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Scattolin D, Maso AD, Ferro A, Frega S, Bonanno L, Guarneri V, Pasello G. The emerging role of Schlafen-11 (SLFN11) in predicting response to anticancer treatments: Focus on small cell lung cancer. Cancer Treat Rev 2024; 128:102768. [PMID: 38797062 DOI: 10.1016/j.ctrv.2024.102768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
Small cell lung cancer (SCLC) is characterized by a dismal prognosis. Many efforts have been made so far for identifying novel biomarkers for a personalized treatment for SCLC patients. Schlafen 11 (SLFN11) is a protein differently expressed in many cancers and recently emerged as a new potential biomarker. Lower expression of SLFN11 correlates with a worse prognosis in SCLC and other tumors. SLFN11 has a role in tumorigenesis, inducing replication arrest in the presence of DNA damage through the block of the replication fork. SLFN11 interacts also with chromatin accessibility, proteotoxic stress and mammalian target of rapamycin signalling pathway. The expression of SLFN11 is regulated by epigenetic mechanisms, including promoter methylation, histone deacetylation, and the histone methylation. The downregulation of SLFN11 correlates with a worse response to topoisomerase I and II inhibitors, alkylating agents, and poly ADP-ribose polymerase inhibitors in different cancer types. Some studies exploring strategies for overcoming drug resistance in tumors with low levels of SLFN11 showed promising results. One of these strategies includes the interaction with the Ataxia Telangiectasia and Rad3-related pathway, constitutively activated and leading to cell survival and tumor growth in the presence of low levels of SLFN11. Furthermore, the expression of SLFN11 is dynamic through time and different anticancer therapy and liquid biopsy seems to be an attractive tool for catching SLFN11 different expressions. Despite this, further investigations exploring SLFN11 as a predictive biomarker, its longitudinal changes, and new strategies to overcome drug resistances are needed.
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Affiliation(s)
- Daniela Scattolin
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | | | - Alessandra Ferro
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Stefano Frega
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Laura Bonanno
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Valentina Guarneri
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Giulia Pasello
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy.
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Zhou J, Zhang MY, Gao AA, Zhu C, He T, Herman JG, Guo MZ. Epigenetic silencing schlafen-11 sensitizes esophageal cancer to ATM inhibitor. World J Gastrointest Oncol 2024; 16:2060-2073. [PMID: 38764821 PMCID: PMC11099458 DOI: 10.4251/wjgo.v16.i5.2060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/26/2024] [Accepted: 04/01/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND Targeting DNA damage response (DDR) pathway is a cutting-edge strategy. It has been reported that Schlafen-11 (SLFN11) contributes to increase chemosensitivity by participating in DDR. However, the detailed mechanism is unclear. AIM To investigate the role of SLFN11 in DDR and the application of synthetic lethal in esophageal cancer with SLFN11 defects. METHODS To reach the purpose, eight esophageal squamous carcinoma cell lines, 142 esophageal dysplasia (ED) and 1007 primary esophageal squamous cell carcinoma (ESCC) samples and various techniques were utilized, including methylation-specific polymerase chain reaction, CRISPR/Cas9 technique, Western blot, colony formation assay, and xenograft mouse model. RESULTS Methylation of SLFN11 was exhibited in 9.15% of (13/142) ED and 25.62% of primary (258/1007) ESCC cases, and its expression was regulated by promoter region methylation. SLFN11 methylation was significantly associated with tumor differentiation and tumor size (both P < 0.05). However, no significant associations were observed between promoter region methylation and age, gender, smoking, alcohol consumption, TNM stage, or lymph node metastasis. Utilizing DNA damaged model induced by low dose cisplatin, SLFN11 was found to activate non-homologous end-joining and ATR/CHK1 signaling pathways, while inhibiting the ATM/CHK2 signaling pathway. Epigenetic silencing of SLFN11 was found to sensitize the ESCC cells to ATM inhibitor (AZD0156), both in vitro and in vivo. CONCLUSION SLFN11 is frequently methylated in human ESCC. Methylation of SLFN11 is sensitive marker of ATM inhibitor in ESCC.
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Affiliation(s)
- Jing Zhou
- School of Medicine, NanKai University, Tianjin 300071, China
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Mei-Ying Zhang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Ai-Ai Gao
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Cheng Zhu
- School of Medicine, NanKai University, Tianjin 300071, China
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Tao He
- Departments of Pathology, Characteristic Medical Center of The Chinese People’s Armed Police Force, Tianjin 300162, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, United States
| | - Ming-Zhou Guo
- School of Medicine, NanKai University, Tianjin 300071, China
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
- National Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing 100853, China
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Perez RE, Eckerdt F, Platanias LC. Schlafens: Emerging Therapeutic Targets. Cancers (Basel) 2024; 16:1805. [PMID: 38791884 PMCID: PMC11119473 DOI: 10.3390/cancers16101805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
The interferon (IFN) family of immunomodulatory cytokines has been a focus of cancer research for over 50 years with direct and indirect implications in cancer therapy due to their properties to inhibit malignant cell proliferation and modulate immune responses. Among the transcriptional targets of the IFNs is a family of genes referred to as Schlafens. The products of these genes, Schlafen proteins, exert important roles in modulating cellular proliferation, differentiation, immune responses, viral replication, and chemosensitivity of malignant cells. Studies have demonstrated that abnormal expression of various Schlafens contributes to the pathophysiology of various cancers. Schlafens are now emerging as promising biomarkers and potentially attractive targets for drug development in cancer research. Here, we highlight research suggesting the use of Schlafens as cancer biomarkers and the rationale for the development of specific drugs targeting Schlafen proteins.
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Affiliation(s)
- Ricardo E. Perez
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611, USA; (R.E.P.); (F.E.)
- Division of Hematology-Oncology, Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Frank Eckerdt
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611, USA; (R.E.P.); (F.E.)
- Division of Hematology-Oncology, Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Leonidas C. Platanias
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611, USA; (R.E.P.); (F.E.)
- Division of Hematology-Oncology, Department of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
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Simić I, Guzonjić A, Kotur Stevuljević J, Ćeriman Krstić V, Samardžić N, Savić Vujović K, Jovanović D. Correlation of Systemic Inflammation Parameters and Serum SLFN11 in Small Cell Lung Cancer-A Prospective Pilot Study. Biomedicines 2024; 12:976. [PMID: 38790938 PMCID: PMC11117707 DOI: 10.3390/biomedicines12050976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/17/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND AND OBJECTIVES The objective of this research was to analyze the correlation of the neutrophil-to-lymphocyte ratio (NLR), C-reactive protein (CRP), soluble programmed cell death ligand 1 (sPD-L1), and Schlafen 11 (SLFN11) with the response to first-line chemotherapy in a cohort of small cell lung cancer (SCLC) patients, and to determine their potential as predictive serum biomarkers. MATERIALS AND METHODS A total of 60 SCLC patients were included. Blood samples were taken to determine CRP, sPD-L1, and SLFN11 levels. The first sampling was performed before the start of chemotherapy, the second after two cycles, and the third after four cycles of chemotherapy. RESULTS The patients who died earlier during the study had NLR and SLFN11 concentrations significantly higher compared to the survivor group. In the group of survivors, after two cycles of chemotherapy, the NLR ratio decreased significantly (p < 0.01), but after four cycles, the NLR ratio increased (p < 0.05). Their serum SLFN11 concentration increased significantly (p < 0.001) after two cycles of chemotherapy, but after four cycles, the level of SLFN11 fell significantly (p < 0.01). CRP, NLR, and SLFN11 were significant predictors of patient survival according to Kaplan-Meier analysis. The combination of inflammatory parameters and SLFN11 with a cutoff value above the 75th percentile of the predicted probability was associated with significantly lower overall survival in SCLC patients (average survival of 3.6 months vs. 4.8 months). CONCLUSION The combination of inflammatory markers and the levels of two specific proteins (sPD-L1, SLFN11) could potentially serve as a non-invasive biomarker for predicting responses to DNA-damaging therapeutic agents in SCLC.
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Affiliation(s)
- Ivana Simić
- Medical Affairs, Merck Sharp & Dohme d.o.o., Omladinskih brigada 90a, 11070 Belgrade, Serbia
| | - Azra Guzonjić
- Department for Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (A.G.); (J.K.S.)
| | - Jelena Kotur Stevuljević
- Department for Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (A.G.); (J.K.S.)
| | - Vesna Ćeriman Krstić
- Faculty of Medicine, University of Belgrade, Dr Subotica 8, 11000 Belgrade, Serbia;
- Clinic for Pulmonology, University Clinical Center of Serbia, Dr Koste Todorovica 26, 11000 Belgrade, Serbia;
| | - Natalija Samardžić
- Clinic for Pulmonology, University Clinical Center of Serbia, Dr Koste Todorovica 26, 11000 Belgrade, Serbia;
| | - Katarina Savić Vujović
- Department of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, Dr Subotica 8, 11000 Belgrade, Serbia;
| | - Dragana Jovanović
- Internal Medicine Clinic “Akta Medica”, Cara Nikolaja II, 11000 Belgrade, Serbia;
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Postel-Vinay S, Coves J, Texier M, Aldea M, Gazzah A, Dómine M, Planchard D, De Las Peñas R, Sala Gonzalez MA, Viteri S, Perez J, Ortega AL, Moran T, Camps C, Lopez-Martin A, Provencio M, Soria JC, Besse B, Massuti B, Rosell R. Olaparib maintenance versus placebo in platinum-sensitive non-small cell lung cancer: the Phase 2 randomized PIPSeN trial. Br J Cancer 2024; 130:417-424. [PMID: 38097741 PMCID: PMC10844295 DOI: 10.1038/s41416-023-02514-5] [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: 04/29/2023] [Revised: 11/02/2023] [Accepted: 11/21/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Platinum-sensitivity is a phenotypic biomarker of Poly (ADP-ribose) polymerase inhibitors (PARPi) sensitivity in histotypes where PARPi are approved. Approximately one-third of non-small cell lung cancers (NSCLC) are platinum-sensitive. The double-blind, randomized phase II PIPSeN (NCT02679963) study evaluated olaparib, a PARPi, as maintenance therapy for patients with platinum-sensitive advanced NSCLC. METHODS Chemonaïve patients with ECOG performance status of 0-1, platinum-sensitive, EGFR- and ALK-wild-type, stage IIIB-IV NSCLC were randomized (R) to receive either olaparib (O) maintenance or a placebo (P). The primary objective was progression-free survival (PFS) from R. Secondary objectives included overall survival (OS) and safety. With an anticipated hazard ratio of 0.65, 144 patients were required to be randomized, and approximately 500 patients enrolled. RESULTS The trial was prematurely terminated because anti-PD(L)1 therapy was approved during the trial recruitment. A total of 182 patients were enrolled, with 60 patients randomized: 33 and 27 in the O and P arms, respectively. Patient and tumor characteristics were well-balanced between arms, except for alcohol intake (33% vs 11% in the O and P arms, respectively, p = 0.043). The median PFS was 2.9 and 2.0 months in the O and P arms, respectively (logrank p = 0.99). The median OS was 9.4 and 9.5 months in the O and P arms, respectively (p = 0.28). Grade ≥3 toxicities occurred in 15 and 8 patients in O and P arms, with no new safety concerns. CONCLUSION PIPSeN was terminated early after enrollment of only 50% of the pre-planned population, thus being statistically underpowered. Olaparib maintenance did neither improve median PFS nor OS in this patient population.
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Affiliation(s)
- Sophie Postel-Vinay
- Drug Development Department, DITEP, Gustave Roussy, Villejuif, France.
- ERC StG group, Inserm Unit U981, Gustave Roussy, Villejuif, France.
- University College of London, Cancer Institute, London, UK.
| | - Juan Coves
- Medical Oncology Department, Hospital Son Llátzer, Palma de Mallorca, Spain
| | | | - Mihaela Aldea
- Department of Medical Oncology, Thoracic tumor board and International Cancer for Thoracic Cancers (CICT), Villejuif, France
| | - Anas Gazzah
- Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
- ERC StG group, Inserm Unit U981, Gustave Roussy, Villejuif, France
- Department of Medical Oncology, Thoracic tumor board and International Cancer for Thoracic Cancers (CICT), Villejuif, France
| | - Manuel Dómine
- Medical Oncology Department, Hospital Universitario Fundación Jiménez Díaz, IIS-FJD, Madrid, Spain
| | - David Planchard
- Department of Medical Oncology, Thoracic tumor board and International Cancer for Thoracic Cancers (CICT), Villejuif, France
- Faculty of Medicine, Paris-Saclay University, Paris, France
| | - Ramon De Las Peñas
- Medical Oncology Department, Consorcio Hospitalario Provincial de Castellón, Castellón de la Plana, Spain
| | | | - Santiago Viteri
- Instituto Oncológico Dr. Rosell, Hospital Universitario Dexeus, Grupo Quirón Salud, Barcelona, Spain
| | - Javier Perez
- Medical Oncology Department, Hospital Virgen de los Lirios de Alcoy, Alcoy, Spain
| | - Ana Laura Ortega
- Medical Oncology Department, Hospital Universitario de Jaén, Jaén, Spain
| | - Teresa Moran
- Institut Català d'Oncologia Badalona, Hospital Universitari Germans Trias i Pujol, Badalona; Badalona Applied Research Group in Oncology, Barcelona, Spain
| | - Carlos Camps
- Hospital General Universitario de Valencia, Medical Oncology Department; TRIAL Mixed Unit, Centro Investigación Príncipe Felipe-Fundación Investigación Hospital General Universitario de Valencia, Valencia, Spain
| | - Ana Lopez-Martin
- Medical Oncology Department, Hospital Universitario Severo Ochoa, Madrid, Spain
| | - Mariano Provencio
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Universidad Autónoma Madrid, IDIPHIM, Madrid, Spain
| | | | - Benjamin Besse
- Department of Medical Oncology, Thoracic tumor board and International Cancer for Thoracic Cancers (CICT), Villejuif, France
- Faculty of Medicine, Paris-Saclay University, Paris, France
| | - Bartomeu Massuti
- Medical Oncology Department, Hospital Universitario Dr. Balmis de Alicante, Alicante, Spain
| | - Rafael Rosell
- Germans Trias i Pujol Research Institute and Hospital (IGTP), Badalona; Translational Cancer Research Unit, Instituto Oncológico Dr Rosell, Dexeus University Hospital, Barcelona, Spain
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Watanabe K, Seki N. Biology and Development of DNA-Targeted Drugs, Focusing on Synthetic Lethality, DNA Repair, and Epigenetic Modifications for Cancer: A Review. Int J Mol Sci 2024; 25:752. [PMID: 38255825 PMCID: PMC10815806 DOI: 10.3390/ijms25020752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
DNA-targeted drugs constitute a specialized category of pharmaceuticals developed for cancer treatment, directly influencing various cellular processes involving DNA. These drugs aim to enhance treatment efficacy and minimize side effects by specifically targeting molecules or pathways crucial to cancer growth. Unlike conventional chemotherapeutic drugs, recent discoveries have yielded DNA-targeted agents with improved effectiveness, and a new generation is anticipated to be even more specific and potent. The sequencing of the human genome in 2001 marked a transformative milestone, contributing significantly to the advancement of targeted therapy and precision medicine. Anticipated progress in precision medicine is closely tied to the continuous development in the exploration of synthetic lethality, DNA repair, and expression regulatory mechanisms, including epigenetic modifications. The integration of technologies like circulating tumor DNA (ctDNA) analysis further enhances our ability to elucidate crucial regulatory factors, promising a more effective era of precision medicine. The combination of genomic knowledge and technological progress has led to a surge in clinical trials focusing on precision medicine. These trials utilize biomarkers for identifying genetic alterations, molecular profiling for potential therapeutic targets, and tailored cancer treatments addressing multiple genetic changes. The evolving landscape of genomics has prompted a paradigm shift from tumor-centric to individualized, genome-directed treatments based on biomarker analysis for each patient. The current treatment strategy involves identifying target genes or pathways, exploring drugs affecting these targets, and predicting adverse events. This review highlights strategies incorporating DNA-targeted drugs, such as PARP inhibitors, SLFN11, methylguanine methyltransferase (MGMT), and ATR kinase.
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Affiliation(s)
- Kiyotaka Watanabe
- Department of Medicine, School of Medicine, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605, Japan
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Akashi H, Yachida N, Ueda H, Yamaguchi M, Yamawaki K, Tamura R, Suda K, Ishiguro T, Adachi S, Nagase Y, Ueda Y, Ueda M, Abiko K, Kagabu M, Baba T, Nakaoka H, Enomoto T, Murai J, Yoshihara K. SLFN11 is a BRCA Independent Biomarker for the Response to Platinum-Based Chemotherapy in High-Grade Serous Ovarian Cancer and Clear Cell Ovarian Carcinoma. Mol Cancer Ther 2024; 23:106-116. [PMID: 37717249 DOI: 10.1158/1535-7163.mct-23-0257] [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: 04/27/2023] [Revised: 07/12/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
BRCA1/2 mutations are robust biomarkers for platinum-based chemotherapy in epithelial ovarian cancers. However, BRCA1/2 mutations in clear cell ovarian carcinoma (CCC) are less frequent compared with high-grade serous ovarian cancer (HGSC). The discovery of biomarkers that can be applied to CCC is an unmet need in chemotherapy. Schlafen 11 (SLFN11) has attracted attention as a novel sensitizer for DNA-damaging agents including platinum. In this study, we investigated the utility of SLFN11 in HGSC and CCC for platinum-based chemotherapy. SLFN11 expression was analyzed retrospectively by IHC across 326 ovarian cancer samples. The clinicopathologic significance of SLFN11 expression was analyzed across 57 advanced HGSC as a discovery set, 96 advanced HGSC as a validation set, and 57 advanced CCC cases, all of whom received platinum-based chemotherapy. BRCA1/2 mutation was analyzed using targeted-gene sequencing. In the HGSC cohort, the SLFN11-positive and BRCA mutation group showed significantly longer whereas the SLFN11-negative and BRCA wild-type group showed significantly shorter progression-free survival and overall survival. Moreover, SLFN11-positive HGSC shrunk significantly better than SLFN11-negative HGSC after neoadjuvant chemotherapy. Comparable results were obtained with CCC but without consideration of BRCA1/2 mutation due to a small population. Multivariate analysis identified SLFN11 as an independent factor for better survival in HGSC and CCC. The SLFN11-dependent sensitivity to platinum and PARP inhibitors were validated with genetically modified non-HGSC ovarian cancer cell lines. Our study reveals that SLFN11 predicts platinum sensitivity in HGSC and CCC independently of BRCA1/2 mutation status, indicating that SLFN11 assessment can guide treatment selection in HGSC and CCC.
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Affiliation(s)
- Hidehiko Akashi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Haruka Ueda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Manako Yamaguchi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kaoru Yamawaki
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Sosuke Adachi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yoshikazu Nagase
- Department of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yutaka Ueda
- Department of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Masashi Ueda
- Department of Obstetrics and Gynecology, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Kaoru Abiko
- Department of Obstetrics and Gynecology, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Masahiro Kagabu
- Department of Obstetrics and Gynecology, Iwate Medical University School of Medicine, Shiwa, Japan
| | - Tsukasa Baba
- Department of Obstetrics and Gynecology, Iwate Medical University School of Medicine, Shiwa, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation Chiyoda-ku, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Department of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Toon, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Ohnmacht AJ, Rajamani A, Avar G, Kutkaite G, Gonçalves E, Saur D, Menden MP. The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity. Commun Biol 2023; 6:825. [PMID: 37558831 PMCID: PMC10412573 DOI: 10.1038/s42003-023-05198-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: 01/14/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023] Open
Abstract
Aberrant DNA methylation accompanies genetic alterations during oncogenesis and tumour homeostasis and contributes to the transcriptional deregulation of key signalling pathways in cancer. Despite increasing efforts in DNA methylation profiling of cancer patients, there is still a lack of epigenetic biomarkers to predict treatment efficacy. To address this, we analyse 721 cancer cell lines across 22 cancer types treated with 453 anti-cancer compounds. We systematically detect the predictive component of DNA methylation in the context of transcriptional and mutational patterns, i.e., in total 19 DNA methylation biomarkers across 17 drugs and five cancer types. DNA methylation constitutes drug sensitivity biomarkers by mediating the expression of proximal genes, thereby enhancing biological signals across multi-omics data modalities. Our method reproduces anticipated associations, and in addition, we find that the NEK9 promoter hypermethylation may confer sensitivity to the NEDD8-activating enzyme (NAE) inhibitor pevonedistat in melanoma through downregulation of NEK9. In summary, we envision that epigenomics will refine existing patient stratification, thus empowering the next generation of precision oncology.
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Affiliation(s)
- Alexander Joschua Ohnmacht
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Anantharamanan Rajamani
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Ismaninger Str. 22, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Göksu Avar
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Ginte Kutkaite
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Emanuel Gonçalves
- Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001, Lisbon, Portugal
- INESC-ID, 1000-029, Lisbon, Portugal
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Ismaninger Str. 22, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Michael Patrick Menden
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany.
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany.
- Department of Biochemistry and Pharmacology, University of Melbourne, Victoria, VIC, 3010, Australia.
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9
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Patel SR, Das M. Small Cell Lung Cancer: Emerging Targets and Strategies for Precision Therapy. Cancers (Basel) 2023; 15:4016. [PMID: 37627044 PMCID: PMC10452729 DOI: 10.3390/cancers15164016] [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: 06/27/2023] [Revised: 08/04/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Small cell lung cancer is an aggressive subtype of lung cancer with limited treatment options. Precision medicine has revolutionized cancer treatment for many tumor types but progress in SCLC has been slower due to the lack of targetable biomarkers. This review article provides an overview of emerging strategies for precision therapy in SCLC. Targeted therapies include targeted kinase inhibitors, monoclonal antibodies, angiogenesis inhibitors, antibody-drug conjugates, PARP inhibitors, and epigenetic modulators. Angiogenesis inhibitors and DNA-damaging agents, such as PARP and ATR inhibitors, have been explored in SCLC with limited success to date although trials are ongoing. The potential of targeting DLL3, a NOTCH ligand, through antibody-drug conjugates, bispecific T-cell engagers, and CAR T-cell therapy, has opened up new therapeutic options moving forward. Additionally, new research in epigenetic therapeutics in reversing transcriptional repression, modulating anti-tumor immunity, and utilizing antibody-drug conjugates to target cell surface-specific targets in SCLC are also being investigated. While progress in precision therapy for SCLC has been challenging, recent advancements provide optimism for improved treatment outcomes. However, several challenges remain and will need to be addressed, including drug resistance and tumor heterogeneity. Further research and biomarker-selected clinical trials are necessary to develop effective precision therapies for SCLC patients.
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Affiliation(s)
- Shruti R. Patel
- Department of Medicine, Division of Medical Oncology, Stanford Cancer Institute, Stanford University, Palo Alto, CA 94305, USA;
| | - Millie Das
- Department of Medicine, Division of Medical Oncology, Stanford Cancer Institute, Stanford University, Palo Alto, CA 94305, USA;
- Department of Medicine, Oncology Section, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
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10
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Yamada Y. Histogenetic and disease-relevant phenotypes in thymic epithelial tumors (TETs): The potential significance for future TET classification. Pathol Int 2023; 73:265-280. [PMID: 37278579 DOI: 10.1111/pin.13343] [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: 03/06/2023] [Accepted: 05/18/2023] [Indexed: 06/07/2023]
Abstract
Thymic epithelial tumors (TETs) encompass morphologically various subtypes. Thus, it would be meaningful to explore the expression phenotypes that delineate each TET subtype or overarching multiple subtypes. If these profiles are related to thymic physiology, they will improve our biological understanding of TETs and may contribute to the establishment of a more rational TET classification. Against this background, pathologists have attempted to identify histogenetic features in TETs for a long time. As part of this work, our group has reported several TET expression profiles that are histotype-dependent and related to the nature of thymic epithelial cells (TECs). For example, we found that beta5t, a constituent of thymoproteasome unique to cortical TECs, is expressed mainly in type B thymomas, for which the nomenclature of cortical thymoma was once considered. Another example is the discovery that most thymic carcinomas, especially thymic squamous cell carcinomas, exhibit expression profiles similar to tuft cells, a recently discovered special type of medullary TEC. This review outlines the currently reported histogenetic phenotypes of TETs, including those related to thymoma-associated myasthenia gravis, summarizes their genetic signatures, and provides a perspective for the future direction of TET classification.
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Affiliation(s)
- Yosuke Yamada
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
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11
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Hostallero DE, Wei L, Wang L, Cairns J, Emad A. Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:535-550. [PMID: 36775056 PMCID: PMC10787192 DOI: 10.1016/j.gpb.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/28/2022] [Accepted: 01/31/2023] [Indexed: 02/12/2023]
Abstract
Prediction of the response of cancer patients to different treatments and identification of biomarkers of drug response are two major goals of individualized medicine. Here, we developed a deep learning framework called TINDL, completely trained on preclinical cancer cell lines (CCLs), to predict the response of cancer patients to different treatments. TINDL utilizes a tissue-informed normalization to account for the tissue type and cancer type of the tumors and to reduce the statistical discrepancies between CCLs and patient tumors. Moreover, by making the deep learning black box interpretable, this model identifies a small set of genes whose expression levels are predictive of drug response in the trained model, enabling identification of biomarkers of drug response. Using data from two large databases of CCLs and cancer tumors, we showed that this model can distinguish between sensitive and resistant tumors for 10 (out of 14) drugs, outperforming various other machine learning models. In addition, our small interfering RNA (siRNA) knockdown experiments on 10 genes identified by this model for one of the drugs (tamoxifen) confirmed that tamoxifen sensitivity is substantially influenced by all of these genes in MCF7 cells, and seven of these genes in T47D cells. Furthermore, genes implicated for multiple drugs pointed to shared mechanism of action among drugs and suggested several important signaling pathways. In summary, this study provides a powerful deep learning framework for prediction of drug response and identification of biomarkers of drug response in cancer. The code can be accessed at https://github.com/ddhostallero/tindl.
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Affiliation(s)
- David Earl Hostallero
- Department of Electrical and Computer Engineering, McGill University, Montreal, QC H3A, Canada; Mila - Quebec Artificial Intelligence Institute, Montreal, QC H2S, Canada
| | - Lixuan Wei
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Junmei Cairns
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.
| | - Amin Emad
- Department of Electrical and Computer Engineering, McGill University, Montreal, QC H3A, Canada; Mila - Quebec Artificial Intelligence Institute, Montreal, QC H2S, Canada; The Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A, Canada.
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12
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Concannon K, Morris BB, Gay CM, Byers LA. Combining targeted DNA repair inhibition and immune-oncology approaches for enhanced tumor control. Mol Cell 2023; 83:660-680. [PMID: 36669489 PMCID: PMC9992136 DOI: 10.1016/j.molcel.2022.12.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/08/2022] [Accepted: 12/27/2022] [Indexed: 01/20/2023]
Abstract
Targeted therapy and immunotherapy have revolutionized cancer treatment. However, the ability of cancer to evade the immune system remains a major barrier for effective treatment. Related to this, several targeted DNA-damage response inhibitors (DDRis) are being tested in the clinic and have been shown to potentiate anti-tumor immune responses. Seminal studies have shown that these agents are highly effective in a pan-cancer class of tumors with genetic defects in key DNA repair genes such as BRCA1/2, BRCA-related genes, ataxia telangiectasia mutated (ATM), and others. Here, we review the molecular consequences of targeted DDR inhibition, from tumor cell death to increased engagement of the anti-tumor immune response. Additionally, we discuss mechanistic and clinical rationale for pairing targeted DDRis with immunotherapy for enhanced tumor control. We also review biomarkers for patient selection and promising new immunotherapy approaches poised to form the foundation of next-generation DDRi and immunotherapy combinations.
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Affiliation(s)
- Kyle Concannon
- Department of Hematology/Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin B Morris
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carl M Gay
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren A Byers
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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13
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Barbier S, Beaufils B, de Miguel R, Reyre M, Le Meitour Y, Lortie A, de Boisferon MH, Chaumeron S, Espirito A, Fossati L, Lagarde P, Klinz S, Thiagalingam A, Lezmi S, Meyer-Losic F. Liposomal Irinotecan Shows a Larger Therapeutic Index than Non-liposomal Irinotecan in Patient-Derived Xenograft Models of Pancreatic Cancer. Oncol Ther 2023; 11:111-128. [PMID: 36645622 PMCID: PMC9935793 DOI: 10.1007/s40487-022-00215-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/23/2022] [Indexed: 01/17/2023] Open
Abstract
INTRODUCTION Liposomal irinotecan promotes controlled sustained release of irinotecan (CPT-11), therefore, we hypothesize that the therapeutic index (quantitative measurement of the relative efficacy/safety ratio of a drug) will be higher for liposomal than non-liposomal irinotecan. METHODS We compared the therapeutic indexes of liposomal and non-liposomal irinotecan in mice bearing subcutaneous patient-derived xenograft (PDX) pancreatic tumors under dosing regimens approximating the clinical setting. Following preliminary drug sensitivity/antitumor activity analyses on three PDX tumor models, one model was selected for analyses of efficacy, biomarker, toxicology, pharmacokinetics in mice receiving liposomal irinotecan (2.5, 10, 50 mg/kg/week) or non-liposomal irinotecan (10, 25, 50 mg/kg/week). The maximum tolerated dose (MTD) for each treatment was 50 mg/kg/week. RESULTS Using the selected IM-PAN-001 model at the MTD (both treatments, 50 mg/kg/week), antitumor activity, phospho-histone gamma-H2AX protein staining in cancer cell nuclei, histological tumor regression, and plasma levels of CPT-11 and its active metabolite SN-38 after 24 h were greater with liposomal than non-liposomal irinotecan, but tumor SN-38 levels were similar. At the lowest doses assessed, antitumor activity, histological tumor regression, and jejunum and bone marrow toxicity were similar. Based on these findings, liposomal and non-liposomal irinotecan had therapeutic indexes of 20 and 5, respectively. CONCLUSION This non-clinical study showed a fourfold broader therapeutic index with liposomal than non-liposomal irinotecan in mice bearing IM-PAN-001 PDX pancreatic tumors, even at optimal dosing for the two drugs. These findings support the clinical benefit observed with liposomal irinotecan in patients with pancreatic cancer.
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Affiliation(s)
- Sandrine Barbier
- Ipsen Innovation, 5 Avenue du Canada, Z.I. Courtaboeuf, 91940, Les Ulis, France.
| | - Benjamin Beaufils
- Ipsen Innovation, 5 Avenue du Canada, Z.I. Courtaboeuf, 91940, Les Ulis, France
| | - Ricardo de Miguel
- Ipsen Innovation, 5 Avenue du Canada, Z.I. Courtaboeuf, 91940, Les Ulis, France
| | - Melissa Reyre
- Ipsen Innovation, 5 Avenue du Canada, Z.I. Courtaboeuf, 91940, Les Ulis, France
| | - Yannick Le Meitour
- Ipsen Innovation, 5 Avenue du Canada, Z.I. Courtaboeuf, 91940, Les Ulis, France
| | - Andreanne Lortie
- Ipsen Innovation, 5 Avenue du Canada, Z.I. Courtaboeuf, 91940, Les Ulis, France
| | | | | | | | - Lina Fossati
- Ipsen Innovation, 5 Avenue du Canada, Z.I. Courtaboeuf, 91940, Les Ulis, France
| | - Pauline Lagarde
- Ipsen Innovation, 5 Avenue du Canada, Z.I. Courtaboeuf, 91940, Les Ulis, France
| | | | | | - Stéphane Lezmi
- Ipsen Innovation, 5 Avenue du Canada, Z.I. Courtaboeuf, 91940, Les Ulis, France
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14
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da Costa AABA, Chowdhury D, Shapiro GI, D'Andrea AD, Konstantinopoulos PA. Targeting replication stress in cancer therapy. Nat Rev Drug Discov 2023; 22:38-58. [PMID: 36202931 PMCID: PMC11132912 DOI: 10.1038/s41573-022-00558-5] [Citation(s) in RCA: 90] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2022] [Indexed: 02/06/2023]
Abstract
Replication stress is a major cause of genomic instability and a crucial vulnerability of cancer cells. This vulnerability can be therapeutically targeted by inhibiting kinases that coordinate the DNA damage response with cell cycle control, including ATR, CHK1, WEE1 and MYT1 checkpoint kinases. In addition, inhibiting the DNA damage response releases DNA fragments into the cytoplasm, eliciting an innate immune response. Therefore, several ATR, CHK1, WEE1 and MYT1 inhibitors are undergoing clinical evaluation as monotherapies or in combination with chemotherapy, poly[ADP-ribose]polymerase (PARP) inhibitors, or immune checkpoint inhibitors to capitalize on high replication stress, overcome therapeutic resistance and promote effective antitumour immunity. Here, we review current and emerging approaches for targeting replication stress in cancer, from preclinical and biomarker development to clinical trial evaluation.
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Affiliation(s)
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, USA.
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15
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Morfouace M, Horak P, Kreutzfeldt S, Stevovic A, de Rojas T, Denisova E, Hutter B, Bautista F, Oliveira J, Defachelles AS, White J, Kasper B, Preusser M, Golfinopoulos V, Pfister S, Van der Graaf W, Wardelmann E, Shenjere P, Fröhling S, McCabe MG. Comprehensive molecular profiling of sarcomas in adolescent and young adult patients: Results of the EORTC SPECTA-AYA international proof-of-concept study. Eur J Cancer 2023; 178:216-226. [PMID: 36470093 DOI: 10.1016/j.ejca.2022.10.020] [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: 06/21/2022] [Revised: 09/30/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Adolescent and young adult (AYA) patients with cancer are poorly recruited to molecularly targeted trials and have not witnessed the advances in cancer treatment and survival seen in other age groups. We report here a pan-European proof-of-concept study to identify actionable alterations in some of the worst prognosis AYA cancers: bone and soft tissue sarcomas. DESIGN Patients aged 12-29 years with newly diagnosed or recurrent, intermediate or high-grade bone and soft tissue sarcomas were recruited from six European countries. Pathological diagnoses were centrally reviewed. Formalin-fixed tissues were analysed by whole exome sequencing, methylation profiling and RNA sequencing and were discussed in a multidisciplinary, international molecular tumour board. RESULTS Of 71 patients recruited, 48 (median 20 years, range 12-28) met eligibility criteria. Central pathological review confirmed, modified and re-classified the diagnosis in 41, 3, and 4 cases, respectively. Median turnaround time to discussion at molecular tumour board was 8.4 weeks. whole exome sequencing (n = 48), methylation profiling (n = 44, 85%) and RNA sequencing (n = 24, 50%) led to therapeutic recommendations for 81% patients, including 4 with germ line alterations. The most common were for agents targeted towards tyrosine kinases (n = 20 recommendations), DNA repair (n = 18) and the PI3K/mTOR/AKT pathway (n = 15). Recommendations were generally based on weak evidence such as activity in a different tumour type (n = 68, 61%), reflecting the dearth of relevant molecular clinical trial data in the same tumour type. CONCLUSIONS We demonstrate here that comprehensive molecular profiling of AYA patients' samples is feasible and deliverable in a European programme.
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Affiliation(s)
- Marie Morfouace
- European Organisation for the Research and Treatment of Cancer (EORTC), Brussels, Belgium
| | - Peter Horak
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Simon Kreutzfeldt
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Aleksandra Stevovic
- European Organisation for the Research and Treatment of Cancer (EORTC), Brussels, Belgium
| | - Teresa de Rojas
- European Organisation for the Research and Treatment of Cancer (EORTC), Brussels, Belgium; Pediatric Oncogenomics Unit, University Children's Hospital Niño Jesús, Madrid, Spain
| | - Evgeniya Denisova
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Hutter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Francisco Bautista
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands; Department of Pediatric Oncology and Hematology, Hospital Niño Jesús, Madrid, Spain
| | - Júlio Oliveira
- Department of Medical Oncology, Instituto Português de Oncologia (IPO), Porto, Portugal
| | | | - Jeff White
- Department of Medical Oncology, Beatson West of Scotland Cancer Centre, Glasgow, UK
| | - Bernd Kasper
- Sarcoma Unit, Mannheim University Medical Center, Mannheim, Germany
| | - Matthias Preusser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Vassilis Golfinopoulos
- European Organisation for the Research and Treatment of Cancer (EORTC), Brussels, Belgium
| | - Stefan Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Pediatric Neurooncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Winette Van der Graaf
- Department of Medical Oncology, Netherlands Cancer Institute (NKI), Amsterdam, Netherlands; Department of Medical Oncology, Erasmus Medical Center Cancer Institute, Rotterdam, Netherlands
| | - Eva Wardelmann
- Gerhard-Domagk Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Patrick Shenjere
- Department of Pathology, The Christie NHS Foundation Trust, Manchester, UK
| | - Stefan Fröhling
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Martin G McCabe
- Division of Cancer Sciences, University of Manchester, Manchester, UK.
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O'Connor MJ, Forment JV. Mechanisms of PARP Inhibitor Resistance. Cancer Treat Res 2023; 186:25-42. [PMID: 37978129 DOI: 10.1007/978-3-031-30065-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) represent the first medicines based on the targeting of the DNA damage response (DDR). PARPi have become standard of care for first-line maintenance treatment in ovarian cancer and have also been approved in other cancer indications including breast, pancreatic and prostate. Despite their efficacy, resistance to PARPi has been reported clinically and represents a growing patient population with unmet clinical need. Here, we describe the various mechanisms of PARPi resistance that have been identified in pre-clinical models and in the clinic.
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Affiliation(s)
- Mark J O'Connor
- Oncology R&D, AstraZeneca, Discovery Centre, Cambridge Biomedical Campus, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK.
| | - Josep V Forment
- Oncology R&D, AstraZeneca, Discovery Centre, Cambridge Biomedical Campus, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
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Increased Expression of the RBPMS Splice Variants Inhibits Cell Proliferation in Ovarian Cancer Cells. Int J Mol Sci 2022; 23:ijms232314742. [PMID: 36499073 PMCID: PMC9738375 DOI: 10.3390/ijms232314742] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
RNA-Binding Protein with Multiple Splicing (RBPMS) is a member of family proteins that bind to nascent RNA transcripts and regulate their splicing, localization, and stability. Evidence indicates that RBPMS controls the activity of transcription factors associated with cell growth and proliferation, including AP-1 and Smads. Three major RBPMS protein splice variants (RBPMSA, RBPMSB, and RBPMSC) have been described in the literature. We previously reported that reduced RBPMS levels decreased the sensitivity of ovarian cancer cells to cisplatin treatment. However, little is known about the biological role of the RBPMS splice variants in ovarian cancer cells. We performed RT-PCR and Western blots and observed that both RBPMSA and RBPMSC are reduced at the mRNA and protein levels in cisplatin resistant as compared with cisplatin sensitive ovarian cancer cells. The mRNA and protein levels of RBPMSB were not detectable in any of the ovarian cancer cells tested. To better understand the biological role of each RBPMSA and RBPMSC, we transfected these two splice variants in the A2780CP20 and OVCAR3CIS cisplatin resistant ovarian cancer cells and performed cell proliferation, cell migration, and invasion assays. Compared with control clones, a significant reduction in the number of colonies, colony size, cell migration, and invasion was observed with RBPMSA and RBPMSC overexpressed cells. Moreover, A2780CP20-RBPMSA and A2780CP20-RBPMSC clones showed reduced senescence-associated β-galactosidase (β-Gal)-levels when compared with control clones. A2780CP20-RBPMSA clones were more sensitive to cisplatin treatment as compared with A2780CP20-RBPMSC clones. The A2780CP20-RBPMSA and A2780CP20-RBPMSC clones subcutaneously injected into athymic nude mice formed smaller tumors as compared with A2780CP20-EV control group. Additionally, immunohistochemical analysis showed lower proliferation (Ki67) and angiogenesis (CD31) staining in tissue sections of A2780CP20-RBPMSA and A2780CP20-RBPMSC tumors compared with controls. RNAseq studies revealed many common RNA transcripts altered in A2780CP20-RBPMSA and A2780CP20-RBPMSC clones. Unique RNA transcripts deregulated by each RBPMS variant were also observed. Kaplan-Meier (KM) plotter database information identified clinically relevant RBPMSA and RBPMSC downstream effectors. These studies suggest that increased levels of RBPMSA and RBPMSC reduce cell proliferation in ovarian cancer cells. However, only RBPMSA expression levels were associated with the sensitivity of ovarian cancer cells to cisplatin treatment.
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Pulmonary cancers across different histotypes share hybrid tuft cell/ionocyte-like molecular features and potentially druggable vulnerabilities. Cell Death Dis 2022; 13:979. [PMID: 36402755 PMCID: PMC9675833 DOI: 10.1038/s41419-022-05428-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022]
Abstract
Tuft cells are chemosensory epithelial cells in the respiratory tract and several other organs. Recent studies revealed tuft cell-like gene expression signatures in some pulmonary adenocarcinomas, squamous cell carcinomas (SQCC), small cell carcinomas (SCLC), and large cell neuroendocrine carcinomas (LCNEC). Identification of their similarities could inform shared druggable vulnerabilities. Clinicopathological features of tuft cell-like (tcl) subsets in various lung cancer histotypes were studied in two independent tumor cohorts using immunohistochemistry (n = 674 and 70). Findings were confirmed, and additional characteristics were explored using public datasets (RNA seq and immunohistochemical data) (n = 555). Drug susceptibilities of tuft cell-like SCLC cell lines were also investigated. By immunohistochemistry, 10-20% of SCLC and LCNEC, and approximately 2% of SQCC expressed POU2F3, the master regulator of tuft cells. These tuft cell-like tumors exhibited "lineage ambiguity" as they co-expressed NCAM1, a marker for neuroendocrine differentiation, and KRT5, a marker for squamous differentiation. In addition, tuft cell-like tumors co-expressed BCL2 and KIT, and tuft cell-like SCLC and LCNEC, but not SQCC, also highly expressed MYC. Data from public datasets confirmed these features and revealed that tuft cell-like SCLC and LCNEC co-clustered on hierarchical clustering. Furthermore, only tuft cell-like subsets among pulmonary cancers significantly expressed FOXI1, the master regulator of ionocytes, suggesting their bidirectional but immature differentiation status. Clinically, tuft cell-like SCLC and LCNEC had a similar prognosis. Experimentally, tuft cell-like SCLC cell lines were susceptible to PARP and BCL2 co-inhibition, indicating synergistic effects. Taken together, pulmonary tuft cell-like cancers maintain histotype-related clinicopathologic characteristics despite overlapping unique molecular features. From a therapeutic perspective, identification of tuft cell-like LCNECs might be crucial given their close kinship with tuft cell-like SCLC.
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19
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Yamada Y, Bohnenberger H, Kriegsmann M, Kriegsmann K, Sinn P, Goto N, Nakanishi Y, Seno H, Chigusa Y, Fujimoto M, Minamiguchi S, Haga H, Simon R, Sauter G, Ströbel P, Marx A. Tuft cell-like carcinomas: novel cancer subsets present in multiple organs sharing a unique gene expression signature. Br J Cancer 2022; 127:1876-1885. [PMID: 35999270 PMCID: PMC9643388 DOI: 10.1038/s41416-022-01957-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Tuft cells are chemosensory epithelial cells playing a role in innate immunity. Recent studies revealed cancers with a tuft cell-like gene expression signature in the thorax. We wondered whether this signature might also occur in extrathoracic cancers. METHODS We examined mRNA expression of tuft cell markers (POU2F3, GFI1B, TRPM5, SOX9, CHAT, and AVIL) in 19 different types of cancers in multiple extrathoracic organs with The Cancer Genome Atlas (TCGA) (N = 6322). Four different extrathoracic cancers in our local archives (N = 909) were analysed by immunohistochemistry. RESULTS Twenty-two (0.35%) extrathoracic tumours with co-expression of POU2F3 and other tuft cell markers were identified in various TCGA datasets. Twelve of the 22 "tuft cell-like tumours" shared poor differentiation and a gene expression pattern, including KIT, anti-apoptotic BCL2, and ionocyte-associated genes. In our archival cases, eleven (1.21%) tumours co-expressing POU2F3, KIT, and BCL2 on immunohistochemistry, i.e., were presumable tuft cell-like cancers. In three among five TCGA cohorts, the tuft cell-like cancer subsets expressed SLFN11, a promising biomarker of PARP inhibitor susceptibility. CONCLUSIONS Tuft cell-like carcinomas form distinct subsets in cancers of many organs. It appears warranted to investigate their shared gene expression signature as a predictive biomarker for novel therapeutic strategies.
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Affiliation(s)
- Yosuke Yamada
- Institute of Pathology, University Medical Centre Mannheim and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan.
| | - Hanibal Bohnenberger
- Institute of Pathology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Mark Kriegsmann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Lung Cancer Research (DZL), Heidelberg, Germany
| | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Sinn
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Norihiro Goto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuki Nakanishi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yoshitsugu Chigusa
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | | | - Hironori Haga
- Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Alexander Marx
- Institute of Pathology, University Medical Centre Mannheim and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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20
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Metzner FJ, Wenzl SJ, Kugler M, Krebs S, Hopfner KP, Lammens K. Mechanistic understanding of human SLFN11. Nat Commun 2022; 13:5464. [PMID: 36115853 PMCID: PMC9482658 DOI: 10.1038/s41467-022-33123-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/01/2022] [Indexed: 11/12/2022] Open
Abstract
Schlafen 11 (SLFN11) is an interferon-inducible antiviral restriction factor with tRNA endoribonuclease and DNA binding functions. It is recruited to stalled replication forks in response to replication stress and inhibits replication of certain viruses such as the human immunodeficiency virus 1 (HIV-1) by modulating the tRNA pool. SLFN11 has been identified as a predictive biomarker in cancer, as its expression correlates with a beneficial response to DNA damage inducing anticancer drugs. However, the mechanism and interdependence of these two functions are largely unknown. Here, we present cryo-electron microscopy (cryo-EM) structures of human SLFN11 in its dimeric apoenzyme state, bound to tRNA and in complex with single-strand DNA. Full-length SLFN11 neither hydrolyses nor binds ATP and the helicase domain appears in an autoinhibited state. Together with biochemical and structure guided mutagenesis studies, our data give detailed insights into the mechanism of endoribonuclease activity as well as suggestions on how SLFN11 may block stressed replication forks. Schlafen 11 serves as an antiviral restriction factor and a predictive biomarker in cancer. Here, the authors use cryoelectron microscopy and biochemical assays to understand tRNA endoribonuclease and DNA binding functions of human Schlafen 11.
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21
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Fischietti M, Eckerdt F, Perez RE, Guillen Magaña JN, Mazewski C, Ho S, Gonzalez C, Streich LD, Beauchamp EM, Heimberger AB, Baran AH, Yue F, James CD, Platanias LC. SLFN11 Negatively Regulates Noncanonical NFκB Signaling to Promote Glioblastoma Progression. CANCER RESEARCH COMMUNICATIONS 2022; 2:966-978. [PMID: 36382088 PMCID: PMC9648417 DOI: 10.1158/2767-9764.crc-22-0192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Glioblastoma (GBM) is an aggressive and incurable brain tumor in nearly all instances, whose disease progression is driven in part by the glioma stem cell (GSC) subpopulation. Here, we explored the effects of Schlafen family member 11 (SLFN11) in the molecular, cellular, and tumor biology of GBM. CRISPR/Cas9-mediated knockout of SLFN11 inhibited GBM cell proliferation and neurosphere growth and was associated with reduced expression of progenitor/stem cell marker genes, such as NES, SOX2, and CD44. Loss of SLFN11 stimulated expression of NFκB target genes, consistent with a negative regulatory role for SLFN11 on the NFκB pathway. Furthermore, our studies identify p21 as a direct transcriptional target of NFκB2 in GBM whose expression was stimulated by loss of SLFN11. Genetic disruption of SLFN11 blocked GBM growth and significantly extended survival in an orthotopic patient-derived xenograft model. Together, our results identify SLFN11 as a novel component of signaling pathways that contribute to GBM and GSC with implications for future diagnostic and therapeutic strategies.
Significance:
We identify a negative regulatory role for SLFN11 in noncanonical NFκB signaling that results in suppression of the cell-cycle inhibitor p21. We provide evidence that SLFN11 contributes to regulation of stem cell markers in GBM, promoting the malignant phenotype. In addition, SLFN11 targeting triggers p21 expression and antitumor responses. Our studies define a highly novel function for SLFN11 and identify it as a potential therapeutic target for GBM.
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Affiliation(s)
- Mariafausta Fischietti
- 1Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
- 2Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Frank Eckerdt
- 1Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
- 2Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- 3Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ricardo E. Perez
- 1Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
- 2Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | - Candice Mazewski
- 1Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
- 2Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Sang Ho
- 1Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Christopher Gonzalez
- 1Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Lukas D. Streich
- 4Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Elspeth M. Beauchamp
- 1Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
- 2Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- 5Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Amy B. Heimberger
- 3Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Aneta H. Baran
- 1Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
- 2Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- 5Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Feng Yue
- 1Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
- 6Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - C. David James
- 1Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
- 3Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Leonidas C. Platanias
- 1Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
- 2Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- 5Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
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22
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Kristeleit RS, Moore K. Life after SOLO-2: Is Olaparib really inducing platinum resistance in BRCA-mutated (BRCAm), PARP inhibitor (PARPi) resistant, recurrent ovarian cancer? Ann Oncol 2022; 33:989-991. [PMID: 35964823 DOI: 10.1016/j.annonc.2022.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- R S Kristeleit
- Department of Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK.
| | - K Moore
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, USA
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23
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Onji H, Murai J. Reconsidering the mechanisms of action of PARP inhibitors based on clinical outcomes. Cancer Sci 2022; 113:2943-2951. [PMID: 35766436 PMCID: PMC9459283 DOI: 10.1111/cas.15477] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/19/2022] [Accepted: 06/25/2022] [Indexed: 11/30/2022] Open
Abstract
PARP inhibitors (PARPis) were initially developed as DNA repair inhibitors that inhibit the catalytic activity of PARP1 and PARP2 and are expected to induce synthetic lethality in BRCA‐ or homologous recombination (HR)‐deficient tumors. However, the clinical indications for PARPis are not necessarily limited to BRCA mutations or HR deficiency; BRCA wild‐type and HR‐proficient cancers can also derive some benefit from PARPis. These facts are interpretable by an additional primary antitumor mechanism of PARPis named PARP trapping, resulting from the stabilization of PARP‐DNA complexes. Favorable response to platinum derivatives (cisplatin and carboplatin) in preceding treatment is used as a clinical biomarker for some PARPis, implying that sensitivity factors for platinum derivatives and PARPis are mainly common. Such common sensitivity factors include not only HR defects (HRD) but also additional factors. One of them is Schlafen 11 (SLFN11), a putative DNA/RNA helicase, that sensitizes cancer cells to a broad type of DNA‐damaging agents, including platinum and topoisomerase inhibitors. Mechanistically, SLFN11 induces a lethal replication block in response to replication stress (ie, DNA damage). As SLFN11 acts upon replication stress, trapping PARPis can activate SLFN11. Preclinical models show the importance of SLFN11 in PARPi sensitivity. However, the relevance of SLFN11 in PARPi response is less evident in clinical data compared with the significance of SLFN11 for platinum sensitivity. In this review, we consider the reasons for variable indications of PARPis resulting from clinical outcomes and review the mechanisms of action for PARPis as anticancer agents.
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Affiliation(s)
- Hiroshi Onji
- Department of Obstetrics and Gynecology, Ehime University Graduate School of Medicine, Japan.,Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Japan
| | - Junko Murai
- Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
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24
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Can Schlafen 11 Help to Stratify Ovarian Cancer Patients Treated with DNA-Damaging Agents? Cancers (Basel) 2022; 14:cancers14102353. [PMID: 35625957 PMCID: PMC9139752 DOI: 10.3390/cancers14102353] [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: 03/25/2022] [Revised: 04/25/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
Platinum-based chemotherapy has been the cornerstone of systemic treatment in ovarian cancer. Since no validated molecular predictive markers have been identified yet, the response to platinum-based chemotherapy has been evaluated clinically, based on platinum-free interval. The new promising marker Schlafen 11 seems to correlate with sensitivity or resistance to DNA-damaging agents, including platinum compounds or PARP inhibitors in various types of cancer. We provide background information about the function of Schlafen 11, its evaluation in tumor tissue, and its prevalence in ovarian cancer. We discuss the current evidence of the correlation of Schlafen 11 expression in ovarian cancer with treatment outcomes and the potential use of Schlafen 11 as the key predictive and prognostic marker that could help to better stratify ovarian cancer patients treated with platinum-based chemotherapy or PARP inhibitors. We also provide perspectives on future directions in the research on this promising marker.
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25
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Dynamic expression of Schlafen 11 (SLFN11) in circulating tumour cells as a liquid biomarker in small cell lung cancer. Br J Cancer 2022; 127:569-576. [PMID: 35440668 PMCID: PMC9346119 DOI: 10.1038/s41416-022-01811-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/10/2022] [Accepted: 03/29/2022] [Indexed: 11/09/2022] Open
Abstract
INTRODUCTION Small cell lung cancer (SCLC) is an aggressive malignancy with no established biomarkers. Schlafen 11(SLFN11), a DNA/RNA helicase that sensitises cancer cells to DNA-damaging agents, has emerged as a promising predictive biomarker for several drug classes including platinum and PARP inhibitors. Detection of SLFN11 in circulating tumour cells (CTCs) may provide a valuable alternative to tissue sampling. METHODS SLFN11 expression was evaluated in tumour samples and characterised in circulating tumour cells (CTC) longitudinally to determine its potential role as a biomarker of response. RESULTS Among 196 SCLC tumours, 51% expressed SLFN11 by IHC. In addition, 20/29 extra-thoracic high-grade neuroendocrine tumours expressed SLFN11 expression. In 64 blood samples from 42 SCLC patients, 83% (53/64) of samples had detectable CTCs, and SLFN11-positive CTCs were detected in 55% (29/53). Patients actively receiving platinum treatment had the lowest number of CTCs and a lower percentage of SLFN11-positive CTCs (p = 0.014). Analysis from patients with longitudinal samples suggest a decrease in CTC number and in SLFN11 expression that correlates with clinical response. CONCLUSIONS SLFN11 levels can be monitored in CTCs from SCLC patients using non-invasive liquid biopsies. The ability to detect SLFN11 in CTCs from SCLC patients adds a valuable tool for the detection and longitudinal monitoring of this promising biomarker.
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26
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Schlafens Can Put Viruses to Sleep. Viruses 2022; 14:v14020442. [PMID: 35216035 PMCID: PMC8875196 DOI: 10.3390/v14020442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 12/21/2022] Open
Abstract
The Schlafen gene family encodes for proteins involved in various biological tasks, including cell proliferation, differentiation, and T cell development. Schlafens were initially discovered in mice, and have been studied in the context of cancer biology, as well as their role in protecting cells during viral infection. This protein family provides antiviral barriers via direct and indirect effects on virus infection. Schlafens can inhibit the replication of viruses with both RNA and DNA genomes. In this review, we summarize the cellular functions and the emerging relationship between Schlafens and innate immunity. We also discuss the functions and distinctions of this emerging family of proteins as host restriction factors against viral infection. Further research into Schlafen protein function will provide insight into their mechanisms that contribute to intrinsic and innate host immunity.
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27
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Metzner FJ, Huber E, Hopfner KP, Lammens K. Structural and biochemical characterization of human Schlafen 5. Nucleic Acids Res 2022; 50:1147-1161. [PMID: 35037067 PMCID: PMC8789055 DOI: 10.1093/nar/gkab1278] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 11/15/2022] Open
Abstract
The Schlafen family belongs to the interferon-stimulated genes and its members are involved in cell cycle regulation, T cell quiescence, inhibition of viral replication, DNA-repair and tRNA processing. Here, we present the cryo-EM structure of full-length human Schlafen 5 (SLFN5) and the high-resolution crystal structure of the highly conserved N-terminal core domain. We show that the core domain does not resemble an ATPase-like fold and neither binds nor hydrolyzes ATP. SLFN5 binds tRNA as well as single- and double-stranded DNA, suggesting a potential role in transcriptional regulation. Unlike rat Slfn13 or human SLFN11, human SLFN5 did not cleave tRNA. Based on the structure, we identified two residues in proximity to the zinc finger motif that decreased DNA binding when mutated. These results indicate that Schlafen proteins have divergent enzymatic functions and provide a structural platform for future biochemical and genetic studies.
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Affiliation(s)
- Felix J Metzner
- Department of Biochemistry, Gene Center, Feodor-Lynen-Straße 25, 81377 München, Germany
| | - Elisabeth Huber
- Department of Biochemistry, Gene Center, Feodor-Lynen-Straße 25, 81377 München, Germany
| | - Karl-Peter Hopfner
- Department of Biochemistry, Gene Center, Feodor-Lynen-Straße 25, 81377 München, Germany
| | - Katja Lammens
- Department of Biochemistry, Gene Center, Feodor-Lynen-Straße 25, 81377 München, Germany
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28
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Prados-Carvajal R, Irving E, Lukashchuk N, Forment JV. Preventing and Overcoming Resistance to PARP Inhibitors: A Focus on the Clinical Landscape. Cancers (Basel) 2021; 14:44. [PMID: 35008208 PMCID: PMC8750220 DOI: 10.3390/cancers14010044] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/17/2021] [Accepted: 12/19/2021] [Indexed: 12/12/2022] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are now a first-line maintenance treatment in ovarian cancer and have been approved in other cancer types, including breast, pancreatic and prostate. Despite their efficacy, and as is the case for other targeted therapies, resistance to PARPi has been reported clinically and is generating a growing patient population of unmet clinical need. Here, we discuss the mechanisms of resistance that have been described in pre-clinical models and focus on those that have been already identified in the clinic, highlighting the key challenges to fully characterise the clinical landscape of PARPi resistance and proposing ways of preventing and overcoming it.
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Affiliation(s)
- Rosario Prados-Carvajal
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK; (R.P.-C.); (E.I.)
| | - Elsa Irving
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK; (R.P.-C.); (E.I.)
| | - Natalia Lukashchuk
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK;
| | - Josep V. Forment
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK; (R.P.-C.); (E.I.)
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29
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Cleary JM, Wolpin BM, Dougan SK, Raghavan S, Singh H, Huffman B, Sethi NS, Nowak JA, Shapiro GI, Aguirre AJ, D'Andrea AD. Opportunities for Utilization of DNA Repair Inhibitors in Homologous Recombination Repair-Deficient and Proficient Pancreatic Adenocarcinoma. Clin Cancer Res 2021; 27:6622-6637. [PMID: 34285063 PMCID: PMC8678153 DOI: 10.1158/1078-0432.ccr-21-1367] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/04/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022]
Abstract
Pancreatic cancer is rapidly progressive and notoriously difficult to treat with cytotoxic chemotherapy and targeted agents. Recent demonstration of the efficacy of maintenance PARP inhibition in germline BRCA mutated pancreatic cancer has raised hopes that increased understanding of the DNA damage response pathway will lead to new therapies in both homologous recombination (HR) repair-deficient and proficient pancreatic cancer. Here, we review the potential mechanisms of exploiting HR deficiency, replicative stress, and DNA damage-mediated immune activation through targeted inhibition of DNA repair regulatory proteins.
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Affiliation(s)
- James M Cleary
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.
| | - Brian M Wolpin
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Stephanie K Dougan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Srivatsan Raghavan
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Harshabad Singh
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Brandon Huffman
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Nilay S Sethi
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Jonathan A Nowak
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew J Aguirre
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, Massachusetts
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30
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Taniyama D, Sakamoto N, Takashima T, Takeda M, Pham QT, Ukai S, Maruyama R, Harada K, Babasaki T, Sekino Y, Hayashi T, Sentani K, Pommier Y, Murai J, Yasui W. Prognostic impact of Schlafen 11 in bladder cancer patients treated with platinum-based chemotherapy. Cancer Sci 2021; 113:784-795. [PMID: 34808009 PMCID: PMC8819307 DOI: 10.1111/cas.15207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 12/15/2022] Open
Abstract
The utility of Schlafen 11 (SLFN11) expression as a predictive biomarker for platinum‐based chemotherapy has been established for cancers from different histologies. However, the therapeutic relevance of SLFN11 in bladder cancer (BC) is unknown. Here, we examined the clinicopathologic significance of SLFN11 expression across 120 BC cases by immunohistochemistry. We divided the cases into two cohorts, one including 50 patients who received adjuvant or neoadjuvant platinum‐based chemotherapy, and the other including 70 BC patients treated by surgical resection without chemotherapy. In the cohort of 50 BC cases treated with platinum‐based chemotherapy, the SLFN11‐positive group (n = 25) showed significantly better overall survival than the SLFN11‐negative group (n = 25, P = .012). Schlafen 11 expression correlated significantly with the expression of luminal subtype marker GATA3. Multivariate analyses identified SLFN11 expression as an independent prognostic predictor (odds ratio, 0.32; 95% confidence interval, 0.11‐0.91; P = .033). Conversely, in the cohort of 70 BC cases not receiving platinum‐based chemotherapy, the SLFN11‐positive group (n = 29) showed significantly worse overall survival than the SLFN11‐negative group (n = 41, P = .034). In vitro analyses using multiple BC cell lines confirmed that SLFN11 KO rendered cells resistant to cisplatin. The epigenetic modifying drugs 5‐azacytidine and entinostat restored SLFN11 expression and resensitized cells to cisplatin and carboplatin in SLFN11‐negative BC cell lines. We conclude that SLFN11 is a predictive biomarker for BC patients who undergo platinum‐based chemotherapy and that the combination of epigenetic modifiers could rescue refractory BC patients to platinum derivatives by reactivating SLFN11 expression.
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Affiliation(s)
- Daiki Taniyama
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Naoya Sakamoto
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tsuyoshi Takashima
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Masahiko Takeda
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Quoc Thang Pham
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shoichi Ukai
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ryota Maruyama
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenji Harada
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takashi Babasaki
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yohei Sekino
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tetsutaro Hayashi
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuhiro Sentani
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Wataru Yasui
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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31
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A wake-up call for cancer DNA damage: the role of Schlafen 11 (SLFN11) across multiple cancers. Br J Cancer 2021; 125:1333-1340. [PMID: 34294893 PMCID: PMC8576031 DOI: 10.1038/s41416-021-01476-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/25/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
DNA-damaging agents exploit increased genomic instability, a hallmark of cancer. Recently, inhibitors targeting the DNA damage response (DDR) pathways, such as PARP inhibitors, have also shown promising therapeutic potential. However, not all tumors respond well to these treatments, suggesting additional determinants of response are required. Schlafen 11 (SLFN11), a putative DNA/RNA helicase that induces irreversible replication block, is emerging as an important regulator of cellular response to DNA damage. Preclinical and emerging clinical trial data suggest that SLFN11 is a predictive biomarker of response to a wide range of therapeutics that cause DNA damage including platinum salts and topoisomerase I/II inhibitors, as well as PARP inhibitors, which has raised exciting possibilities for its clinical application. In this article, we review the function, prevalence, and clinical testing of SLFN11 in tumor biopsy samples and circulating tumor cells. We discuss mounting evidence of SLFN11 as a key predictive biomarker for a wide range of cancer therapeutics and as a prognostic marker across several cancer types. Furthermore, we discuss emerging areas of investigation such as epigenetic reactivation of SLFN11 and its role in activating immune response. We then provide perspectives on open questions and future directions in studying this important biomarker.
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32
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Murai Y, Jo U, Murai J, Fukuda S, Takebe N, Pommier Y. Schlafen 11 expression in human acute leukemia cells with gain-of-function mutations in the interferon-JAK signaling pathway. iScience 2021; 24:103173. [PMID: 34693224 PMCID: PMC8517841 DOI: 10.1016/j.isci.2021.103173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/16/2021] [Accepted: 09/22/2021] [Indexed: 12/28/2022] Open
Abstract
Schlafen11 (SLFN11) is referred to as interferon (IFN)-inducible. Based on cancer genomic databases, we identified human acute myeloid and lymphoblastic leukemia cells with gain-of-function mutations in the Janus kinase (JAK) family as exhibiting high SLFN11 expression. In these cells, the clinical JAK inhibitors cerdulatinib, ruxolitinib, and tofacitinib reduced SLFN11 expression, but IFN did not further induce SLFN11 despite phosphorylated STAT1. We provide evidence that suppression of SLFN11 by JAK inhibitors is caused by inactivation of the non-canonical IFN pathway controlled by AKT and ERK. Accordingly, the AKT and ERK inhibitors MK-2206 and SCH77284 suppressed SLFN11 expression. Both also suppressed the E26 transformation-specific (ETS)-family genes ETS-1 and FLI-1 that act as transcription factors for SLFN11. Moreover, SLFN11 expression was inhibited by the ETS inhibitor TK216. Our study reveals that SLFN11 expression is regulated via the JAK, AKT and ERK, and ETS axis. Pharmacological suppression of SLFN11 warrants future studies.
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Affiliation(s)
- Yasuhisa Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Ukhyun Jo
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Shinsaku Fukuda
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Naoko Takebe
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Developmental Therapeutics Branch and Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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Willis SE, Winkler C, Roudier MP, Baird T, Marco-Casanova P, Jones EV, Rowe P, Rodriguez-Canales J, Angell HK, Ng FSL, Waring PM, Hodgson D, Ledermann JA, Weberpals JI, Dean E, Harrington EA, Barrett JC, Pierce AJ, Leo E, Jones GN. Retrospective analysis of Schlafen11 (SLFN11) to predict the outcomes to therapies affecting the DNA damage response. Br J Cancer 2021; 125:1666-1676. [PMID: 34663950 PMCID: PMC8651811 DOI: 10.1038/s41416-021-01560-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/06/2021] [Accepted: 09/17/2021] [Indexed: 02/08/2023] Open
Abstract
Background The absence of the putative DNA/RNA helicase Schlafen11 (SLFN11) is thought to cause resistance to DNA-damaging agents (DDAs) and PARP inhibitors. Methods We developed and validated a clinically applicable SLFN11 immunohistochemistry assay and retrospectively correlated SLFN11 tumour levels to patient outcome to the standard of care therapies and olaparib maintenance. Results High SLFN11 associated with improved prognosis to the first-line treatment with DDAs platinum-plus-etoposide in SCLC patients, but was not strongly linked to paclitaxel–platinum response in ovarian cancer patients. Multivariate analysis of patients with relapsed platinum-sensitive ovarian cancer from the randomised, placebo-controlled Phase II olaparib maintenance Study19 showed SLFN11 tumour levels associated with sensitivity to olaparib. Study19 patients with high SLFN11 had a lower progression-free survival (PFS) hazard ratio compared to patients with low SLFN11, although both groups had the benefit of olaparib over placebo. Whilst caveated by small sample size, this trend was maintained for PFS, but not overall survival, when adjusting for BRCA status across the olaparib and placebo treatment groups, a key driver of PARP inhibitor sensitivity. Conclusion We provide clinical evidence supporting the role of SLFN11 as a DDA therapy selection biomarker in SCLC and highlight the need for further clinical investigation into SLFN11 as a PARP inhibitor predictive biomarker.
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Affiliation(s)
- Sophie E Willis
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | | | - Tarrion Baird
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Emma V Jones
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Philip Rowe
- GMD, Oncology R&D, AstraZeneca, Macclesfield, UK
| | | | - Helen K Angell
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Felicia S L Ng
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Paul M Waring
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Darren Hodgson
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, MA, USA
| | - Jonathan A Ledermann
- Cancer Research UK and UCL Cancer Trials Centre, UCL Cancer Institute, London, UK
| | | | - Emma Dean
- Clinical, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - J Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Gemma N Jones
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK.
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Yap TA, Krebs MG, Postel-Vinay S, El-Khouiery A, Soria JC, Lopez J, Berges A, Cheung SA, Irurzun-Arana I, Goldwin A, Felicetti B, Jones GN, Lau A, Frewer P, Pierce AJ, Clack G, Stephens C, Smith SA, Dean E, Hollingsworth SJ. Ceralasertib (AZD6738), an Oral ATR Kinase Inhibitor, in Combination with Carboplatin in Patients with Advanced Solid Tumors: A Phase I Study. Clin Cancer Res 2021; 27:5213-5224. [PMID: 34301752 PMCID: PMC9401487 DOI: 10.1158/1078-0432.ccr-21-1032] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/28/2021] [Accepted: 07/19/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE This study reports the safety, tolerability, MTD, recommended phase II dose (RP2D), pharmacokinetic/pharmacodynamic profile, and preliminary antitumor activity of ceralasertib combined with carboplatin in patients with advanced solid tumors. It also examined exploratory predictive and pharmacodynamic biomarkers. PATIENTS AND METHODS Eligible patients (n = 36) received a fixed dose of carboplatin (AUC5) with escalating doses of ceralasertib (20 mg twice daily to 60 mg once daily) in 21-day cycles. Sequential and concurrent combination dosing schedules were assessed. RESULTS Two ceralasertib MTD dose schedules, 20 mg twice daily on days 4-13 and 40 mg once daily on days 1-2, were tolerated with carboplatin AUC5; the latter was declared the RP2D. The most common treatment-emergent adverse events (Common Terminology Criteria for Adverse Events grade ≥3) were anemia (39%), thrombocytopenia (36%), and neutropenia (25%). Dose-limiting toxicities of grade 4 thrombocytopenia (n = 2; including one grade 4 platelet count decreased) and a combination of grade 4 thrombocytopenia and grade 3 neutropenia occurred in 3 patients. Ceralasertib was quickly absorbed (tmax ∼1 hour), with a terminal plasma half-life of 8-11 hours. Upregulation of pRAD50, indicative of ataxia telangiectasia mutated (ATM) activation, was observed in tumor biopsies during ceralasertib treatment. Two patients with absent or low ATM or SLFN11 protein expression achieved confirmed RECIST v1.1 partial responses. Eighteen of 34 (53%) response-evaluable patients had RECIST v1.1 stable disease. CONCLUSIONS The RP2D for ceralasertib plus carboplatin was established as ceralasertib 40 mg once daily on days 1-2 administered with carboplatin AUC5 every 3 weeks, with pharmacokinetic and pharmacodynamic studies confirming pharmacodynamic modulation and preliminary evidence of antitumor activity observed.
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Affiliation(s)
- Timothy A. Yap
- Royal Marsden Hospital and The Institute of Cancer Research, London, United Kingdom.,Corresponding Author: Timothy A. Yap, Department of Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, 1400 Holcombe Blvd, Houston, TX 77030. Phone: 713-563-1784; E-mail:
| | - Matthew G. Krebs
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Sophie Postel-Vinay
- ATIP-Avenir Group, INSERM Unit U981, Institut Gustave Roussy and Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, and Department of Drug Development, DITEP, Institut Gustave Roussy, Villejuif, France
| | | | - Jean-Charles Soria
- ATIP-Avenir Group, INSERM Unit U981, Institut Gustave Roussy and Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, and Department of Drug Development, DITEP, Institut Gustave Roussy, Villejuif, France
| | - Juanita Lopez
- Royal Marsden Hospital and The Institute of Cancer Research, London, United Kingdom
| | - Alienor Berges
- Quantitative Clinical Pharmacology, AstraZeneca, Cambridge, United Kingdom
| | - S.Y. Amy Cheung
- Quantitative Clinical Pharmacology, AstraZeneca, Cambridge, United Kingdom
| | | | - Andrew Goldwin
- Early Clinical Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Brunella Felicetti
- Early Clinical Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Gemma N. Jones
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Alan Lau
- Oncology Bioscience, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Paul Frewer
- Oncology Biometrics, AstraZeneca, Cambridge, United Kingdom
| | - Andrew J. Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Glen Clack
- Early Clinical Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Christine Stephens
- Early Clinical Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Simon A. Smith
- Early Clinical Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Emma Dean
- Early Clinical Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
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Jo U, Murai Y, Takebe N, Thomas A, Pommier Y. Precision Oncology with Drugs Targeting the Replication Stress, ATR, and Schlafen 11. Cancers (Basel) 2021; 13:4601. [PMID: 34572827 PMCID: PMC8465591 DOI: 10.3390/cancers13184601] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022] Open
Abstract
Precision medicine aims to implement strategies based on the molecular features of tumors and optimized drug delivery to improve cancer diagnosis and treatment. DNA replication is a logical approach because it can be targeted by a broad range of anticancer drugs that are both clinically approved and in development. These drugs increase deleterious replication stress (RepStress); however, how to selectively target and identify the tumors with specific molecular characteristics are unmet clinical needs. Here, we provide background information on the molecular processes of DNA replication and its checkpoints, and discuss how to target replication, checkpoint, and repair pathways with ATR inhibitors and exploit Schlafen 11 (SLFN11) as a predictive biomarker.
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Affiliation(s)
- Ukhyun Jo
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
| | - Yasuhisa Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
| | - Naoko Takebe
- Developmental Therapeutics Branch and Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, MD 20892-4264, USA;
| | - Anish Thomas
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-4264, USA; (Y.M.); (A.T.)
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Schlafens: Emerging Proteins in Cancer Cell Biology. Cells 2021; 10:cells10092238. [PMID: 34571887 PMCID: PMC8465726 DOI: 10.3390/cells10092238] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/29/2022] Open
Abstract
Schlafens (SLFN) are a family of genes widely expressed in mammals, including humans and rodents. These intriguing proteins play different roles in regulating cell proliferation, cell differentiation, immune cell growth and maturation, and inhibiting viral replication. The emerging evidence is implicating Schlafens in cancer biology and chemosensitivity. Although Schlafens share common domains and a high degree of homology, different Schlafens act differently. In particular, they show specific and occasionally opposing effects in some cancer types. This review will briefly summarize the history, structure, and non-malignant biological functions of Schlafens. The roles of human and mouse Schlafens in different cancer types will then be outlined. Finally, we will discuss the implication of Schlafens in the anti-tumor effect of interferons and the use of Schlafens as predictors of chemosensitivity.
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Takashima T, Taniyama D, Sakamoto N, Yasumoto M, Asai R, Hattori T, Honma R, Thang PQ, Ukai S, Maruyama R, Harada K, Kuraoka K, Tanabe K, Sasaki AT, Ohdan H, Morii E, Murai J, Yasui W. Schlafen 11 predicts response to platinum-based chemotherapy in gastric cancers. Br J Cancer 2021; 125:65-77. [PMID: 33785877 PMCID: PMC8257722 DOI: 10.1038/s41416-021-01364-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Although unresectable or recurrent gastric cancers (GC) are frequently treated with platinum-based chemotherapy, response to treatment remains unpredictable. Because Schlafen 11 (SLFN11) is recently identified as a critical determinant of platinum sensitivity, we investigated the potential clinical utility of SLFN11 in the treatment of GC. METHODS We analysed the correlation between SLFN11 expression and overall survival in 169 GC patients by our established immunohistochemical approach. The impact of SLFN11 expression on the response to platinum and transition of SLFN11 expression upon long-term treatment with platinum were examined using GC cell lines and organoids. RESULTS GC patients with high-SLFN11 expression exhibited significantly better survival than those with low-SLFN11 expression, and the significance increased when we selected patients treated with platinum-based chemotherapy. Knockout of SLFN11 and reactivation of SLFN11 in GC cells conferred resistance and sensitivity to platinum, respectively. In GC cells and organoids, long-term treatment with oxaliplatin suppressed SLFN11 expression while imparting drug resistance. The acquired resistance to oxaliplatin was reversed by reactivation of SLFN11 with epigenetic modifying drugs. CONCLUSIONS This is the first report revealing definitive clinical implications of SLFN11 in the treatment of GC patients and providing novel strategies for the drug selection based on SLFN11 expression.
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Affiliation(s)
- Tsuyoshi Takashima
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Daiki Taniyama
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Naoya Sakamoto
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
| | - Maika Yasumoto
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ryuichi Asai
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takuya Hattori
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ririno Honma
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Pham Quoc Thang
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shoichi Ukai
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ryota Maruyama
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenji Harada
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuya Kuraoka
- Institute for Clinical Research, National Hospital Organization, Kure Medical Center and Chugoku Cancer Center, Hiroshima, Japan
- Department of Diagnostic Pathology, National Hospital Organization, Kure Medical Center and Chugoku Cancer Center, Hiroshima, Japan
| | - Kazuaki Tanabe
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Hideki Ohdan
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
| | - Wataru Yasui
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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PARP inhibition in UV-associated angiosarcoma preclinical models. J Cancer Res Clin Oncol 2021; 147:2579-2590. [PMID: 34085099 PMCID: PMC8310857 DOI: 10.1007/s00432-021-03678-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/27/2021] [Indexed: 10/27/2022]
Abstract
PURPOSE Angiosarcoma (AS) is a rare vasoformative sarcoma, with poor overall survival and a high need for novel treatment options. Clinically, AS consists of different subtypes, including AS related to previous UV exposure (UV AS) which could indicate susceptibility to DNA damage repair inhibition. We, therefore, investigated the presence of biomarkers PARP1 (poly(ADP-ribose)polymerase-1) and Schlafen-11 (SLFN11) in UV AS. Based on experiences in other sarcomas, we examined (combination) treatment of PARP inhibitor (PARPi) olaparib and temozolomide (TMZ) in UV AS cell lines. METHODS Previously collected UV AS (n = 47) and non-UV AS (n = 96) patient samples and two UV AS cell lines (MO-LAS and AS-M) were immunohistochemically assessed for PARP1 and SLFN11 expression. Both cell lines were treated with single agents PARPi olaparib and TMZ, and the combination treatment. Next, cell viability and treatment synergy were analyzed. In addition, effects on apoptosis and DNA damage were examined. RESULTS In 46/47 UV AS samples (98%), PARP1 expression was present. SLFN11 was expressed in 80% (37/46) of cases. Olaparib and TMZ combination treatment was synergistic in both cell lines, with significantly increased apoptosis compared to single agent treatment. Furthermore, a significant increase in DNA damage marker γH2AX was present in both cell lines after combination therapy. CONCLUSION We showed combination treatment of olaparib with TMZ was synergistic in UV AS cell lines. Expression of PARP1 and SLFN11 was present in the majority of UV AS tumor samples. Together, these results suggest combination treatment of olaparib and TMZ is a potential novel AS subtype-specific treatment option for UV AS patients.
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Murai Y, Jo U, Murai J, Jenkins LM, Huang SYN, Chakka S, Chen L, Cheng K, Fukuda S, Takebe N, Pommier Y. SLFN11 Inactivation Induces Proteotoxic Stress and Sensitizes Cancer Cells to Ubiquitin Activating Enzyme Inhibitor TAK-243. Cancer Res 2021; 81:3067-3078. [PMID: 33863777 DOI: 10.1158/0008-5472.can-20-2694] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/10/2020] [Accepted: 04/13/2021] [Indexed: 11/16/2022]
Abstract
Schlafen11 (SLFN11) inactivation occurs in approximately 50% of cancer cell lines and in a large fraction of patient tumor samples, which leads to chemoresistance. Therefore, new therapeutic approaches are needed to target SLFN11-deficient cancers. To that effect, we conducted a drug screen with the NCATS mechanistic drug library of 1,978 compounds in isogenic SLFN11-knockout (KO) and wild-type (WT) leukemia cell lines. Here we report that TAK-243, a first-in-class ubiquitin activating enzyme UBA1 inhibitor in clinical development, causes preferential cytotoxicity in SLFN11-KO cells; this effect is associated with claspin-mediated DNA replication inhibition by CHK1 independently of ATR. Additional analyses showed that SLFN11-KO cells exhibit consistently enhanced global protein ubiquitylation, endoplasmic reticulum (ER) stress, unfolded protein response (UPR), and protein aggregation. TAK-243 suppressed global protein ubiquitylation and activated the UPR transducers PERK, phosphorylated eIF2α, phosphorylated IRE1, and ATF6 more effectively in SLFN11-KO cells than in WT cells. Proteomic analysis using biotinylated mass spectrometry and RNAi screening also showed physical and functional interactions of SLFN11 with translation initiation complexes and protein folding machinery. These findings uncover a previously unknown function of SLFN11 as a regulator of protein quality control and attenuator of ER stress and UPR. Moreover, they suggest the potential value of TAK-243 in SLFN11-deficient tumors. SIGNIFICANCE: This study uncovers that SLFN11 deficiency induces proteotoxic stress and sensitizes cancer cells to TAK-243, suggesting that profiling SLFN11 status can serve as a therapeutic biomarker for cancer therapy.
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Affiliation(s)
- Yasuhisa Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.,Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Ukhyun Jo
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Shar-Yin N Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Sirisha Chakka
- National Center for Advancing Translational Sciences, Functional Genomics Laboratory, NIH, Rockville, Maryland
| | - Lu Chen
- National Center for Advancing Translational Sciences, Functional Genomics Laboratory, NIH, Rockville, Maryland
| | - Ken Cheng
- National Center for Advancing Translational Sciences, Functional Genomics Laboratory, NIH, Rockville, Maryland
| | - Shinsaku Fukuda
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Naoko Takebe
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.,Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.
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The role of Schlafen 11 (SLFN11) as a predictive biomarker for targeting the DNA damage response. Br J Cancer 2020; 124:857-859. [PMID: 33328609 PMCID: PMC7921443 DOI: 10.1038/s41416-020-01202-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/09/2020] [Accepted: 11/17/2020] [Indexed: 01/25/2023] Open
Abstract
The therapeutic landscape of drugs targeting the DNA damage response (DDR) is rapidly expanding; however, an urgent unmet need remains for validated predictive biomarkers of response. SLFN11 has emerged as a promising predictor of sensitivity to DNA-damaging chemotherapies, and recently, been associated with sensitivity to PARP inhibition. We discuss its use as a predictive biomarker of response for targeting the DDR.
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