institute, Nottingham, UK
| | - Nigel P Mongan
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington, UK; Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Emad Rakha
- Translational Medical Science, School of Medicine, the University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, UK; Department of Pathology, Faculty of Medicine, Menoufia University, Egypt; Pathology Department, Hamad Medical Corporation, Doha, Qatar.
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5
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El‐Botty R, Vacher S, Mainguené J, Briaux A, Ibadioune S, Dahmani A, Montaudon E, Nemati F, Huguet L, Sourd L, Morriset L, Château‐Joubert S, Dubois T, Maire V, Lidereau R, Rapinat A, Gentien D, Coussy F, Bièche I, Marangoni E. HORMAD1 overexpression predicts response to anthracycline-cyclophosphamide and survival in triple-negative breast cancers. Mol Oncol 2023; 17:2017-2028. [PMID: 36852691 PMCID: PMC10552896 DOI: 10.1002/1878-0261.13412] [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: 04/27/2022] [Revised: 01/23/2023] [Accepted: 02/27/2023] [Indexed: 03/01/2023] Open
Abstract
Triple negative breast cancers (TNBCs) represent 15-20% of all breast cancers and are associated with higher recurrence and distant metastasis rate. Standard of care for early stage TNBC is anthracyclines combined with cyclophosphamide (AC) followed by taxanes, in the neo-adjuvant or adjuvant setting. This work aimed to identify predictive biomarkers of AC response in patient-derived xenograft (PDX) models of TNBC and to validate them in the clinical setting. By gene and protein expression analysis of 39 PDX with different responses to AC, we found that high expression of HORMAD1 was associated with better response to AC. Both gene and protein expression were associated with promoter hypomethylation. In a cohort of 526 breast cancer patients, HORMAD1 was overexpressed in 71% of TNBC. In a second cohort of 186 TNBC patients treated with AC, HORMAD1 expression was associated with longer metastasis-free survival (MFS). In summary, HORMAD1 overexpression was predictive of an improved response to AC in PDX and is an independent prognostic factor in TNBC patients treated with AC.
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Affiliation(s)
- Rania El‐Botty
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
| | - Sophie Vacher
- Department of Genetics, Institut CuriePSL Research UniversityParisFrance
| | - Juliette Mainguené
- Department of Genetics, Institut CuriePSL Research UniversityParisFrance
- Medical Oncology Department, Institut CuriePSL Research UniversityParisFrance
| | - Adrien Briaux
- Department of Genetics, Institut CuriePSL Research UniversityParisFrance
| | - Sabrina Ibadioune
- Department of Genetics, Institut CuriePSL Research UniversityParisFrance
| | - Ahmed Dahmani
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
| | - Elodie Montaudon
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
| | - Fariba Nemati
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
| | - Léa Huguet
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
| | - Laura Sourd
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
| | - Ludivine Morriset
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
| | | | - Thierry Dubois
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
| | - Virginie Maire
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
| | - Rosette Lidereau
- Department of Genetics, Institut CuriePSL Research UniversityParisFrance
| | - Audrey Rapinat
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
| | - David Gentien
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
| | - Florence Coussy
- Department of Genetics, Institut CuriePSL Research UniversityParisFrance
- Medical Oncology Department, Institut CuriePSL Research UniversityParisFrance
| | - Ivan Bièche
- Department of Genetics, Institut CuriePSL Research UniversityParisFrance
- Faculty of Pharmaceutical and Biological SciencesParis City University, Inserm U1016France
| | - Elisabetta Marangoni
- Translational Research Department, Institut CuriePSL Research UniversityParisFrance
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Kim JY, Park S, Cho EY, Lee JE, Jung HH, Chae BJ, Kim SW, Nam SJ, Cho SY, Park YH, Ahn JS, Lee S, Im YH. Genomic characteristics of triple negative apocrine carcinoma: a comparison to triple negative breast cancer. Exp Mol Med 2023:10.1038/s12276-023-01030-z. [PMID: 37394589 PMCID: PMC10394068 DOI: 10.1038/s12276-023-01030-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/15/2023] [Accepted: 04/06/2023] [Indexed: 07/04/2023] Open
Abstract
Apocrine carcinoma is a rare breast cancer subtype. As such, the genomic characteristics of apocrine carcinoma with triple negative immunohistochemical results (TNAC), which has been treated as triple negative breast cancer (TNBC), have not been revealed. In this study, we evaluated the genomic characteristics of TNAC compared to TNBC with low Ki-67 (LK-TNBC). In the genetic analysis of 73 TNACs and 32 LK-TNBCs, the most frequently mutated driver gene in TNAC was TP53 (16/56, 28.6%), followed by PIK3CA (9/56, 16.1%), ZNF717 (8/56, 14.3%), and PIK3R1 (6/56, 10.71%). Mutational signature analysis showed enrichment of defective DNA mismatch repair (MMR)-related signatures (SBS6 and SBS21) and the SBS5 signature in TNAC, whereas an APOBEC activity-associated mutational signature (SBS13) was more prominent in LK-TNBC (Student's t test, p < 0.05). In intrinsic subtyping, 38.4% of TNACs were classified as luminal A, 27.4% as luminal B, 26.0% as HER2-enriched (HER2-E), 2.7% as basal, and 5.5% as normal-like. The basal subtype was the most dominant subtype (43.8%) in LK-TNBC (p < 0.001), followed by luminal B (21.9%), HER2-E (21.9%), and luminal A (12.5%). In the survival analysis, TNAC had a five-year disease-free survival (DFS) rate of 92.2% compared to 59.1% for LK-TNBC (P = 0.001) and a five-year overall survival (OS) rate of 95.3% compared to 74.6% for LK-TNBC (P = 0.0099). TNAC has different genetic characteristics and better survival outcomes than LK-TNBC. In particular, normal-like and luminal A subtypes in TNAC have much better DFS and OS than other intrinsic subtypes. Our findings are expected to impact medical practice for patients diagnosed with TNAC.
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Affiliation(s)
- Ji-Yeon Kim
- Division of Hematology-Oncology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
- Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea.
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Seoul, 06351, Republic of Korea.
| | - Sabin Park
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Eun Yoon Cho
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Jeong Eon Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Seoul, 06351, Republic of Korea
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Hae Hyun Jung
- Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Seoul, 06351, Republic of Korea
| | - Byung Joo Chae
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Seok Won Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Seok Jin Nam
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Soo Youn Cho
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Seoul, 06351, Republic of Korea
| | - Jin Seok Ahn
- Division of Hematology-Oncology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Semin Lee
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
| | - Young-Hyuck Im
- Division of Hematology-Oncology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
- Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea.
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Seoul, 06351, Republic of Korea.
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Tran J, Thaper A, Lopetegui-Lia N, Ali A. Locoregional recurrence in triple negative breast cancer: past, present, and future. Expert Rev Anticancer Ther 2023; 23:1085-1093. [PMID: 37750222 DOI: 10.1080/14737140.2023.2262760] [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: 07/17/2023] [Accepted: 09/20/2023] [Indexed: 09/27/2023]
Abstract
INTRODUCTION Triple negative breast cancer (TNBC) is a rare but aggressive biological subtype of breast cancer associated with higher locoregional and distant recurrence rates and lower overall survival despite advancements in diagnostic and treatment strategies. AREAS COVERED This review explores the evolving landscape of locoregional recurrence (LRR) in TNBC with improved surgical and radiation therapy delivery techniques including salvage breast conserving surgery (SBCS), re-irradiation, and thermo-radiation. We review current retrospective and prospective, albeit limited, clinical data highlighting the optimal management of locoregionally recurrent TNBC. We also discuss tumor genomic profiling and transcriptome analysis and review potential investigational directions. EXPERT OPINION Significant progress has been made in the prevention of LRR but rates remain suboptimal, particularly in the TNBC population, and outcomes following LRR are poor. Further prospective studies are needed to identify the most effective and safest systemic therapy regimens and to whom it should be offered. There has been growing interest in the role of molecular markers, genomic signatures, and tumor microenvironment in predicting outcomes and guiding LRR treatment. Transcriptome analyses and biomarker-driven investigations are currently being studied and represent a promising era of development in the management of LRR.
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Affiliation(s)
- Jennifer Tran
- Department of Hematology and Medical Oncology, Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Arushi Thaper
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Nerea Lopetegui-Lia
- Department of Hematology and Medical Oncology, Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Azka Ali
- Department of Hematology and Medical Oncology, Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
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Monaco ML, Idris OA, Essani K. Triple-Negative Breast Cancer: Basic Biology and Immuno-Oncolytic Viruses. Cancers (Basel) 2023; 15:cancers15082393. [PMID: 37190321 DOI: 10.3390/cancers15082393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is the most lethal subtype of breast cancer. TNBC diagnoses account for approximately one-fifth of all breast cancer cases globally. The lack of receptors for estrogen, progesterone, and human epidermal growth factor 2 (HER-2, CD340) results in a lack of available molecular-based therapeutics. This increases the difficulty of treatment and leaves more traditional as well as toxic therapies as the only available standards of care in many cases. Recurrence is an additional serious problem, contributing substantially to its higher mortality rate as compared to other breast cancers. Tumor heterogeneity also poses a large obstacle to treatment approaches. No driver of tumor development has been identified for TNBC, and large variations in mutational burden between tumors have been described previously. Here, we describe the biology of six different subtypes of TNBC, based on differential gene expression. Subtype differences can have a large impact on metastatic potential and resistance to treatment. Emerging antibody-based therapeutics, such as immune checkpoint inhibitors, have available targets for small subsets of TNBC patients, leading to partial responses and relatively low overall efficacy. Immuno-oncolytic viruses (OVs) have recently become significant in the pursuit of effective treatments for TNBC. OVs generally share the ability to ignore the heterogeneous nature of TNBC cells and allow infection throughout a treated tumor. Recent genetic engineering has allowed for the enhancement of efficacy against certain tumor types while avoiding the most common side effects in non-cancerous tissues. In this review, TNBC is described in order to address the challenges it presents to potential treatments. The OVs currently described preclinically and in various stages of clinical trials are also summarized, as are their strategies to enhance therapeutic potential.
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Affiliation(s)
- Michael L Monaco
- Laboratory of Virology, Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Omer A Idris
- Laboratory of Virology, Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Karim Essani
- Laboratory of Virology, Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA
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9
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Zhang W, Li E, Wang L, Lehmann BD, Chen XS. Transcriptome Meta-Analysis of Triple-Negative Breast Cancer Response to Neoadjuvant Chemotherapy. Cancers (Basel) 2023; 15:2194. [PMID: 37190123 PMCID: PMC10137141 DOI: 10.3390/cancers15082194] [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: 03/04/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease with varying responses to neoadjuvant chemotherapy (NAC). The identification of biomarkers to predict NAC response and inform personalized treatment strategies is essential. In this study, we conducted large-scale gene expression meta-analyses to identify genes associated with NAC response and survival outcomes. The results showed that immune, cell cycle/mitotic, and RNA splicing-related pathways were significantly associated with favorable clinical outcomes. Furthermore, we integrated and divided the gene association results from NAC response and survival outcomes into four quadrants, which provided more insights into potential NAC response mechanisms and biomarker discovery.
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Affiliation(s)
- Wei Zhang
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Emma Li
- California Academy of Mathematics and Science, 1000 E Victoria St, Carson, CA 90747, USA
| | - Lily Wang
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Brian D. Lehmann
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - X. Steven Chen
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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10
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Wang W, Rana PS, Markovic V, Sossey-Alaoui K. The WAVE3/β-catenin oncogenic signaling regulates chemoresistance in triple negative breast cancer. Breast Cancer Res 2023; 25:31. [PMID: 36949468 PMCID: PMC10035207 DOI: 10.1186/s13058-023-01634-3] [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: 09/07/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Metastatic breast cancer is responsible for the death of the majority of breast cancer patients. In fact, metastatic BC is the 2nd leading cause of cancer-related deaths in women in the USA and worldwide. Triple negative breast cancer (TNBC), which lacks expression of hormone receptors (ER-α and PR) and ErbB2/HER2, is especially lethal due to its highly metastatic behavior, propensity to recur rapidly, and for its resistance to standard of care therapies, through mechanisms that remain incompletely understood. WAVE3 has been established as a promoter of TNBC development and metastatic progression. In this study, we investigated the molecular mechanisms whereby WAVE3 promotes therapy-resistance and cancer stemness in TNBC, through the regulation of β-catenin stabilization. METHODS The Cancer Genome Atlas dataset was used to assess the expression of WAVE3 and β-catenin in breast cancer tumors. Kaplan-Meier Plotter analysis was used to correlate expression of WAVE3 and β-catenin with breast cancer patients' survival probability. MTT assay was used to quantify cell survival. CRISPR/Cas9-mediated gene editing, 2D and 3D tumorsphere growth and invasion assays, Immunofluorescence, Western blotting, Semi-quantitative and real-time quantitative PCR analyses were applied to study the WAVE3/β-catenin oncogenic signaling in TNBC. Tumor xenograft assays were used to study the role of WAVE3 in mediating chemotherapy resistance of TNBC tumors. RESULTS Genetic inactivation of WAVE3 in combination of chemotherapy resulted in inhibition of 2D growth and 3D tumorsphere formation and invasion of TNBC cells in vitro, as well as tumor growth and metastasis in vivo. In addition, while re-expression of phospho-active WAVE3 in the WAVE3-deficient TNBC cells restored the oncogenic activity of WAVE3, re-expression of phospho-mutant WAVE3 did not. Further studies revealed that dual blocking of WAVE3 expression or phosphorylation in combination with chemotherapy treatment inhibited the activity and expression and stabilization of β-catenin. Most importantly, the combination of WAVE3-deficiency or WAVE3-phospho-deficiency and chemotherapy suppressed the oncogenic behavior of chemoresistant TNBC cells, both in vitro and in vivo. CONCLUSION We identified a novel WAVE3/β-catenin oncogenic signaling axis that modulates chemoresistance of TNBC. This study suggests that a targeted therapeutic strategy against WAVE3 could be effective for the treatment of chemoresistant TNBC tumors.
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Affiliation(s)
- Wei Wang
- Department of Medicine, MetroHealth Medical Center, Cleveland, OH, 44109, USA
- Case Western Reserve University School of Medicine, Case Western Reserve University, Cleveland, OH, 44016, USA
| | - Priyanka S Rana
- Department of Medicine, MetroHealth Medical Center, Cleveland, OH, 44109, USA
- Case Western Reserve University School of Medicine, Case Western Reserve University, Cleveland, OH, 44016, USA
| | - Vesna Markovic
- Case Western Reserve University School of Medicine, Case Western Reserve University, Cleveland, OH, 44016, USA
| | - Khalid Sossey-Alaoui
- Department of Medicine, MetroHealth Medical Center, Cleveland, OH, 44109, USA.
- Case Western Reserve University School of Medicine, Case Western Reserve University, Cleveland, OH, 44016, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
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11
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Fu L, Li Z, Ren Y, Yu H, Liu B, Qiu Y. CRISPR/Cas genome editing in triple negative breast cancer: Current situation and future directions. Biochem Pharmacol 2023; 209:115449. [PMID: 36754153 DOI: 10.1016/j.bcp.2023.115449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023]
Abstract
Triple negative breast cancer (TNBC) has been well-known to be closely associated with the abnormal expression of both oncogenes and tumor suppressors. Although several pathogenic mutations in TNBC have been identified, the current therapeutic strategy is usually aimed at symptom relief rather than correcting mutations in the DNA sequence. Of note, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) has been gradually regarded as a breakthrough gene-editing tool with potential therapeutic applications in human cancers, including TNBC. Thus, in this review, we focus on summarizing the molecular subtypes of TNBC, as well as the CRISPR system and its potential applications in TNBC treatment. Moreover, we further discuss several emerging strategies for utilizing the CRISPR/Cas system to aid in the precise diagnosis of TNBC, as well as the limitations of the CRISPR/Cas system. Taken together, these findings would demonstrate that CRISPR/Cas system is not only an effective genome editing tool in TNBC, but a promising strategy for the future therapeutic purposes.
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Affiliation(s)
- Leilei Fu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Zixiang Li
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Yueting Ren
- Department of Pharmacology and Toxicology, Temerity faculty of medicine, University of Toronto, Canada
| | - Haiyang Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Yuling Qiu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
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12
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Blood-Based mRNA Tests as Emerging Diagnostic Tools for Personalised Medicine in Breast Cancer. Cancers (Basel) 2023; 15:cancers15041087. [PMID: 36831426 PMCID: PMC9954278 DOI: 10.3390/cancers15041087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Molecular diagnostic tests help clinicians understand the underlying biological mechanisms of their patients' breast cancer (BC) and facilitate clinical management. Several tissue-based mRNA tests are used routinely in clinical practice, particularly for assessing the BC recurrence risk, which can guide treatment decisions. However, blood-based mRNA assays have only recently started to emerge. This review explores the commercially available blood mRNA diagnostic assays for BC. These tests enable differentiation of BC from non-BC subjects (Syantra DX, BCtect), detection of small tumours <10 mm (early BC detection) (Syantra DX), detection of different cancers (including BC) from a single blood sample (multi-cancer blood test Aristotle), detection of BC in premenopausal and postmenopausal women and those with high breast density (Syantra DX), and improvement of diagnostic outcomes of DNA testing (variant interpretation) (+RNAinsight). The review also evaluates ongoing transcriptomic research on exciting possibilities for future assays, including blood transcriptome analyses aimed at differentiating lymph node positive and negative BC, distinguishing BC and benign breast disease, detecting ductal carcinoma in situ, and improving early detection further (expression changes can be detected in blood up to eight years before diagnosing BC using conventional approaches, while future metastatic and non-metastatic BC can be distinguished two years before BC diagnosis).
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13
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Peng P, Qiang X, Li G, Li L, Ni S, Yu Q, Sourd L, Marangoni E, Hu C, Wang D, Wu D, Wu F. Tinengotinib (TT-00420), a Novel Spectrum-Selective Small-Molecule Kinase Inhibitor, Is Highly Active Against Triple-Negative Breast Cancer. Mol Cancer Ther 2023; 22:205-214. [PMID: 36223547 PMCID: PMC9890131 DOI: 10.1158/1535-7163.mct-22-0012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/24/2022] [Accepted: 10/07/2022] [Indexed: 02/05/2023]
Abstract
Triple-negative breast cancer (TNBC) is a highly heterogeneous cancer lacking actionable targets. Using a phenotypic screen of TNBC cells, we discovered a novel multiple kinase inhibitor tinengotinib (TT-00420) that strongly inhibited Aurora A/B, FGFR1/2/3, VEGFRs, JAK1/2, and CSF1R in biochemical assays. Exposure to tinengotinib specifically inhibited proliferation across all subtypes of TNBC in vitro and in vivo, while leaving luminal breast cancer cells intact. Incubation of HCC1806 with tinengotinib led to dose-dependent downregulation of genes essential for TNBC cell growth and proliferation. Studies revealed that the potential mechanism of action of tinengotinib involved, predominantly, inhibition of Aurora A or B kinase activity, while inhibition of other pathways contributed to suppression of potency and activity. In vitro treatment of TNBC cell lines or in vivo administration in a syngeneic model with tinengotinib resulted in up-regulation of CXCL10 and 11 or diminished tumor-associated macrophage (TAM) infiltration. Tinengotinib represents a novel combinatorial inhibitory mechanism to treat TNBC. The phase I trial of tinengotinib was completed (ClinicalTrials.gov identifier: NCT03654547).
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Affiliation(s)
- Peng Peng
- Department of Medicinal Chemistry, Pharmacology, Project Management, Drug Metabolism and Pharmacokinetics, TransThera Sciences (Nanjing), Inc., Nanjing, Jiangsu, P.R. China.,Corresponding Author: Peng Peng, TransThera Sciences (Nanjing), Inc., Fl 3, Bld 9, Phase 2 Accelerator, Biotech and Pharmaceutical Valley, Jiangbei New Area, Nanjing, Jiangsu 210032, P.R. China. E-mail:
| | - Xiaoyan Qiang
- Department of Medicinal Chemistry, Pharmacology, Project Management, Drug Metabolism and Pharmacokinetics, TransThera Sciences (Nanjing), Inc., Nanjing, Jiangsu, P.R. China
| | - Guoyu Li
- Department of Medicinal Chemistry, Pharmacology, Project Management, Drug Metabolism and Pharmacokinetics, TransThera Sciences (Nanjing), Inc., Nanjing, Jiangsu, P.R. China
| | - Lin Li
- Department of Medicinal Chemistry, Pharmacology, Project Management, Drug Metabolism and Pharmacokinetics, TransThera Sciences (Nanjing), Inc., Nanjing, Jiangsu, P.R. China
| | - Shumao Ni
- Department of Medicinal Chemistry, Pharmacology, Project Management, Drug Metabolism and Pharmacokinetics, TransThera Sciences (Nanjing), Inc., Nanjing, Jiangsu, P.R. China
| | - Qi Yu
- Department of Medicinal Chemistry, Pharmacology, Project Management, Drug Metabolism and Pharmacokinetics, TransThera Sciences (Nanjing), Inc., Nanjing, Jiangsu, P.R. China
| | - Laura Sourd
- Translational Research Department, Institute Curie, PSL Research University, Paris, France
| | - Elisabetta Marangoni
- Translational Research Department, Institute Curie, PSL Research University, Paris, France
| | - Chao Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Di Wu
- Department of Medicinal Chemistry, Pharmacology, Project Management, Drug Metabolism and Pharmacokinetics, TransThera Sciences (Nanjing), Inc., Nanjing, Jiangsu, P.R. China
| | - Frank Wu
- Department of Medicinal Chemistry, Pharmacology, Project Management, Drug Metabolism and Pharmacokinetics, TransThera Sciences (Nanjing), Inc., Nanjing, Jiangsu, P.R. China
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14
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Soliman H, Hogue D, Han H, Mooney B, Costa R, Lee MC, Niell B, Williams A, Chau A, Falcon S, Soyano A, Armaghani A, Khakpour N, Weinfurtner RJ, Hoover S, Kiluk J, Laronga C, Rosa M, Khong H, Czerniecki B. Oncolytic T-VEC virotherapy plus neoadjuvant chemotherapy in nonmetastatic triple-negative breast cancer: a phase 2 trial. Nat Med 2023; 29:450-457. [PMID: 36759673 DOI: 10.1038/s41591-023-02210-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 01/06/2023] [Indexed: 02/11/2023]
Abstract
Talimogene laherparepvec (T-VEC) is an oncolytic virus hypothesized to enhance triple-negative breast cancer (TNBC) responses to neoadjuvant chemotherapy (NAC). This article describes the phase 2 trial of T-VEC plus NAC (ClinicalTrials.gov ID: NCT02779855 ). Patients with stage 2-3 TNBC received five intratumoral T-VEC injections with paclitaxel followed by doxorubicin and cyclophosphamide and surgery to assess residual cancer burden index (RCB). The primary end point was RCB0 rate. Secondary end points were RCB0-1 rate, recurrence rate, toxicity and immune correlates. Thirty-seven patients were evaluated. Common T-VEC toxicities were fevers, chills, headache, fatigue and injection site pain. NAC toxicities were as expected. Four thromboembolic events occurred. The primary end point was met with an estimated RCB0 rate = 45.9% and RCB0-1 descriptive rate = 65%. The 2-year disease-free rate is equal to 89% with no recurrences in RCB0-1 patients. Immune activation during treatment correlated with response. T-VEC plus NAC in TNBC may increase RCB0-1 rates. These results support continued investigation of T-VEC plus NAC for TNBC.
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Affiliation(s)
- Hatem Soliman
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA.
| | - Deanna Hogue
- Clinical Trials Office, Moffitt Cancer Center, Tampa, FL, USA
| | - Hyo Han
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Blaise Mooney
- Department of Radiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Ricardo Costa
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Marie C Lee
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Bethany Niell
- Department of Radiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Angela Williams
- Department of Radiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Alec Chau
- Department of Radiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Shannon Falcon
- Department of Radiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Aixa Soyano
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Avan Armaghani
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Nazanin Khakpour
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Susan Hoover
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - John Kiluk
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Christine Laronga
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Marilin Rosa
- Department of Pathology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hung Khong
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Brian Czerniecki
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, FL, USA
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15
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Systemically Identifying Triple-Negative Breast Cancer Subtype-Specific Prognosis Signatures, Based on Single-Cell RNA-Seq Data. Cells 2023; 12:cells12030367. [PMID: 36766710 PMCID: PMC9913740 DOI: 10.3390/cells12030367] [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: 11/23/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 01/21/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly heterogeneous disease with different molecular subtypes. Although progress has been made, the identification of TNBC subtype-associated biomarkers is still hindered by traditional RNA-seq or array technologies, since bulk data detected by them usually have some non-disease tissue samples, or they are confined to measure the averaged properties of whole tissues. To overcome these constraints and discover TNBC subtype-specific prognosis signatures (TSPSigs), we proposed a single-cell RNA-seq-based bioinformatics approach for identifying TSPSigs. Notably, the TSPSigs we developed mostly were found to be disease-related and involved in cancer development through investigating their enrichment analysis results. In addition, the prognostic power of TSPSigs was successfully confirmed in four independent validation datasets. The multivariate analysis results showed that TSPSigs in two TNBC subtypes-BL1 and LAR, were two independent prognostic factors. Further, analysis results of the TNBC cell lines revealed that the TSPSigs expressions and drug sensitivities had significant associations. Based on the preceding data, we concluded that TSPSigs could be exploited as novel candidate prognostic markers for TNBC patients and applied to individualized treatment in the future.
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16
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Choi H, Kim K. Theranostics for Triple-Negative Breast Cancer. Diagnostics (Basel) 2023; 13:diagnostics13020272. [PMID: 36673082 PMCID: PMC9857659 DOI: 10.3390/diagnostics13020272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/11/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with poor prognosis. Current endocrine therapy or anti HER-2 therapy is not available for these patients. Chemotherapeutic treatment response varies among patients due to the disease heterogeneity. To overcome these challenges, theranostics for treating TNBC have been widely investigated. Anticancer material conjugated nanoparticles with target-binding ligand and tracer agents enable simultaneous drug delivery and visualization of the lesion with minimal off-target toxicity. In this review, we summarize recently FDA-approved targeted therapies for TNBC, such as poly-ADP-ribose polymerase (PARP) inhibitors, check point inhibitors, and antibody-drug conjugates. Particularly, novel theranostic approaches including lipid-based, polymer-based, and carbon-based nanocarriers are discussed, which can provide basic overview of nano-therapeutic modalities in TNBC diagnosis and treatment.
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Affiliation(s)
- Hyeryeon Choi
- Department of Surgery, Eulji Medical Center, Eulji University School of Medicine, Seoul 01830, Republic of Korea
| | - Kwangsoon Kim
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Correspondence:
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17
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Bassiouni R, Idowu MO, Gibbs LD, Robila V, Grizzard PJ, Webb MG, Song J, Noriega A, Craig DW, Carpten JD. Spatial Transcriptomic Analysis of a Diverse Patient Cohort Reveals a Conserved Architecture in Triple-Negative Breast Cancer. Cancer Res 2023; 83:34-48. [PMID: 36283023 PMCID: PMC9812886 DOI: 10.1158/0008-5472.can-22-2682] [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: 08/23/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 02/03/2023]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive disease that disproportionately affects African American (AA) women. Limited targeted therapeutic options exist for patients with TNBC. Here, we employ spatial transcriptomics to interrogate tissue from a racially diverse TNBC cohort to comprehensively annotate the transcriptional states of spatially resolved cellular populations. A total of 38,706 spatial features from a cohort of 28 sections from 14 patients were analyzed. Intratumoral analysis of spatial features from individual sections revealed heterogeneous transcriptional substructures. However, integrated analysis of all samples resulted in nine transcriptionally distinct clusters that mapped across all individual sections. Furthermore, novel use of join count analysis demonstrated nonrandom directional spatial dependencies of the transcriptionally defined shared clusters, supporting a conserved spatio-transcriptional architecture in TNBC. These findings were substantiated in an independent validation cohort comprising 17,861 spatial features representing 15 samples from 8 patients. Stratification of samples by race revealed race-associated differences in hypoxic tumor content and regions of immune-rich infiltrate. Overall, this study combined spatial and functional molecular analyses to define the tumor architecture of TNBC, with potential implications in understanding TNBC disparities. SIGNIFICANCE Spatial transcriptomics profiling of a diverse cohort of triple-negative breast cancers and innovative informatics approaches reveal a conserved cellular architecture across cancers and identify proportional differences in tumor cell composition by race.
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Affiliation(s)
- Rania Bassiouni
- Department of Translational Genomics, Keck School of Medicine, University of Southern California; Los Angeles, CA
| | - Michael O. Idowu
- Department of Pathology, Virginia Commonwealth University; Richmond, VA
| | - Lee D. Gibbs
- Department of Translational Genomics, Keck School of Medicine, University of Southern California; Los Angeles, CA
| | - Valentina Robila
- Department of Pathology, Virginia Commonwealth University; Richmond, VA
| | | | - Michelle G. Webb
- Department of Translational Genomics, Keck School of Medicine, University of Southern California; Los Angeles, CA
| | - Jiarong Song
- Department of Translational Genomics, Keck School of Medicine, University of Southern California; Los Angeles, CA
| | - Ashley Noriega
- Department of Translational Genomics, Keck School of Medicine, University of Southern California; Los Angeles, CA
| | - David W. Craig
- Department of Translational Genomics, Keck School of Medicine, University of Southern California; Los Angeles, CA
- Translational and Clinical Sciences Program, Norris Comprehensive Cancer Center, University of Southern California; Los Angeles, CA
| | - John D. Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California; Los Angeles, CA
- Translational and Clinical Sciences Program, Norris Comprehensive Cancer Center, University of Southern California; Los Angeles, CA
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18
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Tsang JY, Tse GM. Update on triple-negative breast cancers - highlighting subtyping update and treatment implication. Histopathology 2023; 82:17-35. [PMID: 36468263 DOI: 10.1111/his.14784] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/14/2022] [Accepted: 08/19/2022] [Indexed: 12/12/2022]
Abstract
Triple-negative breast cancer (TNBC) remains a major challenge in breast cancer management. Continuing research in the past years aimed at understanding the biology of this tumour and developing more effective therapeutic options. It is now clear that TNBC is vastly heterogeneous with diverse histological, molecular, immunological profiles and clinical differences. Current evidence suggested the existence of at least four predominant subtypes based on expression profiling across studies. These subtypes exhibited specific genomic alterations and tumour microenvironment. Subtype-specific therapeutic strategies were identified. Recognising these subtypes allows not only an improved prognostication but also a better treatment decision. Herein, we provide an overview of the recent findings on TNBC heterogeneity at different levels and corresponding subtyping. The characteristic of subtypes and the implication of these subtypings in therapeutic approaches are also discussed.
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Affiliation(s)
- Julia Y Tsang
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Gary M Tse
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
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19
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Akhouayri L, Ostano P, Mello-Grand M, Gregnanin I, Crivelli F, Laurora S, Liscia D, Leone F, Santoro A, Mulè A, Guarino D, Maggiore C, Carlino A, Magno S, Scatolini M, Di Leone A, Masetti R, Chiorino G. Identification of a minimum number of genes to predict triple-negative breast cancer subgroups from gene expression profiles. Hum Genomics 2022; 16:70. [PMID: 36536459 PMCID: PMC9764480 DOI: 10.1186/s40246-022-00436-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a very heterogeneous disease. Several gene expression and mutation profiling approaches were used to classify it, and all converged to the identification of distinct molecular subtypes, with some overlapping across different approaches. However, a standardised tool to routinely classify TNBC in the clinics and guide personalised treatment is lacking. We aimed at defining a specific gene signature for each of the six TNBC subtypes proposed by Lehman et al. in 2011 (basal-like 1 (BL1); basal-like 2 (BL2); mesenchymal (M); immunomodulatory (IM); mesenchymal stem-like (MSL); and luminal androgen receptor (LAR)), to be able to accurately predict them. METHODS Lehman's TNBCtype subtyping tool was applied to RNA-sequencing data from 482 TNBC (GSE164458), and a minimal subtype-specific gene signature was defined by combining two class comparison techniques with seven attribute selection methods. Several machine learning algorithms for subtype prediction were used, and the best classifier was applied on microarray data from 72 Italian TNBC and on the TNBC subset of the BRCA-TCGA data set. RESULTS We identified two signatures with the 120 and 81 top up- and downregulated genes that define the six TNBC subtypes, with prediction accuracy ranging from 88.6 to 89.4%, and even improving after removal of the least important genes. Network analysis was used to identify highly interconnected genes within each subgroup. Two druggable matrix metalloproteinases were found in the BL1 and BL2 subsets, and several druggable targets were complementary to androgen receptor or aromatase in the LAR subset. Several secondary drug-target interactions were found among the upregulated genes in the M, IM and MSL subsets. CONCLUSIONS Our study took full advantage of available TNBC data sets to stratify samples and genes into distinct subtypes, according to gene expression profiles. The development of a data mining approach to acquire a large amount of information from several data sets has allowed us to identify a well-determined minimal number of genes that may help in the recognition of TNBC subtypes. These genes, most of which have been previously found to be associated with breast cancer, have the potential to become novel diagnostic markers and/or therapeutic targets for specific TNBC subsets.
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Affiliation(s)
- Laila Akhouayri
- grid.412148.a0000 0001 2180 2473Department of Biomedical Sciences, Genetics and Molecular Biology Laboratory, Faculty of Medicine and Pharmacy, Hassan II-Casablanca University, Casablanca, Morocco ,grid.7605.40000 0001 2336 6580Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Paola Ostano
- grid.452265.2Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
| | | | - Ilaria Gregnanin
- grid.452265.2Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
| | - Francesca Crivelli
- grid.452265.2Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy ,Clinical Research Division, “Degli Infermi” Hospital, Ponderano, BI Italy
| | - Sara Laurora
- grid.452265.2Molecular Oncology Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
| | - Daniele Liscia
- Pathology Department, “Degli Infermi” Hospital, Ponderano, BI Italy
| | - Francesco Leone
- Oncology Department, “Degli Infermi” Hospital, Ponderano, BI Italy
| | - Angela Santoro
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Antonino Mulè
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Donatella Guarino
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Claudia Maggiore
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Angela Carlino
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Stefano Magno
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Maria Scatolini
- grid.452265.2Molecular Oncology Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
| | - Alba Di Leone
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Riccardo Masetti
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giovanna Chiorino
- grid.452265.2Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
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20
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Li S, Lee W, Heo W, Son HY, Her Y, Kim JI, Moon HG. AKR1C2 Promotes Metastasis and Regulates the Molecular Features of Luminal Androgen Receptor Subtype in Triple Negative Breast Cancer Cells. J Breast Cancer 2022; 26:60-76. [PMID: 36762781 PMCID: PMC9981988 DOI: 10.4048/jbc.2023.26.e1] [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: 06/20/2022] [Revised: 11/12/2022] [Accepted: 11/18/2022] [Indexed: 01/07/2023] Open
Abstract
PURPOSE Patients with triple-negative breast cancer (TNBC) have an increased risk of distant metastasis compared to those with other subtypes. In this study, we aimed to identify the genes associated with distant metastasis in TNBC and their underlying mechanisms. METHODS We established patient-derived xenograft (PDX) models using surgically resected breast cancer tissues from 31 patients with TNBC. Among these, 15 patients subsequently developed distant metastases. Candidate metastasis-associated genes were identified using RNA sequencing. In vitro wound healing, proliferation, migration, and invasion assays and in vivo tumor xenograft and metastasis assays were performed to determine the functional importance of aldo-keto reductase family 1 member C2 (AKR1C2). Additionally, we used the METABRIC dataset to investigate the potential role of AKR1C2 in regulating TNBC subtypes and their downstream signaling activities. RESULTS RNA sequencing of primary and PDX tumors showed that genes involved in steroid hormone biosynthesis, including AKR1C2, were significantly upregulated in patients who subsequently developed metastasis. In vitro and in vivo assays showed that silencing of AKR1C2 resulted in reduced cell proliferation, migration, invasion, tumor growth, and incidence of lung metastasis. AKR1C2 was upregulated in the luminal androgen receptor (LAR) subtype of TNBC in the METABRIC dataset, and AKR1C2 silencing resulted in the downregulation of LAR classifier genes in TNBC cell lines. The androgen receptor (AR) gene was a downstream mediator of AKR1C2-associated phenotypes in TNBC cells. AKR1C2 expression was associated with gene expression pathways that regulate AR expression, including JAK-STAT signaling or interleukin 6 (IL-6). The levels of phospho-signal transducer and activator of transcription and IL-6, along with secreted IL-6, were significantly downregulated in AKR1C2-silenced TNBC cells. CONCLUSION Our data indicate that AKR1C2 is an important regulator of cancer growth and metastasis in TNBC and may be a critical determinant of LAR subtype features.
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Affiliation(s)
- Songbin Li
- Interdisciplinary Graduate Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Woochan Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.,Genomic Medicine Institute, Medical Research Center, Seoul, Korea
| | - Woohang Heo
- Center for Medical Innovation, Seoul National University Hospital, Seoul, Korea
| | - Hye-Youn Son
- Center for Medical Innovation, Seoul National University Hospital, Seoul, Korea
| | - Yujeong Her
- Interdisciplinary Graduate Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.,Genomic Medicine Institute, Medical Research Center, Seoul, Korea
| | - Hyeong-Gon Moon
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Surgery, Seoul National University Hospital, Seoul, Korea.,Department of Surgery, Seoul National University College of Medicine, Seoul, Korea.
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21
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Furukawa N, Stearns V, Santa-Maria CA, Popel AS. The tumor microenvironment and triple-negative breast cancer aggressiveness: shedding light on mechanisms and targeting. Expert Opin Ther Targets 2022; 26:1041-1056. [PMID: 36657483 PMCID: PMC10189896 DOI: 10.1080/14728222.2022.2170779] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
INTRODUCTION In contrast to other breast cancer subtypes, there are currently limited options of targeted therapies for triple-negative breast cancer (TNBC). Immense research has demonstrated that not only cancer cells but also stromal cells and immune cells in the tumor microenvironment (TME) play significant roles in the progression of TNBC. It is thus critical to understand the components of the TME of TNBC and the interactions between the various cell populations. AREAS COVERED The components of the TME of TNBC identified by single-cell technologies are reviewed. Furthermore, the molecular interactions between the cells and the potential therapeutic targets contributing to the progression of TNBC are discussed. EXPERT OPINION Single-cell omics studies have contributed to the classification of cells in the TME and the identification of important cell types involved in the progression and the treatment of the tumor. The interactions between cancer cells and stromal cells/immune cells in the TME have led to the discovery of potential therapeutic targets. Experimental data with spatial and temporal resolution will further boost the understanding of the TME of TNBC.
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Affiliation(s)
- Natsuki Furukawa
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Vered Stearns
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Cesar A. Santa-Maria
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Aleksander S. Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
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22
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Hamilton AM, Hoadley KA, Troester MA. Race and Ancestry in Immune Response to Breast Cancer. Cancer Discov 2022; 12:2496-2497. [PMID: 36321309 PMCID: PMC10071672 DOI: 10.1158/2159-8290.cd-22-0852] [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] [Indexed: 11/06/2022]
Abstract
Martini and colleagues performed genetic ancestry estimation on a unique international triple-negative breast cancer (TNBC) study enriched for participants with African ancestry. They identified gene signatures indicative of ancestry in race-associated TNBC and found ancestry-associated immunologic differences that may contribute to racial disparities in breast cancer. See related article by Martini et al., p. 2530 (5).
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Affiliation(s)
- Alina M. Hamilton
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Melissa A. Troester
- 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
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23
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Xu Q, Kaur J, Wylie D, Mittal K, Li H, Kolachina R, Aleskandarany M, Toss MS, Green AR, Yang J, Yankeelov TE, Bhattarai S, Janssen EAM, Kong J, Rakha EA, Kowalski J, Aneja R. A Case Series Exploration of Multi-Regional Expression Heterogeneity in Triple-Negative Breast Cancer Patients. Int J Mol Sci 2022; 23:13322. [PMID: 36362107 PMCID: PMC9655720 DOI: 10.3390/ijms232113322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 08/13/2023] Open
Abstract
Extensive intratumoral heterogeneity (ITH) is believed to contribute to therapeutic failure and tumor recurrence, as treatment-resistant cell clones can survive and expand. However, little is known about ITH in triple-negative breast cancer (TNBC) because of the limited number of single-cell sequencing studies on TNBC. In this study, we explored ITH in TNBC by evaluating gene expression-derived and imaging-derived multi-region differences within the same tumor. We obtained tissue specimens from 10 TNBC patients and conducted RNA sequencing analysis of 2-4 regions per tumor. We developed a novel analysis framework to dissect and characterize different types of variability: between-patients (inter-tumoral heterogeneity), between-patients across regions (inter-tumoral and region heterogeneity), and within-patient, between-regions (regional intratumoral heterogeneity). We performed a Bayesian changepoint analysis to assess and classify regional variability as low (convergent) versus high (divergent) within each patient feature (TNBC and PAM50 subtypes, immune, stroma, tumor counts and tumor infiltrating lymphocytes). Gene expression signatures were categorized into three types of variability: between-patients (108 genes), between-patients across regions (183 genes), and within-patients, between-regions (778 genes). Based on the between-patient gene signature, we identified two distinct patient clusters that differed in menopausal status. Significant intratumoral divergence was observed for PAM50 classification, tumor cell counts, and tumor-infiltrating T cell abundance. Other features examined showed a representation of both divergent and convergent results. Lymph node stage was significantly associated with divergent tumors. Our results show extensive intertumoral heterogeneity and regional ITH in gene expression and image-derived features in TNBC. Our findings also raise concerns regarding gene expression based TNBC subtyping. Future studies are warranted to elucidate the role of regional heterogeneity in TNBC as a driver of treatment resistance.
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Affiliation(s)
- Qi Xu
- Department of Oncology, Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jaspreet Kaur
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Dennis Wylie
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX 78705, USA
| | - Karuna Mittal
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Hongxiao Li
- Department of Mathematics and Statistics, Georgia State University, Atlanta, GA 30303, USA
| | - Rishab Kolachina
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | | | - Michael S. Toss
- University of Nottingham and Nottingham University Hospitals, Nottingham NG7 2UH, UK
| | - Andrew R. Green
- University of Nottingham and Nottingham University Hospitals, Nottingham NG7 2UH, UK
| | - Jianchen Yang
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78705, USA
- Departments of Diagnostic Medicine, Biomedical Engineering, and Oncology, The University of Texas at Austin, Austin, TX 78705, USA
| | - Thomas E. Yankeelov
- Department of Oncology, Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX 78712, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78705, USA
- Departments of Diagnostic Medicine, Biomedical Engineering, and Oncology, The University of Texas at Austin, Austin, TX 78705, USA
| | - Shristi Bhattarai
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Emiel A. M. Janssen
- Department of Pathology, Stavanger University Hospital, 4011 Stavanger, Norway
| | - Jun Kong
- Department of Mathematics and Statistics, Georgia State University, Atlanta, GA 30303, USA
| | - Emad A. Rakha
- University of Nottingham and Nottingham University Hospitals, Nottingham NG7 2UH, UK
| | - Jeanne Kowalski
- Department of Oncology, Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
- Department of Clinical and Diagnostic Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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24
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Araujo JM, De la Cruz-Ku G, Cornejo M, Doimi F, Dyer R, Gomez HL, Pinto JA. Prognostic Capability of TNBC 3-Gene Score among Triple-Negative Breast Cancer Subtypes. Cancers (Basel) 2022; 14:cancers14174286. [PMID: 36077821 PMCID: PMC9454544 DOI: 10.3390/cancers14174286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Triple-negative breast cancer (TNBC) is a complex and molecularly heterogeneous entity, with the poorest outcome compared with other breast cancer subtypes. Previously, we developed a TNBC 3-gene score with a significant prognostic capability. This study aims to test the 3-gene score in the different TNBC subtypes. Methods: Data from 204 TNBC patients treated with neoadjuvant chemotherapy were retrieved from public datasets and pooled (GSE25066, GSE58812, and GSE16446). After removing batch effects, cases were classified into Lehman’s TNBC subtypes and then the TNBC 3-gene score was used to evaluate the risk of distant recurrence in each subgroup. In addition, the association with tumor-infiltrating lymphocyte (TILs) levels was evaluated in a retrospective group of 72 TNBC cases. Results: The TNBC 3-gene score was able to discriminate patients with different risks within the pooled cohort (HR = 2.41 for high vs. low risk; 95%CI: 1.50−3.86). The score showed predictive capability in the immunomodulatory subtype (HR = 4.16; 95%CI: 1.63−10.60) and in the mesenchymal stem-like subtype (HR = 18.76; 95%CI: 1.68−208.97). In the basal-like 1, basal-like-2, and mesenchymal subtypes, the observed differential risk patterns showed no statistical significance. The score had poor predictive capability in the luminal androgen receptor subtype (p = 0.765). In addition, a low TNBC 3-gene score was related to a high level of TIL infiltration (p < 0.001). Conclusions: The TNBC 3-gene score is able to predict the risk of distant recurrence in TNBC patients, specifically in the immunomodulatory and mesenchymal stem-like subtype. Despite a small sample size in each subgroup, an improved prognostic capability was seen in TNBC subtypes with tumor-infiltrating components.
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Affiliation(s)
- Jhajaira M. Araujo
- Centro de Investigación Básica y Traslacional, AUNA Ideas, Lima 15036, Peru
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima 15067, Peru
| | - Gabriel De la Cruz-Ku
- Department of Surgery, University of Massachusetts, Worcester, MA 01604, USA
- Universidad Cientifica del Sur, Lima 15067, Peru
| | - Melanie Cornejo
- Centro de Investigación Básica y Traslacional, AUNA Ideas, Lima 15036, Peru
| | - Franco Doimi
- Departamento de Patología, Oncosalud-AUNA, Lima 15036, Peru
| | - Richard Dyer
- Departamento de Patología, Oncosalud-AUNA, Lima 15036, Peru
| | - Henry L. Gomez
- Departamento de Medicina Oncológica, Oncosalud-AUNA, Lima 15036, Peru
| | - Joseph A. Pinto
- Centro de Investigación Básica y Traslacional, AUNA Ideas, Lima 15036, Peru
- Correspondence: ; Tel.: +51-1-5137900 (ext. 2231)
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25
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High PANX1 Expression Leads to Neutrophil Recruitment and the Formation of a High Adenosine Immunosuppressive Tumor Microenvironment in Basal-like Breast Cancer. Cancers (Basel) 2022; 14:cancers14143369. [PMID: 35884429 PMCID: PMC9323990 DOI: 10.3390/cancers14143369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 12/07/2022] Open
Abstract
Background: A high adenosine level is an important characteristic of the tumor microenvironment (TME) in breast cancer. Pannexin 1 (PANX1) can release intracellular ATP to the extracellular space and elevate extracellular ATP (exATP) levels under physiological conditions. Methods: We performed public database bioinformatics analysis, surgical specimen histological validation, RNA sequencing, and exATP/extracellular adenosine (exADO) assays to reveal the role of PANX1 in regulating the immune microenvironment of basal-like breast cancer. Results: Our results revealed that PANX1 acted as a poor prognostic factor for breast cancer and had high expression in basal-like breast cancer. PANX1 expression was positively correlated with exATP and exADO levels in basal-like breast cancer TME. PANX1 expression was also positively correlated with tumor-associated neutrophil (TAN) infiltration in breast cancer TME and TANs highly expressed ENTPD1 (CD39)/NT5E (CD73). Conclusions: This study suggests that high PANX1 expression is associated with high TAN infiltration and adenosine production to induce local immunosuppression in basal-like breast cancer TME.
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26
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Expression and Clinical Significance of CMTM6 and PD-L1 in Triple-Negative Breast Cancer. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8118909. [PMID: 35845949 PMCID: PMC9283057 DOI: 10.1155/2022/8118909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 01/02/2023]
Abstract
The CKLF-like MARVEL transmembrane domain containing 6 (CMTM6) plays an extremely important role of the programed death receptor ligand-1 (PD-L1) protein. Our study is aimed at investigating the expression of CMTM6 and PD-L1 proteins in triple-negative breast cancer and their correlation with the clinical pathological data of patients. We selected 89 cases of triple-negative breast cancer and 62 cases of normal breast tissue specimens. Immunohistochemical methods were used to detect the expression levels of CMTM6 and PD-L1 and to carefully study differences in their expression. The expression of CMTM6 and PD-L1 in TNBC was higher than that in normal breast tissue, and the expression of the two was positively correlated (p < 0.05). In TNBC, CMTM6 expression is positively correlated with tumor size, lymph node metastasis, Ki67 proliferation index, and TNM stage (p < 0.05). PD-L1 expression is positively correlated with tumor size, lymph node metastasis, Ki67 proliferation index, TNM stage, and vascular infiltration (p < 0.05). Kaplan-Meier analysis showed that the positive expression of CMTM6 and PD-L1 had no correlation with the survival rate of patients (p > 0.05). According to KM-plotter, we found that a higher CMTM6 expression was positively related with relapse-free survival rate of patients (p < 0.05). A higher PD-L1 expression was positively correlated with relapse-free, overall, and distant metastasis survival rate of patients (p < 0.05). In timer database, we found a positive correlation between the expression of CMTM6 and PD-L1 in triple-negative breast cancer. Both CMTM6 and PD-L1 are highly expressed in TNBC, and their expressions are positively related. In the future, the two gene might become targets for the treatment of TNBC, providing a basis of clinical treatment of TNBC.
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27
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Menghi F, Banda K, Kumar P, Straub R, Dobrolecki L, Rodriguez IV, Yost SE, Chandok H, Radke MR, Somlo G, Yuan Y, Lewis MT, Swisher EM, Liu ET. Genomic and epigenomic
BRCA
alterations predict adaptive resistance and response to platinum-based therapy in patients with triple-negative breast and ovarian carcinomas. Sci Transl Med 2022; 14:eabn1926. [PMID: 35857626 PMCID: PMC9585706 DOI: 10.1126/scitranslmed.abn1926] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Triple-negative breast cancer (TNBC) and ovarian carcinomas (OvCas) with
BRCA1
promoter methylation (
BRCA1
meth) respond more poorly to alkylating agents compared to those bearing mutations in
BRCA1
and
BRCA2
(
BRCA
mut). This is a conundrum given the biologically equivalent homologous recombination deficiency (HRD) induced by these genetic and epigenetic
BRCA
perturbations. We dissected this problem through detailed genomic analyses of TNBC and OvCa cohorts and experimentation with patient-derived xenografts and genetically engineered cell lines. We found that despite identical downstream genomic mutational signatures associated with
BRCA1
meth and
BRCA
mut states,
BRCA1
meth uniformly associates with poor outcomes. Exposure of
BRCA1
meth TNBCs to platinum chemotherapy, either as clinical treatment of a patient or as experimental in vivo exposure of preclinical patient derived xenografts, resulted in allelic loss of
BRCA1
methylation and increased
BRCA1
expression and platinum resistance. These data suggest that, unlike
BRCA
mut cancers, where
BRCA
loss is a genetically “fixed” deficiency state,
BRCA1
meth cancers are highly adaptive to genotoxin exposure and, through reversal of promoter methylation, recover
BRCA1
expression and become resistant to therapy. We further found a specific augmented immune transcriptional signal associated with enhanced response to platinum chemotherapy but only in patients with BRCA-proficient cancers. We showed how integrating both this cancer immune signature and the presence of
BRCA
mutations results in more accurate predictions of patient response when compared to either HRD status or
BRCA
status alone. This underscores the importance of defining
BRCA
heterogeneity in optimizing the predictive precision of assigning response probabilities in TNBC and OvCa.
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Affiliation(s)
- Francesca Menghi
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Kalyan Banda
- Division of Medical Oncology, UW Medical Center, Seattle, WA 98195, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pooja Kumar
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Robert Straub
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | - Isabel V. Rodriguez
- Department of Obstetrics and Gynecology, UW Medical Center, Seattle, WA 98195, USA
| | - Susan E. Yost
- Division of Medical Oncology and Therapeutic Research, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Marc R. Radke
- Department of Obstetrics and Gynecology, UW Medical Center, Seattle, WA 98195, USA
| | - George Somlo
- Division of Medical Oncology and Therapeutic Research, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Yuan Yuan
- Division of Medical Oncology and Therapeutic Research, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Michael T. Lewis
- Departments of Molecular and Cellular Biology and Radiology, Lester and Sue Smith Breast Center, Dan L Duncan Comprehensive Cancer Center, Houston, TX 77030, USA
| | - Elizabeth M. Swisher
- Department of Obstetrics and Gynecology, UW Medical Center, Seattle, WA 98195, USA
| | - Edison T. Liu
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
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28
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Yam C, Abuhadra N, Sun R, Adrada BE, Ding QQ, White JB, Ravenberg EE, Clayborn AR, Valero V, Tripathy D, Damodaran S, Arun BK, Litton JK, Ueno NT, Murthy RK, Lim B, Baez L, Li X, Buzdar AU, Hortobagyi GN, Thompson AM, Mittendorf EA, Rauch GM, Candelaria RP, Huo L, Moulder SL, Chang JT. Molecular Characterization and Prospective Evaluation of Pathologic Response and Outcomes with Neoadjuvant Therapy in Metaplastic Triple-Negative Breast Cancer. Clin Cancer Res 2022; 28:2878-2889. [PMID: 35507014 PMCID: PMC9250637 DOI: 10.1158/1078-0432.ccr-21-3100] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 02/28/2022] [Accepted: 04/29/2022] [Indexed: 01/03/2023]
Abstract
PURPOSE Metaplastic breast cancer (MpBC) is a rare subtype of breast cancer that is commonly triple-negative and poorly responsive to neoadjuvant therapy in retrospective studies. EXPERIMENTAL DESIGN To better define clinical outcomes and correlates of response, we analyzed the rate of pathologic complete response (pCR) to neoadjuvant therapy, survival outcomes, and genomic and transcriptomic profiles of the pretreatment tumors in a prospective clinical trial (NCT02276443). A total of 211 patients with triple-negative breast cancer (TNBC), including 39 with MpBC, received doxorubicin-cyclophosphamide-based neoadjuvant therapy. RESULTS Although not meeting the threshold for statistical significance, patients with MpBCs were less likely to experience a pCR (23% vs. 40%; P = 0.07), had shorter event-free survival (29.4 vs. 32.2 months, P = 0.15), metastasis-free survival (30.3 vs. 32.4 months, P = 0.22); and overall survival (32.6 vs. 34.3 months, P = 0.21). This heterogeneity is mirrored in the molecular profiling. Mutations in PI3KCA (23% vs. 9%, P = 0.07) and its pathway (41% vs. 18%, P = 0.02) were frequently observed and enriched in MpBCs. The gene expression profiles of each histologically defined subtype were distinguishable and characterized by distinctive gene signatures. Among nonmetaplastic (non-Mp) TNBCs, 10% possessed a metaplastic-like gene expression signature and had pCR rates and survival outcomes similar to MpBC. CONCLUSIONS Further investigations will determine if metaplastic-like tumors should be treated more similarly to MpBC in the clinic. The 23% pCR rate in this study suggests that patients with MpBC should be considered for NAT. To improve this rate, a pathway analysis predicted enrichment of histone deacetylase (HDAC) and RTK/MAPK pathways in MpBC, which may serve as new targetable vulnerabilities.
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Affiliation(s)
- Clinton Yam
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nour Abuhadra
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Beatriz E. Adrada
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qing-Qing Ding
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason B. White
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elizabeth E. Ravenberg
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alyson R. Clayborn
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vicente Valero
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Senthilkumar Damodaran
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Banu K. Arun
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer K. Litton
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naoto T. Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rashmi K. Murthy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bora Lim
- Department of Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Luis Baez
- PROncology (Private Practice), University of Puerto Rico. San Juan, Puerto Rico
| | - Xiaoxian Li
- Department of Pathology & Laboratory Medicine, Winship Cancer Institute - Emory University Hospital, Atlanta, GA, USA
| | - Aman U. Buzdar
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gabriel N. Hortobagyi
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alistair M. Thompson
- Division of Surgical Oncology, Section of Breast Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth A. Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MD, USA.,Breast Oncology Program, Dana-Farber/Brigham and Women’s Cancer Center, Boston, MA, USA
| | - Gaiane M. Rauch
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rosalind P. Candelaria
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lei Huo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stacy L. Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey T. Chang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, TX, USA
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29
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Eustace AJ, Lee MJ, Colley G, Roban J, Downing T, Buchanan PJ. Aberrant calcium signalling downstream of mutations in TP53 and the PI3K/AKT pathway genes promotes disease progression and therapy resistance in triple negative breast cancer. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:560-576. [PMID: 36176752 PMCID: PMC9511797 DOI: 10.20517/cdr.2022.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/04/2022] [Accepted: 05/25/2022] [Indexed: 06/16/2023]
Abstract
Triple-negative breast cancer (TNBC) is characterized as an aggressive form of breast cancer (BC) associated with poor patient outcomes. For the majority of patients, there is a lack of approved targeted therapies. Therefore, chemotherapy remains a key treatment option for these patients, but significant issues around acquired resistance limit its efficacy. Thus, TNBC has an unmet need for new targeted personalized medicine approaches. Calcium (Ca2+) is a ubiquitous second messenger that is known to control a range of key cellular processes by mediating signalling transduction and gene transcription. Changes in Ca2+ through altered calcium channel expression or activity are known to promote tumorigenesis and treatment resistance in a range of cancers including BC. Emerging evidence shows that this is mediated by Ca2+ modulation, supporting the function of tumour suppressor genes (TSGs) and oncogenes. This review provides insight into the underlying alterations in calcium signalling and how it plays a key role in promoting disease progression and therapy resistance in TNBC which harbours mutations in tumour protein p53 (TP53) and the PI3K/AKT pathway.
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Affiliation(s)
- Alex J. Eustace
- DCU Cancer Research, Dublin City University, Dublin D9, Ireland
- National Institute Cellular Biotechnology, Dublin City University, Dublin D9, Ireland
- School of Biotechnology, Dublin City University, Dublin D9, Ireland
| | - Min Jie Lee
- School of Biotechnology, Dublin City University, Dublin D9, Ireland
| | - Grace Colley
- National Institute Cellular Biotechnology, Dublin City University, Dublin D9, Ireland
- School of Biotechnology, Dublin City University, Dublin D9, Ireland
| | - Jack Roban
- School of Biotechnology, Dublin City University, Dublin D9, Ireland
| | - Tim Downing
- DCU Cancer Research, Dublin City University, Dublin D9, Ireland
- School of Biotechnology, Dublin City University, Dublin D9, Ireland
| | - Paul J. Buchanan
- DCU Cancer Research, Dublin City University, Dublin D9, Ireland
- National Institute Cellular Biotechnology, Dublin City University, Dublin D9, Ireland
- School of Nursing, Psychotherapy, and Community Health, Dublin City University, Dublin D9, Ireland
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30
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Wolf DM, Yau C, Wulfkuhle J, Brown-Swigart L, Gallagher RI, Lee PRE, Zhu Z, Magbanua MJ, Sayaman R, O'Grady N, Basu A, Delson A, Coppé JP, Lu R, Braun J, Asare SM, Sit L, Matthews JB, Perlmutter J, Hylton N, Liu MC, Pohlmann P, Symmans WF, Rugo HS, Isaacs C, DeMichele AM, Yee D, Berry DA, Pusztai L, Petricoin EF, Hirst GL, Esserman LJ, van 't Veer LJ. Redefining breast cancer subtypes to guide treatment prioritization and maximize response: Predictive biomarkers across 10 cancer therapies. Cancer Cell 2022; 40:609-623.e6. [PMID: 35623341 PMCID: PMC9426306 DOI: 10.1016/j.ccell.2022.05.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/16/2022] [Accepted: 05/06/2022] [Indexed: 12/26/2022]
Abstract
Using pre-treatment gene expression, protein/phosphoprotein, and clinical data from the I-SPY2 neoadjuvant platform trial (NCT01042379), we create alternative breast cancer subtypes incorporating tumor biology beyond clinical hormone receptor (HR) and human epidermal growth factor receptor-2 (HER2) status to better predict drug responses. We assess the predictive performance of mechanism-of-action biomarkers from ∼990 patients treated with 10 regimens targeting diverse biology. We explore >11 subtyping schemas and identify treatment-subtype pairs maximizing the pathologic complete response (pCR) rate over the population. The best performing schemas incorporate Immune, DNA repair, and HER2/Luminal phenotypes. Subsequent treatment allocation increases the overall pCR rate to 63% from 51% using HR/HER2-based treatment selection. pCR gains from reclassification and improved patient selection are highest in HR+ subsets (>15%). As new treatments are introduced, the subtyping schema determines the minimum response needed to show efficacy. This data platform provides an unprecedented resource and supports the usage of response-based subtypes to guide future treatment prioritization.
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Affiliation(s)
- Denise M Wolf
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA.
| | - Christina Yau
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Julia Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Lamorna Brown-Swigart
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
| | - Rosa I Gallagher
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Pei Rong Evelyn Lee
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
| | - Zelos Zhu
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark J Magbanua
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
| | - Rosalyn Sayaman
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
| | - Nicholas O'Grady
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amrita Basu
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amy Delson
- Breast Science Advocacy Core, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jean Philippe Coppé
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
| | - Ruixiao Lu
- Quantum Leap Healthcare Collaborative, San Francisco, CA 94118, USA
| | - Jerome Braun
- Quantum Leap Healthcare Collaborative, San Francisco, CA 94118, USA
| | - Smita M Asare
- Quantum Leap Healthcare Collaborative, San Francisco, CA 94118, USA
| | - Laura Sit
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey B Matthews
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Nola Hylton
- Department of Radiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Minetta C Liu
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Paula Pohlmann
- MedStar Georgetown University Hospital, Georgetown University, Washington, DC 20057, USA
| | - W Fraser Symmans
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hope S Rugo
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA
| | - Angela M DeMichele
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Douglas Yee
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Lajos Pusztai
- Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Gillian L Hirst
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura J Esserman
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura J van 't Veer
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA.
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31
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Thompson KJ, Leon-Ferre RA, Sinnwell JP, Zahrieh D, Suman V, Metzger F, Asad S, Stover D, Carey L, Sikov W, Ingle J, Liu M, Carter J, Klee E, Weinshilboum R, Boughey J, Wang L, Couch F, Goetz M, Kalari K. Luminal androgen receptor breast cancer subtype and investigation of the microenvironment and neoadjuvant chemotherapy response. NAR Cancer 2022; 4:zcac018. [PMID: 35734391 PMCID: PMC9204893 DOI: 10.1093/narcan/zcac018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/28/2022] [Accepted: 06/13/2022] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype with low overall survival rates and high molecular heterogeneity; therefore, few targeted therapies are available. The luminal androgen receptor (LAR) is the most consistently identified TNBC subtype, but the clinical utility has yet to be established. Here, we constructed a novel genomic classifier, LAR-Sig, that distinguishes the LAR subtype from other TNBC subtypes and provide evidence that it is a clinically distinct disease. A meta-analysis of seven TNBC datasets (n = 1086 samples) from neoadjuvant clinical trials demonstrated that LAR patients have significantly reduced response (pCR) rates than non-LAR TNBC patients (odds ratio = 2.11, 95% CI: 1.33, 2.89). Moreover, deconvolution of the tumor microenvironment confirmed an enrichment of luminal epithelium corresponding with a decrease in basal and myoepithelium in LAR TNBC tumors. Increased immunosuppression in LAR patients may lead to a decreased presence of cycling T-cells and plasma cells. While, an increased presence of myofibroblast-like cancer-associated cells may impede drug delivery and treatment. In summary, the lower levels of tumor infiltrating lymphocytes (TILs), reduced immune activity in the micro-environment, and lower pCR rates after NAC, suggest that new therapeutic strategies for the LAR TNBC subtype need to be developed.
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Affiliation(s)
- Kevin J Thompson
- Mayo Clinic, Department of Quantitative Health Sciences, Rochester, MN, USA
| | | | - Jason P Sinnwell
- Mayo Clinic, Department of Quantitative Health Sciences, Rochester, MN, USA
| | - David M Zahrieh
- Mayo Clinic, Department of Quantitative Health Sciences, Rochester, MN, USA
| | - Vera J Suman
- Mayo Clinic, Department of Quantitative Health Sciences, Rochester, MN, USA
| | | | - Sarah Asad
- The Ohio State University Wexner Medical Center, Molecular, Cellular, and Developmental Biology, Columbus, OH, USA
| | - Daniel G Stover
- The Ohio State University Wexner Medical Center, Molecular, Cellular, and Developmental Biology, Columbus, OH, USA
| | - Lisa Carey
- University of North Carolina at Chapel Hill School of Medicine, Medical Science, Chapel Hill, NC, USA
| | - William M Sikov
- Warren Alpert Medical School of Brown University, Department of Medicine Women, Providence, RI, USA
- Infants Hospital of Rhode Island, Department of Obstetrics & Gynecology, Providence, RI, USA
| | - James N Ingle
- Mayo Clinic, Department of Oncology, Rochester, MN, USA
| | - Minetta C Liu
- Mayo Clinic, Department of Oncology, Rochester, MN, USA
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN, USA
| | - Jodi M Carter
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN, USA
| | - Eric W Klee
- Mayo Clinic, Department of Quantitative Health Sciences, Rochester, MN, USA
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN, USA
| | - Richard M Weinshilboum
- Mayo Clinic, Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, USA
| | | | - Liewei Wang
- Mayo Clinic, Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, USA
| | - Fergus J Couch
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN, USA
| | - Matthew P Goetz
- Mayo Clinic, Department of Oncology, Rochester, MN, USA
- Mayo Clinic, Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, USA
| | - Krishna R Kalari
- Mayo Clinic, Department of Quantitative Health Sciences, Rochester, MN, USA
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32
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Reassessment of Reliability and Reproducibility for Triple-Negative Breast Cancer Subtyping. Cancers (Basel) 2022; 14:cancers14112571. [PMID: 35681552 PMCID: PMC9179838 DOI: 10.3390/cancers14112571] [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: 04/07/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Triple-negative breast cancer (TNBC) is a heterogeneous disease. A proper classification system is needed to develop targetable biomarkers and guide personalized treatment in clinical practice. However, there has been no consensus on the molecular subtypes of TNBC, probably due to discrepancies in technical and computational methods chosen by different research groups. In this paper, we reassessed each major step for TNBC subtyping and provided suggestions, which promote rational workflow design and ensure reliable and reproducible results for future studies. We presented a recommended pipeline to the existing data, validated established TNBC subtypes with a larger sample size, and revealed two intermediate subtypes with prognostic significance. This work provides perspectives on issues and limitations regarding TNBC subtyping, indicating promising directions for developing targeted therapy based on the molecular characteristics of each TNBC subtype. Abstract Triple-negative breast cancer (TNBC) is a heterogeneous disease with diverse, often poor prognoses and treatment responses. In order to identify targetable biomarkers and guide personalized care, scientists have developed multiple molecular classification systems for TNBC based on transcriptomic profiling. However, there is no consensus on the molecular subtypes of TNBC, likely due to discrepancies in technical and computational methods used by different research groups. Here, we reassessed the major steps for TNBC subtyping, validated the reproducibility of established TNBC subtypes, and identified two more subtypes with a larger sample size. By comparing results from different workflows, we demonstrated the limitations of formalin-fixed, paraffin-embedded samples, as well as batch effect removal across microarray platforms. We also refined the usage of computational tools for TNBC subtyping. Furthermore, we integrated high-quality multi-institutional TNBC datasets (discovery set: n = 457; validation set: n = 165). Performing unsupervised clustering on the discovery and validation sets independently, we validated four previously discovered subtypes: luminal androgen receptor, mesenchymal, immunomodulatory, and basal-like immunosuppressed. Additionally, we identified two potential intermediate states of TNBC tumors based on their resemblance with more than one well-characterized subtype. In summary, we addressed the issues and limitations of previous TNBC subtyping through comprehensive analyses. Our results promote the rational design of future subtyping studies and provide new insights into TNBC patient stratification.
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33
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Abou-Fadel J, Bhalli M, Grajeda B, Zhang J. CmP Signaling Network Leads to Identification of Prognostic Biomarkers for Triple-Negative Breast Cancer in Caucasian Women. Genet Test Mol Biomarkers 2022; 26:198-219. [PMID: 35481969 DOI: 10.1089/gtmb.2021.0221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Objective: Triple-negative breast cancer (TNBC) constitutes ∼15% of all diagnosed invasive breast cancer cases with limited options for treatment since immunotherapies that target ER, PR, and HER2 receptors are ineffective. Progesterone (PRG) can induce its effects through either classic, nonclassic, or combined responses by binding to classic nuclear PRG receptors (nPRs) or nonclassic membrane PRG receptors (mPRs). Under PRG-induced actions, we previously demonstrated that the CCM signaling complex (CSC) can couple both nPRs and mPRs into a CmPn signaling network, which plays an important role during nPR(+) breast cancer tumorigenesis. We recently defined the novel CmP signaling network in African American women (AAW)-derived TNBC cells, which overlapped with our previously defined CmPn network in nPR(+) breast cancer cells. Methods: Under mPR-specific steroid actions, we measured alterations to key tumorigenic pathways in Caucasian American women (CAW)- derived TNBC cells, with RNAseq/proteomic and systems biology approaches. Exemption from ethics approval from IRB: This study only utilized cultured NBC cell lines with publicly available TNBC clinical data sets. Results: Our results demonstrated that TNBCs in CAW share similar altered signaling pathways, as TNBCs in AAW, under mPR-specific steroid actions, demonstrating the overall aggressive nature of TNBCs, regardless of racial differences. Furthermore, in this report, we have deconvoluted the CmP signalosome, using systems biology approaches and CAW-TNBC clinical data, to identify 21 new CAW-TNBC-specific prognostic biomarkers that reinforce the definitive role of CSC and mPR signaling during CAW-TNBC tumorigenesis. Conclusion: This new set of potential prognostic biomarkers may revolutionize molecular mechanisms and currently known concepts of tumorigenesis in CAW-TNBCs, leading to hopeful new therapeutic strategies.
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Affiliation(s)
- Johnathan Abou-Fadel
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, Texas, USA
| | - Muaz Bhalli
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, Texas, USA
| | - Brian Grajeda
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Jun Zhang
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, Texas, USA
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34
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Llera AS, Abdelhay ESFW, Artagaveytia N, Daneri-Navarro A, Müller B, Velazquez C, Alcoba EB, Alonso I, Alves da Quinta DB, Binato R, Bravo AI, Camejo N, Carraro DM, Castro M, Castro-Cervantes JM, Cataldi S, Cayota A, Cerda M, Colombo A, Crocamo S, Del Toro-Arreola A, Delgadillo-Cisterna R, Delgado L, Dreyer-Breitenbach M, Fejerman L, Fernández EA, Fernández J, Fernández W, Franco-Topete RA, Gabay C, Gaete F, Garibay-Escobar A, Gómez J, Greif G, Gross TG, Guerrero M, Henderson MK, Lopez-Muñoz ME, Lopez-Vazquez A, Maldonado S, Morán-Mendoza AJ, Nagai MA, Oceguera-Villanueva A, Ortiz-Martínez MA, Quintero J, Quintero-Ramos A, Reis RM, Retamales J, Rivera-Claisse E, Rocha D, Rodríguez R, Rosales C, Salas-González E, Sanchotena V, Segovia L, Sendoya JM, Silva-García AA, Trinchero A, Valenzuela O, Vedham V, Zagame L, Podhajcer OL. The Transcriptomic Portrait of Locally Advanced Breast Cancer and Its Prognostic Value in a Multi-Country Cohort of Latin American Patients. Front Oncol 2022; 12:835626. [PMID: 35433488 PMCID: PMC9007037 DOI: 10.3389/fonc.2022.835626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Purposes Most molecular-based published studies on breast cancer do not adequately represent the unique and diverse genetic admixture of the Latin American population. Searching for similarities and differences in molecular pathways associated with these tumors and evaluating its impact on prognosis may help to select better therapeutic approaches. Patients and Methods We collected clinical, pathological, and transcriptomic data of a multi-country Latin American cohort of 1,071 stage II-III breast cancer patients of the Molecular Profile of Breast Cancer Study (MPBCS) cohort. The 5-year prognostic ability of intrinsic (transcriptomic-based) PAM50 and immunohistochemical classifications, both at the cancer-specific (OSC) and disease-free survival (DFS) stages, was compared. Pathway analyses (GSEA, GSVA and MetaCore) were performed to explore differences among intrinsic subtypes. Results PAM50 classification of the MPBCS cohort defined 42·6% of tumors as LumA, 21·3% as LumB, 13·3% as HER2E and 16·6% as Basal. Both OSC and DFS for LumA tumors were significantly better than for other subtypes, while Basal tumors had the worst prognosis. While the prognostic power of traditional subtypes calculated with hormone receptors (HR), HER2 and Ki67 determinations showed an acceptable performance, PAM50-derived risk of recurrence best discriminated low, intermediate and high-risk groups. Transcriptomic pathway analysis showed high proliferation (i.e. cell cycle control and DNA damage repair) associated with LumB, HER2E and Basal tumors, and a strong dependency on the estrogen pathway for LumA. Terms related to both innate and adaptive immune responses were seen predominantly upregulated in Basal tumors, and, to a lesser extent, in HER2E, with respect to LumA and B tumors. Conclusions This is the first study that assesses molecular features at the transcriptomic level in a multicountry Latin American breast cancer patient cohort. Hormone-related and proliferation pathways that predominate in PAM50 and other breast cancer molecular classifications are also the main tumor-driving mechanisms in this cohort and have prognostic power. The immune-related features seen in the most aggressive subtypes may pave the way for therapeutic approaches not yet disseminated in Latin America. Clinical Trial Registration ClinicalTrials.gov (Identifier: NCT02326857).
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Affiliation(s)
- Andrea Sabina Llera
- Molecular and Cellular Therapy Laboratory, Fundación Instituto Leloir-CONICET, Buenos Aires, Argentina
| | | | - Nora Artagaveytia
- Hospital de Clínicas Manuel Quintela, Universidad de la República, Montevideo, Uruguay
| | | | | | | | - Elsa B Alcoba
- Hospital Municipal de Oncología María Curie, Buenos Aires, Argentina
| | - Isabel Alonso
- Centro Hospitalario Pereira Rossell, Montevideo, Uruguay
| | - Daniela B Alves da Quinta
- Molecular and Cellular Therapy Laboratory, Fundación Instituto Leloir-CONICET, Buenos Aires, Argentina.,Universidad Argentina de la Empresa (UADE), Instituto de Tecnología (INTEC), Buenos Aires, Argentina
| | - Renata Binato
- Bone Marrow Transplantation Unit, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | - Natalia Camejo
- Hospital de Clínicas Manuel Quintela, Universidad de la República, Montevideo, Uruguay
| | - Dirce Maria Carraro
- Laboratory of Genomics and Molecular Biology/Centro Internacional de Pesquisa (CIPE), AC Camargo Cancer Center, Sao Paulo, Brazil
| | - Mónica Castro
- Instituto de Oncología Angel Roffo, Buenos Aires, Argentina
| | | | | | | | - Mauricio Cerda
- Integrative Biology Program, Instituto de Ciencias Biomédicas (ICBM), Centro de Informática Médica y Telemedicina, Facultad de Medicina, Instituto de Neurociencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Alicia Colombo
- Department of Pathology, Facultad de Medicina y Hospital Clínico, Universidad de Chile, Santiago, Chile
| | - Susanne Crocamo
- Oncology Department, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | | | - Lucía Delgado
- Hospital de Clínicas Manuel Quintela, Universidad de la República, Montevideo, Uruguay
| | - Marisa Dreyer-Breitenbach
- Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Laura Fejerman
- Department of Public Health Sciences and Comprehensive Cancer Center, University of California Davis, Davis, CA, United States
| | - Elmer A Fernández
- Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas [Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE) CONICET/Universidad Católica de Córdoba], Córdoba, Argentina.,Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | | | | | - Ramón A Franco-Topete
- Organismo Público Descentralizado (OPD), Hospital Civil de Guadalajara, Universidad de Guadalajara, Guadalajara, Mexico
| | - Carolina Gabay
- Instituto de Oncología Angel Roffo, Buenos Aires, Argentina
| | | | | | - Jorge Gómez
- Texas A&M University, Houston, TX, United States
| | | | - Thomas G Gross
- Center for Global Health, National Cancer Institute, Rockville, MD, United States
| | | | - Marianne K Henderson
- Center for Global Health, National Cancer Institute, Rockville, MD, United States
| | | | | | | | | | - Maria Aparecida Nagai
- Center for Translational Research in Oncology, Cancer Institute of São Paulo (ICESP), Sao Paulo University Medical School, Sao Paulo, Brazil
| | | | | | | | | | - Rui M Reis
- Molecular Oncology Research Center, Hospital de Câncer de Barretos, Barretos, Brazil
| | - Javier Retamales
- Grupo Oncológico Cooperativo Chileno de Investigación, Santiago, Chile
| | | | - Darío Rocha
- Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | | | - Cristina Rosales
- Hospital Municipal de Oncología María Curie, Buenos Aires, Argentina
| | | | | | | | - Juan Martín Sendoya
- Molecular and Cellular Therapy Laboratory, Fundación Instituto Leloir-CONICET, Buenos Aires, Argentina
| | - Aida A Silva-García
- Organismo Público Descentralizado (OPD), Hospital Civil de Guadalajara, Universidad de Guadalajara, Guadalajara, Mexico
| | | | | | - Vidya Vedham
- Center for Global Health, National Cancer Institute, Rockville, MD, United States
| | - Livia Zagame
- Instituto Jalisciense de Cancerologia, Guadalajara, Mexico
| | | | - Osvaldo L Podhajcer
- Molecular and Cellular Therapy Laboratory, Fundación Instituto Leloir-CONICET, Buenos Aires, Argentina
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Liao M, Qin R, Huang W, Zhu HP, Peng F, Han B, Liu B. Targeting regulated cell death (RCD) with small-molecule compounds in triple-negative breast cancer: a revisited perspective from molecular mechanisms to targeted therapies. J Hematol Oncol 2022; 15:44. [PMID: 35414025 PMCID: PMC9006445 DOI: 10.1186/s13045-022-01260-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/28/2022] [Indexed: 02/08/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a subtype of human breast cancer with one of the worst prognoses, with no targeted therapeutic strategies currently available. Regulated cell death (RCD), also known as programmed cell death (PCD), has been widely reported to have numerous links to the progression and therapy of many types of human cancer. Of note, RCD can be divided into numerous different subroutines, including autophagy-dependent cell death, apoptosis, mitotic catastrophe, necroptosis, ferroptosis, pyroptosis and anoikis. More recently, targeting the subroutines of RCD with small-molecule compounds has been emerging as a promising therapeutic strategy, which has rapidly progressed in the treatment of TNBC. Therefore, in this review, we focus on summarizing the molecular mechanisms of the above-mentioned seven major RCD subroutines related to TNBC and the latest progress of small-molecule compounds targeting different RCD subroutines. Moreover, we further discuss the combined strategies of one drug (e.g., narciclasine) or more drugs (e.g., torin-1 combined with chloroquine) to achieve the therapeutic potential on TNBC by regulating RCD subroutines. More importantly, we demonstrate several small-molecule compounds (e.g., ONC201 and NCT03733119) by targeting the subroutines of RCD in TNBC clinical trials. Taken together, these findings will provide a clue on illuminating more actionable low-hanging-fruit druggable targets and candidate small-molecule drugs for potential RCD-related TNBC therapies.
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Affiliation(s)
- Minru Liao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Rui Qin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Hong-Ping Zhu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.,Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Fu Peng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
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36
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Decision Theory versus Conventional Statistics for Personalized Therapy of Breast Cancer. J Pers Med 2022; 12:jpm12040570. [PMID: 35455687 PMCID: PMC9028435 DOI: 10.3390/jpm12040570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
Estrogen and progesterone receptors being present or not represents one of the most important biomarkers for therapy selection in breast cancer patients. Conventional measurement by immunohistochemistry (IHC) involves errors, and numerous attempts have been made to increase precision by additional information from gene expression. This raises the question of how to fuse information, in particular, if there is disagreement. It is the primary domain of Dempster–Shafer decision theory (DST) to deal with contradicting evidence on the same item (here: receptor status), obtained through different techniques. DST is widely used in technical settings, such as self-driving cars and aviation, and is also promising to deliver significant advantages in medicine. Using data from breast cancer patients already presented in previous work, we focus on comparing DST with classical statistics in this work, to pave the way for its application in medicine. First, we explain how DST not only considers probabilities (a single number per sample), but also incorporates uncertainty in a concept of ‘evidence’ (two numbers per sample). This allows for very powerful displays of patient data in so-called ternary plots, a novel and crucial advantage for medical interpretation. Results are obtained according to conventional statistics (ODDS) and, in parallel, according to DST. Agreement and differences are evaluated, and the particular merits of DST discussed. The presented application demonstrates how decision theory introduces new levels of confidence in diagnoses derived from medical data.
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37
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Nalio Ramos R, Missolo-Koussou Y, Gerber-Ferder Y, Bromley CP, Bugatti M, Núñez NG, Tosello Boari J, Richer W, Menger L, Denizeau J, Sedlik C, Caudana P, Kotsias F, Niborski LL, Viel S, Bohec M, Lameiras S, Baulande S, Lesage L, Nicolas A, Meseure D, Vincent-Salomon A, Reyal F, Dutertre CA, Ginhoux F, Vimeux L, Donnadieu E, Buttard B, Galon J, Zelenay S, Vermi W, Guermonprez P, Piaggio E, Helft J. Tissue-resident FOLR2 + macrophages associate with CD8 + T cell infiltration in human breast cancer. Cell 2022; 185:1189-1207.e25. [PMID: 35325594 DOI: 10.1016/j.cell.2022.02.021] [Citation(s) in RCA: 153] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 10/08/2021] [Accepted: 02/15/2022] [Indexed: 12/12/2022]
Abstract
Macrophage infiltration is a hallmark of solid cancers, and overall macrophage infiltration correlates with lower patient survival and resistance to therapy. Tumor-associated macrophages, however, are phenotypically and functionally heterogeneous. Specific subsets of tumor-associated macrophage might be endowed with distinct roles on cancer progression and antitumor immunity. Here, we identify a discrete population of FOLR2+ tissue-resident macrophages in healthy mammary gland and breast cancer primary tumors. FOLR2+ macrophages localize in perivascular areas in the tumor stroma, where they interact with CD8+ T cells. FOLR2+ macrophages efficiently prime effector CD8+ T cells ex vivo. The density of FOLR2+ macrophages in tumors positively correlates with better patient survival. This study highlights specific roles for tumor-associated macrophage subsets and paves the way for subset-targeted therapeutic interventions in macrophages-based cancer therapies.
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Affiliation(s)
- Rodrigo Nalio Ramos
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Yoann Missolo-Koussou
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Yohan Gerber-Ferder
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Christian P Bromley
- Cancer Inflammation and Immunity Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Manchester, UK
| | - Mattia Bugatti
- Department of Pathology, University of Brescia, Brescia 25123, Italy
| | - Nicolas Gonzalo Núñez
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Jimena Tosello Boari
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Wilfrid Richer
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Laurie Menger
- PSL University, Institut Curie Research Center, INSERM U932, 75005 Paris, France
| | - Jordan Denizeau
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Christine Sedlik
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Pamela Caudana
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Fiorella Kotsias
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Leticia L Niborski
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Sophie Viel
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Mylène Bohec
- PSL University, Institut Curie Research Center, Institut Curie Genomics of Excellence Platform, 75005 Paris, France
| | - Sonia Lameiras
- PSL University, Institut Curie Research Center, Institut Curie Genomics of Excellence Platform, 75005 Paris, France
| | - Sylvain Baulande
- PSL University, Institut Curie Research Center, Institut Curie Genomics of Excellence Platform, 75005 Paris, France
| | - Laëtitia Lesage
- PSL University, Institut Curie Hospital, Department of Pathology, 75005 Paris, France
| | - André Nicolas
- PSL University, Institut Curie Hospital, Department of Pathology, 75005 Paris, France
| | - Didier Meseure
- PSL University, Institut Curie Hospital, Department of Pathology, 75005 Paris, France
| | - Anne Vincent-Salomon
- PSL University, Institut Curie Hospital, Department of Pathology, 75005 Paris, France
| | - Fabien Reyal
- PSL University, Institut Curie Hospital, Department of Surgery, 75005 Paris, France
| | | | - Florent Ginhoux
- Université Paris-Saclay, Institut Gustave Roussy, INSERM U1015, Villejuif, France; Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Lene Vimeux
- University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, 75014 Paris, France
| | - Emmanuel Donnadieu
- University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, 75014 Paris, France
| | - Bénédicte Buttard
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers, Laboratory of Integrative Cancer Immunology, Paris, France
| | - Jérôme Galon
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers, Laboratory of Integrative Cancer Immunology, Paris, France
| | - Santiago Zelenay
- Cancer Inflammation and Immunity Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Manchester, UK
| | - William Vermi
- PSL University, Institut Curie Research Center, INSERM U932, 75005 Paris, France; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Pierre Guermonprez
- Université de Paris, Centre for Inflammation Research, CNRS ERL8252, INSERM1149, Paris, France
| | - Eliane Piaggio
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France
| | - Julie Helft
- PSL University, Institut Curie Research Center, INSERM U932 & SiRIC, Translational Immunotherapy Team, 75005 Paris, France.
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Prognostic Impact of High Baseline Stromal Tumor-Infiltrating Lymphocytes in the Absence of Pathologic Complete Response in Early-Stage Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:cancers14051323. [PMID: 35267631 PMCID: PMC8909018 DOI: 10.3390/cancers14051323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary High stromal tumor-infiltrating lymphocytes (sTILs) are associated with an improved pathologic complete response (pCR) and survival in triple-negative breast cancer (TNBC). We hypothesized that high baseline sTILs would have a favorable prognostic impact in TNBC patients without a pCR. In this study of 318 early-stage TNBC patients in a prospective clinical trial, event-free survival (EFS) in patients without a pCR was not significantly different between those with high sTILs and those with low sTILs (p = 0.7). Therefore, high baseline sTILs do not confer a benefit in EFS in the absence of a pCR. RNA-seq analysis predicted more CD8+ T cells in the high-sTIL group with favorable EFS compared with the high-sTIL group with unfavorable EFS, suggesting the type of lymphocytes within the TIL fraction may be an important parameter to consider for de-escalation strategies. The implications of our findings in the setting of immune checkpoint inhibitor therapy remain to be investigated. Abstract High stromal tumor-infiltrating lymphocytes (sTILs) are associated with an improved pathologic complete response (pCR) and survival in triple-negative breast cancer (TNBC). We hypothesized that high baseline sTILs would have a favorable prognostic impact in TNBC patients without a pCR after neoadjuvant chemotherapy (NACT). In this prospective NACT study, pretreatment biopsies from 318 patients with early-stage TNBC were evaluated for sTILs. Recursive partitioning analysis (RPA) was applied to search for the sTIL cutoff best associated with a pCR. With ≥20% sTILs identified as the optimal cutoff, 33% patients had high sTILs (pCR rate 64%) and 67% had low sTILs (pCR rate 29%). Patients were stratified according to the sTIL cutoff (low vs. high) and response to NACT (pCR vs. residual disease (RD)). The primary endpoint was event-free survival (EFS), with hazard ratios calculated using the Cox proportional hazards regression model and the 3-year restricted mean survival time (RMST) as primary measures. Within the high-sTIL group, EFS was better in patients with a pCR compared with those with RD (HR 0.05; 95% CI 0.01–0.39; p = 0.004). The difference in the 3-year RMST for EFS between the two groups was 5.6 months (95% CI 2.3–8.8; p = 0.001). However, among patients with RD, EFS was not significantly different between those with high sTILs and those with low sTILs (p = 0.7). RNA-seq analysis predicted more CD8+ T cells in the high-sTIL group with favorable EFS compared with the high-sTIL group with unfavorable EFS. This study did not demonstrate that high baseline sTILs confer a benefit in EFS in the absence of a pCR.
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Williams SD, Sakwe AM. Reduced Expression of Annexin A6 Induces Metabolic Reprogramming That Favors Rapid Fatty Acid Oxidation in Triple-Negative Breast Cancer Cells. Cancers (Basel) 2022; 14:1108. [PMID: 35267416 PMCID: PMC8909273 DOI: 10.3390/cancers14051108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/17/2022] [Accepted: 02/20/2022] [Indexed: 12/01/2022] Open
Abstract
The ability of cancer cells to alter their metabolism is one of the major mechanisms underlying rapid tumor progression and/or therapeutic resistance in solid tumors, including the hard-to-treat triple-negative breast cancer (TNBC) subtype. Here, we assessed the contribution of the tumor suppressor, Annexin A6 (AnxA6), in the metabolic adaptation of basal-like (AnxA6-low) versus mesenchymal-like (AnxA6-high), as well as in lapatinib-resistant TNBC cells. Using model basal-like and mesenchymal-like TNBC cell lines, we show that TNBC cells also exhibit metabolic heterogeneity. The downregulation of AnxA6 in TNBC cells generally attenuated mitochondrial respiration, glycolytic flux, and cellular ATP production capacity resulting in a quiescent metabolic phenotype. We also show that AnxA6 depletion in mesenchymal-like TNBC cells was associated with a rapid uptake and mitochondrial fatty acid oxidation and diminished lipid droplet accumulation and altered the lipogenic metabolic phenotype of these cells to a lypolytic metabolic phenotype. The overexpression or chronic lapatinib-induced upregulation of AnxA6 in AnxA6-low TNBC cells reversed the quiescent/lypolytic phenotype to a more lipogenic/glycolytic phenotype with gluconeogenic precursors as additional metabolites. Collectively, these data suggest that the expression status of AnxA6 in TNBC cells underlies distinct metabolic adaptations of basal-like and mesenchymal-like TNBC subsets in response to cellular stress and/or therapeutic intervention and suggest AnxA6 as a biomarker for metabolic subtyping of TNBC subsets.
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Affiliation(s)
| | - Amos M. Sakwe
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN 37208, USA;
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40
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Yoo TK, Kang J, Lee A, Chae BJ. A triple-negative breast cancer surrogate subtype classification that correlates with gene expression subtypes. Breast Cancer Res Treat 2022; 191:599-610. [PMID: 35018542 DOI: 10.1007/s10549-021-06437-8] [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: 08/18/2021] [Accepted: 10/25/2021] [Indexed: 11/02/2022]
Abstract
BACKGROUND This study developed a triple-negative breast cancer (TNBC) surrogate subtype classification that represents TNBC subtypes based on the Vanderbilt subtype classification. METHODS Patients who underwent primary curative surgery for TNBC were included. Representative FFPE blocks were used for gene expression analysis and tissue microarray construction for immunohistochemical (IHC) staining. The Vanderbilt subtypes were re-classified into four groups: basal-like (BL), mesenchymal-like (M), immunomodulatory (IM) and luminal androgen receptor (LAR) subtype. Classification and regression tree (CART) modeling was applied to develop a surrogate subtype classification. RESULTS A total of 145 patients were included. The study cohort was allocated to the Vanderbilt 4 subtypes as LAR (n = 22, 15.2%), IM (n = 32, 22.1%), M (n = 38, 26.2%), BL (n = 25, 17.2%) and unclassified (n = 28, 19.3%). After excluding nine (6.2%) patients due to poor IHC staining quality, CART modeling was performed. TNBC surrogate subtypes were defined as follows: LAR subtype, androgen receptor Allred score 8; IM subtype, LAR-negative with a tumor-infiltrating lymphocyte (TIL) score > 70%; M subtype, LAR-negative with a TIL score < 20%; BL subtype, LAR-negative with a TIL score 20-70% and diffuse, strong p16 staining. The study cohort was classified by the surrogate subtypes as LAR (n = 26, 17.9%), IM (n = 21, 14.5%), M (n = 44, 30.3%), BL1 (n = 27, 18.6%) and unclassified (n = 18, 12.4%). Surrogate subtypes predicted TNBC Vanderbilt 4 subtypes with an accuracy of 0.708. CONCLUSION We have developed a TNBC surrogate subtype classification that correlates with the Vanderbilt subtype. It is a practical and accessible diagnostic test that can be easily applied in clinical practice.
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Affiliation(s)
- Tae-Kyung Yoo
- Department of Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-Daero, Seocho-Gu, Seoul, 06591, Republic of Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpo-Daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Jun Kang
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-Daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Awon Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-Daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Byung Joo Chae
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Republic of Korea.
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YB1 Is a Major Contributor to Health Disparities in Triple Negative Breast Cancer. Cancers (Basel) 2021; 13:cancers13246262. [PMID: 34944882 PMCID: PMC8699660 DOI: 10.3390/cancers13246262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Triple negative breast cancer (TNBC) is a devastating disease that affects many women, due to the lack of FDA-approved targeted therapy. In the absence of cell surface receptors ER, PR, and Her2 that can be targeted with hormonal and antibody treatments, cytotoxic chemotherapy remains the major course of treatment, with a dismal response and rapid recurrence due to the acquisition of resistance. TNBC is also twice as more prevalent in African American (AA) when compared to Caucasian American (CA) women. This study investigated the role of the YB1 gene in the disparities in TNBC between AA and CA women. We found that YB1 is highly expressed in TNBC tumors of AA origin when compared to CAs. Increased expression levels and activity of YB1 correlates with poor disease outcomes, resistance to chemotherapy, and the activation of the cancer stem cell (CSC) phenotype, with higher levels in AA than in CA TNBC tumors. More importantly, we found that the targeted inhibition of the expression and activity of YB1 significantly inhibited the oncogenic behavior of AA tumors through sensitization to chemotherapy and inhibition of CSCs. Our study is the first to show that YB1 activity may be a major biological contributor to the health disparities in TNBC, and that development of therapies that specifically target YB1 could reduce these disparities. Abstract Triple negative breast cancer (TNBC) is the most aggressive amongst all breast cancer (BC) subtypes. While TNBC tumors represent less than 20% of all BC subtypes, they are responsible for the most BC-related deaths. More significantly, when considering TNBC incidence across all racial/ethnic groups, TNBC accounts for less than 20% of all BCs. However, in non-Hispanic black women, the incidence rate of TNBC is more than 40%, which may be a contributing factor to the higher BC-related death rate in this population. These disparities remain strong even after accounting for differences in socioeconomic status, healthcare access, and lifestyle factors. Increased evidence now points to biological mechanisms that are intrinsic to the tumor that contribute to disparate TNBC disease burdens. Here, we show that YB1, a multifunction gene, plays a major role in the TNBC disparities between African American (AA) and Caucasian American (CA) women. We show in three independent TNBC tumors cohorts, that YB1 is significantly highly expressed in AA TNBC tumors when compared to CAs, and that increased levels of YB1 correlate with poor survival of AA patients with TNBC. We used a combination of genetic manipulation of YB1 and chemotherapy treatment, both in vitro and in animal models of TNBC to show that YB1 oncogenic activity is more enhanced in TNBC cell lines of AA origin, by increasing their tumorigenic and aggressive behaviors, trough the activation of cancer stem cell phenotype and resistance to chemotherapeutic treatments.
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Moore J, Ma L, Lazar AA, Barcellos-Hoff MH. Mammary tumor-derived transplants as breast cancer models to evaluate tumor-immune interactions and therapeutic responses. Cancer Res 2021; 82:365-376. [PMID: 34903599 DOI: 10.1158/0008-5472.can-21-0253] [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: 01/22/2021] [Revised: 06/25/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022]
Abstract
In breast cancer, the type and distribution of infiltrating immune cells are associated with clinical outcome. Moreover, infiltrated cancers with abundant tumor infiltrating lymphocytes (TIL) are more likely to respond to immunotherapy, while those in which CD8+ T cells are completely absent (deserts) or excluded are less likely to respond. Detailed understanding of this biology is limited by a lack of preclinical breast cancer models that recapitulate TIL distributions and their associated biology. Here we established mammary tumor-derived transplants (mTDT) from 12 Trp53 null mammary tumors in syngeneic BALB/cJ mice and examined the stability of their growth rate, TIL distribution, and transcriptomic profiles. All mTDT were estrogen receptor negative. Half of the parental tumors were classified as infiltrated, and the rest were divided between excluded and desert phenotypes. After two orthotopic passages, most (70%) mTDT from infiltrated parents recapitulated this pattern, whereas the desert or excluded parental patterns were maintained in about half of daughter mTDT. Approximately 30% of mTDT gave rise to lung or liver metastases, but metastasis was not associated with a TIL phenotype. Unsupervised transcriptomic analysis clustered mTDT according to their TIL spatial patterns. Infiltrated mTDT transplanted subcutaneously and orthotopically were resistant to anti-PD-L1. Profiling implicated prolonged antigen stimulation and loss of effector function of lymphocytes rather than T cell exhaustion in the lack of response of infiltrated mTDT to checkpoint blockade. In summary, the molecular diversity and immune complexity of mTDT will facilitate the dissection of mechanisms of breast cancer response to immunotherapies.
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Affiliation(s)
- Jade Moore
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Lin Ma
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Ann A Lazar
- Department of Oral Epidemiology, School of Dentistry, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco School of Medicine, San Francisco, California
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.
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Immune Milieu and Genomic Alterations Set the Triple-Negative Breast Cancer Immunomodulatory Subtype Tumor Behavior. Cancers (Basel) 2021; 13:cancers13246256. [PMID: 34944876 PMCID: PMC8699570 DOI: 10.3390/cancers13246256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Triple-negative breast cancer (TNBC) is an aggressive and highly heterogeneous breast cancer subtype, both molecular and transcriptomic. Gene expression patterns identified seven TNBC subtypes; basal-like 1 (BL1), basal-like 2 (BL2), immunomodulatory (IM), mesenchymal (M), mesenchymal stem-like (MSL), luminal androgen receptor (LAR), and unstable (UNS). Herein, we contrasted the IM subtype with non-IM TNBC, including clinical, histopathological, and molecular variables. Our results showed that the IM subtype featured an increased FOXP3+ TILs infiltration and a higher CTLA-4 and PD-L1 expression compared with non-IM tumors. Long intergenic non-coding RNAs associated with the immune response through transcriptomic and enrichment analyses characterized the IM-subtype enriched by the β-catenin signaling pathway. Additionally, DNA sequencing identified differences in mutation rates as well as some specific mutations. These results should motivate the design of future clinical trials in which the benefit of immune-based therapy in this subgroup of patients could be evaluated. Abstract Triple-negative breast cancer (TNBC) is an aggressive and heterogeneous disease. Seven subtypes have been described based on gene expression patterns. Herein, we characterized the tumor biology and clinical behavior of the immunomodulatory (IM) subtype. Methods: Formalin-fixed paraffin-embedded tumor samples from 68 high-risk (stage III-IV) TNBC patients were analyzed through microarrays, immunohistochemistry, and DNA sequencing. Results: The IM subtype was identified in 24% of TNBC tumor samples and characterized by a higher intratumoral (intT) and stromal (strml) infiltration of FOXP3+ TILs (Treg) compared with non-IM subtypes. Further, PD-L1+ (>1%) expression was significantly higher, as well as CTLA-4+ intT and strml expression in the IM subtype. Differential expression and gene set enrichment analysis identified biological processes associated with the immune system. Pathway analysis revealed enrichment of the β-catenin signaling pathway. The non-coding analysis led to seven Long Intergenic Non-Protein Coding RNAs (lincRNAs) (6 up-regulated and 1 down-regulated) that were associated with a favorable prognosis in the TNBC-IM subtype. The DNA sequencing highlighted two genes relevant to immune system responses: CTNNB1 (Catenin β-1) and IDH1. Conclusion: the IM subtype showed a distinct immune microenvironment, as well as subtype-specific genomic alterations. Characterizing TNBC at a molecular and transcriptomic level might guide immune-based therapy in this subgroup of patients.
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Hanamura T, Christenson JL, O'Neill KI, Rosas E, Spoelstra NS, Williams MM, Richer JK. Secreted indicators of androgen receptor activity in breast cancer pre-clinical models. Breast Cancer Res 2021; 23:102. [PMID: 34736512 PMCID: PMC8567567 DOI: 10.1186/s13058-021-01478-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/19/2021] [Indexed: 01/01/2023] Open
Abstract
PURPOSE Accumulating evidence has attracted attention to the androgen receptor (AR) as a biomarker and therapeutic target in breast cancer. We hypothesized that AR activity within the tumor has clinical implications and investigated whether androgen responsive serum factors might serve as a minimally invasive indicator of tumor AR activity. METHODS Based on a comprehensive gene expression analysis of an AR-positive, triple negative breast cancer patient-derived xenograft (PDX) model, 163 dihydrotestosterone (DHT)-responsive genes were defined as an androgen responsive gene set. Among them, we focused on genes that were DHT-responsive that encode secreted proteins, namely KLK3, AZGP1 and PIP, that encode the secreted factors prostate specific antigen (PSA), zinc-alpha-2-glycoprotein (ZAG) and prolactin induced protein (PIP), respectively. Using AR-positive breast cancer cell lines representing all breast cancer subtypes, expression of candidate factors was assessed in response to agonist DHT and antagonist enzalutamide. Gene set enrichment analysis (GSEA) was performed on publically available gene expression datasets from breast cancer patients to analyze the relationship between genes encoding the secreted factors and other androgen responsive gene sets in each breast cancer subtype. RESULTS Anti-androgen treatment decreased proliferation in all cell lines tested representing various tumor subtypes. Expression of the secreted factors was regulated by AR activation in the majority of breast cancer cell lines. In GSEA, the candidate genes were positively correlated with an androgen responsive gene set across breast cancer subtypes. CONCLUSION KLK3, AZGP1 and PIP are AR regulated and reflect tumor AR activity. Further investigations are needed to examine the potential efficacy of these factors as serum biomarkers.
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Affiliation(s)
- Toru Hanamura
- Department of Pathology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Jessica L Christenson
- Department of Pathology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Kathleen I O'Neill
- Department of Pathology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Emmanuel Rosas
- Department of Pathology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Nicole S Spoelstra
- Department of Pathology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Michelle M Williams
- Department of Pathology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave., Aurora, CO, 80045, USA
| | - Jennifer K Richer
- Department of Pathology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave., Aurora, CO, 80045, USA.
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Napieralski R, Schricker G, Auer G, Aubele M, Perkins J, Magdolen V, Ulm K, Hamann M, Walch A, Weichert W, Kiechle M, Wilhelm OG. PITX2 DNA-Methylation: Predictive versus Prognostic Value for Anthracycline-Based Chemotherapy in Triple-Negative Breast Cancer Patients. Breast Care (Basel) 2021; 16:523-531. [PMID: 34720812 DOI: 10.1159/000510468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/24/2020] [Indexed: 12/31/2022] Open
Abstract
Background PITX2 DNA methylation has been shown to predict outcomes in high-risk breast cancer patients after anthracycline-based chemotherapy. To determine its prognostic versus predictive value, the impact of PITX2 DNA methylation on outcomes was studied in an untreated cohort vs. an anthracycline-treated triple-negative breast cancer (TNBC) cohort. Material and Methods The percent DNA methylation ratio (PMR) of paired-like homeodomain transcription factor 2 (PITX2) was determined by a validated methylation-specific real-time PCR test. Patient samples of routinely collected archived formalin-fixed paraffin-embedded (FFPE) tissue and clinical data from 144 TNBC patients of 2 independent cohorts (i.e., 66 untreated patients and 78 patients treated with anthracycline-based chemotherapy) were analyzed. Results The risk of 5- and 10-year overall survival (OS) increased continuously with rising PITX2 DNA methylation in the anthracycline-treated population, but it increased only slightly during 10-year follow-up time in the untreated patient population. PITX2 DNA methylation with a PMR cutoff of 2 did not show significance for poor vs. good outcomes (OS) in the untreated patient cohort (HR = 1.55; p = 0.259). In contrast, the PITX2 PMR cutoff of 2 identified patients with poor (PMR >2) vs. good (PMR ≤2) outcomes (OS) with statistical significance in the anthracycline-treated cohort (HR = 3.96; p = 0.011). The results in the subgroup of patients who did receive anthracyclines only (no taxanes) confirmed this finding (HR = 5.71; p = 0.014). Conclusion In this hypothesis-generating study PITX2 DNA methylation demonstrated predominantly predictive value in anthracycline treatment in TNBC patients. The risk of poor outcome (OS) correlates with increasing PITX2 DNA methylation.
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Affiliation(s)
| | | | - Gert Auer
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | | | | | - Viktor Magdolen
- Department of Gynecology and Obstetrics and Comprehensive Cancer Center (CCCTUM), Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Kurt Ulm
- Institute of Medical Informatics, Statistics and Epidemiology, Technische Universität München, Munich, Germany
| | - Moritz Hamann
- Department of Gynecology Rotkreuzklinikum München, Munich, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Munich, Germany
| | - Wilko Weichert
- Institute of Pathology, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Marion Kiechle
- Department of Gynecology and Obstetrics and Comprehensive Cancer Center (CCCTUM), Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
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Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes. Nat Commun 2021; 12:6276. [PMID: 34725325 PMCID: PMC8560912 DOI: 10.1038/s41467-021-26502-6] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/08/2021] [Indexed: 12/11/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a collection of biologically diverse cancers characterized by distinct transcriptional patterns, biology, and immune composition. TNBCs subtypes include two basal-like (BL1, BL2), a mesenchymal (M) and a luminal androgen receptor (LAR) subtype. Through a comprehensive analysis of mutation, copy number, transcriptomic, epigenetic, proteomic, and phospho-proteomic patterns we describe the genomic landscape of TNBC subtypes. Mesenchymal subtype tumors display high mutation loads, genomic instability, absence of immune cells, low PD-L1 expression, decreased global DNA methylation, and transcriptional repression of antigen presentation genes. We demonstrate that major histocompatibility complex I (MHC-I) is transcriptionally suppressed by H3K27me3 modifications by the polycomb repressor complex 2 (PRC2). Pharmacological inhibition of PRC2 subunits EZH2 or EED restores MHC-I expression and enhances chemotherapy efficacy in murine tumor models, providing a rationale for using PRC2 inhibitors in PD-L1 negative mesenchymal tumors. Subtype-specific differences in immune cell composition and differential genetic/pharmacological vulnerabilities suggest additional treatment strategies for TNBC. Triple negative breast cancer can be divided into additional subtypes. Here, using omics analyses, the authors show that in the mesenchymal subtype expression of MHC-1 is repressed and that this can be restored by using drugs that target subunits of the epigenetic modifier PRC2.
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Breast Cancer Consensus Subtypes: A system for subtyping breast cancer tumors based on gene expression. NPJ Breast Cancer 2021; 7:136. [PMID: 34642313 PMCID: PMC8511026 DOI: 10.1038/s41523-021-00345-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 09/21/2021] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is heterogeneous in prognoses and drug responses. To organize breast cancers by gene expression independent of statistical methodology, we identified the Breast Cancer Consensus Subtypes (BCCS) as the consensus groupings of six different subtyping methods. Our classification software identified seven BCCS subtypes in a study cohort of publicly available data (n = 5950) including METABRIC, TCGA-BRCA, and data assayed by Affymetrix arrays. All samples were fresh-frozen from primary tumors. The estrogen receptor-positive (ER+) BCCS subtypes were: PCS1 (18%) good prognosis, stromal infiltration; PCS2 (15%) poor prognosis, highly proliferative; PCS3 (13%) poor prognosis, highly proliferative, activated IFN-gamma signaling, cytotoxic lymphocyte infiltration, high tumor mutation burden; PCS4 (18%) good prognosis, hormone response genes highly expressed. The ER− BCCS subtypes were: NCS1 (11%) basal; NCS2 (10%) elevated androgen response; NCS3 (5%) cytotoxic lymphocyte infiltration; unclassified tumors (9%). HER2+ tumors were heterogeneous with respect to BCCS.
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Recurrence biomarkers of triple negative breast cancer treated with neoadjuvant chemotherapy and anti-EGFR antibodies. NPJ Breast Cancer 2021; 7:124. [PMID: 34535679 PMCID: PMC8448841 DOI: 10.1038/s41523-021-00334-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
To find metastatic recurrence biomarkers of triple-negative breast cancer (TNBC) treated by neoadjuvant chemotherapy and anti-EGFR antibodies (NAT), we evaluated tumor genomic, transcriptomic, and immune features, using MSK-IMPACT assay, gene arrays, Nanostring technology, and TIL assessment on H&E. Six patients experienced a rapid fatal recurrence (RR) and other 6 had later non-fatal recurrences (LR). Before NAT, RR had low expression of 6 MHC class I and 13 MHC class II genes but were enriched in upregulated genes involved in the cell cycle-related pathways. Their TIL number before NAT in RR was very low (<5%) and did not increase after treatment. In post-NAT residual tumors, RR cases showed high expression of SOX2 and CXCR4. Our results indicate that high expression of cell cycle genes, combined with cold immunological phenotype, may predict strong TNBC resistance to NAT and rapid progression after it. This biomarker combination is worth validation in larger studies.
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Balkrishna A, Mittal R, Arya V. Unveiling Novel Therapeutic Drug Targets and Prognostic Markers of Triple Negative Breast Cancer. Curr Cancer Drug Targets 2021; 21:907-918. [PMID: 34503412 DOI: 10.2174/1568009621666210908113010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 11/22/2022]
Abstract
Triple negative breast cancer represents multiple genomic and transcriptomic heterogeneities. Genetic and epigenetic changes emerging in TNBC help it in acquiring resistance against immunological response. Distant metastasis, lack of clinically targeted therapies and prognostic markers make it the most aggressive form of breast cancer. In this review, we showed that driver alterations in targeted genes AR, ERR, TIL, TAM, miRNA, mTOR and immunosuppressive cytokines are predominantly involved in complicating TNBC by inducing cell proliferation, invasion and metastasis, and by inhibiting apoptosis. The role of node status, cathepsin-D, Ki-67 index, CD3+TIL, BRCA1 promoter methylation value and p53 as an efficient prognostic factor have also been studied to predict the disease free and overall survival rate in TNBC patients. The present review article is an attempt to gain an insight with a new vision on the etiology of TNBC, its treatment strategies and prognostic marker to identify the outcome of standard therapies and to re-design future treatment strategies to provide maximum benefit to patients.
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Affiliation(s)
- Acharya Balkrishna
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar. India
| | - Rashmi Mittal
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar. India
| | - Vedpriya Arya
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar. India
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Hossain F, Majumder S, David J, Miele L. Precision Medicine and Triple-Negative Breast Cancer: Current Landscape and Future Directions. Cancers (Basel) 2021; 13:cancers13153739. [PMID: 34359640 PMCID: PMC8345034 DOI: 10.3390/cancers13153739] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/10/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The implementation of precision medicine will revolutionize cancer treatment paradigms. Notably, this goal is not far from reality: genetically similar cancers can be treated similarly. The heterogeneous nature of triple-negative breast cancer (TNBC) made it a suitable candidate to practice precision medicine. Using TNBC molecular subtyping and genomic profiling, a precision medicine-based clinical trial is ongoing. This review summarizes the current landscape and future directions of precision medicine and TNBC. Abstract Triple-negative breast cancer (TNBC) is an aggressive and heterogeneous subtype of breast cancer associated with a high recurrence and metastasis rate that affects African-American women disproportionately. The recent approval of targeted therapies for small subgroups of TNBC patients by the US ‘Food and Drug Administration’ is a promising development. The advancement of next-generation sequencing, particularly somatic exome panels, has raised hopes for more individualized treatment plans. However, the use of precision medicine for TNBC is a work in progress. This review will discuss the potential benefits and challenges of precision medicine for TNBC. A recent clinical trial designed to target TNBC patients based on their subtype-specific classification shows promise. Yet, tumor heterogeneity and sub-clonal evolution in primary and metastatic TNBC remain a challenge for oncologists to design adaptive precision medicine-based treatment plans.
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Affiliation(s)
- Fokhrul Hossain
- Department of Genetics, Louisiana State University Health Sciences Center (LSUHSC), New Orleans, LA 70112, USA; (S.M.); (L.M.)
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center (LSUHSC), New Orleans, LA 70112, USA
- Correspondence:
| | - Samarpan Majumder
- Department of Genetics, Louisiana State University Health Sciences Center (LSUHSC), New Orleans, LA 70112, USA; (S.M.); (L.M.)
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center (LSUHSC), New Orleans, LA 70112, USA
| | - Justin David
- School of Medicine, Louisiana State University Health Sciences Center (LSUHSC), New Orleans, LA 70112, USA;
| | - Lucio Miele
- Department of Genetics, Louisiana State University Health Sciences Center (LSUHSC), New Orleans, LA 70112, USA; (S.M.); (L.M.)
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center (LSUHSC), New Orleans, LA 70112, USA
- School of Medicine, Louisiana State University Health Sciences Center (LSUHSC), New Orleans, LA 70112, USA;
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