1
|
Glaviano A, Wander SA, Baird RD, Yap KCH, Lam HY, Toi M, Carbone D, Geoerger B, Serra V, Jones RH, Ngeow J, Toska E, Stebbing J, Crasta K, Finn RS, Diana P, Vuina K, de Bruin RAM, Surana U, Bardia A, Kumar AP. Mechanisms of sensitivity and resistance to CDK4/CDK6 inhibitors in hormone receptor-positive breast cancer treatment. Drug Resist Updat 2024; 76:101103. [PMID: 38943828 DOI: 10.1016/j.drup.2024.101103] [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: 02/28/2024] [Revised: 05/17/2024] [Accepted: 06/10/2024] [Indexed: 07/01/2024]
Abstract
Cell cycle dysregulation is a hallmark of cancer that promotes eccessive cell division. Cyclin-dependent kinase 4 (CDK4) and cyclin-dependent kinase 6 (CDK6) are key molecules in the G1-to-S phase cell cycle transition and are crucial for the onset, survival, and progression of breast cancer (BC). Small-molecule CDK4/CDK6 inhibitors (CDK4/6i) block phosphorylation of tumor suppressor Rb and thus restrain susceptible BC cells in G1 phase. Three CDK4/6i are approved for the first-line treatment of patients with advanced/metastatic hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2-) BC in combination with endocrine therapy (ET). Though this has improved the clinical outcomes for survival of BC patients, there is no established standard next-line treatment to tackle drug resistance. Recent studies suggest that CDK4/6i can modulate other distinct effects in both BC and breast stromal compartments, which may provide new insights into aspects of their clinical activity. This review describes the biochemistry of the CDK4/6-Rb-E2F pathway in HR+ BC, then discusses how CDK4/6i can trigger other effects in BC/breast stromal compartments, and finally outlines the mechanisms of CDK4/6i resistance that have emerged in recent preclinical studies and clinical cohorts, emphasizing the impact of these findings on novel therapeutic opportunities in BC.
Collapse
Affiliation(s)
- Antonino Glaviano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo 90123, Italy
| | - Seth A Wander
- Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Richard D Baird
- Cancer Research UK Cambridge Centre, Hills Road, Cambridge CB2 0QQ, UK
| | - Kenneth C-H Yap
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Hiu Yan Lam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Masakazu Toi
- School of Medicine, Kyoto University, Kyoto, Japan
| | - Daniela Carbone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo 90123, Italy
| | - Birgit Geoerger
- Gustave Roussy Cancer Center, Department of Pediatric and Adolescent Oncology, Inserm U1015, Université Paris-Saclay, Villejuif, France
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Robert H Jones
- Cardiff University and Velindre Cancer Centre, Museum Avenue, Cardiff CF10 3AX, UK
| | - Joanne Ngeow
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Experimental Medicine Building, 636921, Singapore; Cancer Genetics Service (CGS), National Cancer Centre Singapore, 168583, Singapore
| | - Eneda Toska
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Justin Stebbing
- School of Life Sciences, Anglia Ruskin University, Cambridge, UK; Division of Cancer, Imperial College London, Hammersmith Campus, London, UK
| | - Karen Crasta
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117593, Singapore; Healthy Longetivity Translational Program, Yong Loo Lin School of Medicine, National University of Singapore, 117456, Singapore
| | - Richard S Finn
- Department of Oncology, Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Patrizia Diana
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo 90123, Italy
| | - Karla Vuina
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Robertus A M de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Uttam Surana
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; SiNOPSEE Therapeutics Pte Ltd, A⁎STARTCentral, 139955, Singapore
| | - Aditya Bardia
- Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.
| |
Collapse
|
2
|
Liu J, Ma J, Wen J, Zhou X. A Cell Cycle-Aware Network for Data Integration and Label Transferring of Single-Cell RNA-Seq and ATAC-Seq. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401815. [PMID: 38887194 DOI: 10.1002/advs.202401815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/22/2024] [Indexed: 06/20/2024]
Abstract
In recent years, the integration of single-cell multi-omics data has provided a more comprehensive understanding of cell functions and internal regulatory mechanisms from a non-single omics perspective, but it still suffers many challenges, such as omics-variance, sparsity, cell heterogeneity, and confounding factors. As it is known, the cell cycle is regarded as a confounder when analyzing other factors in single-cell RNA-seq data, but it is not clear how it will work on the integrated single-cell multi-omics data. Here, a cell cycle-aware network (CCAN) is developed to remove cell cycle effects from the integrated single-cell multi-omics data while keeping the cell type-specific variations. This is the first computational model to study the cell-cycle effects in the integration of single-cell multi-omics data. Validations on several benchmark datasets show the outstanding performance of CCAN in a variety of downstream analyses and applications, including removing cell cycle effects and batch effects of scRNA-seq datasets from different protocols, integrating paired and unpaired scRNA-seq and scATAC-seq data, accurately transferring cell type labels from scRNA-seq to scATAC-seq data, and characterizing the differentiation process from hematopoietic stem cells to different lineages in the integration of differentiation data.
Collapse
Affiliation(s)
- Jiajia Liu
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jian Ma
- Department of Electronic Information and Computer Engineering, The Engineering & Technical College of Chengdu University of Technology, Leshan, Sichuan, 614000, China
| | - Jianguo Wen
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| |
Collapse
|
3
|
Using single-cell transcriptomics to predict which tumors will respond to targeted therapy. NATURE CANCER 2024; 5:825-826. [PMID: 38684925 DOI: 10.1038/s43018-024-00757-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
|
4
|
Sinha S, Vegesna R, Mukherjee S, Kammula AV, Dhruba SR, Wu W, Kerr DL, Nair NU, Jones MG, Yosef N, Stroganov OV, Grishagin I, Aldape KD, Blakely CM, Jiang P, Thomas CJ, Benes CH, Bivona TG, Schäffer AA, Ruppin E. PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors. NATURE CANCER 2024; 5:938-952. [PMID: 38637658 DOI: 10.1038/s43018-024-00756-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/08/2024] [Indexed: 04/20/2024]
Abstract
Tailoring optimal treatment for individual cancer patients remains a significant challenge. To address this issue, we developed PERCEPTION (PERsonalized Single-Cell Expression-Based Planning for Treatments In ONcology), a precision oncology computational pipeline. Our approach uses publicly available matched bulk and single-cell (sc) expression profiles from large-scale cell-line drug screens. These profiles help build treatment response models based on patients' sc-tumor transcriptomics. PERCEPTION demonstrates success in predicting responses to targeted therapies in cultured and patient-tumor-derived primary cells, as well as in two clinical trials for multiple myeloma and breast cancer. It also captures the resistance development in patients with lung cancer treated with tyrosine kinase inhibitors. PERCEPTION outperforms published state-of-the-art sc-based and bulk-based predictors in all clinical cohorts. PERCEPTION is accessible at https://github.com/ruppinlab/PERCEPTION . Our work, showcasing patient stratification using sc-expression profiles of their tumors, will encourage the adoption of sc-omics profiling in clinical settings, enhancing precision oncology tools based on sc-omics.
Collapse
Affiliation(s)
- Sanju Sinha
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA.
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
| | - Rahulsimham Vegesna
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Sumit Mukherjee
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Ashwin V Kammula
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
- University of Maryland, College Park, MD, USA
| | | | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nishanth Ulhas Nair
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Matthew G Jones
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute, Cambridge, MA, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | | | - Ivan Grishagin
- Rancho BioSciences, San Diego, CA, USA
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Peng Jiang
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cyril H Benes
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub Investigator, San Francisco, CA, USA
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA.
| |
Collapse
|
5
|
Swarbrick A, Fernandez-Martinez A, Perou CM. Gene-Expression Profiling to Decipher Breast Cancer Inter- and Intratumor Heterogeneity. Cold Spring Harb Perspect Med 2024; 14:a041320. [PMID: 37137498 PMCID: PMC10759991 DOI: 10.1101/cshperspect.a041320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Breast cancer is heterogeneous and differs substantially across different tumors (intertumor heterogeneity) and even within an individual tumor (intratumor heterogeneity). Gene-expression profiling has considerably impacted our understanding of breast cancer biology. Four main "intrinsic subtypes" of breast cancer (i.e., luminal A, luminal B, HER2-enriched, and basal-like) have been consistently identified by gene expression, showing significant prognostic and predictive value in multiple clinical scenarios. Thanks to the molecular profiling of breast tumors, breast cancer is a paradigm of treatment personalization. Several standardized prognostic gene-expression assays are presently being used in the clinic to guide treatment decisions. Moreover, the development of single-cell-level resolution molecular profiling has allowed us to appreciate that breast cancer is also heterogeneous within a single tumor. There is an evident functional heterogeneity within the neoplastic and tumor microenvironment cells. Finally, emerging insights from these studies suggest a substantial cellular organization of neoplastic and tumor microenvironment cells, thus defining breast cancer ecosystems and highlighting the importance of spatial localizations.
Collapse
Affiliation(s)
- Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Aranzazu Fernandez-Martinez
- Lineberger Comprehensive Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| | - Charles M Perou
- Lineberger Comprehensive Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| |
Collapse
|
6
|
Tang C, Fu S, Jin X, Li W, Xing F, Duan B, Cheng X, Chen X, Wang S, Zhu C, Li G, Chuai G, He Y, Wang P, Liu Q. Personalized tumor combination therapy optimization using the single-cell transcriptome. Genome Med 2023; 15:105. [PMID: 38041202 PMCID: PMC10691165 DOI: 10.1186/s13073-023-01256-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND The precise characterization of individual tumors and immune microenvironments using transcriptome sequencing has provided a great opportunity for successful personalized cancer treatment. However, the cancer treatment response is often characterized by in vitro assays or bulk transcriptomes that neglect the heterogeneity of malignant tumors in vivo and the immune microenvironment, motivating the need to use single-cell transcriptomes for personalized cancer treatment. METHODS Here, we present comboSC, a computational proof-of-concept study to explore the feasibility of personalized cancer combination therapy optimization using single-cell transcriptomes. ComboSC provides a workable solution to stratify individual patient samples based on quantitative evaluation of their personalized immune microenvironment with single-cell RNA sequencing and maximize the translational potential of in vitro cellular response to unify the identification of synergistic drug/small molecule combinations or small molecules that can be paired with immune checkpoint inhibitors to boost immunotherapy from a large collection of small molecules and drugs, and finally prioritize them for personalized clinical use based on bipartition graph optimization. RESULTS We apply comboSC to publicly available 119 single-cell transcriptome data from a comprehensive set of 119 tumor samples from 15 cancer types and validate the predicted drug combination with literature evidence, mining clinical trial data, perturbation of patient-derived cell line data, and finally in-vivo samples. CONCLUSIONS Overall, comboSC provides a feasible and one-stop computational prototype and a proof-of-concept study to predict potential drug combinations for further experimental validation and clinical usage using the single-cell transcriptome, which will facilitate and accelerate personalized tumor treatment by reducing screening time from a large drug combination space and saving valuable treatment time for individual patients. A user-friendly web server of comboSC for both clinical and research users is available at www.combosc.top . The source code is also available on GitHub at https://github.com/bm2-lab/comboSC .
Collapse
Affiliation(s)
- Chen Tang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xuan Jin
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wannian Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Bin Duan
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xiaojie Cheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaohan Chen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shuguang Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chenyu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Gaoyang Li
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Guohui Chuai
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China.
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, Tongji University, Shanghai, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China.
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, Tongji University, Shanghai, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| |
Collapse
|
7
|
Antonarelli G, Taurelli Salimbeni B, Marra A, Esposito A, Locatelli MA, Trapani D, Pescia C, Fusco N, Curigliano G, Criscitiello C. The CDK4/6 inhibitors biomarker landscape: The most relevant biomarkers of response or resistance for further research and potential clinical utility. Crit Rev Oncol Hematol 2023; 192:104148. [PMID: 37783318 DOI: 10.1016/j.critrevonc.2023.104148] [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: 07/31/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/04/2023] Open
Abstract
Cyclin-Dependent Kinase 4/6 inhibitors (CDK4/6is) in combination with Endocrine Therapy (ET) represent the standard frontline therapy for patients with Hormone Receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative metastatic Breast Cancer (mBC). Clinical activity and efficacy of CDK4/6is-based therapies have been proven both in the endocrine sensitive and resistant settings. Therapy resistance eventually underpins clinical progression to any CDK4/6is-based therapies, yet there is a lack of validated molecular biomarkers predictive of either intrinsic or acquired resistance to CDK4/6is in clinical practice. As the "post-CDK4/6is" landscape for the management of HR-positive/HER2-negative mBC is rapidly evolving with the introduction of novel therapies, there is an urgent need for the definition of clinically relevant molecular biomarkers of intrinsic/acquired resistance mechanisms to CDK4/6is. This narrative review outlines the role of currently approved CDK4/6is-based therapies, describes the most relevant molecular biomarkers of CDK4/6is-resistance, and ultimately provides a perspective on the clinical and research scenario.
Collapse
Affiliation(s)
- Gabriele Antonarelli
- Department of Oncology and Haemato-Oncology (DIPO), University of Milan, Milan, Italy; Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
| | - Beatrice Taurelli Salimbeni
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
| | - Antonio Marra
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
| | - Angela Esposito
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
| | - Marzia Adelia Locatelli
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
| | - Dario Trapani
- Department of Oncology and Haemato-Oncology (DIPO), University of Milan, Milan, Italy; Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
| | - Carlo Pescia
- Division of Pathology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Nicola Fusco
- Department of Oncology and Haemato-Oncology (DIPO), University of Milan, Milan, Italy; Division of Pathology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Giuseppe Curigliano
- Department of Oncology and Haemato-Oncology (DIPO), University of Milan, Milan, Italy; Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy
| | - Carmen Criscitiello
- Department of Oncology and Haemato-Oncology (DIPO), University of Milan, Milan, Italy; Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy.
| |
Collapse
|
8
|
Liu P, Deng X, Zhou H, Xie J, Kong Y, Zou Y, Yang A, Li X. Multi-omics analyses unravel DNA damage repair-related clusters in breast cancer with experimental validation. Front Immunol 2023; 14:1297180. [PMID: 38022619 PMCID: PMC10644223 DOI: 10.3389/fimmu.2023.1297180] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Background As one of the most common malignancies worldwide, breast cancer (BC) exhibits high heterogeneity of molecular phenotypes. The evolving view regarding DNA damage repair (DDR) is that it is context-specific and heterogeneous, but its role in BC remains unclear. Methods Multi-dimensional data of transcriptomics, genomics, and single-cell transcriptome profiling were obtained to characterize the DDR-related features of BC. We collected 276 DDR-related genes based on the Molecular Signature Database (MSigDB) database and previous studies. We acquired public datasets included the SCAN-B dataset (GEO: GSE96058), METABRIC database, and TCGA-BRCA database. Corresponding repositories such as transcriptomics, genomics, and clinical information were also downloaded. We selected scRNA-seq data from GEO: GSE176078, GSE114727, GSE161529, and GSE158724. Bulk RNA-seq data from GEO: GSE176078, GSE18728, GSE5462, GSE20181, and GSE130788 were extracted for independent analyses. Results The DDR classification was constructed in the SCAN-B dataset (GEO: GSE96058) and METABRIC database, Among BC patients, there were two clusters with distinct clinical and molecular characteristics: the DDR-suppressed cluster and the DDR-active cluster. A superior survival rate is found for tumors in the DDR-suppressed cluster, while those with the DDR-activated cluster tend to have inferior prognoses and clinically aggressive behavior. The DDR classification was validated in the TCGA-BRCA cohort and shown similar results. We also found that two clusters have different pathway activities at the genomic level. Based on the intersection of the different expressed genes among these cohorts, we found that PRAME might play a vital role in DDR. The DDR classification was then enabled by establishing a DDR score, which was verified through multilayer cohort analysis. Furthermore, our results revealed that malignant cells contributed more to the DDR score at the single-cell level than nonmalignant cells. Particularly, immune cells with immunosuppressive properties (such as FOXP3+ CD4+ T cells) displayed higher DDR scores among those with distinguishable characteristics. Conclusion Collectively, this study performs general analyses of DDR heterogeneity in BC and provides insight into the understanding of individualized molecular and clinicopathological mechanisms underlying unique DDR profiles.
Collapse
Affiliation(s)
- Peng Liu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huamao Zhou
- The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Jindong Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanan Kong
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yutian Zou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Anli Yang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xing Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| |
Collapse
|
9
|
Luo Y, Liang H. Single-cell dissection of tumor microenvironmental response and resistance to cancer therapy. Trends Genet 2023; 39:758-772. [PMID: 37658004 PMCID: PMC10529478 DOI: 10.1016/j.tig.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 09/03/2023]
Abstract
Cancer treatment strategies have evolved significantly over the years, with chemotherapy, targeted therapy, and immunotherapy as major pillars. Each modality leads to unique treatment outcomes by interacting with the tumor microenvironment (TME), which imposes a fundamental selective pressure on cancer progression. The advent of single-cell profiling technologies has revolutionized our understanding of the intricate and heterogeneous nature of the TME at an unprecedented resolution. This review delves into the commonalities and differential manifestations of how cancer therapies reshape the microenvironment in diverse cancer types. We highlight how groundbreaking immune checkpoint blockade (ICB) strategies alone or in combination with tumor-targeting treatments are endowed with comprehensive mechanistic insights when decoded at the single-cell level, aiming to drive forward future research directions on personalized treatments.
Collapse
Affiliation(s)
- Yikai Luo
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
10
|
Thakur S, Haider S, Natrajan R. Implications of tumour heterogeneity on cancer evolution and therapy resistance: lessons from breast cancer. J Pathol 2023; 260:621-636. [PMID: 37587096 DOI: 10.1002/path.6158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 08/18/2023]
Abstract
Tumour heterogeneity is pervasive amongst many cancers and leads to disease progression, and therapy resistance. In this review, using breast cancer as an exemplar, we focus on the recent advances in understanding the interplay between tumour cells and their microenvironment using single cell sequencing and digital spatial profiling technologies. Further, we discuss the utility of lineage tracing methodologies in pre-clinical models of breast cancer, and how these are being used to unravel new therapeutic vulnerabilities and reveal biomarkers of breast cancer progression. © 2023 The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Shefali Thakur
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| |
Collapse
|
11
|
Lee JS, Hackbart H, Cui X, Yuan Y. CDK4/6 Inhibitor Resistance in Hormone Receptor-Positive Metastatic Breast Cancer: Translational Research, Clinical Trials, and Future Directions. Int J Mol Sci 2023; 24:11791. [PMID: 37511548 PMCID: PMC10380517 DOI: 10.3390/ijms241411791] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
The emergence of CDK4/6 inhibitors, such as palbociclib, ribociclib, and abemaciclib, has revolutionized the treatment landscape for hormone receptor-positive breast cancer. These agents have demonstrated significant clinical benefits in terms of both progression-free survival and overall survival. However, resistance to CDK4/6 inhibitors remains a challenge, limiting their long-term efficacy. Understanding the complex mechanisms driving resistance is crucial for the development of novel therapeutic strategies and the improvement of patient outcomes. Translational research efforts, such as preclinical models and biomarker studies, offer valuable insight into resistance mechanisms and may guide the identification of novel combination therapies. This review paper aims to outline the reported mechanisms underlying CDK4/6 inhibitor resistance, drawing insights from both clinical data and translational research in order to help direct the future of treatment for hormone receptor-positive metastatic breast cancer.
Collapse
Affiliation(s)
- Jin Sun Lee
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Hannah Hackbart
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xiaojiang Cui
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yuan Yuan
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| |
Collapse
|
12
|
van Amerongen R, Bentires-Alj M, van Boxtel AL, Clarke RB, Fre S, Suarez EG, Iggo R, Jechlinger M, Jonkers J, Mikkola ML, Koledova ZS, Sørlie T, Vivanco MDM. Imagine beyond: recent breakthroughs and next challenges in mammary gland biology and breast cancer research. J Mammary Gland Biol Neoplasia 2023; 28:17. [PMID: 37450065 PMCID: PMC10349020 DOI: 10.1007/s10911-023-09544-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
On 8 December 2022 the organizing committee of the European Network for Breast Development and Cancer labs (ENBDC) held its fifth annual Think Tank meeting in Amsterdam, the Netherlands. Here, we embraced the opportunity to look back to identify the most prominent breakthroughs of the past ten years and to reflect on the main challenges that lie ahead for our field in the years to come. The outcomes of these discussions are presented in this position paper, in the hope that it will serve as a summary of the current state of affairs in mammary gland biology and breast cancer research for early career researchers and other newcomers in the field, and as inspiration for scientists and clinicians to move the field forward.
Collapse
Affiliation(s)
- Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands.
| | - Mohamed Bentires-Alj
- Laboratory of Tumor Heterogeneity, Metastasis and Resistance, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Antonius L van Boxtel
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Robert B Clarke
- Manchester Breast Centre, Division of Cancer Sciences, School of Medical Sciences, University of Manchester, Manchester, UK
| | - Silvia Fre
- Institut Curie, Genetics and Developmental Biology Department, PSL Research University, CNRS UMR3215, U93475248, InsermParis, France
| | - Eva Gonzalez Suarez
- Transformation and Metastasis Laboratory, Molecular Oncology, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Richard Iggo
- INSERM U1312, University of Bordeaux, 33076, Bordeaux, France
| | - Martin Jechlinger
- Cell Biology and Biophysics Department, EMBL, Heidelberg, Germany
- Molit Institute of Personalized Medicine, Heilbronn, Germany
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Marja L Mikkola
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, P.O.B. 56, 00014, Helsinki, Finland
| | - Zuzana Sumbalova Koledova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Maria dM Vivanco
- Cancer Heterogeneity Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Technological Park Bizkaia, 48160, Derio, Spain
| |
Collapse
|
13
|
Sawant M, Wilson A, Sridaran D, Mahajan K, O'Conor CJ, Hagemann IS, Luo J, Weimholt C, Li T, Roa JC, Pandey A, Wu X, Mahajan NP. Epigenetic reprogramming of cell cycle genes by ACK1 promotes breast cancer resistance to CDK4/6 inhibitor. Oncogene 2023; 42:2263-2277. [PMID: 37330596 PMCID: PMC10348910 DOI: 10.1038/s41388-023-02747-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 05/16/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023]
Abstract
Hormone receptor-positive, HER2-negative advanced breast cancers exhibit high sensitivity to CDK4/6 inhibitors such as palbociclib. However, most patients inevitably develop resistance, thus identification of new actionable therapeutic targets to overcome the recurrent disease is an urgent need. Immunohistochemical studies of tissue microarray revealed increased activation of non-receptor tyrosine kinase, ACK1 (also known as TNK2) in most of the breast cancer subtypes, independent of their hormone receptor status. Chromatin immunoprecipitation studies demonstrated that the nuclear target of activated ACK1, pY88-H4 epigenetic marks, were deposited at cell cycle genes, CCNB1, CCNB2 and CDC20, which in turn initiated their efficient transcription. Pharmacological inhibition of ACK1 using its inhibitor, (R)-9b dampened CCNB1, CCNB2 and CDC20 expression, caused G2/M arrest, culminating in regression of palbociclib-resistant breast tumor growth. Further, (R)-9b suppressed expression of CXCR4 receptor, which resulted in significant impairment of metastasis of breast cancer cells to lung. Overall, our pre-clinical data identifies activated ACK1 as an oncogene that epigenetically controls the cell cycle genes governing the G2/M transition in breast cancer cells. ACK1 inhibitor, (R)-9b could be a novel therapeutic option for the breast cancer patients that have developed resistance to CDK4/6 inhibitors.
Collapse
Affiliation(s)
- Mithila Sawant
- Department of Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Audrey Wilson
- Department of Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Dhivya Sridaran
- Department of Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Kiran Mahajan
- Department of Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Christopher J O'Conor
- Department of Pathology and Immunology, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Ian S Hagemann
- Department of Pathology and Immunology, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Jingqin Luo
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Cody Weimholt
- Department of Pathology and Immunology, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Tiandao Li
- Bioinformatics Research Core, Center of Regenerative Medicine, Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Juan Carlos Roa
- Department of Pathology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xinyan Wu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Nupam P Mahajan
- Department of Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA.
- Division of Urologic Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA.
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA.
| |
Collapse
|
14
|
Zhang S, Xu Q, Sun W, Zhou J, Zhou J. Immunomodulatory effects of CDK4/6 inhibitors. Biochim Biophys Acta Rev Cancer 2023; 1878:188912. [PMID: 37182667 DOI: 10.1016/j.bbcan.2023.188912] [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: 02/01/2023] [Revised: 04/23/2023] [Accepted: 05/10/2023] [Indexed: 05/16/2023]
Abstract
The dysregulation of the cell cycle is one of the hallmarks of cancer. Cyclin-dependent kinase 4 (CDK4) and CDK6 play crucial roles in regulating cell cycle and other cellular functions. CDK4/6 inhibitors have achieved great success in treating breast cancers and are currently being tested extensively in other tumor types as well. Accumulating evidence suggests that CDK4/6 inhibitors exert antitumor effects through immunomodulation aside from cell cycle arrest. Here we outline the immunomodulatory activities of CDK4/6 inhibitors, discuss the immune mechanisms of drug resistance and explore avenues to harness their immunotherapeutic potential when combined with immune checkpoint inhibitors (ICIs) or chimeric antigen receptor (CAR) T-cell therapy to improve the clinical outcomes.
Collapse
Affiliation(s)
- Shumeng Zhang
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiaomai Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenjia Sun
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianya Zhou
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jianying Zhou
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
15
|
Emond R, Griffiths JI, Grolmusz VK, Nath A, Chen J, Medina EF, Sousa RS, Synold T, Adler FR, Bild AH. Cell facilitation promotes growth and survival under drug pressure in breast cancer. Nat Commun 2023; 14:3851. [PMID: 37386030 PMCID: PMC10310817 DOI: 10.1038/s41467-023-39242-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 06/05/2023] [Indexed: 07/01/2023] Open
Abstract
The interplay of positive and negative interactions between drug-sensitive and resistant cells influences the effectiveness of treatment in heterogeneous cancer cell populations. Here, we study interactions between estrogen receptor-positive breast cancer cell lineages that are sensitive and resistant to ribociclib-induced cyclin-dependent kinase 4 and 6 (CDK4/6) inhibition. In mono- and coculture, we find that sensitive cells grow and compete more effectively in the absence of treatment. During treatment with ribociclib, sensitive cells survive and proliferate better when grown together with resistant cells than when grown in monoculture, termed facilitation in ecology. Molecular, protein, and genomic analyses show that resistant cells increase metabolism and production of estradiol, a highly active estrogen metabolite, and increase estrogen signaling in sensitive cells to promote facilitation in coculture. Adding estradiol in monoculture provides sensitive cells with increased resistance to therapy and cancels facilitation in coculture. Under partial inhibition of estrogen signaling through low-dose endocrine therapy, estradiol supplied by resistant cells facilitates sensitive cell growth. However, a more complete blockade of estrogen signaling, through higher-dose endocrine therapy, diminished the facilitative growth of sensitive cells. Mathematical modeling quantifies the strength of competition and facilitation during CDK4/6 inhibition and predicts that blocking facilitation has the potential to control both resistant and sensitive cancer cell populations and inhibit the emergence of a refractory population during cell cycle therapy.
Collapse
Affiliation(s)
- Rena Emond
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, Monrovia, CA, 91016, USA
| | - Jason I Griffiths
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, Monrovia, CA, 91016, USA
| | - Vince Kornél Grolmusz
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, Monrovia, CA, 91016, USA
| | - Aritro Nath
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, Monrovia, CA, 91016, USA
| | - Jinfeng Chen
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, Monrovia, CA, 91016, USA
| | - Eric F Medina
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, Monrovia, CA, 91016, USA
| | - Rachel S Sousa
- Department of Mathematics, University of Utah, Salt Lake City, UT, 84112, USA
- Department of Mathematical, Computational, and Systems Biology, University of California, Irvine, CA, 92697, USA
| | - Timothy Synold
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, Monrovia, CA, 91016, USA
| | - Frederick R Adler
- Department of Mathematics, University of Utah, Salt Lake City, UT, 84112, USA.
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA.
| | - Andrea H Bild
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, Monrovia, CA, 91016, USA.
| |
Collapse
|
16
|
Sun G, Wei Y, Zhou B, Wang M, Luan R, Bai Y, Li H, Wang S, Zheng D, Wang C, Wang S, Zeng K, Liu S, Lin L, He M, Zhang Q, Zhao Y. BAP18 facilitates CTCF-mediated chromatin accessible to regulate enhancer activity in breast cancer. Cell Death Differ 2023; 30:1260-1278. [PMID: 36828916 PMCID: PMC10154423 DOI: 10.1038/s41418-023-01135-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/26/2023] Open
Abstract
The estrogen receptor alpha (ERα) signaling pathway is a crucial target for ERα-positive breast cancer therapeutic strategies. Co-regulators and other transcription factors cooperate for effective ERα-related enhancer activation. Recent studies demonstrate that the transcription factor CTCF is essential to participate in ERα/E2-induced enhancer transactivation. However, the mechanism of how CTCF is achieved remains unknown. Here, we provided evidence that BAP18 is required for CTCF recruitment on ERα-enriched enhancers, facilitating CTCF-mediated chromatin accessibility to promote enhancer RNAs transcription. Consistently, GRO-seq demonstrates that the enhancer activity is positively correlated with BAP18 enrichment. Furthermore, BAP18 interacts with SMARCA1/BPTF to accelerate the recruitment of CTCF to ERα-related enhancers. Interestingly, BAP18 is involved in chromatin accessibility within enhancer regions, thereby increasing enhancer transactivation and enhancer-promoter looping. BAP18 depletion increases the sensitivity of anti-estrogen and anti-enhancer treatment in MCF7 cells. Collectively, our study indicates that BAP18 coordinates with CTCF to enlarge the transactivation of ERα-related enhancers, providing a better understanding of BAP18/CTCF coupling chromatin remodeling and E-P looping in the regulation of enhancer transcription.
Collapse
Affiliation(s)
- Ge Sun
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Yuntao Wei
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang City, 110042, Liaoning Province, China
| | - Baosheng Zhou
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Manlin Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Ruina Luan
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Yu Bai
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Hao Li
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Shan Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Dantong Zheng
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Chunyu Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Shengli Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Kai Zeng
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Shuchang Liu
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Lin Lin
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Mingcong He
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Qiang Zhang
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang City, 110042, Liaoning Province, China
| | - Yue Zhao
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China.
| |
Collapse
|
17
|
Zhou FH, Downton T, Freelander A, Hurwitz J, Caldon CE, Lim E. CDK4/6 inhibitor resistance in estrogen receptor positive breast cancer, a 2023 perspective. Front Cell Dev Biol 2023; 11:1148792. [PMID: 37035239 PMCID: PMC10073728 DOI: 10.3389/fcell.2023.1148792] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
CDK4/6 inhibitors have become game-changers in the treatment of estrogen receptor-positive (ER+) breast cancer, and in combination with endocrine therapy are the standard of care first-line treatment for ER+/HER2-negative advanced breast cancer. Although CDK4/6 inhibitors prolong survival for these patients, resistance is inevitable and there is currently no clear standard next-line treatment. There is an urgent unmet need to dissect the mechanisms which drive intrinsic and acquired resistance to CDK4/6 inhibitors and endocrine therapy to guide the subsequent therapeutic decisions. We will review the insights gained from preclinical studies and clinical cohorts into the diverse mechanisms of CDK4/6 inhibitor action and resistance, and highlight potential therapeutic strategies in the context of CDK4/6 inhibitor resistance.
Collapse
Affiliation(s)
- Fiona H. Zhou
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, University of NSW, Sydney, NSW, Australia
| | - Teesha Downton
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, University of NSW, Sydney, NSW, Australia
| | - Allegra Freelander
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, University of NSW, Sydney, NSW, Australia
| | - Joshua Hurwitz
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, University of NSW, Sydney, NSW, Australia
| | - C. Elizabeth Caldon
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, University of NSW, Sydney, NSW, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, University of NSW, Sydney, NSW, Australia
| |
Collapse
|
18
|
Nolan E, Lindeman GJ, Visvader JE. Deciphering breast cancer: from biology to the clinic. Cell 2023; 186:1708-1728. [PMID: 36931265 DOI: 10.1016/j.cell.2023.01.040] [Citation(s) in RCA: 88] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/14/2023] [Accepted: 01/30/2023] [Indexed: 03/17/2023]
Abstract
Breast cancer remains a leading cause of cancer-related mortality in women, reflecting profound disease heterogeneity, metastasis, and therapeutic resistance. Over the last decade, genomic and transcriptomic data have been integrated on an unprecedented scale and revealed distinct cancer subtypes, critical molecular drivers, clonal evolutionary trajectories, and prognostic signatures. Furthermore, multi-dimensional integration of high-resolution single-cell and spatial technologies has highlighted the importance of the entire breast cancer ecosystem and the presence of distinct cellular "neighborhoods." Clinically, a plethora of new targeted therapies has emerged, now being rapidly incorporated into routine care. Resistance to therapy, however, remains a crucial challenge for the field.
Collapse
Affiliation(s)
- Emma Nolan
- Auckland Cancer Society Research Centre, University of Auckland, Auckland 1023, New Zealand
| | - Geoffrey J Lindeman
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC 3050, Australia; Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Jane E Visvader
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia.
| |
Collapse
|
19
|
Taleb NN, West J. Working with Convex Responses: Antifragility from Finance to Oncology. ENTROPY (BASEL, SWITZERLAND) 2023; 25:e25020343. [PMID: 36832709 PMCID: PMC9955868 DOI: 10.3390/e25020343] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 06/07/2023]
Abstract
We extend techniques and learnings about the stochastic properties of nonlinear responses from finance to medicine, particularly oncology, where it can inform dosing and intervention. We define antifragility. We propose uses of risk analysis for medical problems, through the properties of nonlinear responses (convex or concave). We (1) link the convexity/concavity of the dose-response function to the statistical properties of the results; (2) define "antifragility" as a mathematical property for local beneficial convex responses and the generalization of "fragility" as its opposite, locally concave in the tails of the statistical distribution; (3) propose mathematically tractable relations between dosage, severity of conditions, and iatrogenics. In short, we propose a framework to integrate the necessary consequences of nonlinearities in evidence-based oncology and more general clinical risk management.
Collapse
Affiliation(s)
| | - Jeffrey West
- Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA
| |
Collapse
|
20
|
Andrade de Oliveira K, Sengupta S, Yadav AK, Clarke R. The complex nature of heterogeneity and its roles in breast cancer biology and therapeutic responsiveness. Front Endocrinol (Lausanne) 2023; 14:1083048. [PMID: 36909339 PMCID: PMC9997040 DOI: 10.3389/fendo.2023.1083048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/02/2023] [Indexed: 02/25/2023] Open
Abstract
Heterogeneity is a complex feature of cells and tissues with many interacting components. Depending on the nature of the research context, interacting features of cellular, drug response, genetic, molecular, spatial, temporal, and vascular heterogeneity may be present. We describe the various forms of heterogeneity with examples of their interactions and how they play a role in affecting cellular phenotype and drug responses in breast cancer. While cellular heterogeneity may be the most widely described and invoked, many forms of heterogeneity are evident within the tumor microenvironment and affect responses to the endocrine and cytotoxic drugs widely used in standard clinical care. Drug response heterogeneity is a critical determinant of clinical response and curative potential and also is multifaceted when encountered. The interactive nature of some forms of heterogeneity is readily apparent. For example, the process of metastasis has the properties of both temporal and spatial heterogeneity within the host, whereas each individual metastatic deposit may exhibit cellular, genetic, molecular, and vascular heterogeneity. This review describes the many forms of heterogeneity, their integrated activities, and offers some insights into how heterogeneity may be understood and studied in the future.
Collapse
Affiliation(s)
- Karla Andrade de Oliveira
- The Hormel Institute, University of Minnesota, Austin, MN, United States
- Department of Biochemistry and Pharmacology, Universidade Federal do Piaui, Piauí, Brazil
| | - Surojeet Sengupta
- The Hormel Institute, University of Minnesota, Austin, MN, United States
| | - Anil Kumar Yadav
- The Hormel Institute, University of Minnesota, Austin, MN, United States
| | - Robert Clarke
- The Hormel Institute, University of Minnesota, Austin, MN, United States
- *Correspondence: Robert Clarke,
| |
Collapse
|
21
|
Bishara I, Chen J, Griffiths JI, Bild AH, Nath A. A machine learning framework for scRNA-seq UMI threshold optimization and accurate classification of cell types. Front Genet 2022; 13:982019. [PMID: 36506328 PMCID: PMC9732024 DOI: 10.3389/fgene.2022.982019] [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: 06/30/2022] [Accepted: 11/04/2022] [Indexed: 11/27/2022] Open
Abstract
Recent advances in single cell RNA sequencing (scRNA-seq) technologies have been invaluable in the study of the diversity of cancer cells and the tumor microenvironment. While scRNA-seq platforms allow processing of a high number of cells, uneven read quality and technical artifacts hinder the ability to identify and classify biologically relevant cells into correct subtypes. This obstructs the analysis of cancer and normal cell diversity, while rare and low expression cell populations may be lost by setting arbitrary high cutoffs for UMIs when filtering out low quality cells. To address these issues, we have developed a novel machine-learning framework that: 1. Trains cell lineage and subtype classifier using a gold standard dataset validated using marker genes 2. Systematically assess the lowest UMI threshold that can be used in a given dataset to accurately classify cells 3. Assign accurate cell lineage and subtype labels to the lower read depth cells recovered by setting the optimal threshold. We demonstrate the application of this framework in a well-curated scRNA-seq dataset of breast cancer patients and two external datasets. We show that the minimum UMI threshold for the breast cancer dataset could be lowered from the original 1500 to 450, thereby increasing the total number of recovered cells by 49%, while achieving a classification accuracy of >0.9. Our framework provides a roadmap for future scRNA-seq studies to determine optimal UMI threshold and accurately classify cells for downstream analyses.
Collapse
Affiliation(s)
- Isaac Bishara
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, United States,Irell & Manella Graduate School of Biological Science, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Jinfeng Chen
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, United States,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jason I. Griffiths
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Andrea H. Bild
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Aritro Nath
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, United States,*Correspondence: Aritro Nath,
| |
Collapse
|
22
|
Bidard FC, Kaklamani VG, Neven P, Streich G, Montero AJ, Forget F, Mouret-Reynier MA, Sohn JH, Taylor D, Harnden KK, Khong H, Kocsis J, Dalenc F, Dillon PM, Babu S, Waters S, Deleu I, García Sáenz JA, Bria E, Cazzaniga M, Lu J, Aftimos P, Cortés J, Liu S, Tonini G, Laurent D, Habboubi N, Conlan MG, Bardia A. Elacestrant (oral selective estrogen receptor degrader) Versus Standard Endocrine Therapy for Estrogen Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Advanced Breast Cancer: Results From the Randomized Phase III EMERALD Trial. J Clin Oncol 2022; 40:3246-3256. [PMID: 35584336 PMCID: PMC9553388 DOI: 10.1200/jco.22.00338] [Citation(s) in RCA: 212] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Patients with pretreated estrogen receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative advanced breast cancer have poor prognosis. Elacestrant is a novel, oral selective ER degrader that demonstrated activity in early studies. METHODS This randomized, open-label, phase III trial enrolled patients with ER-positive/HER2-negative advanced breast cancer who had one-two lines of endocrine therapy, required pretreatment with a cyclin-dependent kinase 4/6 inhibitor, and ≤ 1 chemotherapy. Patients were randomly assigned to elacestrant 400 mg orally once daily or standard-of-care (SOC) endocrine monotherapy. Primary end points were progression-free survival (PFS) by blinded independent central review in all patients and patients with detectable ESR1 mutations. RESULTS Patients were randomly assigned to elacestrant (n = 239) or SOC (n = 238). ESR1 mutation was detected in 47.8% of patients, and 43.4% received two prior endocrine therapies. PFS was prolonged in all patients (hazard ratio = 0.70; 95% CI, 0.55 to 0.88; P = .002) and patients with ESR1 mutation (hazard ratio = 0.55; 95% CI, 0.39 to 0.77; P = .0005). Treatment-related grade 3/4 adverse events occurred in 7.2% receiving elacestrant and 3.1% receiving SOC. Treatment-related adverse events leading to treatment discontinuations were 3.4% in the elacestrant arm versus 0.9% in SOC. Nausea of any grade occurred in 35.0% receiving elacestrant and 18.8% receiving SOC (grade 3/4, 2.5% and 0.9%, respectively). CONCLUSION Elacestrant is the first oral selective ER degrader demonstrating a significant PFS improvement versus SOC both in the overall population and in patients with ESR1 mutations with manageable safety in a phase III trial for patients with ER-positive/HER2-negative advanced breast cancer.
Collapse
Affiliation(s)
- Francois-Clement Bidard
- Institut Curie, Paris and Saint Cloud, France,Versailles Saint Quentin/Paris-Saclay University, Saint Cloud, France
| | | | - Patrick Neven
- Universitaire Ziekenhuizen (UZ)—Leuven Cancer Institute, Leuven, Belgium
| | | | - Alberto J. Montero
- University Hospitals Seidman Cancer Center-Case Western Reserve University, Cleveland, OH
| | - Frédéric Forget
- Centre Hospitalier de l'Ardenne—Site de Libramont, Libramont-Chevigny, Belgium
| | | | - Joo Hyuk Sohn
- Yonsei Cancer Center, Yonsei University Health System-Medical Oncology, Seoul, Republic of Korea
| | - Donatienne Taylor
- Université catholique de Louvain, CHU UCL Namur—Site Sainte-Elisabeth, Namur, Belgium
| | | | - Hung Khong
- Moffit Cancer Center & Research Institute, Tampa, FL
| | | | | | | | - Sunil Babu
- Fort Wayne Medical Oncology and Hematology, Fort Wayne, IN
| | | | | | - José A. García Sáenz
- Instituto de Investigación Sanitaria Hospital Clinico San Carlos (IdISSC), Madrid, Spain
| | - Emilio Bria
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Roma, Italy
| | | | - Janice Lu
- University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Philippe Aftimos
- Institut Jules Bordet – Université Libre de Bruxelles, Brussels, Belgium
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Quironsalud Group, Barcelona, Spain,Scientific Department, Medica Scientia Innovation Research, Valencia, Spain,Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain,Universidad Europea de Madrid, Faculty of Biomedical and Health Sciences, Department of Medicine, Madrid, Spain
| | | | | | - Dirk Laurent
- Berlin Chemie AG/Menarini Group, Berlin, Germany
| | | | | | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA,Aditya Bardia, MD, Harvard Medical School, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114; Twitter: @DrAdityaBardia; e-mail:
| |
Collapse
|
23
|
Multianalyte liquid biopsy to aid the diagnostic workup of breast cancer. NPJ Breast Cancer 2022; 8:112. [PMID: 36167819 PMCID: PMC9515081 DOI: 10.1038/s41523-022-00480-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 09/16/2022] [Indexed: 11/19/2022] Open
Abstract
Breast cancer (BC) affects 1 in every 8 women in the United States and is currently the most prevalent cancer worldwide. Precise staging at diagnosis and prognosis are essential components for the clinical management of BC patients. In this study, we set out to evaluate the feasibility of the high-definition single cell (HDSCA) liquid biopsy (LBx) platform to stratify late-stage BC, early-stage BC, and normal donors using peripheral blood samples. Utilizing 5 biomarkers, we identified rare circulating events with epithelial, mesenchymal, endothelial and hematological origin. We detected a higher level of CTCs in late-stage patients, compared to the early-stage and normal donors. Additionally, we observed more tumor-associated large extracellular vesicles (LEVs) in the early-stage, compared to late-stage and the normal donor groups. Overall, we were able to detect reproducible patterns in the enumeration of rare cells and LEVs of cancer vs. normal donors and early-stage vs. late-stage BC with high accuracy, allowing for robust stratification. Our findings illustrate the feasibility of the LBx assay to provide robust detection of rare circulating events in peripheral blood draws and to stratify late-stage BC, early-stage BC, and normal donor samples.
Collapse
|
24
|
Mechanical signatures of human colon cancers. Sci Rep 2022; 12:12475. [PMID: 35864200 PMCID: PMC9304395 DOI: 10.1038/s41598-022-16669-3] [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: 03/22/2022] [Accepted: 07/13/2022] [Indexed: 11/26/2022] Open
Abstract
Besides the standard parameters used for colorectal cancer (CRC) management, new features are needed in clinical practice to improve progression-free and overall survival. In some cancers, the microenvironment mechanical properties can contribute to cancer progression and metastasis formation, or constitute a physical barrier for drug penetration or immune cell infiltration. These mechanical properties remain poorly known for colon tissues. Using a multidisciplinary approach including clinical data, physics and geostatistics, we characterized the stiffness of healthy and malignant colon specimens. For this purpose, we analyzed a prospective cohort of 18 patients with untreated colon adenocarcinoma using atomic force microscopy to generate micrometer-scale mechanical maps. We characterized the stiffness of normal epithelium samples taken far away or close to the tumor area and selected tumor tissue areas. These data showed that normal epithelium was softer than tumors. In tumors, stroma areas were stiffer than malignant epithelial cell areas. Among the clinical parameters, tumor left location, higher stage, and RAS mutations were associated with increased tissue stiffness. Thus, in patients with CRC, measuring tumor tissue rigidity may have a translational value and an impact on patient care.
Collapse
|
25
|
In Silico Investigations of Multi-Drug Adaptive Therapy Protocols. Cancers (Basel) 2022; 14:cancers14112699. [PMID: 35681680 PMCID: PMC9179496 DOI: 10.3390/cancers14112699] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
The standard of care for cancer patients aims to eradicate the tumor by killing the maximum number of cancer cells using the maximum tolerated dose (MTD) of a drug. MTD causes significant toxicity and selects for resistant cells, eventually making the tumor refractory to treatment. Adaptive therapy aims to maximize time to progression (TTP), by maintaining sensitive cells to compete with resistant cells. We explored both dose modulation (DM) protocols and fixed dose (FD) interspersed with drug holiday protocols. In contrast to previous single drug protocols, we explored the determinants of success of two-drug adaptive therapy protocols, using an agent-based model. In almost all cases, DM protocols (but not FD protocols) increased TTP relative to MTD. DM protocols worked well when there was more competition, with a higher cost of resistance, greater cell turnover, and when crowded proliferating cells could replace their neighbors. The amount that the drug dose was changed, mattered less. The more sensitive the protocol was to tumor burden changes, the better. In general, protocols that used as little drug as possible, worked best. Preclinical experiments should test these predictions, especially dose modulation protocols, with the goal of generating successful clinical trials for greater cancer control.
Collapse
|
26
|
Clinical Translation: Targeting the Estrogen Receptor. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:297-309. [DOI: 10.1007/978-3-031-11836-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
27
|
Ribociclib Induces Broad Chemotherapy Resistance and EGFR Dependency in ESR1 Wildtype and Mutant Breast Cancer. Cancers (Basel) 2021; 13:cancers13246314. [PMID: 34944934 PMCID: PMC8699146 DOI: 10.3390/cancers13246314] [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: 10/10/2021] [Revised: 12/05/2021] [Accepted: 12/11/2021] [Indexed: 12/24/2022] Open
Abstract
While endocrine therapy is highly effective for the treatment of oestrogen receptor-α (ERα)-positive breast cancer, a significant number of patients will eventually experience disease progression and develop treatment-resistant, metastatic cancer. The majority of resistant tumours remain dependent on ERα-action, with activating ESR1 gene mutations occurring in 15-40% of advanced cancers. Therefore, there is an urgent need to discover novel effective therapies that can eradicate cancer cells with aberrant ERα and to understand the cellular response underlying their action. Here, we evaluate the response of MCF7-derived, CRISPR-Cas9-generated cell lines expressing mutant ERα (Y537S) to a large number of drugs. We report sensitivity to numerous clinically approved inhibitors, including CDK4/6 inhibitor ribociclib, which is a standard-of-care therapy in the treatment of metastatic ERα-positive breast cancer and currently under evaluation in the neoadjuvant setting. Ribociclib treatment induces senescence in both wildtype and mutant ERα breast cancer models and leads to a broad-range drug tolerance. Strikingly, viability of cells undergoing ribociclib-induced cellular senescence is maintained via engagement of EGFR signalling, which may be therapeutically exploited in both wildtype and mutant ERα-positive breast cancer. Our study highlights a wide-spread reduction in sensitivity to anti-cancer drugs accompanied with an acquired vulnerability to EGFR inhibitors following CDK4/6 inhibitor treatment.
Collapse
|
28
|
Corti C, Giachetti PPMB, Eggermont AMM, Delaloge S, Curigliano G. Therapeutic vaccines for breast cancer: Has the time finally come? Eur J Cancer 2021; 160:150-174. [PMID: 34823982 PMCID: PMC8608270 DOI: 10.1016/j.ejca.2021.10.027] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022]
Abstract
The ability to exploit the immune system as a weapon against cancer has revolutionised the treatment of cancer patients, especially through immune checkpoint inhibitors (ICIs). However, ICIs demonstrated a modest benefit in treating breast cancer (BC), with the exception of certain subsets of triple-negative BCs. An immune-suppressive tumour microenvironment (TME), typically present in BC, is an important factor in the poor response to immunotherapy. After almost two decades of poor clinical trial results, cancer vaccines (CVs), an active immunotherapy, have come back in the spotlight because of some technological advancements, ultimately boosted by coronavirus disease 2019 pandemic. In particular, neoantigens are emerging as the preferred targets for CVs, with gene-based and viral vector–based platforms in development. Moreover, lipid nanoparticles proved to be immunogenic and efficient delivery vehicles. Past clinical trials investigating CVs focused especially on the metastatic disease, where the TME is more likely compromised by inhibitory mechanisms. In this sense, favouring the use of CVs as monotherapy in premalignant or in the adjuvant setting and establishing combination treatments (i.e. CV plus ICI) in late-stage disease are promising strategies. This review provides a full overview of the past and current breast cancer vaccine landscape.
Collapse
Affiliation(s)
- Chiara Corti
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - Pier P M B Giachetti
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - Alexander M M Eggermont
- Princess Máxima Center, Utrecht, the Netherlands; Department of Cancer Medicine, Institut Gustave Roussy, Villejuif, France
| | - Suzette Delaloge
- Department of Cancer Medicine, Institut Gustave Roussy, Villejuif, France
| | - Giuseppe Curigliano
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy.
| |
Collapse
|