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Schwartz CJ, Marra A, Selenica P, Gazzo A, Tan K, Ross D, Razavi P, Chandarlapaty S, Weigelt B, Reis-Filho JS, Brogi E, Pareja F, Wen HY. RB1 Genetic Alterations in Estrogen Receptor-Positive Breast Carcinomas: Correlation With Neuroendocrine Differentiation. Mod Pathol 2024; 37:100541. [PMID: 38897452 PMCID: PMC11344677 DOI: 10.1016/j.modpat.2024.100541] [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: 04/11/2024] [Revised: 05/28/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Genetic alterations in the retinoblastoma susceptibility gene (RB1) are present in up to 40% of triple-negative breast cancers (BCs) and frequent in tumors with neuroendocrine differentiation, including small cell neuroendocrine carcinoma. Data on RB1 genetic alterations in estrogen receptor (ER)-positive BCs are scarce. In this study, we sought to define the morphologic, immunohistochemical, and genetic features of ER-positive BCs harboring somatic alterations in RB1, with emphasis on neuroendocrine differentiation. ER-positive BCs with pathogenic RB1 genetic alterations were identified in <1% of cases (N = 55) from a cohort of 6026 BCs previously subjected to targeted next-generation sequencing, including 23 primary BCs (pBCs) and 32 recurrent/metastatic BCs (mBCs). In cases where loss of heterozygosity of the wild-type RB1 allele could be assessed (93%, 51/55), most pBCs (82%, 18/22) and mBCs (90%, 26/29) exhibited biallelic RB1 inactivation, primarily through loss-of-function mutation and loss of heterozygosity (98%, 43/44). Upon histologic review, a subset of RB1-altered tumors exhibited neuroendocrine morphology (13%, 7/55), which correlated with expression of neuroendocrine markers (39%, 9/23) in both pBCs (27%, 3/11) and mBCs (50%, 6/12). Loss of Rb protein expression was observed in BCs with biallelic RB1 loss only, with similar frequency in pBCs (82%, 9/11) and mBCs (75%, 9/12). All cases with neuroendocrine marker expression (n = 9) and/or neuroendocrine morphology (n = 7) harbored biallelic genetic inactivation of RB1 and exhibited Rb loss of expression. TP53 (53%, 29/55) and PIK3CA (45%, 25/55) were the most frequently comutated genes across the cohort. Overall, these findings suggest that ER-positive BCs with biallelic RB1 genetic alterations frequently exhibit Rb protein loss, which correlates with neuroendocrine differentiation in select BCs. This study provides insights into the molecular and phenotypic heterogeneity of BCs with RB1 genetic inactivation, underscoring the need for further research into the potential clinical implications associated with these tumors.
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Affiliation(s)
- Christopher J Schwartz
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kiki Tan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dara Ross
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Now with AstraZeneca, Gaithersburg, Maryland
| | - Edi Brogi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hannah Y Wen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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2
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Boscolo Bielo L, Trapani D, Nicolò E, Valenza C, Guidi L, Belli C, Kotteas E, Marra A, Prat A, Fusco N, Criscitiello C, Burstein HJ, Curigliano G. The evolving landscape of metastatic HER2-positive, hormone receptor-positive Breast Cancer. Cancer Treat Rev 2024; 128:102761. [PMID: 38772169 DOI: 10.1016/j.ctrv.2024.102761] [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: 03/02/2024] [Revised: 05/05/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
Therapeutic agents targeting Human Epidermal Growth Factor Receptor 2 (HER2) demonstrated to positively impact the prognosis of HER2-positive breast cancer. HER2-positive breast cancer can present either as hormone receptor-negative or positive, defining Triple-positive breast cancer (TPBC). TPBC demonstrate unique gene expression profiles, showing reduced HER2-driven gene expression, as recapitulated by a higher proportion of Luminal-type intrinsic subtypes. The different molecular landscape of TPBC dictates distinctive clinical features, including reduced chemotherapy sensitivity, different patterns of recurrence, and better overall prognosis. Cross-talk between HER2 and hormone receptor signaling seems to be critical to determine resistance to HER2-directed agents. Accordingly, superior outcomes have been achieved with the use of endocrine therapy, representing the first subtype-specific pharmacological intervention unique to this subgroup. Additional targeted agents capable to tackle resistance mechanisms to anti-HER2, hormone agents, or both might further improve the efficacy of treatments, such as PI3K/AKT/mTOR inhibitors, particularly in a biomarker-enriched setting, and CDK4/6-inhibitors, with preliminary data suggesting a role of PAM50 subtyping to predict higher benefits in luminal tumors. Finally, the distinct biology of triple-positive tumors may yield the rationale for considering combinations within antibody-drug conjugate regimens. Accordingly, in this review, we summarized the current evidence and rationale for considering TPBC as a different entity, in which distinct therapeutical approaches leveraging on the different biological profile of TPBC may result in superior anticancer regimens and improved patient-centric outcomes.
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Affiliation(s)
- Luca Boscolo Bielo
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Dario Trapani
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Eleonora Nicolò
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Carmine Valenza
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Lorenzo Guidi
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Carmen Belli
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy
| | - Elias Kotteas
- Oncology Unit, Sotiria General Hospital, 3rd Dept of Internal Medicine, Athens School of Medicine, Greece
| | - Antonio Marra
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy
| | - Aleix Prat
- Department of Medical Oncology and Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Faculty of Medicine and Health Sciences, University of Barcelona, Spain
| | - Nicola Fusco
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Carmen Criscitiello
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Harold J Burstein
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
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3
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Morrison L, Loibl S, Turner NC. The CDK4/6 inhibitor revolution - a game-changing era for breast cancer treatment. Nat Rev Clin Oncol 2024; 21:89-105. [PMID: 38082107 DOI: 10.1038/s41571-023-00840-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2023] [Indexed: 01/27/2024]
Abstract
Cyclin-dependent kinase (CDK) 4/6 inhibition in combination with endocrine therapy is the standard-of-care treatment for patients with advanced-stage hormone receptor-positive, HER2 non-amplified (HR+HER2-) breast cancer. These agents can also be administered as adjuvant therapy to patients with higher-risk early stage disease. Nonetheless, the clinical success of these agents has created several challenges, such as how to address acquired resistance, identifying which patients are most likely to benefit from therapy prior to treatment, and understanding the optimal timing of administration and sequencing of these agents. In this Review, we describe the rationale for targeting CDK4/6 in patients with breast cancer, including a summary of updated clinical evidence and how this should inform clinical practice. We also discuss ongoing research efforts that are attempting to address the various challenges created by the widespread implementation of these agents.
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Affiliation(s)
- Laura Morrison
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
- Breast Unit, The Royal Marsden Hospital, London, UK
| | - Sibylle Loibl
- German Breast Group, Goethe University, Frankfurt, Germany
| | - Nicholas C Turner
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK.
- Breast Unit, The Royal Marsden Hospital, London, UK.
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4
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Fuentes‐Antrás J, Bedard PL, Cescon DW. Seize the engine: Emerging cell cycle targets in breast cancer. Clin Transl Med 2024; 14:e1544. [PMID: 38264947 PMCID: PMC10807317 DOI: 10.1002/ctm2.1544] [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: 10/09/2023] [Revised: 12/10/2023] [Accepted: 12/31/2023] [Indexed: 01/25/2024] Open
Abstract
Breast cancer arises from a series of molecular alterations that disrupt cell cycle checkpoints, leading to aberrant cell proliferation and genomic instability. Targeted pharmacological inhibition of cell cycle regulators has long been considered a promising anti-cancer strategy. Initial attempts to drug critical cell cycle drivers were hampered by poor selectivity, modest efficacy and haematological toxicity. Advances in our understanding of the molecular basis of cell cycle disruption and the mechanisms of resistance to CDK4/6 inhibitors have reignited interest in blocking specific components of the cell cycle machinery, such as CDK2, CDK4, CDK7, PLK4, WEE1, PKMYT1, AURKA and TTK. These targets play critical roles in regulating quiescence, DNA replication and chromosome segregation. Extensive preclinical data support their potential to overcome CDK4/6 inhibitor resistance, induce synthetic lethality or sensitise tumours to immune checkpoint inhibitors. This review provides a biological and drug development perspective on emerging cell cycle targets and novel inhibitors, many of which exhibit favourable safety profiles and promising activity in clinical trials.
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Affiliation(s)
- Jesús Fuentes‐Antrás
- Division of Medical Oncology and HematologyDepartment of MedicinePrincess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoOntarioCanada
- NEXT OncologyHospital Universitario QuironSalud MadridMadridSpain
| | - Philippe L. Bedard
- Division of Medical Oncology and HematologyDepartment of MedicinePrincess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoOntarioCanada
| | - David W. Cescon
- Division of Medical Oncology and HematologyDepartment of MedicinePrincess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoOntarioCanada
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5
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Ma W, Ma B, Ma J, Zhu R. RB1 5́UTR contains an IRES related to cell cycle control and cancer progression. Gene 2023; 887:147724. [PMID: 37604323 DOI: 10.1016/j.gene.2023.147724] [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: 06/07/2023] [Revised: 08/10/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Retinoblastoma gene1 (RB1) is the first tumor suppressor gene that stands as the guardian of the gate of the G1 period and plays a central role in proliferation and differentiation. However, no reports focused on the possible internal ribosome entry site (IRES) function of the RB1 gene flanking sequence. In this study, we constructed a bicistronic reporter with the RB1 5'untranslated region (5́UTR) inserted between two reporter coding regions. We found RB1 5'UTR harbors an IRES and has higher activity in cancer cell lines than normal cells. Besides, RB1 IRES acquired the highest activity in the G0/G1 phase of the cell cycle, and the RB1 5'UTR mutation collected from retinoblastoma decreased IRES activity compared with RB1 5'UTR wild-type. These data indicated that RB1 IRES is a mechanism of stress regulation and is related to cell cycle control and cancer progression.
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Affiliation(s)
- Wennan Ma
- Changzhou Capmus of Hohai University, Changzhou, Jiangsu Province 213022, PR China
| | - Bei Ma
- Changzhou Capmus of Hohai University, Changzhou, Jiangsu Province 213022, PR China
| | - Jing Ma
- Nanjing Kingsley Biotechnology Co., Ltd, Nanjing, Jiangsu Province 210000, PR China
| | - Ruiyu Zhu
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu Province 214122, PR China.
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6
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Kim H, Whitman AA, Wisniewska K, Kakati RT, Garcia-Recio S, Calhoun BC, Franco HL, Perou CM, Spanheimer PM. Tamoxifen Response at Single-Cell Resolution in Estrogen Receptor-Positive Primary Human Breast Tumors. Clin Cancer Res 2023; 29:4894-4907. [PMID: 37747807 PMCID: PMC10690085 DOI: 10.1158/1078-0432.ccr-23-1248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/18/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
PURPOSE In estrogen receptor-positive (ER+)/HER2- breast cancer, multiple measures of intratumor heterogeneity are associated with a worse response to endocrine therapy. We sought to develop a novel experimental model to measure heterogeneity in response to tamoxifen treatment in primary breast tumors. EXPERIMENTAL DESIGN To investigate heterogeneity in response to treatment, we developed an operating room-to-laboratory pipeline for the collection of live normal breast specimens and human tumors immediately after surgical resection for processing into single-cell workflows for experimentation and genomic analyses. Live primary cell suspensions were treated ex vivo with tamoxifen (10 μmol/L) or control media for 12 hours, and single-cell RNA libraries were generated using the 10X Genomics droplet-based kit. RESULTS In total, we obtained and processed normal breast tissue from two women undergoing reduction mammoplasty and tumor tissue from 10 women with ER+/HER2- invasive breast carcinoma. We demonstrate differences in tamoxifen response by cell type and identify distinctly responsive and resistant subpopulations within the malignant cell compartment of human tumors. Tamoxifen resistance signatures from resistant subpopulations predict poor outcomes in two large cohorts of ER+ breast cancer patients and are enriched in endocrine therapy-resistant tumors. CONCLUSIONS This novel ex vivo model system now provides the foundation to define responsive and resistant subpopulations within heterogeneous human tumors, which can be used to develop precise single cell-based predictors of response to therapy and to identify genes and pathways driving therapeutic resistance.
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Affiliation(s)
- Hyunsoo Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Austin A. Whitman
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Kamila Wisniewska
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Rasha T. Kakati
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Susana Garcia-Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Benjamin C. Calhoun
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Hector L. Franco
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
- Computational Medicine Program, University of North Carolina, Chapel Hill, North Carolina
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
- Computational Medicine Program, University of North Carolina, Chapel Hill, North Carolina
| | - Philip M. Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Surgery, University of North Carolina, Chapel Hill, North Carolina
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7
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Witkiewicz AK, Schultz E, Wang J, Hamilton D, Levine E, O'Connor T, Knudsen ES. Determinants of response to CDK4/6 inhibitors in the real-world setting. NPJ Precis Oncol 2023; 7:90. [PMID: 37704753 PMCID: PMC10499925 DOI: 10.1038/s41698-023-00438-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
Despite widespread use and a known mechanism of action for CDK4/6 inhibitors in combination with endocrine therapy, features of disease evolution and determinants of therapeutic response in the real-world setting remain unclear. Here, a cohort of patients treated with standard-of-care combination regimens was utilized to explore features of disease and determinants of progression-free survival (PFS) and overall survival (OS). In this cohort of 280 patients, >90% of patients were treated with palbociclib in combination with either an aromatase inhibitor (AI) or fulvestrant (FUL). Most of these patients had modified Scarff-Bloom-Richardson (SBR) scores, and ER, HER2, and PR immunohistochemistry. Both the SBR score and lack of PR expression were associated with shorter PFS in patients treated with AI combinations and remained significant in multivariate analyses (HR = 3.86, p = 0.008). Gene expression analyses indicated substantial changes in cell cycle and estrogen receptor signaling during the course of treatment. Furthermore, gene expression-based subtyping indicated that predominant subtypes changed with treatment and progression. The luminal B, HER2, and basal subtypes exhibited shorter PFS in CDK4/6 inhibitor combinations when assessed in the pretreatment biopsies; however, they were not associated with OS. Using unbiased approaches, cell cycle-associated gene sets were strongly associated with shorter PFS in pretreatment biopsies irrespective of endocrine therapy. Estrogen receptor signaling gene sets were associated with longer PFS particularly in the AI-treated cohort. Together, these data suggest that there are distinct pathological and biological features of HR+/HER2- breast cancer associated with response to CDK4/6 inhibitors. Clinical trial registration number: NCT04526587.
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Affiliation(s)
- Agnieszka K Witkiewicz
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.
| | - Emily Schultz
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Jianxin Wang
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Deanna Hamilton
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Ellis Levine
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Tracey O'Connor
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Erik S Knudsen
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.
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8
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Tobiasz J, Polanska J. Proteomic Profile Distinguishes New Subpopulations of Breast Cancer Patients with Different Survival Outcomes. Cancers (Basel) 2023; 15:4230. [PMID: 37686507 PMCID: PMC10486506 DOI: 10.3390/cancers15174230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
As a highly heterogeneous disease, breast cancer (BRCA) demonstrates a diverse molecular portrait. The well-established molecular classification (PAM50) relies on gene expression profiling. It insufficiently explains the observed clinical and histopathological diversity of BRCAs. This study aims to demographically and clinically characterize the six BRCA subpopulations (basal, HER2-enriched, and four luminal ones) revealed by their proteomic portraits. GMM-based high variate protein selection combined with PCA/UMAP was used for dimensionality reduction, while the k-means algorithm allowed patient clustering. The statistical analysis (log-rank and Gehan-Wilcoxon tests, hazard ratio HR as the effect size ES) showed significant differences across identified subpopulations in Disease-Specific Survival (p = 0.0160) and Progression-Free Interval (p = 0.0264). Luminal subpopulations vary in prognosis (Disease-Free Interval, p = 0.0277). The A2 subpopulation is of the poorest, comparable to the HER2-enriched subpopulation, prognoses (HR = 1.748, referenced to Luminal B, small ES), while A3 is of the best (HR = 0.250, large ES). Similar to PAM50 subtypes, no substantial dependency on demographic and clinical factors was detected across Luminal subpopulations, as measured by χ2 test and Cramér's V for ES, and ANOVA with appropriate post hocs combined with η2 or Cohen's d-type ES, respectively. Progesterone receptors can serve as the potential A2 biomarker within Luminal patients. Further investigation of molecular differences is required to examine the potential prognostic or clinical applications.
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Affiliation(s)
- Joanna Tobiasz
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
- Department of Computer Graphics, Vision and Digital Systems, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Joanna Polanska
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
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9
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Zboril EK, Grible JM, Boyd DC, Hairr NS, Leftwich TJ, Esquivel MF, Duong AK, Turner SA, Ferreira-Gonzalez A, Olex AL, Sartorius CA, Dozmorov MG, Harrell JC. Stratification of Tamoxifen Synergistic Combinations for the Treatment of ER+ Breast Cancer. Cancers (Basel) 2023; 15:3179. [PMID: 37370789 PMCID: PMC10296623 DOI: 10.3390/cancers15123179] [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: 05/01/2023] [Revised: 05/24/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer alone accounts for the majority of cancer deaths among women, with the most commonly diagnosed subtype being estrogen receptor positive (ER+). Survival has greatly improved for patients with ER+ breast cancer, due in part to the development of antiestrogen compounds, such as tamoxifen. While treatment of the primary disease is often successful, as many as 30% of patients will experience recurrence and metastasis, mainly due to developed endocrine therapy resistance. In this study, we discovered two tamoxifen combination therapies, with simeprevir and VX-680, that reduce the tumor burden in animal models of ER+ breast cancer more than either compound or tamoxifen alone. Additionally, these tamoxifen combinations reduced the expression of HER2, a hallmark of tamoxifen treatment, which can facilitate acquisition of a treatment-resistant phenotype. These combinations could provide clinical benefit by potentiating tamoxifen treatment in ER+ breast cancer.
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Affiliation(s)
- Emily K. Zboril
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jacqueline M. Grible
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | - David C. Boyd
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
- Integrative Life Sciences Program, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nicole S. Hairr
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | - Tess J. Leftwich
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | - Madelyn F. Esquivel
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | - Alex K. Duong
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | - Scott A. Turner
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | | | - Amy L. Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Carol A. Sartorius
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - J. Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Center for Pharmaceutical Engineering, Virginia Commonwealth University, Richmond, VA 23298, USA
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10
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Ford K, Munson BP, Fong SH, Panwala R, Chu WK, Rainaldi J, Plongthongkum N, Arunachalam V, Kostrowicki J, Meluzzi D, Kreisberg JF, Jensen-Pergakes K, VanArsdale T, Paul T, Tamayo P, Zhang K, Bienkowska J, Mali P, Ideker T. Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation. Sci Rep 2023; 13:7678. [PMID: 37169829 PMCID: PMC10175263 DOI: 10.1038/s41598-023-33329-2] [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: 11/15/2022] [Accepted: 04/11/2023] [Indexed: 05/13/2023] Open
Abstract
Cell-cycle control is accomplished by cyclin-dependent kinases (CDKs), motivating extensive research into CDK targeting small-molecule drugs as cancer therapeutics. Here we use combinatorial CRISPR/Cas9 perturbations to uncover an extensive network of functional interdependencies among CDKs and related factors, identifying 43 synthetic-lethal and 12 synergistic interactions. We dissect CDK perturbations using single-cell RNAseq, for which we develop a novel computational framework to precisely quantify cell-cycle effects and diverse cell states orchestrated by specific CDKs. While pairwise disruption of CDK4/6 is synthetic-lethal, only CDK6 is required for normal cell-cycle progression and transcriptional activation. Multiple CDKs (CDK1/7/9/12) are synthetic-lethal in combination with PRMT5, independent of cell-cycle control. In-depth analysis of mRNA expression and splicing patterns provides multiple lines of evidence that the CDK-PRMT5 dependency is due to aberrant transcriptional regulation resulting in premature termination. These inter-dependencies translate to drug-drug synergies, with therapeutic implications in cancer and other diseases.
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Affiliation(s)
- Kyle Ford
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Brenton P Munson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Samson H Fong
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rebecca Panwala
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wai Keung Chu
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Joseph Rainaldi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nongluk Plongthongkum
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Todd VanArsdale
- Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA
| | - Thomas Paul
- Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA
| | - Pablo Tamayo
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Trey Ideker
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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11
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Kim H, Whitman AA, Wisniewska K, Kakati RT, Garcia-Recio S, Calhoun BC, Franco HL, Perou CM, Spanheimer PM. Tamoxifen Response at Single Cell Resolution in Estrogen Receptor-Positive Primary Human Breast Tumors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535159. [PMID: 37066379 PMCID: PMC10103953 DOI: 10.1101/2023.04.01.535159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
In ER+/HER2- breast cancer, multiple measures of intra-tumor heterogeneity are associated with worse response to endocrine therapy. To investigate heterogeneity in response to treatment, we developed an operating room-to-laboratory pipeline for the collection of live human tumors and normal breast specimens immediately after surgical resection for processing into single-cell workflows for experimentation and genomic analyses. We demonstrate differences in tamoxifen response by cell type and identify distinctly responsive and resistant subpopulations within the malignant cell compartment of human tumors. Tamoxifen resistance signatures from 3 distinct resistant subpopulations are prognostic in large cohorts of ER+ breast cancer patients and enriched in endocrine therapy resistant tumors. This novel ex vivo model system now provides a foundation to define responsive and resistant sub-populations within heterogeneous tumors, to develop precise single cell-based predictors of response to therapy, and to identify genes and pathways driving resistance to therapy.
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Affiliation(s)
- Hyunsoo Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Austin A. Whitman
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Kamila Wisniewska
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Rasha T. Kakati
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Susana Garcia-Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Benjamin C. Calhoun
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Hector L. Franco
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
- Department of Genetics, University of North Carolina, Chapel Hill, NC
- Computational Medicine Program, University of North Carolina, Chapel Hill, NC
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina, Chapel Hill, NC
- Computational Medicine Program, University of North Carolina, Chapel Hill, NC
| | - Philip M. Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
- Department of Surgery, University of North Carolina, Chapel Hill, NC
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12
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Circulating tumor DNA reveals complex biological features with clinical relevance in metastatic breast cancer. Nat Commun 2023; 14:1157. [PMID: 36859416 PMCID: PMC9977734 DOI: 10.1038/s41467-023-36801-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/14/2023] [Indexed: 03/03/2023] Open
Abstract
Liquid biopsy has proven valuable in identifying individual genetic alterations; however, the ability of plasma ctDNA to capture complex tumor phenotypes with clinical value is unknown. To address this question, we have performed 0.5X shallow whole-genome sequencing in plasma from 459 patients with metastatic breast cancer, including 245 patients treated with endocrine therapy and a CDK4/6 inhibitor (ET + CDK4/6i) from 2 independent cohorts. We demonstrate that machine learning multi-gene signatures, obtained from ctDNA, identify complex biological features, including measures of tumor proliferation and estrogen receptor signaling, similar to what is accomplished using direct tumor tissue DNA or RNA profiling. More importantly, 4 DNA-based subtypes, and a ctDNA-based genomic signature tracking retinoblastoma loss-of-heterozygosity, are significantly associated with poor response and survival outcome following ET + CDK4/6i, independently of plasma tumor fraction. Our approach opens opportunities for the discovery of additional multi-feature genomic predictors coming from ctDNA in breast cancer and other cancer-types.
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13
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Chen Y, Zhang XF, Ou-Yang L. Inferring cancer common and specific gene networks via multi-layer joint graphical model. Comput Struct Biotechnol J 2023; 21:974-990. [PMID: 36733706 PMCID: PMC9873583 DOI: 10.1016/j.csbj.2023.01.017] [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: 05/17/2022] [Revised: 01/08/2023] [Accepted: 01/14/2023] [Indexed: 01/19/2023] Open
Abstract
Cancer is a complex disease caused primarily by genetic variants. Reconstructing gene networks within tumors is essential for understanding the functional regulatory mechanisms of carcinogenesis. Advances in high-throughput sequencing technologies have provided tremendous opportunities for inferring gene networks via computational approaches. However, due to the heterogeneity of the same cancer type and the similarities between different cancer types, it remains a challenge to systematically investigate the commonalities and specificities between gene networks of different cancer types, which is a crucial step towards precision cancer diagnosis and treatment. In this study, we propose a new sparse regularized multi-layer decomposition graphical model to jointly estimate the gene networks of multiple cancer types. Our model can handle various types of gene expression data and decomposes each cancer-type-specific network into three components, i.e., globally shared, partially shared and cancer-type-unique components. By identifying the globally and partially shared gene network components, our model can explore the heterogeneous similarities between different cancer types, and our identified cancer-type-unique components can help to reveal the regulatory mechanisms unique to each cancer type. Extensive experiments on synthetic data illustrate the effectiveness of our model in joint estimation of multiple gene networks. We also apply our model to two real data sets to infer the gene networks of multiple cancer subtypes or cell lines. By analyzing our estimated globally shared, partially shared, and cancer-type-unique components, we identified a number of important genes associated with common and specific regulatory mechanisms across different cancer types.
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Affiliation(s)
- Yuanxiao Chen
- Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen Key Laboratory of Media Security, and Guangdong Laboratory of Artificial Intelligence and Digital Economy(SZ), Shenzhen University, Shenzhen, China
| | - Xiao-Fei Zhang
- School of Mathematics and Statistics & Hubei Key Laboratory of Mathematical Sciences, Central China Normal University, Wuhan, China
| | - Le Ou-Yang
- Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen Key Laboratory of Media Security, and Guangdong Laboratory of Artificial Intelligence and Digital Economy(SZ), Shenzhen University, Shenzhen, China,Corresponding author.
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14
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Papadimitriou MC, Pazaiti A, Iliakopoulos K, Markouli M, Michalaki V, Papadimitriou CA. Resistance to CDK4/6 inhibition: Mechanisms and strategies to overcome a therapeutic problem in the treatment of hormone receptor-positive metastatic breast cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119346. [PMID: 36030016 DOI: 10.1016/j.bbamcr.2022.119346] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/09/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Selective CDK4/6 inhibitors, such as palbociclib, ribociclib, and abemaciclib, have been approved in combination with hormone therapy for the treatment of patients with HR+, HER2-negative advanced or metastatic breast cancer (mBC). Despite their promising activity, approximately 10 % of patients have de novo resistance, while the rest of them will develop acquired resistance after 24-28 months when used as first-line therapy and after a shorter period when used as second-line therapy. Various mechanisms of resistance to CDK4/6 inhibitors have been described, including cell cycle-related mechanisms, such as RB loss, p16 amplification, CDK6 or CDK4 amplification, and cyclin E-CDK2 amplification. Other bypass mechanisms involve the activation of FGFR or PI3K/AKT/mTOR pathways. Identifying the different mechanisms by which resistance to CDK4/6 inhibitors occurs may help to design new treatment strategies to improve patient outcomes. This review presents the currently available knowledge on the mechanisms of resistance to CDK4/6 inhibitors, explores possible treatment strategies that could overcome this therapeutic problem, and summarizes relevant recent clinical trials.
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Affiliation(s)
- Marios C Papadimitriou
- Oncology Unit, Second Department of Surgery, Aretaieio University Hospital, National and Kapodistrian University of Athens, Vasilissis Sofias 76, 115 28 Athens, Greece
| | - Anastasia Pazaiti
- Breast Clinic of Oncologic and Reconstructive Surgery, Metropolitan General Hospital, Leoforos Mesogeion 264, 155 62 Cholargos, Greece.
| | - Konstantinos Iliakopoulos
- Second Department of Surgery, Aretaieio University Hospital, National and Kapodistrian University of Athens, Vasilissis Sofias 76, 115 28 Athens, Greece
| | - Mariam Markouli
- Second Department of Surgery, Aretaieio University Hospital, National and Kapodistrian University of Athens, Vasilissis Sofias 76, 115 28 Athens, Greece
| | - Vasiliki Michalaki
- Oncology Unit, Second Department of Surgery, Aretaieio University Hospital, National and Kapodistrian University of Athens, Vasilissis Sofias 76, 115 28 Athens, Greece
| | - Christos A Papadimitriou
- Oncology Unit, Second Department of Surgery, Aretaieio University Hospital, National and Kapodistrian University of Athens, Vasilissis Sofias 76, 115 28 Athens, Greece.
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15
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Biomarkers of Response and Resistance to CDK4/6 Inhibitors in Breast Cancer: Hints from Liquid Biopsy and microRNA Exploration. Int J Mol Sci 2022; 23:ijms232314534. [PMID: 36498861 PMCID: PMC9739115 DOI: 10.3390/ijms232314534] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
New evidence on the impact of dysregulation of the CDK4/6 pathway on breast cancer (BC) cell proliferation has led to the development of selective CDK4/6 inhibitors, which have radically changed the management of advanced BC. Despite the improved outcomes obtained by CDK4/6 inhibitors, approximately 10% of tumors show primary resistance, whereas acquired resistance appears to be an almost ubiquitous occurrence, leading to treatment failure. The identification of differentially expressed genes or genomic mutational signatures able to predict sensitivity or resistance to CDK4/6 inhibitors is critical for medical decision making and for avoiding or counteracting primary or acquired resistance against CDK4/6 inhibitors. In this review, we summarize the main mechanisms of resistance to CDK4/6 inhibitors, focusing on those associated with potentially relevant biomarkers that could predict patients' response/resistance to treatment. Recent advances in biomarker identification are discussed, including the potential use of liquid biopsy for BC management and the role of multiple microRNAs as molecular predictors of cancer cell sensitivity and resistance to CDK4/6 inhibitors.
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16
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Szabova L, Gordon MB, Lu L, Pate N, Bassel L, Iacovelli AJ, Karim B, Homan PJ, Householder DB, Guerin TM, Burkett S, Day AM, Custer W, Weaver Ohler Z. Loss of Brca1 and Trp53 in adult mouse mammary ductal epithelium results in development of hormone receptor-positive or hormone receptor-negative tumors, depending on inactivation of Rb family proteins. Breast Cancer Res 2022; 24:75. [PMID: 36333737 PMCID: PMC9636824 DOI: 10.1186/s13058-022-01566-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Breast cancer is a heterogenous disease with several histological and molecular subtypes. Models that represent these subtypes are essential for translational research aimed at improving clinical strategy for targeted therapeutics. METHODS Different combinations of genetic aberrations (Brca1 and Trp53 loss, and inhibition of proteins of the Rb family) were induced in the mammary gland by injection of adenovirus expressing Cre recombinase into the mammary ducts of adult genetically engineered mice. Mammary tumors with different genetic aberrations were classified into molecular subtypes based on expression of molecular markers and RNAseq analysis. In vitro potency assays and Western blots were used to examine their drug sensitivities. RESULTS Induction of Brca1 and Trp53 loss in mammary ductal epithelium resulted in development of basal-like hormone receptor (HR)-negative mammary tumors. Inhibition of Rb and Trp53 loss or the combination of Rb, Trp53 and Brca1 aberrations resulted in development of luminal ductal carcinoma positive for ER, PR, and Her2 expression. HR positivity in tumors with Rb, Trp53 and Brca1 aberrations indicated that functionality of the Rb pathway rather than Brca1 status affected HR status in these models. Mammary tumor gene expression profiles recapitulated human basal-like or luminal B breast cancer signatures, but HR-positive luminal cancer models were endocrine resistant and exhibited upregulation of PI3K signaling and sensitivity to this pathway inhibition. Furthermore, both tumor subtypes were resistant to CDK4/6 inhibition. CONCLUSIONS Examination of molecular expression profiles and drug sensitivities of tumors indicate that these breast cancer models can be utilized as a translational platform for evaluation of targeted combinations to improve chemotherapeutic response in patients that no longer respond to hormone therapy or that are resistant to CDK4/6 inhibition.
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Affiliation(s)
- Ludmila Szabova
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA.
| | - Melanie B Gordon
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lucy Lu
- Center for Advanced Preclinical Research, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Nathan Pate
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Sanofi,Global Discovery Pathology, Translational In Vivo Models Platform, Framingham, MA, USA
| | - Laura Bassel
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Anthony J Iacovelli
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Genentech, Inc., South San Francisco, CA, USA
| | - Baktiar Karim
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Molecular Histopathology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Philip J Homan
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Deborah B Householder
- Center for Advanced Preclinical Research, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Theresa M Guerin
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Amanda M Day
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Wendi Custer
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Zoe Weaver Ohler
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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17
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Cheng T, Wu Y, Liu Z, Yu Y, Sun S, Guo M, Sun B, Huang C. CDKN2A-mediated molecular subtypes characterize the hallmarks of tumor microenvironment and guide precision medicine in triple-negative breast cancer. Front Immunol 2022; 13:970950. [PMID: 36052076 PMCID: PMC9424905 DOI: 10.3389/fimmu.2022.970950] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Currently, breast cancer (BRCA) has become the most common cancer in the world, whose pathological mechanism is complex. Among its subtypes, triple-negative breast cancer (TNBC) has the worst prognosis. With the increasing number of diagnosed TNBC patients, the urgent need of novel biomarkers is also rising. Cyclin-dependent kinase inhibitor 2A (CDKN2A) has recently emerged as a key regulator associated with ferroptosis and cuproptosis (FAC) and has exhibited a significant effect on BRCA, but its detailed mechanism remains elusive. Herein, we conducted the first converge comprehensive landscape analysis of FAC-related gene CDKN2A in BRCA and disclosed its prognostic value in BRCA. Then, an unsupervised cluster analysis based on CDKN2A-correlated genes unveiled three subtypes, namely cold-immune subtype, IFN-γ activated subtype and FTL-dominant subtype. Subsequent analyses depicting hallmarks of tumor microenvironment (TME) among three subtypes suggested strong association between TNBC and CDKN2A. Given the fact that the most clinically heterogeneous TNBC always displayed the most severe outcomes and lacked relevant drug targets, we further explored the potential of immunotherapy for TNBC by interfering CDKN2A and constructed the CDKN2A-derived prognostic model for TNBC patients by Lasso-Cox. The 21-gene–based prognostic model showed high accuracy and was verified in external independent validation cohort. Moreover, we proposed three drugs for TNBC patients based on our model via targeting epidermal growth factor receptor. In summary, our study indicated the potential of CDKN2A as a pioneering prognostic predictor for TNBC and provided a rationale of immunotherapy for TNBC, and offered fresh perspectives and orientations for cancer treatment via inducing ferroptosis and cuproptosis to develop novel anti-cancer treatment strategies.
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Affiliation(s)
- Tianyi Cheng
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Yingyi Wu
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, Macao SAR, China
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Zhiyu Liu
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Yi Yu
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Shixue Sun
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Min Guo
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Baoqing Sun
- Department of Allergy and Clinical Immunology, Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Baoqing Sun, ; Chen Huang,
| | - Chen Huang
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, Macao SAR, China
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macao, Macao SAR, China
- *Correspondence: Baoqing Sun, ; Chen Huang,
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18
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Watt AC, Goel S. Cellular mechanisms underlying response and resistance to CDK4/6 inhibitors in the treatment of hormone receptor-positive breast cancer. Breast Cancer Res 2022; 24:17. [PMID: 35248122 PMCID: PMC8898415 DOI: 10.1186/s13058-022-01510-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/20/2022] [Indexed: 12/24/2022] Open
Abstract
Pharmacological inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) are now an established standard of care for patients with advanced hormone receptor-positive breast cancer. The canonical mechanism underlying CDK4/6 inhibitor activity is the suppression of phosphorylation of the retinoblastoma tumor suppressor protein, which serves to prevent cancer cell proliferation. Recent data suggest that these agents induce other diverse effects within both tumor and stromal compartments, which serve to explain aspects of their clinical activity. Here, we review these phenomena and discuss how they might be leveraged in the development of novel CDK4/6 inhibitor-containing combination treatments. We also briefly review the various known mechanisms of acquired resistance in the clinical setting.
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Affiliation(s)
- April C Watt
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Shom Goel
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3052, Australia.
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19
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Altered Expression of RB and pRB in Tissue Arrays of Primary Breast Cancers and Matched Axillary Lymph Node Metastases. Breast J 2022; 2022:5221257. [PMID: 35711885 PMCID: PMC9187282 DOI: 10.1155/2022/5221257] [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: 11/28/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 12/02/2022]
Abstract
Objectives The retinoblastoma (RB) pathway is crucial in the development and progression of many cancers. To better understand the biology of progressive breast cancer (BC), we examined protein expression of the RB pathway in primary BCs and matched axillary lymph node metastases (LM). Methods Immunohistochemistry was used to evaluate cyclin D1, CDK4/6, RB, phosphorylated RB (pRB), and E2F1 expression in tissue arrays containing cores of 50 primary BCs and matched LM. The number of positive tumor cells and staining intensity were scored. Results The proteins were localized in the nucleus, while CDK6 was detected in the cytoplasm and CDK4 was found in both. pRB and E2F1 showed higher expression in matched LM than in primary tumors. Expression of these proteins differed significantly by the percentage of positive tumor cells, while proteins in the proximal portion of the RB pathway showed no significant differences. The main path of alteration consisted of high pRB in primary BC, remaining pRB high in the majority of LM, variations occurring in fewer cases. All matched LM of the few primary tumors that had unaltered RB and pRB expression showed changes in RB or pRB expression. Conclusion Expression of pRB and E2F1 was significantly higher in LM than in primary BC. A majority of cancers with LM showed altered RB or pRB expression, suggesting that proteins downstream in the RB pathway play a critical role in metastatic BC and disease progression. So looking at the RB pathway could be an option for chemotherapy decisions in patients with only few LM.
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20
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Loss of function of BRCA1 promotes EMT in mammary tumors through activation of TGFβR2 signaling pathway. Cell Death Dis 2022; 13:195. [PMID: 35236825 PMCID: PMC8891277 DOI: 10.1038/s41419-022-04646-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 01/25/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
Abstract
BRCA1 deficient breast cancers are aggressive and chemoresistant due, in part, to their enrichment of cancer stem cells that can be generated from carcinoma cells by an epithelial-mesenchymal transition (EMT). We previously discovered that BRCA1 deficiency activates EMT in mammary tumorigenesis. How BRCA1 controls EMT and how to effectively target BRCA1-deficient cancers remain elusive. We analyzed murine and human tumors and identified a role for Tgfβr2 in governing the molecular aspects of EMT that occur with Brca1 loss. We utilized CRISPR to delete Tgfβr2 and specific inhibitors to block Tgfβr2 activity and followed up with the molecular analysis of assays for tumor growth and metastasis. We discovered that heterozygous germline deletion, or epithelia-specific deletion of Brca1 in mice, activates Tgfβr2 signaling pathways in mammary tumors. BRCA1 depletion promotes TGFβ-mediated EMT activation in cancer cells. BRCA1 binds to the TGFβR2 locus to repress its transcription. Targeted deletion or pharmaceutical inhibition of Tgfβr2 in Brca1-deficient tumor cells reduces EMT and suppresses tumorigenesis and metastasis. BRCA1 and TGFβR2 expression levels are inversely related in human breast cancers. This study reveals for the first time that a targetable TGFβR signaling pathway is directly activated by BRCA1-deficiency in the induction of EMT in breast cancer progression.
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21
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Mandigo AC, Shafi AA, McCann JJ, Yuan W, Laufer TS, Bogdan D, Gallagher L, Dylgjeri E, Semenova G, Vasilevskaya IA, Schiewer MJ, McNair CM, de Bono JS, Knudsen KE. Novel Oncogenic Transcription Factor Cooperation in RB-Deficient Cancer. Cancer Res 2022; 82:221-234. [PMID: 34625422 PMCID: PMC9397633 DOI: 10.1158/0008-5472.can-21-1159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/14/2021] [Accepted: 09/09/2021] [Indexed: 01/07/2023]
Abstract
The retinoblastoma tumor suppressor (RB) is a critical regulator of E2F-dependent transcription, controlling a multitude of protumorigenic networks including but not limited to cell-cycle control. Here, genome-wide assessment of E2F1 function after RB loss in isogenic models of prostate cancer revealed unexpected repositioning and cooperation with oncogenic transcription factors, including the major driver of disease progression, the androgen receptor (AR). Further investigation revealed that observed AR/E2F1 cooperation elicited novel transcriptional networks that promote cancer phenotypes, especially as related to evasion of cell death. These observations were reflected in assessment of human disease, indicating the clinical relevance of the AR/E2F1 cooperome in prostate cancer. Together, these studies reveal new mechanisms by which RB loss induces cancer progression and highlight the importance of understanding the targets of E2F1 function. SIGNIFICANCE: This study identifies that RB loss in prostate cancer drives cooperation between AR and E2F1 as coregulators of transcription, which is linked to the progression of advanced disease.
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Affiliation(s)
- Amy C Mandigo
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Ayesha A Shafi
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jennifer J McCann
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Wei Yuan
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
| | - Talya S Laufer
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Denisa Bogdan
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
| | - Lewis Gallagher
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
| | - Emanuela Dylgjeri
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Galina Semenova
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Irina A Vasilevskaya
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Matthew J Schiewer
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Chris M McNair
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Johann S de Bono
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
| | - Karen E Knudsen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Radiation Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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22
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Mandigo AC, Tomlins SA, Kelly WK, Knudsen KE. Relevance of pRB Loss in Human Malignancies. Clin Cancer Res 2022; 28:255-264. [PMID: 34407969 PMCID: PMC9306333 DOI: 10.1158/1078-0432.ccr-21-1565] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/24/2021] [Accepted: 08/10/2021] [Indexed: 01/07/2023]
Abstract
The retinoblastoma tumor suppressor protein (pRB) is a known regulator of cell-cycle control; however, recent studies identified critical functions for pRB in regulating cancer-associated gene networks that influence the DNA damage response, apoptosis, and cell metabolism. Understanding the impact of these pRB functions on cancer development and progression in the clinical setting will be essential, given the prevalence of pRB loss of function across disease types. Moreover, the current state of evidence supports the concept that pRB loss results in pleiotropic effects distinct from tumor proliferation. Here, the implications of pRB loss (and resultant pathway deregulation) on disease progression and therapeutic response will be reviewed, based on clinical observation. Developing a better understanding of the pRB-regulated pathways that underpin the aggressive features of pRB-deficient tumors will be essential for further developing pRB as a biomarker of disease progression and for stratifying pRB-deficient tumors into more effective treatment regimens.
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Affiliation(s)
- Amy C. Mandigo
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Scott A. Tomlins
- Departments of Pathology and Urology, Michigan Center for Translational Pathology, Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - William K. Kelly
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E. Knudsen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Corresponding Author: Karen E. Knudsen, Thomas Jefferson University, 233 South 10th Street, BLSB 1050, Philadelphia, PA 19107. Phone: 215-503-5692; E-mail:
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23
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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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24
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Wu D, Tan H, Su W, Cheng D, Wang G, Wang J, Ma DA, Dong GM, Sun P. MZF1 mediates oncogene-induced senescence by promoting the transcription of p16 INK4A. Oncogene 2022; 41:414-426. [PMID: 34773072 PMCID: PMC8758531 DOI: 10.1038/s41388-021-02110-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 01/27/2023]
Abstract
Oncogene induced senescence is a tumor suppressing defense mechanism, in which the cell cycle-dependent protein kinase (CDK) inhibitor p16INK4A (encoded by the CDKN2A gene) plays a key role. We previously reported that a transcriptional co-activator chromodomain helicase DNA binding protein 7 (CHD7) mediates oncogenic ras-induced senescence by inducing transcription of the p16INK4A gene. In the current study, we identified myeloid zinc finger 1 (MZF1) as the transcriptional factor that recruits CHD7 to the p16INK4A promoter, where it mediates oncogenic ras-induced p16INK4A transcription and senescence through CHD7, in primary human cells from multiple origins. Moreover, the expression of MZF1 is induced by oncogenic ras in senescent cells through the c-Jun and Ets1 transcriptional factors upon their activation by the Ras-Raf-1-MEK-ERK signaling pathway. In non-small cell lung cancer (NSCLC) and pancreatic adenocarcinoma (PAAD) where activating ras mutations occur frequently, reduced MZF1 expression is observed in tumors, as compared to corresponding normal tissues, and correlates with poor patient survival. Analysis of single cell RNA-sequencing data from PAAD patients revealed that among the tumor cells with normal RB expression levels, those with reduced levels of MZF1 are more likely to express lower p16INK4A levels. These findings have identified novel signaling components in the pathway that mediates induction of the p16INK4A tumor suppressor and the senescence response, and suggested that MZF1 is a potential tumor suppressor in at least some cancer types, the loss of which contributes to the inactivation of the p16INK4A/RB pathway and disruption of senescence in tumor cells with intact RB.
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Affiliation(s)
- Dan Wu
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - Hua Tan
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Weijun Su
- Nankai University School of Medicine, Tianjin, China
| | - Dongmei Cheng
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - Guanwen Wang
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA,Nankai University School of Medicine, Tianjin, China
| | - Juan Wang
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA,Nankai University School of Medicine, Tianjin, China
| | - Ding A. Ma
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - George M. Dong
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - Peiqing Sun
- Department of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-, Salem, NC, 27157, USA.
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25
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Saleh L, Wilson C, Holen I. CDK4/6 inhibitors: A potential therapeutic approach for triple negative breast cancer. MedComm (Beijing) 2021; 2:514-530. [PMID: 34977868 PMCID: PMC8706744 DOI: 10.1002/mco2.97] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/29/2021] [Accepted: 10/07/2021] [Indexed: 02/06/2023] Open
Abstract
Triple negative breast cancer (TNBC) cells lack expression of the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER-2). Thus, TNBC does not respond to hormone-based therapy. TNBC is also an aggressive subtype associated with poorer prognoses compared to other breast cancers. Conventional chemotherapeutics are used to manage TNBC although systemic relapse is common with limited benefits being reported as well as adverse events being documented. Here, we discuss current therapies for TNBC in the neo- and adjuvant settings, as well as recent advancements in the targeting of PD-L1-positive tumors and inclusion of PARP inhibitors for TNBC patients with BRCA mutations. The recent development of cyclin-dependent kinase (CDK) 4/6 inhibitors in ER-positive breast cancers has demonstrated significant improvements in progression free survival in patients. Here, we review preclinical data of CDK 4/6 inhibitors and describe current clinical trials assessing these in TNBC disease.
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Affiliation(s)
- Lubaid Saleh
- Department of Oncology and MetabolismMedical SchoolUniversity of SheffieldSheffieldUK
| | | | - Ingunn Holen
- Department of Oncology and MetabolismMedical SchoolUniversity of SheffieldSheffieldUK
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26
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Dutta A, Dutreux F, Schacherer J. Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds. eLife 2021; 10:70339. [PMID: 34159898 PMCID: PMC8245132 DOI: 10.7554/elife.70339] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022] Open
Abstract
The dynamics and diversity of the appearance of genetic variants play an essential role in the evolution of the genome and the shaping of biodiversity. Recent population-wide genome sequencing surveys have highlighted the importance of loss of heterozygosity (LOH) events and have shown that they are a neglected part of the genetic diversity landscape. To assess the extent, variability, and spectrum, we explored the accumulation of LOH events in 169 heterozygous diploid Saccharomyces cerevisiae mutation accumulation lines across nine genetic backgrounds. In total, we detected a large set of 22,828 LOH events across distinct genetic backgrounds with a heterozygous level ranging from 0.1% to 1%. LOH events are very frequent with a rate consistently much higher than the mutation rate, showing their importance for genome evolution. We observed that the interstitial LOH (I-LOH) events, resulting in internal short LOH tracts, were much frequent (n = 19,660) than the terminal LOH (T-LOH) events, that is, tracts extending to the end of the chromosome (n = 3168). However, the spectrum, the rate, and the fraction of the genome under LOH vary across genetic backgrounds. Interestingly, we observed that the more the ancestors were heterozygous, the more they accumulated T-LOH events. In addition, frequent short I-LOH tracts are a signature of the lines derived from hybrids with low spore fertility. Finally, we found lines showing almost complete homozygotization during vegetative progression. Overall, our results highlight that the variable dynamics of the LOH accumulation across distinct genetic backgrounds might lead to rapid differential genome evolution during vegetative growth.
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Affiliation(s)
- Abhishek Dutta
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF), Paris, France
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27
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Zhuang Y, Grainger JM, Vedell PT, Yu J, Moyer AM, Gao H, Fan XY, Qin S, Liu D, Kalari KR, Goetz MP, Boughey JC, Weinshilboum RM, Wang L. Establishment and characterization of immortalized human breast cancer cell lines from breast cancer patient-derived xenografts (PDX). NPJ Breast Cancer 2021; 7:79. [PMID: 34145270 PMCID: PMC8213738 DOI: 10.1038/s41523-021-00285-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
The application of patient-derived xenografts (PDX) in drug screening and testing is a costly and time-consuming endeavor. While cell lines permit extensive mechanistic studies, many human breast cancer cell lines lack patient characteristics and clinical treatment information. Establishing cell lines that retain patient's genetic and drug response information would enable greater drug screening and mechanistic studies. Therefore, we utilized breast cancer PDX from the Mayo Breast Cancer Genome Guided Therapy Study (BEAUTY) to establish two immortalized, genomically unique breast cancer cell lines. Through extensive genetic and therapeutic testing, the cell lines were found to retain the same clinical subtype, major somatic alterations, and drug response phenotypes as their corresponding PDX and patient tumor. Our findings demonstrate PDX can be utilized to develop immortalized breast cancer cell lines and provide a valuable tool for understanding the molecular mechanism of drug resistance and exploring novel treatment strategies.
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Affiliation(s)
- Yongxian Zhuang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Jordan M Grainger
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Peter T Vedell
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Jia Yu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Ann M Moyer
- Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Huanyao Gao
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Xiao-Yang Fan
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Sisi Qin
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Matthew P Goetz
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | | | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
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28
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Abstract
The introduction of cyclin-dependent kinase 4/6 inhibitors (CKIs) has marked a major development in the standard treatment of advanced breast cancer. Extensive preclinical, translational and clinical research efforts into CKI agents are ongoing, and clinical application of this class of systemic anti-cancer therapy is anticipated to expand beyond metastatic breast cancer treatment. Emerging evidence indicates that mechanisms by which CKI agents exert their therapeutic effect transcend their initially expected impacts on cell cycle control into the realms of cancer immunology and metabolism. The recent expansion in our understanding of the multifaceted impact of CKIs on tumour biology has the potential to improve clinical study design, therapeutic strategies and ultimately patient outcomes. This review contextualises the current status of CKI therapy by providing an overview of the original and emerging insights into mechanisms of action and the evidence behind their current routine use in breast cancer management. Recent preclinical and clinical studies into CKIs across tumour types are discussed, including a synthesis of the more than 300 clinical trials of CKI-combination treatments registered as of November 2020. Key challenges and opportunities anticipated in the 2020s are explored, including treatment resistance, combination therapy strategies and potential biomarker development.
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29
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Mandigo AC, Yuan W, Xu K, Gallagher P, Pang A, Guan YF, Shafi AA, Thangavel C, Sheehan B, Bogdan D, Paschalis A, McCann JJ, Laufer TS, Gordon N, Vasilevskaya IA, Dylgjeri E, Chand SN, Schiewer MJ, Domingo-Domenech J, Den RB, Holst J, McCue PA, de Bono JS, McNair C, Knudsen KE. RB/E2F1 as a Master Regulator of Cancer Cell Metabolism in Advanced Disease. Cancer Discov 2021; 11:2334-2353. [PMID: 33879449 DOI: 10.1158/2159-8290.cd-20-1114] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/20/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022]
Abstract
Loss of the retinoblastoma (RB) tumor suppressor protein is a critical step in reprogramming biological networks that drive cancer progression, although mechanistic insight has been largely limited to the impact of RB loss on cell-cycle regulation. Here, isogenic modeling of RB loss identified disease stage-specific rewiring of E2F1 function, providing the first-in-field mapping of the E2F1 cistrome and transcriptome after RB loss across disease progression. Biochemical and functional assessment using both in vitro and in vivo models identified an unexpected, prominent role for E2F1 in regulation of redox metabolism after RB loss, driving an increase in the synthesis of the antioxidant glutathione, specific to advanced disease. These E2F1-dependent events resulted in protection from reactive oxygen species in response to therapeutic intervention. On balance, these findings reveal novel pathways through which RB loss promotes cancer progression and highlight potentially new nodes of intervention for treating RB-deficient cancers. SIGNIFICANCE: This study identifies stage-specific consequences of RB loss across cancer progression that have a direct impact on tumor response to clinically utilized therapeutics. The study herein is the first to investigate the effect of RB loss on global metabolic regulation and link RB/E2F1 to redox control in multiple advanced diseases.This article is highlighted in the In This Issue feature, p. 2113.
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Affiliation(s)
- Amy C Mandigo
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Wei Yuan
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Kexin Xu
- The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Peter Gallagher
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Angel Pang
- School of Medical Sciences and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Yi Fang Guan
- School of Medical Sciences and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Ayesha A Shafi
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Chellappagounder Thangavel
- Departments of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Dermatology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Beshara Sheehan
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Denisa Bogdan
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Alec Paschalis
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jennifer J McCann
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Talya S Laufer
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Nicolas Gordon
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Irina A Vasilevskaya
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Emanuela Dylgjeri
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Saswati N Chand
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Matthew J Schiewer
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Robert B Den
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Departments of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jeff Holst
- Department of Dermatology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Peter A McCue
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Johann S de Bono
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Christopher McNair
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. .,Departments of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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30
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Agostinetto E, Eiger D, Punie K, de Azambuja E. Emerging Therapeutics for Patients with Triple-Negative Breast Cancer. Curr Oncol Rep 2021; 23:57. [PMID: 33763756 DOI: 10.1007/s11912-021-01038-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2021] [Indexed: 02/08/2023]
Abstract
PURPOSE OF REVIEW Triple negative breast cancer (TNBC) accounts for approximately 10-15% of all breast cancers and it is associated with a poor prognosis. However, recent new effective treatment strategies have improved its outcomes. The aim of this review is to provide an overview on the emerging therapeutics for TNBC, describing both previously approved therapies that are currently being repurposed, as well as new target therapies that may improve patient outcomes. RECENT FINDINGS Emerging therapies are forthcoming in TNBC's treatment landscape, including new post-neoadjuvant chemotherapy strategies, PARP inhibitors, immune checkpoint inhibitors, and antibody-drug conjugates. Combination of different therapies such as AKT/PI3K/mTOR-inhibitors, other immunotherapeutic agents, CDK-inhibitors, antiandrogens, antiangiogenics, and histone deacetylase inhibitors is under clinical investigation. The treatment landscape for TNBC is gradually evolving towards a more personalized approach with promising expectations.
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Affiliation(s)
- Elisa Agostinetto
- Academic Trials Promoting Team, Institut Jules Bordet and l'Université Libre de Bruxelles (U.L.B), Rue Héger-Bordet 1, 1000, Brussels, Belgium.,Department of Medical Oncology and Hematology, Humanitas Clinical and Research Center - IRCCS, Humanitas Cancer Center, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Daniel Eiger
- Academic Trials Promoting Team, Institut Jules Bordet and l'Université Libre de Bruxelles (U.L.B), Rue Héger-Bordet 1, 1000, Brussels, Belgium
| | - Kevin Punie
- Department of General Medical Oncology and Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Evandro de Azambuja
- Academic Trials Promoting Team, Institut Jules Bordet and l'Université Libre de Bruxelles (U.L.B), Rue Héger-Bordet 1, 1000, Brussels, Belgium.
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31
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Differential gene expression analysis of palbociclib-resistant TNBC via RNA-seq. Breast Cancer Res Treat 2021; 186:677-686. [PMID: 33599863 PMCID: PMC8019424 DOI: 10.1007/s10549-021-06127-5] [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: 05/30/2020] [Accepted: 02/02/2021] [Indexed: 11/05/2022]
Abstract
Purpose The management of triple-negative breast cancer (TNBC) remains a significant clinical challenge due to the lack of effective targeted therapies. Inhibitors of the cyclin-dependent kinases 4 and 6 (CDK4/6) are emerging as promising therapeutic agents against TNBC; however, cells can rapidly acquire resistance through multiple mechanisms that are yet to be identified. Therefore, determining the mechanisms underlying resistance to CDK4/6 inhibition is crucial to develop combination therapies that can extend the efficacy of the CDK4/6 inhibitors or delay resistance. This study aims to identify differentially expressed genes (DEG) associated with acquired resistance to palbociclib in ER− breast cancer cells. Methods We performed next-generation transcriptomic sequencing (RNA-seq) and pathway analysis in ER− MDA-MB-231 palbociclib-sensitive (231/pS) and palbociclib-resistant (231/pR) cells. Results We identified 2247 up-regulated and 1427 down-regulated transcripts in 231/pR compared to 231/pS cells. DEGs were subjected to functional analysis using Gene Ontology (GO) and the KEGG database which identified many transduction pathways associated with breast cancer, including the PI3K/AKT, PTEN and mTOR pathways. Additionally, Ingenuity Pathway Analysis (IPA) revealed that resistance to palbociclib is closely associated with altered cholesterol and fatty acid biosynthesis suggesting that resistance to palbociclib may be dependent on lipid metabolic reprograming. Conclusion This study provides evidence that lipid metabolism is altered in TNBC with acquired resistance to palbociclib. Further studies are needed to determine if the observed lipid metabolic rewiring can be exploited to overcome therapy resistance in TNBC. Supplementary Information The online version contains supplementary material available at 10.1007/s10549-021-06127-5.
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32
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DNA damage response inhibitors: An avenue for TNBC treatment. Biochim Biophys Acta Rev Cancer 2021; 1875:188521. [PMID: 33556453 DOI: 10.1016/j.bbcan.2021.188521] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/30/2021] [Accepted: 01/30/2021] [Indexed: 01/13/2023]
Abstract
The DNA damage response (DDR) is critical for the maintenance of genomic stability by sensing DNA damage, regulating cell cycle and initiating DNA repair. Drugs targeting DDR pathways have been increasingly exploited in treating various tumors. Triple negative breast cancer (TNBC) is a highly heterogeneous and aggressive tumor with constitutive activation of oncogenes, inducing replication stress and DNA damage, which require the DDR for survival. In addition, emerging studies have demonstrated that TNBC harbors aberrant genetic alterations in DDR pathways, such as a high frequency of p53 dysfunction and BRCA1/2 mutations. DDR alterations force TNBC to rely on the existing DDR pathways for survival, and make TNBC particularly sensitive to specific DDR inhibitors, such as high sensitivity of TNBC with BRCA1/2 mutations to PARP inhibitors. This review first and comprehensively covers the current status of the development of DDR inhibitors and discusses the mechanism of targeting the DDR in TNBC. Preclinical and clinical studies on inhibitors of the ATR-CHK1-WEE1 pathway and PARP inhibitors, the most studied inhibitors, and some other DDR inhibitors as monotherapy or combination therapy in TNBC are summarized. We also highlight the possible predictive biomarkers for these DDR inhibitors and their potential combination strategies with chemotherapy, radiotherapy or other targeted agents to optimize the efficacy of DDR inhibitors in TNBC treatment. In conclusion, this review discussed the recent considerations related to the use of DDR inhibitors for TNBC and provides a perspective to address future directions and potential therapeutic strategies for patients with TNBC.
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33
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Bai F, Liu S, Liu X, Hollern DP, Scott A, Wang C, Zhang L, Fan C, Fu L, Perou CM, Zhu WG, Pei XH. PDGFRβ is an essential therapeutic target for BRCA1-deficient mammary tumors. Breast Cancer Res 2021; 23:10. [PMID: 33478572 PMCID: PMC7819225 DOI: 10.1186/s13058-021-01387-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/03/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Basal-like breast cancers (BLBCs) are a leading cause of cancer death due to their capacity to metastasize and lack of effective therapies. More than half of BLBCs have a dysfunctional BRCA1. Although most BRCA1-deficient cancers respond to DNA-damaging agents, resistance and tumor recurrence remain a challenge to survival outcomes for BLBC patients. Additional therapies targeting the pathways aberrantly activated by BRCA1 deficiency are urgently needed. METHODS Most BRCA1-deficient BLBCs carry a dysfunctional INK4-RB pathway. Thus, we created genetically engineered mice with Brca1 loss and deletion of p16INK4A, or separately p18INK4C, to model the deficient INK4-RB signaling in human BLBC. By using these mutant mice and human BRCA1-deficient and proficient breast cancer tissues and cells, we tested if there exists a druggable target in BRCA1-deficient breast cancers. RESULTS Heterozygous germline or epithelium-specific deletion of Brca1 in p18INK4C- or p16INK4A-deficient mice activated Pdgfrβ signaling, induced epithelial-to-mesenchymal transition, and led to BLBCs. Confirming this role, targeted deletion of Pdgfrβ in Brca1-deficient tumor cells promoted cell death, induced mesenchymal-to-epithelial transition, and suppressed tumorigenesis. Importantly, we also found that pharmaceutical inhibition of Pdgfrβ and its downstream target Pkcα suppressed Brca1-deficient tumor initiation and progression and effectively killed BRCA1-deficient cancer cells. CONCLUSIONS Our work offers the first genetic and biochemical evidence that PDGFRβ-PKCα signaling is repressed by BRCA1, which establishes PDGFRβ-PKCα signaling as a therapeutic target for BRCA1-deficient breast cancers.
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Affiliation(s)
- Feng Bai
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Department of Pathology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL, 33136, USA
| | - Shiqin Liu
- Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL, 33136, USA
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xiong Liu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Department of Anatomy and Histology, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Daniel P Hollern
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexandria Scott
- Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL, 33136, USA
| | - Chuying Wang
- Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL, 33136, USA
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lihan Zhang
- Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL, 33136, USA
- The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Li Fu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Department of Pharmacology, Shenzhen University Health Science Center, Shenzhen, 518039, China
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Xin-Hai Pei
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518060, China.
- Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL, 33136, USA.
- Department of Anatomy and Histology, Shenzhen University Health Science Center, Shenzhen, 518060, China.
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David S, Ho G, Day D, Harris M, Tan J, Goel S, Hanna GG, Srivastava R, Kruss G, McDowell L, White M. Enhanced toxicity with CDK 4/6 inhibitors and palliative radiotherapy: Non-consecutive case series and review of the literature. Transl Oncol 2020; 14:100939. [PMID: 33227663 PMCID: PMC7689545 DOI: 10.1016/j.tranon.2020.100939] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 11/25/2022] Open
Abstract
CDK 4/6 inhibitors are commonly used in patients with advanced hormone receptor positive breast cancer. Many patients receive palliative radiotherapy for symptomatic disease concomitantly with a CDK 4/6 inhibitor. There is a paucity of data on the safety of combining a CDK 4/6 inhibitor with palliative radiotherapy. We report on 5 cases at our institution where enhanced radiotherapy toxicity was observed when RT was delivered during or prior to treatment with a CDK 4/6 inhibitor. We review pre-clinical and mechanistic data and hypothesise on possible mechanisms for this phenomenon.
Current first-line systemic treatment in most patients with metastatic hormone receptor-positive, HER-2 negative breast cancer is an aromatase inhibitor in combination with a cyclin dependant kinase (CDK) 4/6 inhibitor. Frequently, these patients require palliative radiotherapy (RT) for symptomatic disease management. There is a paucity of data on the safety of combining a CDK 4/6 inhibitor with palliative RT, with conflicting case reports in the literature. We report on 5 cases at our institution where enhanced radiotherapy toxicity was observed when palliative doses of RT was delivered during or prior to treatment with a CDK 4/6 inhibitor. After review of pre-clinical and mechanistic data, we hypothesise that the effects of CDK4/6 inhibition on normal tissue and the tumour microenvironment may impede tissue recovery and exacerbate acute radiation and radiation recall toxicities. Further studies are required to clarify the potential toxicities of this combination. Clinicians should consider the potential risks when combining CDK 4/6 inhibitors with palliative RT and individualise patient management accordingly.
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Affiliation(s)
- Steven David
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Monash Cancer Centre, East Bentleigh, VIC, Australia.
| | - Gwo Ho
- Monash Cancer Centre, East Bentleigh, VIC, Australia; School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Daphne Day
- Monash Cancer Centre, East Bentleigh, VIC, Australia; School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Marion Harris
- Monash Cancer Centre, East Bentleigh, VIC, Australia
| | - Jennifer Tan
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Monash Cancer Centre, East Bentleigh, VIC, Australia
| | - Shom Goel
- Department of Cancer Medicine, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC, Australia
| | - Gerard G Hanna
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC, Australia
| | | | - Gill Kruss
- Monash Cancer Centre, East Bentleigh, VIC, Australia
| | - Lachlan McDowell
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC, Australia
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Targeted sequencing of crucial cancer causing genes of breast cancer in Saudi patients. Saudi J Biol Sci 2020; 27:2651-2659. [PMID: 32994724 PMCID: PMC7499116 DOI: 10.1016/j.sjbs.2020.05.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 11/20/2022] Open
Abstract
Breast cancer is the most common cancer among women worldwide, causing 15% of cancer-related deaths among women. Breast cancer incidence rate is increasing in most countries. In Saudi Arabia, breast cancer constitutes nearly 22% of the newly diagnosed cancer cases in women. Breast cancer incidence in the women population of Saudi Arabia is 25.9%, with 18.2% mortality. In this study, targeted sequencing of 164 selected genes was performed on germline and somatic DNA derived from the blood and tissue samples of 50 breast cancer patients using customized panel on Ion torrent platform. This study focused on the identification of genetic variations of different cancer-causing genes, raising the hope for identification of personalized prognosis. After final filtration and validation, we found protein-truncating, non-synonymous missense, and splice site mutations in the known susceptibility genes for breast cancer. We identified a total of 14 point mutations and one deletion in BRCA1, BRCA2, and RAD50 genes from the BRCA panel analysis of breast cancer samples. In the customized panel analysis, we identified 37 potential mutations in 25 breast cancer risk associated genes. Out of these, most mutations were observed in TP53. After filtration, we observed 7 mutations in TP53 genes (n = 7:- one stop gain (p.R81X), four non-synonymous (p.R81X, p.Y88C, p.R141H, and p.V25D), and two deletions (c.59delC and c.327delC)). Among the mutations detected in our study, TP53 (p.R81X), VHL (p.E52X), and BRCA2 (p.K3326X) mutations, which lead to an aberrant transcript with a premature stop codon, were reported for the first time in breast cancer patients from Saudi Arabia. Our study will help in identifying the damaging mutations and predisposing genes in Saudi breast cancer patients.
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Yoon EC, Wilson P, Zuo T, Pinto M, Cole K, Harigopal M. High frequency of p16 and SOX10 coexpression but not androgen receptor expression in triple-negative breast cancers. Hum Pathol 2020; 102:13-22. [PMID: 32565323 DOI: 10.1016/j.humpath.2020.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 11/25/2022]
Abstract
Triple-negative breast cancers (TNBCs) represent approximately 12-17% of all breast cancers and have distinctively aggressive clinical courses. Because routine biomarkers for breast cancer do not apply for TNBCs, it is essential to find novel prognostic markers and potential targets for therapeutic agents. p16 and SOX10 are emerging biomarkers with relatively unexplored expressions in TNBCs. We present an analysis of the expression of p16 and SOX10 in combination with that of androgen receptor (AR) and cytokeratin (CK) 5/6 in TNBCs. In addition, we used tissue microarrays (TMAs) to compare frequencies of p16 and SOX10 between TNBCs and non-TNBCs. Fifty-six TNBC samples with clinical data were stained immunohistochemically with p16, SOX10, AR, and CK5/6. Fifty-four cases (96.4%) were invasive ductal carcinoma, not otherwise specified, and 46 cases (82.1%) were Nottingham histologic grade 3. The majority of TNBC cases were positive for p16 (n = 44; 78.6%) and SOX10 (n = 48; 85.7%). AR was positive in 15 cases (26.8%). CK5/6 was positive in 24 cases (42.9%), which were classified as basal-like breast cancer (BLBC) subtype. The frequencies of p16 and SOX10 expression in BLBC and non-BLBC subtypes did not reveal significant statistical difference in a separate analysis. Using archived TNBC and non-TNBC TMAs, we observed that 56% of TNBC cases were positive for p16 compared with 16% of non-TNBC cases (p-value <0.0001). SOX10 was positive in 80% of TNBC cases compared with 35% of non-TNBC cases (p-value <0.0001). A significant correlation was observed between p16 and SOX10 coexpression in TNBC cases (n = 56/80, p = 0.02) but not in non-TNBC cases (n = 23/348; p = 0.626). In conclusion, p16 and SOX10 are frequently expressed in TNBC, regardless of CK5/6 expression. Furthermore, p16 and SOX10 are often coexpressed in TNBCs compared with non-TNBCs.
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Affiliation(s)
- Esther C Yoon
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Parker Wilson
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Tao Zuo
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Marguerite Pinto
- Department of Pathology, Yale University School of Medicine New Haven, New Haven, CT, USA
| | - Kimberly Cole
- Department of Pathology, Yale University School of Medicine New Haven, New Haven, CT, USA
| | - Malini Harigopal
- Department of Pathology, Yale University School of Medicine New Haven, New Haven, CT, USA
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Fassl A, Brain C, Abu-Remaileh M, Stukan I, Butter D, Stepien P, Feit AS, Bergholz J, Michowski W, Otto T, Sheng Q, Loo A, Michael W, Tiedt R, DeAngelis C, Schiff R, Jiang B, Jovanovic B, Nowak K, Ericsson M, Cameron M, Gray N, Dillon D, Zhao JJ, Sabatini DM, Jeselsohn R, Brown M, Polyak K, Sicinski P. Increased lysosomal biomass is responsible for the resistance of triple-negative breast cancers to CDK4/6 inhibition. SCIENCE ADVANCES 2020; 6:eabb2210. [PMID: 32704543 PMCID: PMC7360435 DOI: 10.1126/sciadv.abb2210] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/04/2020] [Indexed: 05/28/2023]
Abstract
Inhibitors of cyclin-dependent kinases CDK4 and CDK6 have been approved for treatment of hormone receptor-positive breast cancers. In contrast, triple-negative breast cancers (TNBCs) are resistant to CDK4/6 inhibition. Here, we demonstrate that a subset of TNBC critically requires CDK4/6 for proliferation, and yet, these TNBC are resistant to CDK4/6 inhibition due to sequestration of CDK4/6 inhibitors into tumor cell lysosomes. This sequestration is caused by enhanced lysosomal biogenesis and increased lysosomal numbers in TNBC cells. We developed new CDK4/6 inhibitor compounds that evade the lysosomal sequestration and are efficacious against resistant TNBC. We also show that coadministration of lysosomotropic or lysosome-destabilizing compounds (an antibiotic azithromycin, an antidepressant siramesine, an antimalaria compound chloroquine) renders resistant tumor cells sensitive to currently used CDK4/6 inhibitors. Lastly, coinhibition of CDK2 arrested proliferation of CDK4/6 inhibitor-resistant cells. These observations may extend the use of CDK4/6 inhibitors to TNBCs that are refractory to current anti-CDK4/6 therapies.
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Affiliation(s)
- Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Brain
- Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Monther Abu-Remaileh
- Whitehead Institutes for Biomedical Research and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Departments of Chemical Engineering and Genetics, Stanford University, Stanford, CA 94305, USA
- Institute for Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, 290 Jane Stanford Way, Stanford, CA 94305, USA
| | - Iga Stukan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deborah Butter
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Piotr Stepien
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Avery S. Feit
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Johann Bergholz
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Wojciech Michowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Tobias Otto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Qing Sheng
- Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Alice Loo
- Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Walter Michael
- Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Ralph Tiedt
- Novartis Institutes for Biomedical Research, Oncology Disease Area, 4057 Basel, Switzerland
| | - Carmine DeAngelis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Baishan Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Bojana Jovanovic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Karolina Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Maria Ericsson
- Electron Microscopy Facility, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Cameron
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Nathanael Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Deborah Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jean J. Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - David M. Sabatini
- Whitehead Institutes for Biomedical Research and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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Knudsen ES, Nambiar R, Rosario SR, Smiraglia DJ, Goodrich DW, Witkiewicz AK. Pan-cancer molecular analysis of the RB tumor suppressor pathway. Commun Biol 2020; 3:158. [PMID: 32242058 PMCID: PMC7118159 DOI: 10.1038/s42003-020-0873-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/26/2020] [Indexed: 12/21/2022] Open
Abstract
The retinoblastoma tumor suppressor gene (RB1) plays a critical role in coordinating multiple pathways that impact cancer initiation, disease progression, and therapeutic responses. Here we probed molecular features associated with the RB-pathway across 31 tumor-types. While the RB-pathway has been purported to exhibit multiple mutually exclusive genetic events, only RB1 alteration is mutually exclusive with deregulation of CDK4/6 activity. An ER+ breast cancer model with targeted RB1 deletion was used to identify signatures of CDK4/6 activity and RB-dependency (CDK4/6-RB integrated signature). This signature was prognostic in tumor-types with gene expression features indicative of slower growth. Single copy loss on chromosome 13q encompassing the RB1 locus is prevalent in many cancers, yielding reduced expression of multiple genes in cis, and is inversely related to the CDK4/6-RB integrated signature supporting a cause-effect relationship. Genes that are positively and inversely correlated with the CDK4/6-RB integrated signature define new tumor-specific pathways associated with RB-pathway activity.
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Affiliation(s)
- Erik S Knudsen
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA. .,Department of Molecular and Cellular Biology, Buffalo, USA. .,Center for Personalized Medicine, Buffalo, USA.
| | - Ram Nambiar
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Molecular and Cellular Biology, Buffalo, USA
| | - Spencer R Rosario
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Genetics and Genomics, Buffalo, USA
| | - Dominic J Smiraglia
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Genetics and Genomics, Buffalo, USA
| | - David W Goodrich
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Pharmacology and Therapeutics, Buffalo, USA
| | - Agnieszka K Witkiewicz
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA. .,Center for Personalized Medicine, Buffalo, USA. .,Department of Pathology, Buffalo, USA.
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Schoninger SF, Blain SW. The Ongoing Search for Biomarkers of CDK4/6 Inhibitor Responsiveness in Breast Cancer. Mol Cancer Ther 2020; 19:3-12. [PMID: 31909732 PMCID: PMC6951437 DOI: 10.1158/1535-7163.mct-19-0253] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/02/2019] [Accepted: 09/05/2019] [Indexed: 12/20/2022]
Abstract
CDK4 inhibitors (CDK4/6i), such as palbociclib, ribociclib, and abemaciclib, are approved in combination with hormonal therapy as a front-line treatment for metastatic HR+, HER2- breast cancer. Their targets, CDK4 and CDK6, are cell-cycle regulatory proteins governing the G1-S phase transition across many tissue types. A key challenge remains to uncover biomarkers to identify those patients that may benefit from this class of drugs. Although CDK4/6i addition to estrogen modulation therapy essentially doubles the median progression-free survival, overall survival is not significantly increased. However, in reality only a subset of treated patients respond. Many patients exhibit primary resistance to CDK4/6 inhibition and do not derive any benefit from these agents, often switching to chemotherapy within 6 months. Some patients initially benefit from treatment, but later develop secondary resistance. This highlights the need for complementary or companion diagnostics to pinpoint patients who would respond. In addition, because CDK4 is a bona fide target in other tumor types where CDK4/6i therapy is currently in clinical trials, the lack of target identification may obscure benefit to a subset of patients there as well. This review summarizes the current status of CDK4/6i biomarker test development, both in clinical trials and at the bench, with particular attention paid to those which have a strong biological basis as well as supportive clinical data.
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Affiliation(s)
| | - Stacy W Blain
- Departments of Pediatrics and Cell Biology, SUNY Downstate Medical Center, Brooklyn, New York.
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Risi E, Biagioni C, Benelli M, Migliaccio I, McCartney A, Bonechi M, Guarducci C, Hilbers F, Di Cosimo S, Huober J, Romagnoli D, Boccalini G, Vitale S, Sotiriou C, Biganzoli L, Di Leo A, Malorni L. An RB-1 loss of function gene signature as a tool to predict response to neoadjuvant chemotherapy plus anti-HER2 agents: a substudy of the NeoALTTO trial (BIG 1-06). Ther Adv Med Oncol 2019; 11:1758835919891608. [PMID: 31853266 PMCID: PMC6906346 DOI: 10.1177/1758835919891608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 11/05/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Chemotherapy added to anti-HER2 agents (H) is the treatment of choice in patients with HER2+ early breast cancer. However, HER2+ tumours are clinically and biologically heterogeneous, and treatment response varies significantly by hormone receptor (HR) status and molecular subtype. Predictive biomarkers are needed in this context. This study assessed whether an RB-1 loss of function gene signature (RBsig) is predictive of response to neoadjuvant chemotherapy in combination with trastuzumab, lapatinib or both, within the NeoALTTO trial. METHODS We collected RNA-sequencing data from pretreatment biopsies derived from the NeoALTTO trial. RBsig expression was computed retrospectively and correlated with pathological complete response (pCR) using receiver-operating characteristic (ROC) curves. The RBsig was dichotomised as High/Low in correspondence to the 25th percentile. Reported p values resulted from Fisher's exact test. RESULTS Of 455 NeoALTTO patients, 244 were eligible for this substudy (HR+ n = 129; HR- n = 115). Overall, pCR rate was significantly higher in patients with RBsig High tumours than those with RBsig Low (35% versus 18% respectively; p = 0.01). The area under the ROC curve (AUC) was 0.60 (95% CI 0.52-0.67). A remarkably low pCR rate of 11% was seen in HR+/RBsig Low patients versus 28% in HR+/RBsig High. CONCLUSIONS These results indicate RBsig may add valuable information to HER2 and HR expression, which may in turn inform treatment choices. HR+/HER2+/RBsig Low breast cancers exhibited the poorest pathological response following chemotherapy plus H. Accordingly, in such patients, endocrine therapy in combination with H and, possibly, a CDK4/6 inhibitor, may potentially prove to be a more effective treatment.
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Affiliation(s)
- Emanuela Risi
- Sandro Pitigliani Medical Oncology Department,
Hospital of Prato, via Suor Niccolina Infermiera 20, Prato, 59100,
Italy
- Sandro Pitigliani Translational Research Unit,
Hospital of Prato, Prato, Italy
| | | | | | - Ilenia Migliaccio
- Sandro Pitigliani Translational Research Unit,
Hospital of Prato, Prato, Italy
| | - Amelia McCartney
- Sandro Pitigliani Medical Oncology Department,
Hospital of Prato, Prato, Italy
| | - Martina Bonechi
- Sandro Pitigliani Translational Research Unit,
Hospital of Prato, Prato, Italy
| | - Cristina Guarducci
- Sandro Pitigliani Translational Research Unit,
Hospital of Prato, Prato, Italy
| | | | - Serena Di Cosimo
- Division of Medical Oncology, Fondazione IRCCS
Istituto Nazionale dei Tumori, Milan, Italy
| | - Jens Huober
- Breast Center, University of Ulm, Ulm,
Germany
| | | | - Giulia Boccalini
- Sandro Pitigliani Translational Research Unit,
Hospital of Prato, Prato, Italy
| | - Stefania Vitale
- Sandro Pitigliani Medical Oncology Department,
Hospital of Prato, Prato, Italy
- Department of Medical Biotechnologies,
University of Siena, Siena, Italy
| | - Christos Sotiriou
- Breast Cancer Translational Research
Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels,
Belgium
| | - Laura Biganzoli
- Sandro Pitigliani Medical Oncology Department,
Hospital of Prato, Prato, Italy
| | - Angelo Di Leo
- Sandro Pitigliani Medical Oncology Department,
Hospital of Prato, Prato, Italy
| | - Luca Malorni
- Sandro Pitigliani Medical Oncology Department,
Hospital of Prato, Prato, Italy
- Sandro Pitigliani Translational Research Unit,
Hospital of Prato, Prato, Italy
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Genetic determinants of the molecular portraits of epithelial cancers. Nat Commun 2019; 10:5666. [PMID: 31827079 PMCID: PMC6906458 DOI: 10.1038/s41467-019-13588-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022] Open
Abstract
The ability to characterize and predict tumor phenotypes is crucial to precision medicine. In this study, we present an integrative computational approach using a genome-wide association analysis and an Elastic Net prediction method to analyze the relationship between DNA copy number alterations and an archive of gene expression signatures. Across breast cancers, we are able to quantitatively predict many gene signatures levels within individual tumors with high accuracy based upon DNA copy number features alone, including proliferation status and Estrogen-signaling pathway activity. We can also predict many other key phenotypes, including intrinsic molecular subtypes, estrogen receptor status, and TP53 mutation. This approach is also applied to TCGA Pan-Cancer, which identify repeatedly predictable signatures across tumor types including immune features in lung squamous and basal-like breast cancers. These Elastic Net DNA predictors could also be called from DNA-based gene panels, thus facilitating their use as biomarkers to guide therapeutic decision making. Effective precision medicine strategies rely on the ability to predict tumour behaviour based on molecular characteristics. Here, the authors build models to predict multiple distinct gene expression patterns using DNA copy number alterations
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Karagoz K, Mehta GA, Khella CA, Khanna P, Gatza ML. Integrative proteogenomic analyses of human tumours identifies ADNP as a novel oncogenic mediator of cell cycle progression in high-grade serous ovarian cancer with poor prognosis. EBioMedicine 2019; 50:191-202. [PMID: 31767542 PMCID: PMC6921307 DOI: 10.1016/j.ebiom.2019.11.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022] Open
Abstract
Background Despite toxic side effects and limited durable response, the current standard-of-care treatment for high grade serous ovarian cancer (HGSOC) remains platinum/taxane-based chemotherapy. Given that the overall prognosis has not improved drastically over the past several decades, there is a critical need to understand the underlying mechanisms that lead to tumour development and progression. Methods We utilized an integrative proteogenomic analysis of HGSOC tumours applying a poor prognosis gene expression signature (PPS) as a conceptual framework to analyse orthogonal genomic and proteomic data from the TCGA (n = 488) and CPTAC (n = 169) studies. Genes identified through in silico analyses were assessed in vitro studies to demonstrate their impact on proliferation and cell cycle progression. Findings These analyses identified DNA amplification and overexpression of the transcription factor ADNP (Activity Dependent Neuroprotector Homeobox) in poorly prognostic tumours. Validation studies confirmed the prognostic capacity of ADNP and suggested an oncogenic role for this protein given the association between ADNP expression and pro-proliferative signalling. In vitro studies confirmed ADNP as a novel and essential mediator of cell proliferation through dysregulation of cell cycle checkpoints. Interpretation We identified ADNP as being amplified and overexpressed in poor prognosis HGSOC in silico analyses and demonstrated that ADNP is a novel and essential oncogene in HGSOC which mediates proliferation through dysregulation of cell cycle checkpoints in vitro. Funding The National Cancer Institute of the National Institutes of Health, the V Foundation for Cancer Research and the New Jersey Commission for Cancer Research.
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Affiliation(s)
- Kubra Karagoz
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States; Department of Radiation Oncology, Robert Wood Johnson Medical School, United States; Rutgers, The State University of New Jersey, New Brunswick NJ, United States
| | - Gaurav A Mehta
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States; Department of Radiation Oncology, Robert Wood Johnson Medical School, United States; Rutgers, The State University of New Jersey, New Brunswick NJ, United States
| | - Christen A Khella
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States; Department of Radiation Oncology, Robert Wood Johnson Medical School, United States; Rutgers, The State University of New Jersey, New Brunswick NJ, United States
| | - Pooja Khanna
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States; Department of Radiation Oncology, Robert Wood Johnson Medical School, United States; Rutgers, The State University of New Jersey, New Brunswick NJ, United States
| | - Michael L Gatza
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States; Department of Radiation Oncology, Robert Wood Johnson Medical School, United States; Rutgers, The State University of New Jersey, New Brunswick NJ, United States.
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43
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CDK4/6 inhibitors in breast cancer: a role in triple-negative disease? Lancet Oncol 2019; 20:1479-1481. [PMID: 31575504 DOI: 10.1016/s1470-2045(19)30627-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 09/23/2019] [Accepted: 09/23/2019] [Indexed: 11/21/2022]
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Liu JC, Granieri L, Shrestha M, Wang DY, Vorobieva I, Rubie EA, Jones R, Ju Y, Pellecchia G, Jiang Z, Palmerini CA, Ben-David Y, Egan SE, Woodgett JR, Bader GD, Datti A, Zacksenhaus E. Identification of CDC25 as a Common Therapeutic Target for Triple-Negative Breast Cancer. Cell Rep 2019; 23:112-126. [PMID: 29617654 PMCID: PMC9357459 DOI: 10.1016/j.celrep.2018.03.039] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/31/2018] [Accepted: 03/11/2018] [Indexed: 12/18/2022] Open
Abstract
CDK4/6 inhibitors are effective against cancer cells expressing the tumor suppressor RB1, but not RB1-deficient cells, posing the challenge of how to target RB1 loss. In triple-negative breast cancer (TNBC), RB1 and PTEN are frequently inactivated together with TP53. We performed kinome/phosphatase inhibitor screens on primary mouse Rb/p53-, Pten/p53-, and human RB1/PTEN/TP53-deficient TNBC cell lines and identified CDC25 phosphatase as a common target. Pharmacological or genetic inhibition of CDC25 suppressed growth of RB1-deficient TNBC cells that are resistant to combined CDK4/6 plus CDK2 inhibition. Minimal cooperation was observed in vitro between CDC25 antagonists and CDK1, CDK2, or CDK4/6 inhibitors, but strong synergy with WEE1 inhibition was apparent. In accordance with increased PI3K signaling following long-term CDC25 inhibition, CDC25 and PI3K inhibitors effectively synergized to suppress TNBC growth both in vitro and in xenotransplantation models. These results provide a rationale for the development of CDC25-based therapies for diverse RB1/PTEN/TP53-deficient and -proficient TNBCs. Liu et al. report that inhibition of the protein phosphatase CDC25 kills diverse triple-negative breast cancer (TNBC) cells. Moreover, CDC25 antagonists cooperate with other drugs, such as PI3K inhibitors, to efficiently suppress growth of human TNBC engrafted into mice.
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Affiliation(s)
- Jeff C Liu
- Toronto General Research Institute - University Health Network, 67 College Street, Toronto, ON, Canada M5G 2M1
| | - Letizia Granieri
- Toronto General Research Institute - University Health Network, 67 College Street, Toronto, ON, Canada M5G 2M1; Department of Agriculture, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Mariusz Shrestha
- Toronto General Research Institute - University Health Network, 67 College Street, Toronto, ON, Canada M5G 2M1; Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Dong-Yu Wang
- Toronto General Research Institute - University Health Network, 67 College Street, Toronto, ON, Canada M5G 2M1
| | - Ioulia Vorobieva
- Toronto General Research Institute - University Health Network, 67 College Street, Toronto, ON, Canada M5G 2M1; Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Elizabeth A Rubie
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON, Canada
| | - Rob Jones
- Toronto General Research Institute - University Health Network, 67 College Street, Toronto, ON, Canada M5G 2M1
| | - YoungJun Ju
- Toronto General Research Institute - University Health Network, 67 College Street, Toronto, ON, Canada M5G 2M1
| | - Giovanna Pellecchia
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Zhe Jiang
- Toronto General Research Institute - University Health Network, 67 College Street, Toronto, ON, Canada M5G 2M1
| | - Carlo A Palmerini
- Department of Agriculture, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Yaacov Ben-David
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, Guizhou 550014, China; State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Sean E Egan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Program in Cell Biology, The Peter Gilgan Center for Research and Learning, The Hospital for Sick Children, Toronto, ON, Canada
| | - James R Woodgett
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Alessandro Datti
- Department of Agriculture, Food, and Environmental Sciences, University of Perugia, Perugia, Italy; Network Biology Collaborative Centre, SMART Laboratory for High-Throughput Screening Programs, Mount Sinai Hospital, Toronto, ON, Canada
| | - Eldad Zacksenhaus
- Toronto General Research Institute - University Health Network, 67 College Street, Toronto, ON, Canada M5G 2M1; Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Medicine, University of Toronto, Toronto, ON, Canada.
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Iida M, Nakamura M, Tokuda E, Toyosawa D, Niwa T, Ohuchi N, Ishida T, Hayashi SI. The p21 levels have the potential to be a monitoring marker for ribociclib in breast cancer. Oncotarget 2019; 10:4907-4918. [PMID: 31448056 PMCID: PMC6690670 DOI: 10.18632/oncotarget.27127] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/21/2019] [Indexed: 11/25/2022] Open
Abstract
Although cyclin-dependent kinase (CDK) 4/6 inhibitors have exhibited remarkable results for patients with estrogen receptor (ER)–positive breast cancer in clinical trials, the mechanism of CDK4/6 inhibitor resistance remains unclear. Thus, this study aimed to investigate the mechanism of CDK4/6 inhibitor resistance using two CDK4/6 inhibitor resistant breast cancer cell lines. We established CDK6 overexpressed cell lines (MCF7-C6) from MCF-7 cells using the stably transfected CDK6 expression vector. Additionally, acquired ribociclib-resistant (RIBR) cell lines were created using ER-positive hormone-resistant cell lines by long-term exposure to ribociclib. CDK6 overexpression and the knockdown of CDK4 experiments highlight the significance of high levels of CDK4 and low levels of CDK6 in CDK4/6 inhibitor sensitivity. Moreover, RIBR cell lines did not exhibit incremental CDK6 compared with ER-positive hormone-resistant cell lines. In MCF7-C6 and RIBR cell lines, p21 levels decreased, and p21 levels were proportional to CDK4/6 inhibitor sensitivity. This study suggests that overexpression of CDK6 is one of the many possible mechanisms of resistance to CDK4/6 inhibitors. Furthermore, p21 levels have the potential to serve as a marker for CDK4/6 inhibitors independent of the resistance mechanism.
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Affiliation(s)
- Masafumi Iida
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Sendai, Japan.,Department of Breast and Endocrine Surgical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Misato Nakamura
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Emi Tokuda
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Daichi Toyosawa
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Toshifumi Niwa
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Noriaki Ohuchi
- Department of Breast and Endocrine Surgical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Takanori Ishida
- Department of Breast and Endocrine Surgical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shin-Ichi Hayashi
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Sendai, Japan
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46
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Lal A, Ramazzotti D, Weng Z, Liu K, Ford JM, Sidow A. Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations. BMC Med Genomics 2019; 12:84. [PMID: 31182087 PMCID: PMC6558765 DOI: 10.1186/s12920-019-0545-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/31/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Germline mutations in the BRCA1 and BRCA2 genes predispose carriers to breast and ovarian cancer, and there remains a need to identify the specific genomic mechanisms by which cancer evolves in these patients. Here we present a systematic genomic analysis of breast tumors with BRCA1 and BRCA2 mutations. METHODS We analyzed genomic data from breast tumors, with a focus on comparing tumors with BRCA1/BRCA2 gene mutations with common classes of sporadic breast tumors. RESULTS We identify differences between BRCA-mutated and sporadic breast tumors in patterns of point mutation, DNA methylation and structural variation. We show that structural variation disproportionately affects tumor suppressor genes and identify specific driver gene candidates that are enriched for structural variation. CONCLUSIONS Compared to sporadic tumors, BRCA-mutated breast tumors show signals of reduced DNA methylation, more ancestral cell divisions, and elevated rates of structural variation that tend to disrupt highly expressed protein-coding genes and known tumor suppressors. Our analysis suggests that BRCA-mutated tumors are more aggressive than sporadic breast cancers because loss of the BRCA pathway causes multiple processes of mutagenesis and gene dysregulation.
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Affiliation(s)
- Avantika Lal
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
- Present address: NVIDIA Corporation, 2788 San Tomas Expy, Santa Clara, CA 95051 USA
| | - Daniele Ramazzotti
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
- Department of Computer Science, Stanford University, Stanford, CA 94305 USA
| | - Ziming Weng
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
| | - Keli Liu
- Department of Statistics, Stanford University, Stanford, CA 94305 USA
| | - James M. Ford
- Department of Medicine, Stanford University, Stanford, CA 94305 USA
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
| | - Arend Sidow
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
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47
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Indovina P, Pentimalli F, Conti D, Giordano A. Translating RB1 predictive value in clinical cancer therapy: Are we there yet? Biochem Pharmacol 2019; 166:323-334. [PMID: 31176618 DOI: 10.1016/j.bcp.2019.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/03/2019] [Indexed: 12/16/2022]
Abstract
The retinoblastoma RB1 gene has been identified in the 80s as the first tumor suppressor. RB1 loss of function, as well alterations in its pathway, occur in most human cancers and often have prognostic value. RB1 has a key role in restraining cell cycle entry and, along with its family members, regulates a myriad of cellular processes and affects cell response to a variety of stimuli, ultimately determining cell fate. Consistently, RB1 status is a crucial determinant of the cell response to antitumoral therapies, impacting on the outcome of both traditional and modern anti-cancer strategies, including precision medicine approaches, such as kinase inhibitors, and immunotherapy. Despite many efforts however, the predictive value of RB1 status in the clinical practice is still underused, mainly owing to the complexity of RB1 function, to differences depending on the cellular context and on the therapeutic strategies, and, not-lastly, to technical issues. Here, we provide an overview of studies analyzing the role of RB1 in response to conventional cytotoxic and cytostatic therapeutic agents in different cancer types, including hormone dependent ones. We also review RB1 predictive value in the response to the last generation CDK4/6 inhibitors, other kinase inhibitors, and immunotherapy and discuss new emerging non-canonical roles of RB1 that could impact on the response to antitumoral treatments.
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Affiliation(s)
- Paola Indovina
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Francesca Pentimalli
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, Napoli 80131, Italy
| | - Daniele Conti
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy.
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48
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Rajasekaran S, Nagarajha Selvan LD, Dotts K, Kumar R, Rishi P, Khetan V, Bisht M, Sivaraman K, Krishnakumar S, Sahoo D, Campbell MJ, Elchuri SV, Miles WO. Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors. Front Oncol 2019; 9:221. [PMID: 31058073 PMCID: PMC6477087 DOI: 10.3389/fonc.2019.00221] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/12/2019] [Indexed: 12/11/2022] Open
Abstract
Retinoblastoma is a rare pediatric tumor of the retina, caused by the homozygous loss of the Retinoblastoma 1 (RB1) tumor suppressor gene. Previous microarray studies have identified changes in the expression profiles of coding genes; however, our understanding of how non-coding genes change in this tumor is absent. This is an important area of research, as in many adult malignancies, non-coding genes including LNC-RNAs are used as biomarkers to predict outcome and/or relapse. To establish a complete and in-depth RNA profile, of both coding and non-coding genes, in Retinoblastoma tumors, we conducted RNA-seq from a cohort of tumors and normal retina controls. This analysis identified widespread transcriptional changes in the levels of both coding and non-coding genes. Unexpectedly, we also found rare RNA fusion products resulting from genomic alterations, specific to Retinoblastoma tumor samples. We then determined whether these gene expression changes, of both coding and non-coding genes, were also found in a completely independent Retinoblastoma cohort. Using our dataset, we then profiled the potential effects of deregulated LNC-RNAs on the expression of neighboring genes, the entire genome, and on mRNAs that contain a putative area of homology. This analysis showed that most deregulated LNC-RNAs do not act locally to change the transcriptional environment, but potentially function to modulate genes at distant sites. From this analysis, we selected a strongly down-regulated LNC-RNA in Retinoblastoma, DRAIC, and found that restoring DRAIC RNA levels significantly slowed the growth of the Y79 Retinoblastoma cell line. Collectively, our work has generated the first non-coding RNA profile of Retinoblastoma tumors and has found that these tumors show widespread transcriptional deregulation.
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Affiliation(s)
- Swetha Rajasekaran
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States.,The Ohio State University Comprehensive Cancer Center, Columbus, OH,, United States.,Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | | | - Kathleen Dotts
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States.,The Ohio State University Comprehensive Cancer Center, Columbus, OH,, United States.,Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Ranjith Kumar
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Pukhraj Rishi
- Shri Bhagwan Mahavir Vitreoretinal Services and Ocular Oncology Services, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Vikas Khetan
- Shri Bhagwan Mahavir Vitreoretinal Services and Ocular Oncology Services, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Madhoolika Bisht
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States.,The Ohio State University Comprehensive Cancer Center, Columbus, OH,, United States.,Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | | | | | - Debashis Sahoo
- Department of Pediatrics and Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, United States
| | - Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Sailaja V Elchuri
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Wayne O Miles
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States.,The Ohio State University Comprehensive Cancer Center, Columbus, OH,, United States.,Center for RNA Biology, The Ohio State University, Columbus, OH, United States
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49
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Wu YM, Cieślik M, Lonigro RJ, Vats P, Reimers MA, Cao X, Ning Y, Wang L, Kunju LP, de Sarkar N, Heath EI, Chou J, Feng FY, Nelson PS, de Bono JS, Zou W, Montgomery B, Alva A, Robinson DR, Chinnaiyan AM. Inactivation of CDK12 Delineates a Distinct Immunogenic Class of Advanced Prostate Cancer. Cell 2019; 173:1770-1782.e14. [PMID: 29906450 DOI: 10.1016/j.cell.2018.04.034] [Citation(s) in RCA: 386] [Impact Index Per Article: 77.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/23/2018] [Accepted: 04/24/2018] [Indexed: 12/15/2022]
Abstract
Using integrative genomic analysis of 360 metastatic castration-resistant prostate cancer (mCRPC) samples, we identified a novel subtype of prostate cancer typified by biallelic loss of CDK12 that is mutually exclusive with tumors driven by DNA repair deficiency, ETS fusions, and SPOP mutations. CDK12 loss is enriched in mCRPC relative to clinically localized disease and characterized by focal tandem duplications (FTDs) that lead to increased gene fusions and marked differential gene expression. FTDs associated with CDK12 loss result in highly recurrent gains at loci of genes involved in the cell cycle and DNA replication. CDK12 mutant cases are baseline diploid and do not exhibit DNA mutational signatures linked to defects in homologous recombination. CDK12 mutant cases are associated with elevated neoantigen burden ensuing from fusion-induced chimeric open reading frames and increased tumor T cell infiltration/clonal expansion. CDK12 inactivation thereby defines a distinct class of mCRPC that may benefit from immune checkpoint immunotherapy.
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Affiliation(s)
- Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin Cieślik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert J Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Melissa A Reimers
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yu Ning
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lisha Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lakshmi P Kunju
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Navonil de Sarkar
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Elisabeth I Heath
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Jonathan Chou
- Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Felix Y Feng
- Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA; Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California at San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Johann S de Bono
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Weiping Zou
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, Seattle, WA 98109, USA; Veterans Affairs Puget Sound Health Care System, University of Washington, Seattle, WA 98109, USA
| | - Ajjai Alva
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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50
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Alexandrou S, George SM, Ormandy CJ, Lim E, Oakes SR, Caldon CE. The Proliferative and Apoptotic Landscape of Basal-like Breast Cancer. Int J Mol Sci 2019; 20:ijms20030667. [PMID: 30720718 PMCID: PMC6387372 DOI: 10.3390/ijms20030667] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/21/2019] [Accepted: 01/28/2019] [Indexed: 02/07/2023] Open
Abstract
Basal-like breast cancer (BLBC) is an aggressive molecular subtype that represents up to 15% of breast cancers. It occurs in younger patients, and typically shows rapid development of locoregional and distant metastasis, resulting in a relatively high mortality rate. Its defining features are that it is positive for basal cytokeratins and, epidermal growth factor receptor and/or c-Kit. Problematically, it is typically negative for the estrogen receptor and human epidermal growth factor receptor 2 (HER2), which means that it is unsuitable for either hormone therapy or targeted HER2 therapy. As a result, there are few therapeutic options for BLBC, and a major priority is to define molecular subgroups of BLBC that could be targeted therapeutically. In this review, we focus on the highly proliferative and anti-apoptotic phenotype of BLBC with the goal of defining potential therapeutic avenues, which could take advantage of these aspects of tumor development.
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Affiliation(s)
- Sarah Alexandrou
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
| | - Sandra Marie George
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
| | - Christopher John Ormandy
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, 2052 Sydney, Australia.
| | - Elgene Lim
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, 2052 Sydney, Australia.
| | - Samantha Richelle Oakes
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, 2052 Sydney, Australia.
| | - C Elizabeth Caldon
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, 2052 Sydney, Australia.
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