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Kawai Y, Nagayama A, Miyao K, Takeuchi M, Yokoe T, Kameyama T, Wang X, Seki T, Takahashi M, Hayashida T, Kitagawa Y. A genome-wide CRISPR/Cas9 knockout screen identifies SEMA3F gene for resistance to cyclin-dependent kinase 4 and 6 inhibitors in breast cancer. Breast Cancer 2025; 32:120-131. [PMID: 39352623 DOI: 10.1007/s12282-024-01641-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 09/26/2024] [Indexed: 01/11/2025]
Abstract
BACKGROUND Palbociclib is a cell-cycle targeted small molecule agent used as one of the standards of care in combination with endocrine therapy for patients with hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative advanced breast cancer. Although several gene alterations such as loss of Rb gene and amplification of p16 gene are known to be conventional resistance mechanisms to cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors, the comprehensive landscape of resistance is not yet fully elucidated. The purpose of this study is to identify the novel resistant genes to the CDK4/6 inhibitors in HR-positive HER2-negative breast cancer. METHODS The whole genome knockout screen using CRISPR/Cas9 genome editing was conducted in MCF7 to identify resistant genes to palbociclib. The candidate genes for resistance were selected by NGS analysis and GSEA analysis and validated by cell viability assay and mouse xenograft models. RESULTS We identified eight genes including RET, TIRAP, GNRH1, SEMA3F, SEMA5A, GATA4, NOD1, SSTR1 as candidate genes from the whole genome knockout screen. Among those, knockdown of SEMA3F by siRNA significantly and consistently increased the cell viability in the presence of CDK4/6 inhibitors in vitro and in vivo. Furthermore, the level of p-Rb was maintained in the palbociclib treated SEMA3F-downregulated cells, indicating that the resistance is driven by increased activity of cyclin kinases. CONCLUSION Our observation provided the first evidence of SEMA3F as a regulator of sensitivity to CDK4/6 inhibitors in breast cancer. The detailed mechanisms of resistance deserve further functional studies to develop the better strategy to overcome resistance in CDK4/6 inhibitors.
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Affiliation(s)
- Yuko Kawai
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Aiko Nagayama
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan.
| | - Kazuhiro Miyao
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Makoto Takeuchi
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Takamichi Yokoe
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Tomoe Kameyama
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Xinyue Wang
- Department of Surgery, Keio University Graduate School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Tomoko Seki
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Maiko Takahashi
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Tetsu Hayashida
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
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2
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Herrera-Abreu MT, Guan J, Khalid U, Ning J, Costa MR, Chan J, Li Q, Fortin JP, Wong WR, Perampalam P, Biton A, Sandoval W, Vijay J, Hafner M, Cutts R, Wilson G, Frankum J, Roumeliotis TI, Alexander J, Hickman O, Brough R, Haider S, Choudhary J, Lord CJ, Swain A, Metcalfe C, Turner NC. Inhibition of GPX4 enhances CDK4/6 inhibitor and endocrine therapy activity in breast cancer. Nat Commun 2024; 15:9550. [PMID: 39500869 PMCID: PMC11538343 DOI: 10.1038/s41467-024-53837-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/18/2024] [Indexed: 11/08/2024] Open
Abstract
CDK4/6 inhibition in combination with endocrine therapy is the standard of care for estrogen receptor (ER+) breast cancer, and although cytostasis is frequently observed, new treatment strategies that enhance efficacy are required. Here, we perform two independent genome-wide CRISPR screens to identify genetic determinants of CDK4/6 and endocrine therapy sensitivity. Genes involved in oxidative stress and ferroptosis modulate sensitivity, with GPX4 as the top sensitiser in both screens. Depletion or inhibition of GPX4 increases sensitivity to palbociclib and giredestrant, and their combination, in ER+ breast cancer models, with GPX4 null xenografts being highly sensitive to palbociclib. GPX4 perturbation additionally sensitises triple negative breast cancer (TNBC) models to palbociclib. Palbociclib and giredestrant induced oxidative stress and disordered lipid metabolism, leading to a ferroptosis-sensitive state. Lipid peroxidation is promoted by a peroxisome AGPAT3-dependent pathway in ER+ breast cancer models, rather than the classical ACSL4 pathway. Our data demonstrate that CDK4/6 and ER inhibition creates vulnerability to ferroptosis induction, that could be exploited through combination with GPX4 inhibitors, to enhance sensitivity to the current therapies in breast cancer.
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Affiliation(s)
- M T Herrera-Abreu
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Guan
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - U Khalid
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Ning
- Tumour Modelling Facility, Institute of Cancer Research, London, UK
| | - M R Costa
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - J Chan
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Q Li
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - J-P Fortin
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - W R Wong
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - P Perampalam
- ProCogia Inc. under contract to Hoffmann-La Roche Limited, Toronto, ON, Canada
| | - A Biton
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - W Sandoval
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - J Vijay
- Roche Informatics, Mississauga, ON, Canada
| | - M Hafner
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - R Cutts
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - G Wilson
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Frankum
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - T I Roumeliotis
- Functional proteomics team, The Institute of Cancer Research, London, UK
| | - J Alexander
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - O Hickman
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - R Brough
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - S Haider
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Choudhary
- Functional proteomics team, The Institute of Cancer Research, London, UK
| | - C J Lord
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - A Swain
- Tumour Modelling Facility, Institute of Cancer Research, London, UK
| | - C Metcalfe
- Genentech, 1 DNA Way, South San Francisco, CA, USA.
| | - N C Turner
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
- Breast Unit, The Royal Marsden Hospital, London, UK.
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3
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Park S, Silva E, Singhal A, Kelly MR, Licon K, Panagiotou I, Fogg C, Fong S, Lee JJY, Zhao X, Bachelder R, Parker BA, Yeung KT, Ideker T. A deep learning model of tumor cell architecture elucidates response and resistance to CDK4/6 inhibitors. NATURE CANCER 2024; 5:996-1009. [PMID: 38443662 PMCID: PMC11286358 DOI: 10.1038/s43018-024-00740-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 02/07/2024] [Indexed: 03/07/2024]
Abstract
Cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6is) have revolutionized breast cancer therapy. However, <50% of patients have an objective response, and nearly all patients develop resistance during therapy. To elucidate the underlying mechanisms, we constructed an interpretable deep learning model of the response to palbociclib, a CDK4/6i, based on a reference map of multiprotein assemblies in cancer. The model identifies eight core assemblies that integrate rare and common alterations across 90 genes to stratify palbociclib-sensitive versus palbociclib-resistant cell lines. Predictions translate to patients and patient-derived xenografts, whereas single-gene biomarkers do not. Most predictive assemblies can be shown by CRISPR-Cas9 genetic disruption to regulate the CDK4/6i response. Validated assemblies relate to cell-cycle control, growth factor signaling and a histone regulatory complex that we show promotes S-phase entry through the activation of the histone modifiers KAT6A and TBL1XR1 and the transcription factor RUNX1. This study enables an integrated assessment of how a tumor's genetic profile modulates CDK4/6i resistance.
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Affiliation(s)
- Sungjoon Park
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Erica Silva
- Program in Biomedical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Akshat Singhal
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Marcus R Kelly
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego, San Diego, CA, USA
| | - Kate Licon
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Isabella Panagiotou
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Catalina Fogg
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Samson Fong
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - John J Y Lee
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiaoyu Zhao
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Robin Bachelder
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Barbara A Parker
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego, San Diego, CA, USA
| | - Kay T Yeung
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego, San Diego, CA, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, San Diego, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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Kayser A, Wolff A, Berlin P, Duehring L, Henze L, Mundkowski R, Bergmann W, Müller-Hilke B, Wagner C, Huehns M, Oehmcke-Hecht S, Maletzki C. Selective but not pan-CDK inhibition abrogates 5-FU-driven tissue factor upregulation in colon cancer. Sci Rep 2024; 14:10582. [PMID: 38719932 PMCID: PMC11078971 DOI: 10.1038/s41598-024-61076-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Thromboembolic events are complications in cancer patients and hypercoagulability has been linked to the tissue factor (TF) pathway, making this an attractive target. Here, we investigated the effects of chemotherapeutics and CDK inhibitors (CDKI) abemaciclib/palbociclib (CDK4/6), THZ-1 (CDK7/12/13), and dinaciclib (CDK1/2/5/9) alone and in combination regimens on TF abundance and coagulation. The human colorectal cancer (CRC) cell line HROC173 was treated with 5-FU or gemcitabine to stimulate TF expression. TF+ cells were sorted, recultured, and re-analyzed. The effect of treatment alone or in combination was assessed by functional assays. Low-dose chemotherapy induced a hypercoagulable state and significantly upregulated TF, even after reculture without treatment. Cells exhibited characteristics of epithelial-mesenchymal transition, including high expression of vimentin and mucin. Dinaciclib and THZ-1 also upregulated TF, while abemaciclib and palbociclib downregulated it. Similar results were observed in coagulation assays. The same anticoagulant activity of abemaciclib was seen after incubation with peripheral immune cells from healthy donors and CRC patients. Abemaciclib reversed 5-FU-induced TF upregulation and prolonged clotting times in second-line treatment. Effects were independent of cytotoxicity, senescence, and p27kip1 induction. TF-antibody blocking experiments confirmed the importance of TF in plasma coagulation, with Factor XII playing a minor role. Short-term abemaciclib counteracts 5-FU-induced hypercoagulation and eventually even prevents thromboembolic events.
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Affiliation(s)
- Annika Kayser
- Department of Medicine, Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Annabell Wolff
- Department of Medicine, Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, 18057, Rostock, Germany
| | - Peggy Berlin
- Department of Medicine II, Division of Gastroenterology, Rostock University Medical Center, 18057, Rostock, Germany
| | - Lara Duehring
- Department of Medicine, Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, 18057, Rostock, Germany
| | - Larissa Henze
- Department of Medicine, Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
- Department of Internal Medicine II, Asklepios Hospital Harz, Goslar, Germany
| | - Ralf Mundkowski
- Center of Pharmacology and Toxicology, Institute of Clinical Pharmacology, Rostock University Medical Center, 18057, Rostock, Germany
| | - Wendy Bergmann
- Laboratory for Clinical Immunology, Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, 18057, Rostock, Germany
| | - Brigitte Müller-Hilke
- Laboratory for Clinical Immunology, Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, 18057, Rostock, Germany
| | - Charlotte Wagner
- Department of Medicine, Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Maja Huehns
- Institute of Pathology, Rostock University Medical Center, 18057, Rostock, Germany
| | - Sonja Oehmcke-Hecht
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, 18057, Rostock, Germany.
| | - Claudia Maletzki
- Department of Medicine, Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany.
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5
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Jin P, Duan X, Li L, Zhou P, Zou C, Xie K. Cellular senescence in cancer: molecular mechanisms and therapeutic targets. MedComm (Beijing) 2024; 5:e542. [PMID: 38660685 PMCID: PMC11042538 DOI: 10.1002/mco2.542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 04/26/2024] Open
Abstract
Aging exhibits several hallmarks in common with cancer, such as cellular senescence, dysbiosis, inflammation, genomic instability, and epigenetic changes. In recent decades, research into the role of cellular senescence on tumor progression has received widespread attention. While how senescence limits the course of cancer is well established, senescence has also been found to promote certain malignant phenotypes. The tumor-promoting effect of senescence is mainly elicited by a senescence-associated secretory phenotype, which facilitates the interaction of senescent tumor cells with their surroundings. Targeting senescent cells therefore offers a promising technique for cancer therapy. Drugs that pharmacologically restore the normal function of senescent cells or eliminate them would assist in reestablishing homeostasis of cell signaling. Here, we describe cell senescence, its occurrence, phenotype, and impact on tumor biology. A "one-two-punch" therapeutic strategy in which cancer cell senescence is first induced, followed by the use of senotherapeutics for eliminating the senescent cells is introduced. The advances in the application of senotherapeutics for targeting senescent cells to assist cancer treatment are outlined, with an emphasis on drug categories, and the strategies for their screening, design, and efficient targeting. This work will foster a thorough comprehension and encourage additional research within this field.
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Affiliation(s)
- Ping Jin
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, School of Life SciencesYunnan UniversityKunmingYunnanChina
| | - Xirui Duan
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Lei Li
- Department of Anorectal SurgeryHospital of Chengdu University of Traditional Chinese Medicine and Chengdu University of Traditional Chinese MedicineChengduChina
| | - Ping Zhou
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Cheng‐Gang Zou
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, School of Life SciencesYunnan UniversityKunmingYunnanChina
| | - Ke Xie
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
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6
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Chen P, Wang Y, Zhou B. Insights into targeting cellular senescence with senolytic therapy: The journey from preclinical trials to clinical practice. Mech Ageing Dev 2024; 218:111918. [PMID: 38401690 DOI: 10.1016/j.mad.2024.111918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Abstract
Interconnected, fundamental aging processes are central to many illnesses and diseases. Cellular senescence is a mechanism that halts the cell cycle in response to harmful stimuli. Senescent cells (SnCs) can emerge at any point in life, and their persistence, along with the numerous proteins they secrete, can negatively affect tissue function. Interventions aimed at combating persistent SnCs, which can destroy tissues, have been used in preclinical models to delay, halt, or even reverse various diseases. Consequently, the development of small-molecule senolytic medicines designed to specifically eliminate SnCs has opened potential avenues for the prevention or treatment of multiple diseases and age-related issues in humans. In this review, we explore the most promising approaches for translating small-molecule senolytics and other interventions targeting senescence in clinical practice. This discussion highlights the rationale for considering SnCs as therapeutic targets for diseases affecting individuals of all ages.
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Affiliation(s)
- Peng Chen
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China.
| | - Yulai Wang
- Department of Pharmacy, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei, P.R. China
| | - Benhong Zhou
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
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7
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Aleman M, Arepally GM, Baglin T, Buitrago L, Davizon-Castillo P, Dayal S, Flick MJ, Gerber G, Hisada Y, Kolev K, O’Loghlen A, Rezaie AR, Sparkenbaugh EM, Stavrou EX, Ünlü B, Vercellotti GM. Coagulation and platelet biology at the intersection of health and disease: illustrated capsules of the 11th Symposium on Hemostasis at the University of North Carolina. Res Pract Thromb Haemost 2024; 8:102395. [PMID: 38699410 PMCID: PMC11063502 DOI: 10.1016/j.rpth.2024.102395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 05/05/2024] Open
Abstract
The University of North Carolina Symposia on Hemostasis began in 2002, with The First Symposium on Hemostasis with a Special Focus on FVIIa and Tissue Factor. They have occurred biannually since and have maintained the primary goal of establishing a forum for the sharing of outstanding advances made in the basic sciences of hemostasis. The 2024 11th Symposium on Hemostasis will bring together leading scientists from around the globe to present and discuss the latest research related to coagulation factors and platelet biology. In keeping with the tradition of the conference, we expect novel cross-disciplinary collaborations to result from bringing together fundamental scientists and physician-scientists from different backgrounds and perspectives. The aim of these collaborations is to springboard the next generation of important advances in the field. This year's program was designed to discuss Coagulation and Platelet Biology at the Intersection of Health and Disease. The goal is to develop a better understanding of the pathophysiologic mechanisms leading to hemostatic and thrombotic disorders as this understanding is critical for the continued development of safe and efficacious therapeutics. Included in this review article are illustrated capsules provided by our speakers that highlight the main conclusions of the invited talks.
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Affiliation(s)
- Maria Aleman
- Blood Research Center, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gowthami M. Arepally
- Division of Hematology, Duke University Medical Center, Durham, North Carolina, USA
| | - Trevor Baglin
- Centessa Pharmaceuticals plc, Cheshire, United Kingdom
| | - Lorena Buitrago
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, Rockefeller University, New York, New York, USA
| | - Pavel Davizon-Castillo
- Department of Pediatrics Hematology/Oncology and Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sanjana Dayal
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Matthew J. Flick
- Blood Research Center, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gloria Gerber
- Division of Hematology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yohei Hisada
- Blood Research Center, Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Krasimir Kolev
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Ana O’Loghlen
- Epigenetics & Cellular Senescence Group, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Alireza R. Rezaie
- Department of Biochemistry and Molecular Biology, Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Erica M. Sparkenbaugh
- Blood Research Center, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Blood Research Center, Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Evi X. Stavrou
- Department of Medicine, Hematology and Oncology Division, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Medicine Service, Section of Hematology-Oncology, Louise Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Betül Ünlü
- Einthoven Laboratory for Experimental Vascular Medicine, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
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8
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Gureghian V, Herbst H, Kozar I, Mihajlovic K, Malod-Dognin N, Ceddia G, Angeli C, Margue C, Randic T, Philippidou D, Nomigni MT, Hemedan A, Tranchevent LC, Longworth J, Bauer M, Badkas A, Gaigneaux A, Muller A, Ostaszewski M, Tolle F, Pržulj N, Kreis S. A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma. Cancer Gene Ther 2023; 30:1330-1345. [PMID: 37420093 PMCID: PMC10581906 DOI: 10.1038/s41417-023-00640-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/19/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023]
Abstract
Therapy Induced Senescence (TIS) leads to sustained growth arrest of cancer cells. The associated cytostasis has been shown to be reversible and cells escaping senescence further enhance the aggressiveness of cancers. Chemicals specifically targeting senescent cells, so-called senolytics, constitute a promising avenue for improved cancer treatment in combination with targeted therapies. Understanding how cancer cells evade senescence is needed to optimise the clinical benefits of this therapeutic approach. Here we characterised the response of three different NRAS mutant melanoma cell lines to a combination of CDK4/6 and MEK inhibitors over 33 days. Transcriptomic data show that all cell lines trigger a senescence programme coupled with strong induction of interferons. Kinome profiling revealed the activation of Receptor Tyrosine Kinases (RTKs) and enriched downstream signaling of neurotrophin, ErbB and insulin pathways. Characterisation of the miRNA interactome associates miR-211-5p with resistant phenotypes. Finally, iCell-based integration of bulk and single-cell RNA-seq data identifies biological processes perturbed during senescence and predicts 90 new genes involved in its escape. Overall, our data associate insulin signaling with persistence of a senescent phenotype and suggest a new role for interferon gamma in senescence escape through the induction of EMT and the activation of ERK5 signaling.
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Affiliation(s)
- Vincent Gureghian
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Hailee Herbst
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Ines Kozar
- Laboratoire National de Santé, Dudelange, Luxembourg
| | | | | | - Gaia Ceddia
- Barcelona Supercomputing Center, 08034, Barcelona, Spain
| | - Cristian Angeli
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Christiane Margue
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Tijana Randic
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Demetra Philippidou
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Milène Tetsi Nomigni
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Ahmed Hemedan
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Leon-Charles Tranchevent
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Joseph Longworth
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Mark Bauer
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Apurva Badkas
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Anthoula Gaigneaux
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Arnaud Muller
- LuxGen, TMOH and Bioinformatics platform, Data Integration and Analysis unit, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Fabrice Tolle
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Nataša Pržulj
- Barcelona Supercomputing Center, 08034, Barcelona, Spain
- Department of Computer Science, University College London, London, WC1E 6BT, UK
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Stephanie Kreis
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg.
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9
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Zhu Y, Wang Y, Hu M, Lu X, Sun G. Identification of oncogenes and tumor-suppressor genes with hepatocellular carcinoma: A comprehensive analysis based on TCGA and GEO datasets. Front Genet 2023; 13:934883. [PMID: 36685860 PMCID: PMC9845404 DOI: 10.3389/fgene.2022.934883] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 12/05/2022] [Indexed: 01/05/2023] Open
Abstract
Aim: Existing targeted therapies for hepatocellular carcinoma (HCC) are resistant and have limitations. It is crucial to find new HCC-related target genes. Methods: RNA-sequencing data of HCC were gathered from The Cancer Genome Atlas and Gene Expression Omnibus datasets. Initially, differentially expressed genes between normal and tumor tissues were identified from four Gene Expression Omnibus datasets, GSE36376, GSE102079, GSE54236, and GSE45267. GO terms and KEGG pathway enrichment analyses were performed to explore the potential biological functions of differentially expressed genes. A PPI network was constructed by using the STRING database, and up-regulated and down-regulated hub genes were defined through 12 topological approaches. Subsequently, the correlation bounded by up-regulated genes and down-regulated genes in the diagnosis, prognosis, and clinicopathological features of HCC was analyzed. Beyond a shadow of doubt, the key oncogene PBK and tumor suppressor gene F9 were screened out, and the specific mechanism was investigated through GSEA enrichment analysis and immune correlation analysis. The role of PBK in HCC was further verified by western blot, CCK8, transwell, and tube formation experiments. Results: CDCA5, CDC20, PBK, PRC1, TOP2A, and NCAPG are good indicators of HCC diagnosis and prognosis. The low expressions of F9, AFM, and C8B indicate malignant progression and poor prognosis of HCC. PBK was found to be closely related to VEGF, VEGFR, and PDGFR pathways. Experiments showed that PBK promotes HCC cell proliferation, migration, invasion, and tube formation in HUVEC cells. F9 was negatively correlated with the degree of immune infiltration, and low expression of F9 suggested a poor response to immunotherapy. Conclusion: The role of HCC-related oncogenes and tumor-suppressor genes in diagnosis and prognosis was identified. In addition, we have found that PBK may promote tumor proliferation through angiogenesis and F9 may be a predictor of tumor immunotherapy response.
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Affiliation(s)
- Yue Zhu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yanfei Wang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Integrated Traditional Chinese and Western Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Mengyao Hu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Integrated Traditional Chinese and Western Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Xiaoting Lu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Guoping Sun
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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10
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Ten Years of CRISPRing Cancers In Vitro. Cancers (Basel) 2022; 14:cancers14235746. [PMID: 36497228 PMCID: PMC9738354 DOI: 10.3390/cancers14235746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022] Open
Abstract
Cell lines have always constituted a good investigation tool for cancer research, allowing scientists to understand the basic mechanisms underlying the complex network of phenomena peculiar to the transforming path from a healthy to cancerous cell. The introduction of CRISPR in everyday laboratory activity and its relative affordability greatly expanded the bench lab weaponry in the daily attempt to better understand tumor biology with the final aim to mitigate cancer's impact in our lives. In this review, we aim to report how this genome editing technique affected in the in vitro modeling of different aspects of tumor biology, its several declinations, and analyze the advantages and drawbacks of each of them.
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11
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Zhang L, Pitcher LE, Yousefzadeh MJ, Niedernhofer LJ, Robbins PD, Zhu Y. Cellular senescence: a key therapeutic target in aging and diseases. J Clin Invest 2022; 132:e158450. [PMID: 35912854 PMCID: PMC9337830 DOI: 10.1172/jci158450] [Citation(s) in RCA: 284] [Impact Index Per Article: 94.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cellular senescence is a hallmark of aging defined by stable exit from the cell cycle in response to cellular damage and stress. Senescent cells (SnCs) can develop a characteristic pathogenic senescence-associated secretory phenotype (SASP) that drives secondary senescence and disrupts tissue homeostasis, resulting in loss of tissue repair and regeneration. The use of transgenic mouse models in which SnCs can be genetically ablated has established a key role for SnCs in driving aging and age-related disease. Importantly, senotherapeutics have been developed to pharmacologically eliminate SnCs, termed senolytics, or suppress the SASP and other markers of senescence, termed senomorphics. Based on extensive preclinical studies as well as small clinical trials demonstrating the benefits of senotherapeutics, multiple clinical trials are under way. This Review discusses the role of SnCs in aging and age-related diseases, strategies to target SnCs, approaches to discover and develop senotherapeutics, and preclinical and clinical advances of senolytics.
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Affiliation(s)
- Lei Zhang
- Institute on the Biology of Aging and Metabolism and the Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Louise E. Pitcher
- Institute on the Biology of Aging and Metabolism and the Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Matthew J. Yousefzadeh
- Institute on the Biology of Aging and Metabolism and the Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and Metabolism and the Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Paul D. Robbins
- Institute on the Biology of Aging and Metabolism and the Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yi Zhu
- Robert and Arlene Kogod Center on Aging, and
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
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12
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Mylonas A, O'Loghlen A. Cellular Senescence and Ageing: Mechanisms and Interventions. FRONTIERS IN AGING 2022; 3:866718. [PMID: 35821824 PMCID: PMC9261318 DOI: 10.3389/fragi.2022.866718] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 01/07/2023]
Abstract
The influence of the activation of a cellular phenotype termed senescence and it’s importance in ageing and age-related diseases is becoming more and more evident. In fact, there is a huge effort to tackle these diseases via therapeutic drugs targeting senescent cells named senolytics. However, a clearer understanding of how senescence is activated and the influence it has on specific cellular types and tissues is needed. Here, we describe general triggers and characteristics of senescence. In addition, we describe the influence of senescent cells in ageing and different age-related diseases.
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Affiliation(s)
- Andreas Mylonas
- Epigenetics & Cellular Senescence Group, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Ana O'Loghlen
- Epigenetics & Cellular Senescence Group, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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