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Shen CI, Chang JC, Jain S, Olsen S, Wu CE. Afatinib Plus Bevacizumab Treatment for a Patient With EGFR S645C-Mutant Non-Small Cell Lung Cancer: A Case Report. JCO Precis Oncol 2024; 8:e2400007. [PMID: 38838275 DOI: 10.1200/po.24.00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/21/2024] [Accepted: 04/11/2024] [Indexed: 06/07/2024] Open
Affiliation(s)
- Chia-I Shen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ju-Chen Chang
- Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Suyog Jain
- Medical Affairs, Guardant Health AMEA, Singapore
| | - Steve Olsen
- Medical Affairs, Guardant Health AMEA, Singapore
| | - Chiao-En Wu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan
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2
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Hynds RE, Huebner A, Pearce DR, Hill MS, Akarca AU, Moore DA, Ward S, Gowers KHC, Karasaki T, Al Bakir M, Wilson GA, Pich O, Martínez-Ruiz C, Hossain ASMM, Pearce SP, Sivakumar M, Ben Aissa A, Grönroos E, Chandrasekharan D, Kolluri KK, Towns R, Wang K, Cook DE, Bosshard-Carter L, Naceur-Lombardelli C, Rowan AJ, Veeriah S, Litchfield K, Crosbie PAJ, Dive C, Quezada SA, Janes SM, Jamal-Hanjani M, Marafioti T, McGranahan N, Swanton C. Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models. Nat Commun 2024; 15:4653. [PMID: 38821942 PMCID: PMC11143323 DOI: 10.1038/s41467-024-47547-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/28/2024] [Indexed: 06/02/2024] Open
Abstract
Patient-derived xenograft (PDX) models are widely used in cancer research. To investigate the genomic fidelity of non-small cell lung cancer PDX models, we established 48 PDX models from 22 patients enrolled in the TRACERx study. Multi-region tumor sampling increased successful PDX engraftment and most models were histologically similar to their parent tumor. Whole-exome sequencing enabled comparison of tumors and PDX models and we provide an adapted mouse reference genome for improved removal of NOD scid gamma (NSG) mouse-derived reads from sequencing data. PDX model establishment caused a genomic bottleneck, with models often representing a single tumor subclone. While distinct tumor subclones were represented in independent models from the same tumor, individual PDX models did not fully recapitulate intratumor heterogeneity. On-going genomic evolution in mice contributed modestly to the genomic distance between tumors and PDX models. Our study highlights the importance of considering primary tumor heterogeneity when using PDX models and emphasizes the benefit of comprehensive tumor sampling.
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Affiliation(s)
- Robert E Hynds
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Epithelial Cell Biology in ENT Research Group (EpiCENTR), Developmental Biology and Cancer, Great Ormond Street University College London Institute of Child Health, London, UK.
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - David R Pearce
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ayse U Akarca
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Kate H C Gowers
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Oriol Pich
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - A S Md Mukarram Hossain
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Simon P Pearce
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Monica Sivakumar
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Deepak Chandrasekharan
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Krishna K Kolluri
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Rebecca Towns
- Biological Services Unit, University College London, London, UK
| | - Kaiwen Wang
- School of Medicine, University of Leeds, Leeds, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Leticia Bosshard-Carter
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | | | - Andrew J Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Philip A J Crosbie
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Caroline Dive
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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3
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Valipour J, Taghizadeh F, Esfahani R, Ramesh M, Rastegar T. Role of nuclear factor erythroid 2-related factor 2 (Nrf2) in female and male fertility. Heliyon 2024; 10:e29752. [PMID: 38720768 PMCID: PMC11076650 DOI: 10.1016/j.heliyon.2024.e29752] [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: 09/02/2023] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Oxidative stress refers to a condition where there is an imbalance between the production of reactive oxygen species and their removal by antioxidants. While the function of reactive oxygen species as specific second messengers under physiological conditions is necessary, their overproduction can lead to numerous instances of cell and tissue damage. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a master regulator of many cytoprotective genes that respond to redox stresses. Nrf2 is regularly degraded by kelch-like ECH-associated protein 1 through the ubiquitin-proteasome pathway. The kelch-like ECH-associated protein 1 and Nrf2 complex have attracted attention in both basic and clinical infertility research fields. Oxidative stress is implicated in the pathogenesis of female infertility, including primary ovarian insufficiency, polycystic ovarian syndrome, and endometriosis, as well as male infertility, namely varicocele, cryptorchidism, spermatic cord torsion, and orchitis. Most scientists believe that Nrf2 is a potential therapeutic method in female and male infertility disorders due to its antioxidant effect. Here, the potential roles of oxidative stress and Nrf2 in female and male infertility disorders are reviewed. Moreover, the key role of Nrf2 in the inhibition or induction of these diseases is discussed.
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Affiliation(s)
- Jamal Valipour
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Taghizadeh
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Roghayeh Esfahani
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahya Ramesh
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Tayebeh Rastegar
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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4
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Chen F, Xiao M, Hu S, Wang M. Keap1-Nrf2 pathway: a key mechanism in the occurrence and development of cancer. Front Oncol 2024; 14:1381467. [PMID: 38634043 PMCID: PMC11021590 DOI: 10.3389/fonc.2024.1381467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
The Keap1-Nrf2 signaling pathway is a major regulator of the cytoprotective response, participating in endogenous and exogenous stress caused by ROS (reactive oxygen species). Nrf2 is the core of this pathway. We summarized the literature on Keap1-Nrf2 signaling pathway and summarized the following three aspects: structure, function pathway, and cancer and clinical application status. This signaling pathway is similar to a double-edged sword: on the one hand, Nrf2 activity can protect cells from oxidative and electrophilic stress; on the other hand, increasing Nrf2 activity can enhance the survival and proliferation of cancer cells. Notably, oxidative stress is also considered a marker of cancer in humans. Keap1-Nrf2 signaling pathway, as a typical antioxidant stress pathway, is abnormal in a variety of human malignant tumor diseases (such as lung cancer, liver cancer, and thyroid cancer). In recent years, research on the Keap1-Nrf2 signaling pathway has become increasingly in-depth and detailed. Therefore, it is of great significance for cancer prevention and treatment to explore the molecular mechanism of the occurrence and development of this pathway.
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Affiliation(s)
- Feilong Chen
- Sports Medicine Key Laboratory of Sichuan Province, Expert Centre of Sichuan Province, Institute of Sports Medicine and Health, Chengdu Sport University, Chengdu, China
| | - Mei Xiao
- College of Bioengineering, Chongqing University, Chongqing, China
| | - Shaofan Hu
- Department of Biochemistry and Molecular Biology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Meng Wang
- Department of Biochemistry and Molecular Biology, Third Military Medical University (Army Medical University), Chongqing, China
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5
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Caballé-Perez E, Hernández-Pedro N, Ramos-Ramírez M, Barrios-Bernal P, Romero-Núñez E, Lucio-Lozada J, Ávila-Ríos S, Reyes-Terán G, Cardona AF, Arrieta O. Impact of KRAS G12D subtype and concurrent pathogenic mutations on advanced non-small cell lung cancer outcomes. Clin Transl Oncol 2024; 26:836-850. [PMID: 37490263 PMCID: PMC10981588 DOI: 10.1007/s12094-023-03279-2] [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: 06/26/2023] [Accepted: 07/09/2023] [Indexed: 07/26/2023]
Abstract
PURPOSE Mutations in the Kirsten rat sarcoma viral (KRAS) oncogene constitute a significant driver of lung adenocarcinoma, present in 10-40% of patients, which exhibit heterogeneous clinical outcomes, mainly driven by concurrent genetic alterations. However, characterization of KRAS mutational subtypes and their impact on clinical outcomes in Latin America is limited. METHODS A cohort study was conducted at the National Cancer Institute (INCan) of Mexico. Individuals with advance-staged of adenocarcinoma and KRAS mutations, detected by next-generation sequencing, having undergone at least one line of therapy were included for analysis. Clinical and pathological characteristics were retrieved from institutional database from June 2014 to March 2023. RESULTS KRAS was identified in fifty-four (15.6%) of 346 patients, among which 50 cases were included for analysis. KRASG12D (n = 16, 32%) and KRASG12C (n = 16, 32%) represented the most prevalent subtypes. KRASG12D mutations were associated with female (p = 0.018), never smokers (p = 0.108), and concurrences with EGFR (25.0% vs. 17.6%, p = 0.124) and CDKN2A (18.8% vs. 14.7%, p = 0.157). KRASG12D patients showed a better ORR (66.6% vs. 30.0%; OR 4.66, 95% CI 1.23-17.60, p = 0.023) and on multivariate analysis was significantly associated with better PFS (HR 0.36, 95% CI 0.16-0.80; p = 0.012) and OS (HR 0.24, 95% CI 0.08-0.70; p = 0.009). CONCLUSIONS To our knowledge, this study represents the first effort to comprehensively characterize the molecular heterogeneity of KRAS-mutant NSCLC in Latin American patients. Our data reinforce the current view that KRAS-mutated NSCLC is not a single oncogene-driven disease and emphasizes the prognostic impact of diverse molecular profiles in this genomically defined subset of NSCLC. Further validation is warranted in larger multicenter Latin American cohorts to confirm our findings.
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Affiliation(s)
- Enrique Caballé-Perez
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
- Personalized Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Norma Hernández-Pedro
- Personalized Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Maritza Ramos-Ramírez
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Pedro Barrios-Bernal
- Personalized Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Eunice Romero-Núñez
- Personalized Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - José Lucio-Lozada
- Personalized Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | | | | | - Andrés F Cardona
- Thoracic Oncology Unit and Direction of Research, Science and Education, Luis Carlos Sarmiento Angulo, Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
- Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.
- Personalized Medicine Laboratory, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.
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6
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Lee JY, Bhandare RR, Boddu SHS, Shaik AB, Saktivel LP, Gupta G, Negi P, Barakat M, Singh SK, Dua K, Chellappan DK. Molecular mechanisms underlying the regulation of tumour suppressor genes in lung cancer. Biomed Pharmacother 2024; 173:116275. [PMID: 38394846 DOI: 10.1016/j.biopha.2024.116275] [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: 11/24/2023] [Revised: 01/30/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Tumour suppressor genes play a cardinal role in the development of a large array of human cancers, including lung cancer, which is one of the most frequently diagnosed cancers worldwide. Therefore, extensive studies have been committed to deciphering the underlying mechanisms of alterations of tumour suppressor genes in governing tumourigenesis, as well as resistance to cancer therapies. In spite of the encouraging clinical outcomes demonstrated by lung cancer patients on initial treatment, the subsequent unresponsiveness to first-line treatments manifested by virtually all the patients is inherently a contentious issue. In light of the aforementioned concerns, this review compiles the current knowledge on the molecular mechanisms of some of the tumour suppressor genes implicated in lung cancer that are either frequently mutated and/or are located on the chromosomal arms having high LOH rates (1p, 3p, 9p, 10q, 13q, and 17p). Our study identifies specific genomic loci prone to LOH, revealing a recurrent pattern in lung cancer cases. These loci, including 3p14.2 (FHIT), 9p21.3 (p16INK4a), 10q23 (PTEN), 17p13 (TP53), exhibit a higher susceptibility to LOH due to environmental factors such as exposure to DNA-damaging agents (carcinogens in cigarette smoke) and genetic factors such as chromosomal instability, genetic mutations, DNA replication errors, and genetic predisposition. Furthermore, this review summarizes the current treatment landscape and advancements for lung cancers, including the challenges and endeavours to overcome it. This review envisages inspired researchers to embark on a journey of discovery to add to the list of what was known in hopes of prompting the development of effective therapeutic strategies for lung cancer.
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Affiliation(s)
- Jia Yee Lee
- School of Health Sciences, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
| | - Richie R Bhandare
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates.
| | - Sai H S Boddu
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates
| | - Afzal B Shaik
- St. Mary's College of Pharmacy, St. Mary's Group of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological University Kakinada, Chebrolu, Guntur, Andhra Pradesh 522212, India; Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, India
| | - Lakshmana Prabu Saktivel
- Department of Pharmaceutical Technology, University College of Engineering (BIT Campus), Anna University, Tiruchirappalli 620024, India
| | - Gaurav Gupta
- Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; School of Pharmacy, Suresh Gyan Vihar University, Jaipur, Rajasthan 302017, India
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University, PO Box 9, Solan, Himachal Pradesh 173229, India
| | - Muna Barakat
- Department of Clinical Pharmacy & Therapeutics, Applied Science Private University, Amman-11937, Jordan
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T Road, Phagwara 144411, India; Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Sydney 2007, Australia
| | - Kamal Dua
- Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Sydney 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney 2007, Australia
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia.
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Li J, Shi D, Li S, Shi X, Liu Y, Zhang Y, Wang G, Zhang C, Xia T, Piao HL, Liu HX. KEAP1 promotes anti-tumor immunity by inhibiting PD-L1 expression in NSCLC. Cell Death Dis 2024; 15:175. [PMID: 38413563 PMCID: PMC10899596 DOI: 10.1038/s41419-024-06563-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
Immunotherapy has become a prominent first-line cancer treatment strategy. In non-small cell lung cancer (NSCLC), the expression of PD-L1 induces an immuno-suppressive effect to protect cancer cells from immune elimination, which designates PD-L1 as an important target for immunotherapy. However, little is known about the regulation mechanism and the function of PD-L1 in lung cancer. In this study, we have discovered that KEAP1 serves as an E3 ligase to promote PD-L1 ubiquitination and degradation. We found that overexpression of KEAP1 suppressed tumor growth and promoted cytotoxic T-cell activation in vivo. These results indicate the important role of KEAP1 in anti-cancer immunity. Moreover, the combination of elevated KEAP1 expression with anti-PD-L1 immunotherapy resulted in a synergistic effect on both tumor growth and cytotoxic T-cell activation. Additionally, we found that the expressions of KEAP1 and PD-L1 were associated with NSCLC prognosis. In summary, our findings shed light on the mechanism of PD-L1 degradation and how NSCLC immune escape through KEAP1-PD-L1 signaling. Our results also suggest that KEAP1 agonist might be a potential clinical drug to boost anti-tumor immunity and improve immunotherapies in NSCLC.
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Affiliation(s)
- Jinghan Li
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Daiwang Shi
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Department of Thoracic Surgery, Shengjing Hospital, China Medical University, Shenyang, Liaoning, China
| | - Siyi Li
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiang Shi
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yu Liu
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yi Zhang
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Gebang Wang
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China
| | - Chenlei Zhang
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China
| | - Tian Xia
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Hai-Long Piao
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China.
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
- Department of Biochemistry & Molecular Biology, School of Life Sciences, China Medical University, Shenyang, 110122, China.
| | - Hong-Xu Liu
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China.
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Skalka GL, Tsakovska M, Murphy DJ. Kinase signalling adaptation supports dysfunctional mitochondria in disease. Front Mol Biosci 2024; 11:1354682. [PMID: 38434478 PMCID: PMC10906720 DOI: 10.3389/fmolb.2024.1354682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/15/2024] [Indexed: 03/05/2024] Open
Abstract
Mitochondria form a critical control nexus which are essential for maintaining correct tissue homeostasis. An increasing number of studies have identified dysregulation of mitochondria as a driver in cancer. However, which pathways support and promote this adapted mitochondrial function? A key hallmark of cancer is perturbation of kinase signalling pathways. These pathways include mitogen activated protein kinases (MAPK), lipid secondary messenger networks, cyclic-AMP-activated (cAMP)/AMP-activated kinases (AMPK), and Ca2+/calmodulin-dependent protein kinase (CaMK) networks. These signalling pathways have multiple substrates which support initiation and persistence of cancer. Many of these are involved in the regulation of mitochondrial morphology, mitochondrial apoptosis, mitochondrial calcium homeostasis, mitochondrial associated membranes (MAMs), and retrograde ROS signalling. This review will aim to both explore how kinase signalling integrates with these critical mitochondrial pathways and highlight how these systems can be usurped to support the development of disease. In addition, we will identify areas which require further investigation to fully understand the complexities of these regulatory interactions. Overall, this review will emphasize how studying the interaction between kinase signalling and mitochondria improves our understanding of mitochondrial homeostasis and can yield novel therapeutic targets to treat disease.
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Affiliation(s)
- George L. Skalka
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mina Tsakovska
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel J. Murphy
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- CRUK Scotland Institute, Glasgow, United Kingdom
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9
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Yoshizawa M, Shiozaki A, Ashihara E. Depletion of DNTTIP2 Induces Cell Cycle Arrest in Pancreatic Cancer Cells. Cancer Genomics Proteomics 2024; 21:18-29. [PMID: 38151292 PMCID: PMC10756344 DOI: 10.21873/cgp.20426] [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: 10/08/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND/AIM Pancreatic cancer is one of the most lethal malignant cancers worldwide and the seventh most common cause of cancer-related death in both sexes. Herein, we analyzed open access data and discovered that expression of a gene called deoxynucleotidyltransferase terminal-interacting protein 2 (DNTTIP2) is linked to prognosis of pancreatic ductal adenocarcinoma (PDAC). We then elucidated the role of DNTTIP2 in the proliferation of pancreatic cancer cells in vitro. MATERIALS AND METHODS A WST-8 assay, cell cycle analysis, Annexin-V staining, quantitative reverse transcription-PCR, and western blot analysis were conducted to assess cell proliferation, cell cycle, apoptosis, and expression of DNTTIP2 mRNA and protein, respectively, in DNTTIP2-depleteted MIA-PaCa-2 and PK-1 cells. RESULTS Depletion of DNTTIP2 induced G1 arrest in MIA-PaCa-2 cells by decreasing expression of special AT-rich sequence binding protein 1 (SATB1) and cyclin-dependent kinase 6 (CDK6). In addition, depletion of DNTTIP2 induced G2 arrest in PK-1 cells by decreasing expression of CDK1. Depletion of DNTTIP2 did not induce apoptosis in MIA-PaCa-2 or PK-1 cells. CONCLUSION DNTTIP2 is involved in proliferation of pancreatic cancer cells. Thus, DNTTIP2 is a potential target for inhibiting progression of pancreatic cancers.
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Affiliation(s)
- Masato Yoshizawa
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan;
| | - Atsushi Shiozaki
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eishi Ashihara
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan;
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10
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Riley AK, Grant M, Snell A, Vichas A, Moorthi S, Urisman A, Castel P, Wan L, Berger AH. The deubiquitinase USP9X regulates RIT1 protein abundance and oncogenic phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569313. [PMID: 38077017 PMCID: PMC10705424 DOI: 10.1101/2023.11.30.569313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
RIT1 is a rare and understudied oncogene in lung cancer. Despite structural similarity to other RAS GTPase proteins such as KRAS, oncogenic RIT1 activity does not appear to be tightly regulated by nucleotide exchange or hydrolysis. Instead, there is a growing understanding that the protein abundance of RIT1 is important for its regulation and function. We previously identified the deubiquitinase USP9X as a RIT1 dependency in RIT1-mutant cells. Here, we demonstrate that both wild-type and mutant forms of RIT1 are substrates of USP9X. Depletion of USP9X leads to decreased RIT1 protein stability and abundance and resensitizes cells to EGFR tyrosine kinase inhibitors. Our work expands upon the current understanding of RIT1 protein regulation and presents USP9X as a key regulator of RIT1-driven oncogenic phenotypes.
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Affiliation(s)
- Amanda K. Riley
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Michael Grant
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Aidan Snell
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Athea Vichas
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sitapriya Moorthi
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco, CA, USA
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Lixin Wan
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alice H. Berger
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Herbold Computational Biology Program, Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Lead contact:
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11
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Zavitsanou AM, Pillai R, Hao Y, Wu WL, Bartnicki E, Karakousi T, Rajalingam S, Herrera A, Karatza A, Rashidfarrokhi A, Solis S, Ciampricotti M, Yeaton AH, Ivanova E, Wohlhieter CA, Buus TB, Hayashi M, Karadal-Ferrena B, Pass HI, Poirier JT, Rudin CM, Wong KK, Moreira AL, Khanna KM, Tsirigos A, Papagiannakopoulos T, Koralov SB. KEAP1 mutation in lung adenocarcinoma promotes immune evasion and immunotherapy resistance. Cell Rep 2023; 42:113295. [PMID: 37889752 PMCID: PMC10755970 DOI: 10.1016/j.celrep.2023.113295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/23/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Lung cancer treatment has benefited greatly through advancements in immunotherapies. However, immunotherapy often fails in patients with specific mutations like KEAP1, which are frequently found in lung adenocarcinoma. We established an antigenic lung cancer model and used it to explore how Keap1 mutations remodel the tumor immune microenvironment. Using single-cell technology and depletion studies, we demonstrate that Keap1-mutant tumors diminish dendritic cell and T cell responses driving immunotherapy resistance. This observation was corroborated in patient samples. CRISPR-Cas9-mediated gene targeting revealed that hyperactivation of the NRF2 antioxidant pathway is responsible for diminished immune responses in Keap1-mutant tumors. Importantly, we demonstrate that combining glutaminase inhibition with immune checkpoint blockade can reverse immunosuppression, making Keap1-mutant tumors susceptible to immunotherapy. Our study provides new insight into the role of KEAP1 mutations in immune evasion, paving the way for novel immune-based therapeutic strategies for KEAP1-mutant cancers.
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Affiliation(s)
- Anastasia-Maria Zavitsanou
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA; Vilcek Institute of Graduate Biomedical Sciences, NYU Grossman School of Medicine, New York, NY, USA
| | - Ray Pillai
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, VA New York Harbor Healthcare System, New York, NY, USA; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Yuan Hao
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Warren L Wu
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA; Vilcek Institute of Graduate Biomedical Sciences, NYU Grossman School of Medicine, New York, NY, USA
| | - Eric Bartnicki
- Vilcek Institute of Graduate Biomedical Sciences, NYU Grossman School of Medicine, New York, NY, USA; Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Triantafyllia Karakousi
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA; Vilcek Institute of Graduate Biomedical Sciences, NYU Grossman School of Medicine, New York, NY, USA
| | - Sahith Rajalingam
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Alberto Herrera
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA; Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, USA
| | - Angeliki Karatza
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Ali Rashidfarrokhi
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA; Vilcek Institute of Graduate Biomedical Sciences, NYU Grossman School of Medicine, New York, NY, USA
| | - Sabrina Solis
- Vilcek Institute of Graduate Biomedical Sciences, NYU Grossman School of Medicine, New York, NY, USA; NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Metamia Ciampricotti
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna H Yeaton
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Ellie Ivanova
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Corrin A Wohlhieter
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Terkild B Buus
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA; LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Makiko Hayashi
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Harvey I Pass
- Department of Cardiothoracic Surgery, NYU Langone Health, New York, NY, USA
| | - John T Poirier
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Andre L Moreira
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Kamal M Khanna
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA; Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, VA New York Harbor Healthcare System, New York, NY, USA; Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Thales Papagiannakopoulos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.
| | - Sergei B Koralov
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.
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12
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Wang L, Quan F, Guo Z, Lu Z, Yang D, Shi M. Co-Occurring EGFR S645C and EGFR L858R in a Patient with Lung Adenocarcinoma Induced Primary Resistance to Osimertinib. LUNG CANCER (AUCKLAND, N.Z.) 2023; 14:79-84. [PMID: 37842288 PMCID: PMC10576154 DOI: 10.2147/lctt.s431252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
Approximately 10-20% of patients demonstrate primary resistance to EGFR-TKIs, and different EGFR mutations vary in sensitivity to EGFR-TKIs. We report a case of a 78-year-old male with lung adenocarcinoma that EGFR L858R (AF = 1.32%) coexisting with EGFR S645C (AF = 7.13%) in his diagnosed tissues analyzed by NGS. The patient was primarily resistant to first-line osimertinib and rapidly progressed after pembrolizumab in combination with pemetrexed and bevacizumab, as demonstrated by persistently elevated CEA levels during treatment. ctDNA-based NGS analysis revealed loss of EGFR L858R while persistence of highly abundant EGFR S645C in the pleural fluid and plasma after treatment, suggesting that EGFR L858R may be a subclone. We provide the first clinical evidence of the primary resistance of EGFR S645C to osimertinib and emphasize the importance of identifying clones and subclones. Our patient did not respond to immunotherapy either, and preclinical studies have shown that EGFR S645C activates the MEK signaling pathway, the combination of EGFR-TKIs and MEK inhibitors may be effective.
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Affiliation(s)
- Li Wang
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Fei Quan
- The Medical Department, Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, People’s Republic of China
| | - Zhen Guo
- Radiology Department, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Zhongyu Lu
- The Medical Department, Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, People’s Republic of China
| | - Duoxia Yang
- The Medical Department, Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, People’s Republic of China
| | - Meiqi Shi
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
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13
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Konda P, Garinet S, Van Allen EM, Viswanathan SR. Genome-guided discovery of cancer therapeutic targets. Cell Rep 2023; 42:112978. [PMID: 37572322 DOI: 10.1016/j.celrep.2023.112978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023] Open
Abstract
The success of precision oncology-which aims to match the right therapies to the right patients based on molecular status-is predicated on a robust pipeline of molecular targets against which therapies can be developed. Recent advances in genomics and functional genetics have enabled the unbiased discovery of novel molecular targets at scale. We summarize the promise and challenges in integrating genomic and functional genetic landscapes of cancer to establish the next generation of cancer targets.
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Affiliation(s)
- Prathyusha Konda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Simon Garinet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Srinivas R Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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14
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Mukherjee AG, Gopalakrishnan AV. The mechanistic insights of the antioxidant Keap1-Nrf2 pathway in oncogenesis: a deadly scenario. Med Oncol 2023; 40:248. [PMID: 37480500 DOI: 10.1007/s12032-023-02124-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/06/2023] [Indexed: 07/24/2023]
Abstract
The Nuclear factor erythroid 2-related factor 2 (Nrf2) protein has garnered significant interest due to its crucial function in safeguarding cells and tissues. The Nrf2 protein is crucial in preserving tissue integrity by safeguarding cells against metabolic, xenobiotic and oxidative stress. Due to its various functions, Nrf2 is a potential pharmacological target for reducing the incidence of diseases such as cancer. However, mutations in Keap1-Nrf2 are not consistently favored in all types of cancer. Instead, they seem to interact with specific driver mutations of tumors and their respective tissue origins. The Kelch-like ECH-associated protein 1 (Keap1)-Nrf2 pathway mutations are a powerful cancer adaptation that utilizes inherent cytoprotective pathways, encompassing nutrient metabolism and ROS regulation. The augmentation of Nrf2 activity elicits significant alterations in the characteristics of neoplastic cells, such as resistance to radiotherapy and chemotherapy, safeguarding against apoptosis, heightened invasiveness, hindered senescence, impaired autophagy and increased angiogenesis. The altered activity of Nrf2 can arise from diverse genetic and epigenetic modifications that instantly impact Nrf2 regulation. The present study aims to showcase the correlation between the Keap1-Nrf2 pathway and the progression of cancers, emphasizing genetic mutations, metabolic processes, immune regulation, and potential therapeutic strategies. This article delves into the intricacies of Nrf2 pathway anomalies in cancer, the potential ramifications of uncontrolled Nrf2 activity, and therapeutic interventions to modulate the Keap1-Nrf2 pathway.
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Affiliation(s)
- Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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15
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Johnson A, Ng PKS, Kahle M, Castillo J, Amador B, Wang Y, Zeng J, Holla V, Vu T, Su F, Kim SH, Conway T, Jiang X, Chen K, Shaw KRM, Yap TA, Rodon J, Mills GB, Meric-Bernstam F. Actionability classification of variants of unknown significance correlates with functional effect. NPJ Precis Oncol 2023; 7:67. [PMID: 37454202 DOI: 10.1038/s41698-023-00420-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
Genomically-informed therapy requires consideration of the functional impact of genomic alterations on protein expression and/or function. However, a substantial number of variants are of unknown significance (VUS). The MD Anderson Precision Oncology Decision Support (PODS) team developed an actionability classification scheme that categorizes VUS as either "Unknown" or "Potentially" actionable based on their location within functional domains and/or proximity to known oncogenic variants. We then compared PODS VUS actionability classification with results from a functional genomics platform consisting of mutant generation and cell viability assays. 106 (24%) of 438 VUS in 20 actionable genes were classified as oncogenic in functional assays. Variants categorized by PODS as Potentially actionable (N = 204) were more likely to be oncogenic than those categorized as Unknown (N = 230) (37% vs 13%, p = 4.08e-09). Our results demonstrate that rule-based actionability classification of VUS can identify patients more likely to have actionable variants for consideration with genomically-matched therapy.
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Affiliation(s)
- Amber Johnson
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Kwok-Shing Ng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Kahle
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Julia Castillo
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bianca Amador
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yujia Wang
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Zeng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vijaykumar Holla
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Thuy Vu
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fei Su
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sun-Hee Kim
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tara Conway
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xianli Jiang
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenna R Mills Shaw
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy A Yap
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jordi Rodon
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gordon B Mills
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Funda Meric-Bernstam
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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16
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DeBlasi JM, Falzone A, Caldwell S, Prieto-Farigua N, Prigge JR, Schmidt EE, Chio IIC, Karreth FA, DeNicola GM. Distinct Nrf2 Signaling Thresholds Mediate Lung Tumor Initiation and Progression. Cancer Res 2023; 83:1953-1967. [PMID: 37062029 PMCID: PMC10267679 DOI: 10.1158/0008-5472.can-22-3848] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023]
Abstract
Mutations in the KEAP1-NRF2 (Kelch-like ECH-associated protein 1-nuclear factor-erythroid 2 p45-related factor 2) pathway occur in up to a third of non-small cell lung cancer (NSCLC) cases and often confer resistance to therapy and poor outcomes. Here, we developed murine alleles of the KEAP1 and NRF2 mutations found in human NSCLC and comprehensively interrogated their impact on tumor initiation and progression. Chronic NRF2 stabilization by Keap1 or Nrf2 mutation was not sufficient to induce tumorigenesis, even in the absence of tumor suppressors, p53 or LKB1. When combined with KrasG12D/+, constitutive NRF2 activation promoted lung tumor initiation and early progression of hyperplasia to low-grade tumors but impaired their progression to advanced-grade tumors, which was reversed by NRF2 deletion. Finally, NRF2 overexpression in KEAP1 mutant human NSCLC cell lines was detrimental to cell proliferation, viability, and anchorage-independent colony formation. Collectively, these results establish the context-dependence and activity threshold for NRF2 during the lung tumorigenic process. SIGNIFICANCE Stabilization of the transcription factor NRF2 promotes oncogene-driven tumor initiation but blocks tumor progression, indicating distinct, threshold-dependent effects of the KEAP1/NRF2 pathway in different stages of lung tumorigenesis.
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Affiliation(s)
- Janine M. DeBlasi
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology PhD Program, University of South Florida, Tampa, Florida
| | - Aimee Falzone
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Samantha Caldwell
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Nicolas Prieto-Farigua
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Justin R. Prigge
- Microbiology & Cell Biology Department, Montana State University, Bozeman, Montana
| | - Edward E. Schmidt
- Microbiology & Cell Biology Department, Montana State University, Bozeman, Montana
| | - Iok In Christine Chio
- Department of Genetics and Development, Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
| | - Florian A. Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Gina M. DeNicola
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
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17
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Ostroverkhova D, Przytycka TM, Panchenko AR. Cancer driver mutations: predictions and reality. Trends Mol Med 2023:S1471-4914(23)00067-9. [PMID: 37076339 DOI: 10.1016/j.molmed.2023.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Cancer cells accumulate many genetic alterations throughout their lifetime, but only a few of them drive cancer progression, termed driver mutations. Driver mutations may vary between cancer types and patients, can remain latent for a long time and become drivers at particular cancer stages, or may drive oncogenesis only in conjunction with other mutations. The high mutational, biochemical, and histological tumor heterogeneity makes driver mutation identification very challenging. In this review we summarize recent efforts to identify driver mutations in cancer and annotate their effects. We underline the success of computational methods to predict driver mutations in finding novel cancer biomarkers, including in circulating tumor DNA (ctDNA). We also report on the boundaries of their applicability in clinical research.
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Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Teresa M Przytycka
- National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada; Department of Biology and Molecular Sciences, Queen's University, Kingston, ON, Canada; School of Computing, Queen's University, Kingston, ON, Canada; Ontario Institute of Cancer Research, Toronto, ON, Canada.
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18
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Hu Y, Mu H, Deng Z. RBM14 as a novel epigenetic-activated tumor oncogene is implicated in the reprogramming of glycolysis in lung cancer. World J Surg Oncol 2023; 21:132. [PMID: 37060064 PMCID: PMC10105460 DOI: 10.1186/s12957-023-02928-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/05/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND RNA-binding motif protein 14 (RBM14) is upregulated in a variety of tumors. However, the expression and biological role of RBM14 in lung cancer remain unclear. METHODS Chromatin immunoprecipitation and PCR were carried out to measure the levels of sedimentary YY1, EP300, H3K9ac, and H3K27ac in the RBM14 promoter. Co-immunoprecipitation was used to verify the interaction between YY1 and EP300. Glycolysis was investigated according to glucose consumption, lactate production, and the extracellular acidification rate (ECAR). RESULTS RBM14 level is increased in lung adenocarcinoma (LUAD) cells. The increased RBM14 expression was correlated with TP53 mutation and individual cancer stages. A high level of RBM14 predicted a poorer overall survival of LUAD patients. The upregulated RBM14 in LUAD is induced by DNA methylation and histone acetylation. The transcription factor YY1 directly binds to EP300 and recruits EP300 to the promoter regions of RBM14, which further enhances H3K27 acetylation and promotes RBM14 expression. YY1-induced upregulation of RBM14 promoted cell growth and inhibited apoptosis by affecting the reprogramming of glycolysis. CONCLUSIONS These results indicated that epigenetically activated RBM14 regulated growth and apoptosis by regulating the reprogramming of glycolysis and RBM14 may serve as a promising biomarker and therapeutic target for LUAD.
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Affiliation(s)
- Yan Hu
- Department of Respiratory, The First People's Hospital of Zigong City, No.42, Shangyihao Road, Ziliujing District, Zigong City, 643000, Sichuan, China
| | - Hanshuo Mu
- Medical School, Nantong University, Nantong, 226001, Jiangsu, China
| | - Zhiping Deng
- Department of Respiratory, The First People's Hospital of Zigong City, No.42, Shangyihao Road, Ziliujing District, Zigong City, 643000, Sichuan, China.
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19
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Frankell AM, Dietzen M, Al Bakir M, Lim EL, Karasaki T, Ward S, Veeriah S, Colliver E, Huebner A, Bunkum A, Hill MS, Grigoriadis K, Moore DA, Black JRM, Liu WK, Thol K, Pich O, Watkins TBK, Naceur-Lombardelli C, Cook DE, Salgado R, Wilson GA, Bailey C, Angelova M, Bentham R, Martínez-Ruiz C, Abbosh C, Nicholson AG, Le Quesne J, Biswas D, Rosenthal R, Puttick C, Hessey S, Lee C, Prymas P, Toncheva A, Smith J, Xing W, Nicod J, Price G, Kerr KM, Naidu B, Middleton G, Blyth KG, Fennell DA, Forster MD, Lee SM, Falzon M, Hewish M, Shackcloth MJ, Lim E, Benafif S, Russell P, Boleti E, Krebs MG, Lester JF, Papadatos-Pastos D, Ahmad T, Thakrar RM, Lawrence D, Navani N, Janes SM, Dive C, Blackhall FH, Summers Y, Cave J, Marafioti T, Herrero J, Quezada SA, Peggs KS, Schwarz RF, Van Loo P, Miedema DM, Birkbak NJ, Hiley CT, Hackshaw A, Zaccaria S, Jamal-Hanjani M, McGranahan N, Swanton C. The evolution of lung cancer and impact of subclonal selection in TRACERx. Nature 2023; 616:525-533. [PMID: 37046096 PMCID: PMC10115649 DOI: 10.1038/s41586-023-05783-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/02/2023] [Indexed: 04/14/2023]
Abstract
Lung cancer is the leading cause of cancer-associated mortality worldwide1. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource.
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Affiliation(s)
- Alexander M Frankell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Michelle Dietzen
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Takahiro Karasaki
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ariana Huebner
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Abigail Bunkum
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kristiana Grigoriadis
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - David A Moore
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Wing Kin Liu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Kerstin Thol
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Robert Bentham
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew G Nicholson
- Department of Histopathology, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - John Le Quesne
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Pathology Department, Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sonya Hessey
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Claudia Lee
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Division of Medicine, University College London, London, UK
| | - Paulina Prymas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Antonia Toncheva
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Jon Smith
- Scientific Computing, The Francis Crick Institute, London, UK
| | - Wei Xing
- Scientific Computing, The Francis Crick Institute, London, UK
| | - Jerome Nicod
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Gillian Price
- Department of Medical Oncology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UK
- University of Aberdeen, Aberdeen, UK
| | - Keith M Kerr
- University of Aberdeen, Aberdeen, UK
- Department of Pathology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UK
| | - Babu Naidu
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
| | - Gary Middleton
- University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Kevin G Blyth
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Queen Elizabeth University Hospital, Glasgow, UK
| | - Dean A Fennell
- University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Martin D Forster
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Siow Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Mary Falzon
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Madeleine Hewish
- Royal Surrey Hospital, Royal Surrey Hospitals NHS Foundation Trust, Guilford, UK
- University of Surrey, Guilford, UK
| | | | - Eric Lim
- Academic Division of Thoracic Surgery, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sarah Benafif
- Department of Oncology, University College London Hospitals, London, UK
| | - Peter Russell
- Princess Alexandra Hospital, The Princess Alexandra Hospital NHS Trust, Harlow, UK
| | - Ekaterini Boleti
- Royal Free Hospital, Royal Free London NHS Foundation Trust, London, UK
| | - Matthew G Krebs
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Jason F Lester
- Singleton Hospital, Swansea Bay University Health Board, Swansea, UK
| | | | - Tanya Ahmad
- Department of Oncology, University College London Hospitals, London, UK
| | - Ricky M Thakrar
- Department of Thoracic Medicine, University College London Hospitals, London, UK
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - David Lawrence
- Department of Thoracic Surgery, University College London Hospital NHS Trust, London, UK
| | - Neal Navani
- Department of Thoracic Medicine, University College London Hospitals, London, UK
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Caroline Dive
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Fiona H Blackhall
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Yvonne Summers
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Judith Cave
- Department of Oncology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Department of Haematology, University College London Hospitals, London, UK
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Roland F Schwarz
- Institute for Computational Cancer Biology, Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data (BIFOLD), Berlin, Germany
| | - Peter Van Loo
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Daniël M Miedema
- LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Crispin T Hiley
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Allan Hackshaw
- Cancer Research UK and UCL Cancer Trials Centre, London, UK
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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20
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Al Bakir M, Huebner A, Martínez-Ruiz C, Grigoriadis K, Watkins TBK, Pich O, Moore DA, Veeriah S, Ward S, Laycock J, Johnson D, Rowan A, Razaq M, Akther M, Naceur-Lombardelli C, Prymas P, Toncheva A, Hessey S, Dietzen M, Colliver E, Frankell AM, Bunkum A, Lim EL, Karasaki T, Abbosh C, Hiley CT, Hill MS, Cook DE, Wilson GA, Salgado R, Nye E, Stone RK, Fennell DA, Price G, Kerr KM, Naidu B, Middleton G, Summers Y, Lindsay CR, Blackhall FH, Cave J, Blyth KG, Nair A, Ahmed A, Taylor MN, Procter AJ, Falzon M, Lawrence D, Navani N, Thakrar RM, Janes SM, Papadatos-Pastos D, Forster MD, Lee SM, Ahmad T, Quezada SA, Peggs KS, Van Loo P, Dive C, Hackshaw A, Birkbak NJ, Zaccaria S, Jamal-Hanjani M, McGranahan N, Swanton C. The evolution of non-small cell lung cancer metastases in TRACERx. Nature 2023; 616:534-542. [PMID: 37046095 PMCID: PMC10115651 DOI: 10.1038/s41586-023-05729-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/12/2023] [Indexed: 04/14/2023]
Abstract
Metastatic disease is responsible for the majority of cancer-related deaths1. We report the longitudinal evolutionary analysis of 126 non-small cell lung cancer (NSCLC) tumours from 421 prospectively recruited patients in TRACERx who developed metastatic disease, compared with a control cohort of 144 non-metastatic tumours. In 25% of cases, metastases diverged early, before the last clonal sweep in the primary tumour, and early divergence was enriched for patients who were smokers at the time of initial diagnosis. Simulations suggested that early metastatic divergence more frequently occurred at smaller tumour diameters (less than 8 mm). Single-region primary tumour sampling resulted in 83% of late divergence cases being misclassified as early, highlighting the importance of extensive primary tumour sampling. Polyclonal dissemination, which was associated with extrathoracic disease recurrence, was found in 32% of cases. Primary lymph node disease contributed to metastatic relapse in less than 20% of cases, representing a hallmark of metastatic potential rather than a route to subsequent recurrences/disease progression. Metastasis-seeding subclones exhibited subclonal expansions within primary tumours, probably reflecting positive selection. Our findings highlight the importance of selection in metastatic clone evolution within untreated primary tumours, the distinction between monoclonal versus polyclonal seeding in dictating site of recurrence, the limitations of current radiological screening approaches for early diverging tumours and the need to develop strategies to target metastasis-seeding subclones before relapse.
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Affiliation(s)
- Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kristiana Grigoriadis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Joanne Laycock
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Diana Johnson
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Maryam Razaq
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mita Akther
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Paulina Prymas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Antonia Toncheva
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sonya Hessey
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Abigail Bunkum
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Emma Nye
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | | | - Dean A Fennell
- University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Gillian Price
- Department of Medical Oncology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UK
- University of Aberdeen, Aberdeen, UK
| | - Keith M Kerr
- University of Aberdeen, Aberdeen, UK
- Department of Pathology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UK
| | - Babu Naidu
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Gary Middleton
- University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Yvonne Summers
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Colin R Lindsay
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Fiona H Blackhall
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Judith Cave
- Department of Oncology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Kevin G Blyth
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
- Queen Elizabeth University Hospital, Glasgow, UK
| | - Arjun Nair
- Department of Radiology, University College London Hospitals, London, UK
- UCL Respiratory, Department of Medicine, University College London, London, UK
| | - Asia Ahmed
- Department of Radiology, University College London Hospitals, London, UK
| | - Magali N Taylor
- Department of Radiology, University College London Hospitals, London, UK
| | | | - Mary Falzon
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - David Lawrence
- Department of Thoracic Surgery, University College London Hospital NHS Trust, London, UK
| | - Neal Navani
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Thoracic Medicine, University College London Hospitals, London, UK
| | - Ricky M Thakrar
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Thoracic Medicine, University College London Hospitals, London, UK
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | | | - Martin D Forster
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Siow Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Tanya Ahmad
- Department of Oncology, University College London Hospitals, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Department of Haematology, University College London Hospitals, London, UK
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline Dive
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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21
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Fang X, Lee YH, Jang JH, Kim SJ, Kim SH, Kim DH, Na HK, Kim KO, Baek JH, Surh YJ. ARD1 stabilizes NRF2 through direct interaction and promotes colon cancer progression. Life Sci 2023; 313:121217. [PMID: 36442525 DOI: 10.1016/j.lfs.2022.121217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/11/2022] [Accepted: 11/19/2022] [Indexed: 11/26/2022]
Abstract
AIMS Aberrant overactivation/overexpression of NRF2 is implicated as a driving event in tumor progression, which has been attributed to its mutation or inactivation of the inhibitory protein, KEAP1. However, alternative mechanisms responsible for sustained activation of NRF2 are less understood. MAIN METHODS Human colon cancer cell lines and tissues obtained from colorectal cancer (CRC) patients were used. To examine the expression levels of ARD1 and NRF2, Western blot and immunofluorescence analyses were performed. To investigate the potential relevance of NRF2 and ARD1 to human CRC, NRF2 and ARD1 were individually silenced in human colon cancer cells (HCT-116) by transfection with their specific small interfering RNA (siRNA). To determine the functional role of ARD1 in NRF2 regulation, in situ proximate ligation, co-immunoprecipitation, nano-LC-ESI MS/MS, and in vitro acetylation assays were performed. KEY FINDINGS ARD1 knockdown in human colon cancer cell lines significantly reduced the protein levels of NRF2 without affecting its mRNA expression; however, silencing of NRF2 did not alter ARD1 protein expression. In addition, these two proteins were co-localized and physically interacted with each other both in human colon cancer cells (HCT-116) and human colon tumor tissues. Mechanistically, ARD1 overexpression increased the acetylation levels of NRF2. Moreover, an in vitro acetylation assay and mass spectrometric analysis demonstrated that ARD1 could directly acetylate NRF2. Ectopic expression of mutant forms of ARD1 with defective acetyltransferase activity reduced the stability of NRF2. SIGNIFICANCE In conclusion, ARD1 may potentiate the oncogenic function of NRF2 in human colon cancer by stabilizing this transcription factor.
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Affiliation(s)
- Xizhu Fang
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Yeon-Hwa Lee
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Jeong-Hoon Jang
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Su-Jung Kim
- Department of Molecular Medicine and Biopharmaceutical Science, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Seong Hoon Kim
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Do-Hee Kim
- Department of Chemistry, College of Convergence and Integrated Science, Kyonggi University, Suwon, Gyeonggi-do, South Korea
| | - Hye-Kyung Na
- Department of Food Science and Biotechnology, College of Knowledge-Based Services Engineering, Sungshin Women's University, Seoul, South Korea
| | - Kyung-Ok Kim
- Gachon Medical Research Institute, Gil Medical Center, Gachon University, Incheon, South Korea
| | - Jeong-Heum Baek
- Division of Colon and Rectal Surgery, Department of Surgery, Gil Medical Center, Gachon University College of Medicine, Incheon, South Korea
| | - Young-Joon Surh
- College of Pharmacy, Seoul National University, Seoul, South Korea; Cancer Research Institute, Seoul National University, Seoul, South Korea.
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22
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Liu W, Cui Y, Zheng X, Yu K, Sun G. Application status and future prospects of the PDX model in lung cancer. Front Oncol 2023; 13:1098581. [PMID: 37035154 PMCID: PMC10080030 DOI: 10.3389/fonc.2023.1098581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Lung cancer is one of the most prevalent, fatal, and highly heterogeneous diseases that, seriously threaten human health. Lung cancer is primarily caused by the aberrant expression of multiple genes in the cells. Lung cancer treatment options include surgery, radiation, chemotherapy, targeted therapy, and immunotherapy. In recent decades, significant progress has been made in developing therapeutic agents for lung cancer as well as a biomarker for its early diagnosis. Nonetheless, the alternative applications of traditional pre-clinical models (cell line models) for diagnosis and prognosis prediction are constrained by several factors, including the lack of microenvironment components necessary to affect cancer biology and drug response, and the differences between laboratory and clinical results. The leading reason is that substantial shifts accrued to cell biological behaviors, such as cell proliferative, metastatic, invasive, and gene expression capabilities of different cancer cells after decades of growing indefinitely in vitro. Moreover, the introduction of individualized treatment has prompted the development of appropriate experimental models. In recent years, preclinical research on lung cancer has primarily relied on the patient-derived tumor xenograft (PDX) model. The PDX provides stable models with recapitulate characteristics of the parental tumor such as the histopathology and genetic blueprint. Additionally, PDXs offer valuable models for efficacy screening of new cancer drugs, thus, advancing the understanding of tumor biology. Concurrently, with the heightened interest in the PDX models, potential shortcomings have gradually emerged. This review summarizes the significant advantages of PDXs over the previous models, their benefits, potential future uses and interrogating open issues.
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23
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Lo A, McSharry M, Berger AH. Oncogenic KRAS alters splicing factor phosphorylation and alternative splicing in lung cancer. BMC Cancer 2022; 22:1315. [PMID: 36522653 PMCID: PMC9756471 DOI: 10.1186/s12885-022-10311-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Alternative RNA splicing is widely dysregulated in cancers including lung adenocarcinoma, where aberrant splicing events are frequently caused by somatic splice site mutations or somatic mutations of splicing factor genes. However, the majority of mis-splicing in cancers is unexplained by these known mechanisms. We hypothesize that the aberrant Ras signaling characteristic of lung cancers plays a role in promoting the alternative splicing observed in tumors. METHODS We recently performed transcriptome and proteome profiling of human lung epithelial cells ectopically expressing oncogenic KRAS and another cancer-associated Ras GTPase, RIT1. Unbiased analysis of phosphoproteome data identified altered splicing factor phosphorylation in KRAS-mutant cells, so we performed differential alternative splicing analysis using rMATS to identify significantly altered isoforms in lung epithelial cells. To determine whether these isoforms were uniquely regulated by KRAS, we performed a large-scale splicing screen in which we generated over 300 unique RNA sequencing profiles of isogenic A549 lung adenocarcinoma cells ectopically expressing 75 different wild-type or variant alleles across 28 genes implicated in lung cancer. RESULTS Mass spectrometry data showed widespread downregulation of splicing factor phosphorylation in lung epithelial cells expressing mutant KRAS compared to cells expressing wild-type KRAS. We observed alternative splicing in the same cells, with 2196 and 2416 skipped exon events in KRASG12V and KRASQ61H cells, respectively, 997 of which were shared (p < 0.001 by hypergeometric test). In the high-throughput splicing screen, mutant KRAS induced the greatest number of differential alternative splicing events, second only to the RNA binding protein RBM45 and its variant RBM45M126I. We identified ten high confidence cassette exon events across multiple KRAS variants and cell lines. These included differential splicing of the Myc Associated Zinc Finger (MAZ). As MAZ regulates expression of KRAS, this splice variant may be a mechanism for the cell to modulate wild-type KRAS levels in the presence of oncogenic KRAS. CONCLUSION Proteomic and transcriptomic profiling of lung epithelial cells uncovered splicing factor phosphorylation and mRNA splicing events regulated by oncogenic KRAS. These data suggest that in addition to widespread transcriptional changes, the Ras signaling pathway can promote post-transcriptional splicing changes that may contribute to oncogenic processes.
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Affiliation(s)
- April Lo
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Maria McSharry
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alice H Berger
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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24
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Gopal P, Yard BD, Petty A, Lal JC, Bera TK, Hoang TQ, Buhimschi AD, Abazeed ME. The Mutational Landscape of Cancer's Vulnerability to Ionizing Radiation. Clin Cancer Res 2022; 28:5343-5358. [PMID: 36222846 PMCID: PMC9751780 DOI: 10.1158/1078-0432.ccr-22-1914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/24/2022] [Accepted: 10/10/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Large-scale sequencing efforts have established that cancer-associated genetic alterations are highly diverse, posing a challenge to the identification of variants that regulate complex phenotypes like radiation sensitivity. The impact of the vast majority of rare or common genetic variants on the sensitivity of cancers to radiotherapy remains largely unknown. EXPERIMENTAL DESIGN We developed a scalable gene editing and irradiation platform to assess the role of categories of variants in cells. Variants were prioritized on the basis of genotype-phenotype associations from a previously completed large-scale cancer cell line radiation profiling study. Altogether, 488 alleles (396 unique single-nucleotide variants) from 92 genes were generated and profiled in an immortalized lung cell line, BEAS-2B. We validated our results in other cell lines (TRT-HU1 and NCI-H520), in vivo via the use of both cell line and patient-derived murine xenografts, and in clinical cohorts. RESULTS We show that resistance to radiation is characterized by substantial inter- and intra-gene allelic variation. Some genes (e.g., KEAP1) demonstrated significant intragenic allelic variation in the magnitude of conferred resistance and other genes (e.g., CTNNB1) displayed both resistance and sensitivity in a protein domain-dependent manner. We combined results from our platform with gene expression and metabolite features and identified the upregulation of amino acid transporters that facilitate oxidative reductive capacity and cell-cycle deregulation as key regulators of radiation sensitivity. CONCLUSIONS Our results reveal new insights into the genetic determinants of tumor sensitivity to radiotherapy and nominate a multitude of cancer mutations that are predicted to impact treatment efficacy.
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Affiliation(s)
- Priyanka Gopal
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Brian D. Yard
- Department of Translational Hematology Oncology Research, Cleveland Clinic, Cleveland, Ohio
| | - Aaron Petty
- Department of Translational Hematology Oncology Research, Cleveland Clinic, Cleveland, Ohio
| | - Jessica C. Lal
- Department of Translational Hematology Oncology Research, Cleveland Clinic, Cleveland, Ohio
| | - Titas K. Bera
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Trung Q. Hoang
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Alexandru D. Buhimschi
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Mohamed E. Abazeed
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois.,Corresponding Author: Mohamed E. Abazeed, Feinberg School of Medicine, Northwestern University, 303 E. Superior St/Lurie 7-115, Chicago, IL 60611. Phone: 312-926-2520; Fax: 312-926-6524; E-mail:
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25
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Haghighi M, Caicedo JC, Cimini BA, Carpenter AE, Singh S. High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations. Nat Methods 2022; 19:1550-1557. [PMID: 36344834 PMCID: PMC10012424 DOI: 10.1038/s41592-022-01667-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Cells can be perturbed by various chemical and genetic treatments and the impact on gene expression and morphology can be measured via transcriptomic profiling and image-based assays, respectively. The patterns observed in these high-dimensional profile data can power a dozen applications in drug discovery and basic biology research, but both types of profiles are rarely available for large-scale experiments. Here, we provide a collection of four datasets with both gene expression and morphological profile data useful for developing and testing multimodal methodologies. Roughly a thousand features are measured for each of the two data types, across more than 28,000 chemical and genetic perturbations. We define biological problems that use the shared and complementary information in these two data modalities, provide baseline analysis and evaluation metrics for multi-omic applications, and make the data resource publicly available ( https://broad.io/rosetta/ ).
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Affiliation(s)
| | | | - Beth A Cimini
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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26
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Thornton AM, Tumu M, Brooks AN. An expression-based variant impact phenotyping protocol to predict the impact of gene variants in cell lines. STAR Protoc 2022; 3:101651. [PMID: 36092819 PMCID: PMC9449654 DOI: 10.1016/j.xpro.2022.101651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We describe a bioinformatics protocol for eVIP2 (expression-based variant impact phenotyping). eVIP2 can predict a gene variant’s functional impact by comparing gene expression signatures induced by introduction of wild-type versus mutant cDNAs in cell lines. The predicted functional outcomes of the variants include gain-of-function, loss-of-function, change-of-function, or neutral. eVIP2 improves upon eVIP by being applicable to RNA-seq data and providing pathway-level functional predictions for each mutation. Here, we detail how to run eVIP2 on RNA-seq data from two RNF43 variants. For complete details on the use and execution of this protocol, please refer to Thornton et al. (2021). A user-friendly computational tool to predict variant impact Profiles many variants across multiple genes in a single run Identification of specific signaling pathways affected by each variant Static and interactive visualization of results
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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Affiliation(s)
- Alexis M Thornton
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Manoj Tumu
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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27
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Yin XQ, Yin XH, Yu YQ, Xu L, Zhang M. Genomic Landscape of RTK/RAS Pathway and Tumor Immune Infiltration as Prognostic Indicator of Lung Adenocarcinoma. Front Oncol 2022; 12:924239. [PMID: 35936718 PMCID: PMC9351312 DOI: 10.3389/fonc.2022.924239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/21/2022] [Indexed: 11/30/2022] Open
Abstract
The RTK/RAS pathway is an oncogenic signaling pathway for which many targeted drugs have been developed; however, survival remains poor. A combination of targeted therapy and immunotherapy has emerged as an option for improving cancer treatment responses. In this study, on the basis of the expression, survival, single nucleotide variation (SNV), copy number variation (CNV), and methylation data of lung adenocarcinoma (LUAD) from The Cancer Genome Atlas database, we comprehensively analyzed the genomic changes in the RTK/RAS pathway and their associations with tumor-infiltrating lymphocytes (TIL) and prognosis in LUAD to provide the genomics landscape of RTK/RAS with TIL and prognosis. We found that two rarely mutated genes, mitogen-activated protein kinase kinase 1 and insulin-like growth factor 1 receptor, were significantly associated with the worse survival of patients with LUAD. Patients with LUAD and co-mutation of KRAS proto-oncogene (KRAS) and neurofibromin 1 genes had worse survival, and the underlying mechanism could be insufficient for protein synthesis and intracellular signal deactivation. Methylation of the Rac family small GTPase 1 (RAC1) was associated with better survival. The SNVs of the top mutated genes, including epidermal growth factor receptor (12.7%), neurotrophic receptor tyrosine kinase 3 (7.8%), erb-b2 receptor tyrosine kinase 4 (8.5%), and KRAS (29.6%), were associated with T cell exhaustion in LUAD. To construct nomograms, we further screened the genes whose genomic changes were closely associated with survival and immune infiltration. The nomograms performed well in predicting disease-specific survival (DSS) with a concordance index of 0.7 (0.589, 0.811) and overall survival with a concordance index of 0.689 (0.603, 0.775) in test set; they also showed good correspondence between actual and ideal nomogram predictions. Tumor stage, RAC1 methylation, and type 1 regulatory T cells greatly contributed to DSS and OS nomograms. In summary, we provided a comprehensive genomic profile of the RTK/RAS pathway in LUAD and its association with immune cell infiltration and prognosis of LUAD. This profile would serve as a basis for developing better therapeutic strategies, improving patient prognosis, and understanding the mechanisms of immune disturbance from the perspective of oncogenic pathways of LUAD.
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Affiliation(s)
- Xiang-Qian Yin
- Department of Oncology, The People’s Hospital of Huangpi, Wuhan, China
| | - Xue-Hui Yin
- Department of Oncology, The People’s Hospital of Huangpi, Wuhan, China
| | - Ya-Qin Yu
- Department of Oncology, The People’s Hospital of Huangpi, Wuhan, China
| | - Lang Xu
- Brain Science and Advanced Technology Institute, Wuhan University of Science and Technology, Wuhan, China
- *Correspondence: Lang Xu, ; Mao Zhang,
| | - Mao Zhang
- Department of Oncology, The People’s Hospital of Huangpi, Wuhan, China
- *Correspondence: Lang Xu, ; Mao Zhang,
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28
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Construction of a Novel Clinical Stage-Related Gene Signature for Predicting Outcome and Immune Response in Hepatocellular Carcinoma. J Immunol Res 2022; 2022:6535009. [PMID: 35865652 PMCID: PMC9296277 DOI: 10.1155/2022/6535009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Hepatocellular carcinoma (HCC) with high heterogeneity is one of the most frequent malignant tumors. However, there were no studies to create a clinical stage-related gene signature for HCC patients. Differentially expressed genes (DEGs) associated with clinical stage of HCC were analyzed based on TCGA datasets. Functional enrichment analysis was carried out by the use of stage-related DEGs. Then, the least absolute shrinkage and selection operator (LASSO) regression and univariate Cox regression were performed to reduce the overfit and the number of genes for further analysis. Next, survival and ROC assays were carried out to demonstrate the model using TCGA. Functional analysis and immune microenvironment analysis related to stage-related DEGs were performed. Reverse transcriptase polymerase chain reaction (RT-PCR) and Cell Counting Kit-8 (CCK-8) assays were applied to examine the expression and function of PNCK in HCC. In this research, there were 21 DEGs between HCC specimens with stage (I-II) and HCC specimens with stage (III-IV), including 20 increased genes and 1 decreased genes. A novel seven-gene signature (including PITX2, PNCK, GLIS1, SCNN1G, MMP1, ZNF488, and SHISA9) was created for the prediction of outcomes of HCC patients. The ROC curves confirmed the prognostic value of the new model. Cox assays demonstrated that the seven-gene signature can independently forecast overall survival. The immune analysis revealed that patients with low risk score exhibited more immune activities. Moreover, we confirmed that PNCK expressions were distinctly increased in HCC, and its silence suppressed the proliferation of HCC cells. Overall, our research offered a robust and reliable gene signature which displayed an important value in the prediction of overall survival of HCC patients and might deliver more effective personalized therapies.
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29
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Huang W, Zou L, Hao Z, Wang B, Mao F, Duan Q, Guo D. S645C Point Mutation Suppresses Degradation of EGFR to Promote Progression of Glioblastoma. Front Oncol 2022; 12:904383. [PMID: 35814475 PMCID: PMC9259983 DOI: 10.3389/fonc.2022.904383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/18/2022] [Indexed: 11/24/2022] Open
Abstract
Background The tightly controlled activity of EGFR is important for the homeostasis of self-renewal of human tissue. Mutations in the extracellular domain of EGFR are frequent and function as a novel mechanism for oncogenic EGFR activation in GBM, and impact the response of patients to small-molecule inhibitors. Methods We constructed glioblastoma cell lines stably expressing wild-type EGFR and the mutant of EGFR S645C. We detected cell growth in vitro and in vivo. We evaluated the anti-tumor activity and effectiveness of gefitinib and osimertinib in cells. Results In the present study, we identified an oncogenic substituted mutation of EGFR—S645C. The mutation can promote the proliferation and colony formation of glioblastoma in vitro and in vivo. Mechanistically, the EGFR S645C mutation potentially changes the formation of hydrogen bonds within dimerized EGFR and inhibits the degradation of EGFR to prolong downstream signaling. The mutation induces resistance to gefitinib but presents an opportunity for osimertinib treatment. Conclusion The study indicated a novel oncogenic mutation and advises on the precise treatment of individual patients with the EGFR S645C mutation.
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Affiliation(s)
- Wenda Huang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Zou
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhaonian Hao
- Department of Neurosurgery, Beijing TianTan Hospital, Capital Medical University, Beijing, China
| | - Baofeng Wang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feng Mao
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiuhong Duan
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Dongsheng Guo, ; Qiuhong Duan,
| | - Dongsheng Guo
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Dongsheng Guo, ; Qiuhong Duan,
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30
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Heo J, Lee J, Nam YJ, Kim Y, Yun H, Lee S, Ju H, Ryu CM, Jeong SM, Lee J, Lim J, Cho YM, Jeong EM, Hong B, Son J, Shin DM. The CDK1/TFCP2L1/ID2 cascade offers a novel combination therapy strategy in a preclinical model of bladder cancer. Exp Mol Med 2022; 54:801-811. [PMID: 35729325 PMCID: PMC9256744 DOI: 10.1038/s12276-022-00786-0] [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: 11/11/2021] [Revised: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 01/03/2023] Open
Abstract
Aberrant activation of embryogenesis-related molecular programs in urothelial bladder cancer (BC) is associated with stemness features related to oncogenic dedifferentiation and tumor metastasis. Recently, we reported that overexpression of transcription factor CP2-like protein-1 (TFCP2L1) and its phosphorylation at Thr177 by cyclin-dependent kinase-1 (CDK1) play key roles in regulating bladder carcinogenesis. However, the clinical relevance and therapeutic potential of this novel CDK1-TFCP2L1 molecular network remain elusive. Here, we demonstrated that inhibitor of DNA binding-2 (ID2) functions as a crucial mediator by acting as a direct repressive target of TFCP2L1 to modulate the stemness features and survival of BC cells. Low ID2 and high CDK1 expression were significantly associated with unfavorable clinical characteristics. TFCP2L1 downregulated ID2 by directly binding to its promoter region. Consistent with these findings, ectopic expression of ID2 or treatment with apigenin, a chemical activator of ID2, triggered apoptosis and impaired the proliferation, suppressed the stemness features, and reduced the invasive capacity of BC cells. Combination treatment with the specific CDK1 inhibitor RO-3306 and apigenin significantly suppressed tumor growth in an orthotopic BC xenograft animal model. This study demonstrates the biological role and clinical utility of ID2 as a direct target of the CDK1-TFCP2L1 pathway for modulating the stemness features of BC cells. Combination therapy with apigenin, a powerful antioxidant found in plants such as parsley and camomile, and a drug that inhibits the cell cycle protein CDK1 shows promise for developing therapies for bladder cancer (BC). Switching on genes usually activated in stem cells can cause cancer, including BC. Although CDK1 was known to activate one of these genes in BC cells, no way to suppress the activation had been identified. Jinbeom Heo at University of Ulsan College of Medicine, South Korea, and coworkers investigated CDK1’s role in BC. They found that the transcription factor activated by CDK1 suppressed a protein, ID2, that suppressed stem cell-like characteristics. Simultaneously suppressing CDK1 and boosting ID2 with apigenin strongly repressed tumor growth in a mouse model. These results help point the way to developing new treatment options for BC patients.
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Affiliation(s)
- Jinbeom Heo
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jinyoung Lee
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yun Ji Nam
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - YongHwan Kim
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - HongDuck Yun
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seungun Lee
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyein Ju
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chae-Min Ryu
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Center for Cell Therapy, Asan Medical Center, Seoul, Korea
| | - Seon Min Jeong
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jinwon Lee
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jisun Lim
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yong Mee Cho
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Eui Man Jeong
- Department of Pharmacy, College of Pharmacy, Jeju National University, Jeju, Korea.,Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Bio-Health Materials Core-Facility Center and Practical Translational Research Center, Jeju National University, Jeju, Korea
| | - Bumsik Hong
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Jaekyoung Son
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Dong-Myung Shin
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea. .,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea. .,Center for Cell Therapy, Asan Medical Center, Seoul, Korea.
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31
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Phenotypic drug discovery: recent successes, lessons learned and new directions. Nat Rev Drug Discov 2022; 21:899-914. [DOI: 10.1038/s41573-022-00472-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2022] [Indexed: 12/29/2022]
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Yang L, Guo G, Yu X, Wen Y, Lin Y, Zhang R, Zhao D, Huang Z, Wang G, Yan Y, Zhang X, Chen D, Xing W, Wang W, Zeng W, Zhang L. Mutation-Derived Long Noncoding RNA Signature Predicts Survival in Lung Adenocarcinoma. Front Oncol 2022; 12:780631. [PMID: 35372012 PMCID: PMC8965709 DOI: 10.3389/fonc.2022.780631] [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: 09/21/2021] [Accepted: 02/17/2022] [Indexed: 12/24/2022] Open
Abstract
Background Genomic instability is one of the representative features of cancer evolution. Recent research has revealed that long noncoding RNAs (lncRNAs) play a critical role in maintaining genomic instability. Our work proposed a gene signature (GILncSig) based on genomic instability-derived lncRNAs to probe the possibility of lncRNA signatures as an index of genomic instability, providing a potential new approach to identify genomic instability-related cancer biomarkers. Methods Lung adenocarcinoma (LUAD) gene expression data from an RNA-seq FPKM dataset, somatic mutation information and relevant clinical materials were downloaded from The Cancer Genome Atlas (TCGA). A prognostic model consisting of genomic instability-related lncRNAs was constructed, termed GILncSig, to calculate the risk score. We validated GILncSig using data from the Gene Expression Omnibus (GEO) database. In this study, we used R software for data analysis. Results Through univariate and multivariate Cox regression analyses, five genomic instability-associated lncRNAs (LINC01671, LINC01116, LINC01214, lncRNA PTCSC3, and LINC02555) were identified. We constructed a lncRNA signature (GILncSig) related to genomic instability. LUAD patients were classified into two risk groups by GILncSig. The results showed that the survival rate of LUAD patients in the low-risk group was higher than that of those in the high-risk group. Then, we verified GILncSig in the GEO database. GILncSig was associated with the genomic mutation rate of LUAD. We also used GILncSig to divide TP53 mutant-type patients and TP53 wild-type patients into two groups and performed prognostic analysis. The results suggested that compared with TP53 mutation status, GILncSig may have better prognostic significance. Conclusions By combining the lncRNA expression profiles associated with somatic mutations and the corresponding clinical characteristics of LUAD, a lncRNA signature (GILncSig) related to genomic instability was established.
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Affiliation(s)
- Longjun Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guangran Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiangyang Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Yingsheng Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yongbin Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rusi Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dechang Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zirui Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Gongming Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Yan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Huizhou Municipal Central Hospital, Huizhou, China
| | - Xuewen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dongtai Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Xing
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Weidong Wang
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Weian Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lanjun Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
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Dobson CS, Reich AN, Gaglione S, Smith BE, Kim EJ, Dong J, Ronsard L, Okonkwo V, Lingwood D, Dougan M, Dougan SK, Birnbaum ME. Antigen identification and high-throughput interaction mapping by reprogramming viral entry. Nat Methods 2022; 19:449-460. [PMID: 35396484 PMCID: PMC9012700 DOI: 10.1038/s41592-022-01436-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/01/2022] [Indexed: 01/11/2023]
Abstract
Deciphering immune recognition is critical for understanding a broad range of diseases and for the development of effective vaccines and immunotherapies. Efforts to do so are limited by a lack of technologies capable of simultaneously capturing the complexity of adaptive immunoreceptor repertoires and the landscape of potential antigens. To address this, we present receptor-antigen pairing by targeted retroviruses, which combines viral pseudotyping and molecular engineering approaches to enable one-pot library-on-library interaction screens by displaying antigens on the surface of lentiviruses and encoding their identity in the viral genome. Antigen-specific viral infection of cell lines expressing human T or B cell receptors allows readout of both antigen and receptor identities via single-cell sequencing. The resulting system is modular, scalable and compatible with any cell type. These techniques provide a suite of tools for targeted viral entry, molecular engineering and interaction screens with broad potential applications.
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Affiliation(s)
- Connor S Dobson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anna N Reich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Stephanie Gaglione
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Blake E Smith
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA, USA
| | - Ellen J Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Jiayi Dong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | | | - Vintus Okonkwo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | | | - Michael Dougan
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephanie K Dougan
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael E Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore.
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Concise Review: Gene of The Month KEAP1-mutant non-small cell lung cancer: the catastrophic failure of a cell-protecting hub. J Thorac Oncol 2022; 17:751-757. [DOI: 10.1016/j.jtho.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 11/19/2022]
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Pillai R, Hayashi M, Zavitsanou AM, Papagiannakopoulos T. NRF2: KEAPing Tumors Protected. Cancer Discov 2022; 12:625-643. [PMID: 35101864 DOI: 10.1158/2159-8290.cd-21-0922] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/22/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022]
Abstract
The Kelch-like ECH-associated protein 1 (KEAP1)/nuclear factor erythroid 2-related factor 2 (NRF2) pathway plays a physiologic protective role against xenobiotics and reactive oxygen species. However, activation of NRF2 provides a powerful selective advantage for tumors by rewiring metabolism to enhance proliferation, suppress various forms of stress, and promote immune evasion. Genetic, epigenetic, and posttranslational alterations that activate the KEAP1/NRF2 pathway are found in multiple solid tumors. Emerging clinical data highlight that alterations in this pathway result in resistance to multiple therapies. Here, we provide an overview of how dysregulation of the KEAP1/NRF2 pathway in cancer contributes to several hallmarks of cancer that promote tumorigenesis and lead to treatment resistance. SIGNIFICANCE: Alterations in the KEAP1/NRF2 pathway are found in multiple cancer types. Activation of NRF2 leads to metabolic rewiring of tumors that promote tumor initiation and progression. Here we present the known alterations that lead to NRF2 activation in cancer, the mechanisms in which NRF2 activation promotes tumors, and the therapeutic implications of NRF2 activation.
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Affiliation(s)
- Ray Pillai
- Department of Pathology, Perlmutter Cancer Center, New York University School of Medicine, New York, New York.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, VA New York Harbor Healthcare System, New York, New York.,Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Makiko Hayashi
- Department of Pathology, Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Anastasia-Maria Zavitsanou
- Department of Pathology, Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Thales Papagiannakopoulos
- Department of Pathology, Perlmutter Cancer Center, New York University School of Medicine, New York, New York.
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An oncogenic splice variant of PDGFRα in adult glioblastoma as a therapeutic target for selective CDK4/6 inhibitors. Sci Rep 2022; 12:1275. [PMID: 35075231 PMCID: PMC8786844 DOI: 10.1038/s41598-022-05391-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 01/06/2022] [Indexed: 12/15/2022] Open
Abstract
Understanding human genome alterations is necessary to optimize genome-based cancer therapeutics. However, some newly discovered mutations remain as variants of unknown significance (VUS). Here, the mutation c.1403A > G in exon 10 of the platelet-derived growth factor receptor-alpha (PDGFRA) gene, a VUS found in adult glioblastoma multiforme (GBM), was introduced in human embryonal kidney 293 T (HEK293T) cells using genome editing to investigate its potential oncogenic functions. Genome editing was performed using CRISPR/Cas9; the proliferation, drug sensitivity, and carcinogenic potential of genome-edited cells were investigated. We also investigated the mechanism underlying the observed phenotypes. Three GBM patients carrying the c.1403A > G mutation were studied to validate the in vitro results. The c.1403A > G mutation led to a splice variant (p.K455_N468delinsN) because of the generation of a 3’-acceptor splice site in exon 10. PDGFRA-mutated HEK293T cells exhibited a higher proliferative activity via PDGFRα and the cyclin-dependent kinase (CDK)4/CDK6-cyclin D1 signaling pathway in a ligand-independent manner. They showed higher sensitivity to multi-kinase, receptor tyrosine kinase, and CDK4/CDK6 inhibitors. Of the three GBM patients studied, two harbored the p.K455_N468delinsN splice variant. The splicing mutation c.1403A > G in PDGFRA is oncogenic in nature. Kinase inhibitors targeting PDGFRα and CDK4/CDK6 signaling should be evaluated for treating GBM patients harboring this mutation.
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Massively parallel phenotyping of coding variants in cancer with Perturb-seq. Nat Biotechnol 2022; 40:896-905. [DOI: 10.1038/s41587-021-01160-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 11/11/2021] [Indexed: 02/08/2023]
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38
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Shen M, Qi R, Ren J, Lv D, Yang H. Characterization With KRAS Mutant Is a Critical Determinant in Immunotherapy and Other Multiple Therapies for Non-Small Cell Lung Cancer. Front Oncol 2022; 11:780655. [PMID: 35070984 PMCID: PMC8766810 DOI: 10.3389/fonc.2021.780655] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a frequent type of cancer, which is mainly characterized clinically by high aggressiveness and high mortality. KRAS oncoprotein is the most common molecular protein detected in NSCLC, accounting for 25% of all oncogenic mutations. Constitutive activation of the KRAS oncoprotein triggers an intracellular cascade in cancer cells, leading to uncontrolled cell proliferation of cancer cells and aberrant cell survival states. The results of multiple clinical trials have shown that different KRAS mutation subtypes exhibit different sensitivities to different chemotherapy regimens. Meanwhile, anti-angiogenic drugs have shown differential efficacy for different subtypes of KRAS mutated lung cancer. It was explored to find if the specificity of the KRAS mutation subtype would affect PD-L1 expression, so immunotherapy would be of potential clinical value for the treatment of some types of KRAS mutations. It was discovered that the specificity of the KRAS mutation affected PD-L1, which opened up immunotherapy as a potential clinical treatment option. After several breakthrough studies, the preliminary test data of many early clinical trials showed that it is possible to directly inhibit KRAS G12C mutation, which has been proved to be a targeted treatment that is suitable for about 10%-12% of patients with advanced NSCLC, having a significant impact on the prolongation of their survival and the improvement of their quality of life. This article reviews the latest progress of treatments for NSCLC with KRAS mutation, in order to gain insight into the biological diversity of lung cancer cells and their potential clinical implications, thereby enabling individualized treatment for patients with KRAS-mutant NSCLC.
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Affiliation(s)
- Mo Shen
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Rongbin Qi
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Respiratory Medicine, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
| | - Justin Ren
- Biological Sciences, Northwestern University, Evanston, Evanston, IL, United States
| | - Dongqing Lv
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Respiratory Medicine, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
| | - Haihua Yang
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Radiation Oncology, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
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Ikeuchi H, Hirose T, Ikegami M, Takamochi K, Suzuki K, Mano H, Kohsaka S. Preclinical assessment of combination therapy of EGFR tyrosine kinase inhibitors in a highly heterogeneous tumor model. Oncogene 2022; 41:2470-2479. [PMID: 35304574 PMCID: PMC9033582 DOI: 10.1038/s41388-022-02263-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 01/29/2023]
Abstract
The development of tyrosine kinase inhibitors (TKIs) has improved the treatment of non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations. The current research priority is to provide viable treatments for patients who have drug-resistant EGFR mutations. We evaluated the drug sensitivity of various EGFR mutants to monotherapies and combination therapies of EGFR-TKIs. In vitro, the transforming potential and drug sensitivity of 357 EGFR variants were assessed. In vivo, we tested the sensitivity of EGFR variants to different regimens of EGFR-TKIs by examining changes in the proportion of each variant within the tumor. Out of 357 variants thoroughly examined for transforming activities, 144 (40.3%) and 282 (79.0%) transformed 3T3 and Ba/F3 cells, respectively. Among the latter variants, 50 (17.7%) were found to be resistant or only partly resistant to osimertinib or afatinib. Four of 25 afatinib-resistant variants (16%) were sensitive to osimertinib, whereas 25 of 46 osimertinib-resistant variants (54.3%) were sensitive to afatinib. Despite the lack of a synergistic impact, TKI combination treatment effectively reduced in vivo the heterogeneous tumors composed of 3T3 cells with different EGFR variants. Regimens starting with afatinib and subsequently switched to osimertinib suppressed tumor development more efficiently than the opposite combination. Combination EGFR-TKI treatment may decrease tumor growth and prevent the development of resistant variants. This work created an experimental model of a heterogeneous tumor to find the best combination therapy regimen and proposes a basic notion of EGFR-TKI combination therapy to enhance the prognosis of NSCLC patients.
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Affiliation(s)
- Hiroshi Ikeuchi
- grid.272242.30000 0001 2168 5385Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045 Japan ,grid.258269.20000 0004 1762 2738Department of General Thoracic Surgery, Juntendo University School of Medicine, Tokyo, 113-8431 Japan
| | - Takeshi Hirose
- grid.272242.30000 0001 2168 5385Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045 Japan
| | - Masachika Ikegami
- grid.272242.30000 0001 2168 5385Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045 Japan ,grid.415479.aDepartment of Musculoskeletal Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, 113-8677 Japan
| | - Kazuya Takamochi
- grid.258269.20000 0004 1762 2738Department of General Thoracic Surgery, Juntendo University School of Medicine, Tokyo, 113-8431 Japan
| | - Kenji Suzuki
- grid.258269.20000 0004 1762 2738Department of General Thoracic Surgery, Juntendo University School of Medicine, Tokyo, 113-8431 Japan
| | - Hiroyuki Mano
- grid.272242.30000 0001 2168 5385Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045 Japan
| | - Shinji Kohsaka
- grid.272242.30000 0001 2168 5385Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045 Japan
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Riley AK, Berger AH. Genome-wide CRISPR screening reveals novel therapeutic targets in RIT1-driven lung cancer. Mol Cell Oncol 2021; 8:2000318. [PMID: 35419481 PMCID: PMC8997261 DOI: 10.1080/23723556.2021.2000318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 06/14/2023]
Abstract
In recent work, we performed CRISPR/Cas9 screening in RIT1 (Ras-like in all tissues)-mutant cancer cells. We found that RIT1-mutant cells are vulnerable to loss of mitotic regulators, and mutant RIT1 synergizes with YAP1 (yes-associated protein 1) in oncogenesis. These findings can be leveraged to identify targeted therapies for RIT1-mutant cancer.
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Affiliation(s)
- Amanda K. Riley
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Alice H. Berger
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Lin X, Peng M, Chen Q, Yuan M, Chen R, Deng H, Deng J, Liu O, Weng Y, Chen M, Zhou C. Identification of the Unique Clinical and Genetic Features of Chinese Lung Cancer Patients With EGFR Germline Mutations in a Large-Scale Retrospective Study. Front Oncol 2021; 11:774156. [PMID: 34869019 PMCID: PMC8637204 DOI: 10.3389/fonc.2021.774156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/23/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Epidemiological surveys have suggested that lung cancer has inherited susceptibility and shows familial aggregation. However, the distribution and prevalence of epidermal growth factor receptor (EGFR) germline variants and their roles in lung cancer genetic predisposition in Chinese population remain to be elucidated. METHODS In this study, EGFR germline and somatic variants were retrospectively reviewed from the next-generation sequencing results of 31,906 patients with lung cancer. Clinical information was also collected for patients with confirmed EGFR germline mutations. RESULTS A total of 22 germline EGFR variants were identified in 64 patients with lung cancer, accounting for 0.2% of the total cases studied. Five patients were diagnosed as multiple primary carcinomas. Family history was documented in 31.3% (20/64) of patients, 55% of which were diagnosed as lung cancer. G863D was the most frequent EGFR germline mutation, followed by P848L, D1014N, and K757R. Somatic EGFR-sensitive mutations were identified in 51.6% of patients with germline EGFR mutations. The proportion of L858R mutation, exon 19 deletion, and rare sensitive mutation was 50%, 17.6%, and 32.4%, respectively. D1014N and T790M mutations were common in young patients. The family members of patients with P848L, R776H, V769M, and V774M mutations were more commonly diagnosed with cancers. A total of 19 patients were confirmed to have received EGFR tyrosine kinase inhibitors (TKIs), but the response to EGFR-TKIs differed among patients with different EGFR mutations. CONCLUSION Chinese patients with lung cancer harbored unique and dispersive EGFR germline mutations and showed unique clinical and genetic characteristics, with varied response patterns to EGFR-TKI treatment.
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Affiliation(s)
- Xinqing Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Muyun Peng
- Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Quanfang Chen
- Department of Respiratory Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Mingming Yuan
- Medical Department, Geneplus-Beijing, Beijing, China
| | - Rongrong Chen
- Medical Department, Geneplus-Beijing, Beijing, China
| | - Haiyi Deng
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiaxi Deng
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ouqi Liu
- Department of Respiratory and Critical Medicine, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Yuqing Weng
- Department of Respiratory and Critical Medicine, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Mingjiu Chen
- Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chengzhi Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
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42
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Liu L, Qu J, Heng J, Zhou C, Xiong Y, Yang H, Jiang W, Zeng L, Zhu S, Zhang Y, Tan J, Hu C, Deng P, Yang N. A Large Real-World Study on the Effectiveness of the Combined Inhibition of EGFR and MET in EGFR-Mutant Non-Small-Cell Lung Cancer After Development of EGFR-TKI Resistance. Front Oncol 2021; 11:722039. [PMID: 34660287 PMCID: PMC8517073 DOI: 10.3389/fonc.2021.722039] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/23/2021] [Indexed: 12/16/2022] Open
Abstract
Background MET proto-oncogene amplification (amp) is an important mechanism underlying acquired resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs). However, the optimal treatment strategy after acquiring MET-amp-mediated EGFR-TKI resistance remains controversial. Our study compared three treatment strategies for patients with EGFR-mutant non-small-cell lung cancer (NSCLC) who were detected with MET-amp at EGFR-TKI progression using next-generation sequencing. Methods Of the 70 patients included in the study, 38 received EGFR-TKI + crizotinib, 10 received crizotinib monotherapy, and 22 received chemotherapy. Clinical outcomes and molecular profiles were analyzed. Results The objective response rate was 48.6% for EGFR-TKI + crizotinib group, 40.0% for crizotinib monotherapy group, and 18.2% for chemotherapy group. Patients who received EGFR-TKI + crizotinib had significantly longer progression-free survival than those who received crizotinib or chemotherapy (5.0 vs. 2.3 vs. 2.9 months, p = 0.010), but overall survival was comparable (10.0 vs. 4.1 vs. 8.5 months, p = 0.088). TP53 mutation (58.5%) and EGFR-amp (42.9%) were frequent concurrent mutations of the cohort. Progression-free survival was significantly longer for patients with either concurrent TP53 mutation (n = 17) (6.0 vs. 2.3 vs. 2.9 months, p = 0.009) or EGFR-amp (n = 13) (5.0 vs. 1.2 vs. 2.4 months, p = 0.016) in the EGFR-TKI + crizotinib group than the other two regimen. Potential acquired resistance mechanisms to EGFR-TKI + crizotinib included EGFR-T790M (n = 2), EGFR-L718Q (n = 1), EGFR-S645C (n = 1), MET-D1228H (n = 1), BRAF-V600E (n = 1), NRAS-Q61H (n = 1), KRAS-amp (n = 1), ERBB2-amp (n = 1), CDK4-amp (n = 1), and MYC-amp (n = 1). Conclusion Our study provides real-world clinical evidence from a large cohort that simultaneous inhibition of EGFR and MET could be a more effective therapeutic strategy for patients with MET-amp acquired from EGFR-TKI therapy.
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Affiliation(s)
- Li Liu
- Department of Lung Cancer and Gastroenterology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China
| | - Jingjing Qu
- Department of Respiratory Disease, Thoracic Disease Centre, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jianfu Heng
- Department of Lung Cancer and Gastroenterology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China.,Department of Clinical Pharmaceutical Research Institution, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China
| | - Chunhua Zhou
- Department of Lung Cancer and Gastroenterology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China
| | - Yi Xiong
- Department of Lung Cancer and Gastroenterology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China.,Department of Clinical Pharmaceutical Research Institution, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China
| | - Haiyan Yang
- Department of Lung Cancer and Gastroenterology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China
| | - Wenjuan Jiang
- Department of Lung Cancer and Gastroenterology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China
| | - Liang Zeng
- Department of Lung Cancer and Gastroenterology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China
| | - Songlin Zhu
- Department of Clinical Pharmaceutical Research Institution, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China
| | - Yongchang Zhang
- Department of Lung Cancer and Gastroenterology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China
| | - Jiarong Tan
- Department of Respiratory Medicine, Xiangya Hospital of Central South University, Changsha, China
| | - Chengping Hu
- Department of Respiratory Medicine, Xiangya Hospital of Central South University, Changsha, China
| | - Pengbo Deng
- Department of Respiratory Medicine, Xiangya Hospital of Central South University, Changsha, China
| | - Nong Yang
- Department of Lung Cancer and Gastroenterology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, China
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43
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Arunachalam A, Lakshmanan DK, Ravichandran G, Paul S, Manickam S, Kumar PV, Thilagar S. Regulatory mechanisms of heme regulatory protein BACH1: a potential therapeutic target for cancer. Med Oncol 2021; 38:122. [PMID: 34482423 DOI: 10.1007/s12032-021-01573-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/27/2021] [Indexed: 02/06/2023]
Abstract
A limited number of overexpressed transcription factors are associated with cancer progression in many types of cancer. BTB and CNC homology 1 (BACH1) is the first mammalian heme-binding transcription factor that belongs to the basic region leucine zipper (bZIP) family and a member of CNC (cap 'n' collar). It forms heterodimers with the small musculoaponeurotic fibrosarcoma (MAF) proteins and stimulates or suppresses the expression of target genes under a very low intracellular heme concentration. It possesses a significant regulatory role in heme homeostasis, oxidative stress, cell cycle, apoptosis, angiogenesis, and cancer metastasis progression. This review discusses the current knowledge about how BACH1 regulates cancer metastasis in various types of cancer and other carcinogenic associated factors such as oxidative stress, cell cycle regulation, apoptosis, and angiogenesis. Overall, from the reported studies and outcomes, it could be realized that BACH1 is a potential pharmacological target for discovering new therapeutic anticancer drugs.
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Affiliation(s)
- Abirami Arunachalam
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | - Dinesh Kumar Lakshmanan
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | - Guna Ravichandran
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | - Soumi Paul
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | - Sivakumar Manickam
- Petroleum and Chemical Engineering, Faculty of Engineering, Universiti Teknologi Brunei, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Palanirajan Vijayaraj Kumar
- Department (Pharmaceutical Technology), Faculty of Pharmacy, UCSI University, South Campus, Taman Connaught, 56000, Kuala Lumpur, Malaysia
| | - Sivasudha Thilagar
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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44
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Parrish PCR, Thomas JD, Gabel AM, Kamlapurkar S, Bradley RK, Berger AH. Discovery of synthetic lethal and tumor suppressor paralog pairs in the human genome. Cell Rep 2021; 36:109597. [PMID: 34469736 PMCID: PMC8534300 DOI: 10.1016/j.celrep.2021.109597] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/17/2021] [Accepted: 08/03/2021] [Indexed: 01/26/2023] Open
Abstract
CRISPR screens have accelerated the discovery of important cancer vulnerabilities. However, single-gene knockout phenotypes can be masked by redundancy among related genes. Paralogs constitute two-thirds of the human protein-coding genome, so existing methods are likely inadequate for assaying a large portion of gene function. Here, we develop paired guide RNAs for paralog genetic interaction mapping (pgPEN), a pooled CRISPR-Cas9 single- and double-knockout approach targeting more than 2,000 human paralogs. We apply pgPEN to two cell types and discover that 12% of human paralogs exhibit synthetic lethality in at least one context. We recover known synthetic lethal paralogs MEK1/MEK2, important drug targets CDK4/CDK6, and other synthetic lethal pairs including CCNL1/CCNL2. Additionally, we identify ten tumor suppressor paralog pairs whose compound loss promotes cell proliferation. These findings nominate drug targets and suggest that paralog genetic interactions could shape the landscape of positive and negative selection in cancer.
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Affiliation(s)
- Phoebe C R Parrish
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - James D Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Austin M Gabel
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Shriya Kamlapurkar
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alice H Berger
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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45
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Le Gal K, Schmidt EE, Sayin VI. Cellular Redox Homeostasis. Antioxidants (Basel) 2021; 10:antiox10091377. [PMID: 34573009 PMCID: PMC8469889 DOI: 10.3390/antiox10091377] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 08/26/2021] [Indexed: 01/07/2023] Open
Abstract
Cellular redox homeostasis is an essential and dynamic process that ensures the balance between reducing and oxidizing reactions within cells and regulates a plethora of biological responses and events. The study of these biochemical reactions has proven difficult over time, but recent technical and methodological developments have contributed to the rapid growth of the redox field and to our understanding of its importance in biology. The aim of this short review is to give the reader an overall understanding of redox regulation in the areas of cellular signaling, development, and disease, as well as to introduce some recent discoveries in those fields.
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Affiliation(s)
- Kristell Le Gal
- Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Center for Cancer Research, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Edward E. Schmidt
- Microbiology & Cell Biology, Montana State University, Bozeman, MT 59718, USA;
- McLaughlin Research Institute, Great Falls, MT 59405, USA
- Laboratory of Redox Biology, University of Veterinary Medicine, 1078 Budapest, Hungary
| | - Volkan I. Sayin
- Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Center for Cancer Research, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence:
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46
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Vichas A, Riley AK, Nkinsi NT, Kamlapurkar S, Parrish PCR, Lo A, Duke F, Chen J, Fung I, Watson J, Rees M, Gabel AM, Thomas JD, Bradley RK, Lee JK, Hatch EM, Baine MK, Rekhtman N, Ladanyi M, Piccioni F, Berger AH. Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer. Nat Commun 2021; 12:4789. [PMID: 34373451 PMCID: PMC8352964 DOI: 10.1038/s41467-021-24841-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
CRISPR-based cancer dependency maps are accelerating advances in cancer precision medicine, but adequate functional maps are limited to the most common oncogenes. To identify opportunities for therapeutic intervention in other rarer subsets of cancer, we investigate the oncogene-specific dependencies conferred by the lung cancer oncogene, RIT1. Here, genome-wide CRISPR screening in KRAS, EGFR, and RIT1-mutant isogenic lung cancer cells identifies shared and unique vulnerabilities of each oncogene. Combining this genetic data with small-molecule sensitivity profiling, we identify a unique vulnerability of RIT1-mutant cells to loss of spindle assembly checkpoint regulators. Oncogenic RIT1M90I weakens the spindle assembly checkpoint and perturbs mitotic timing, resulting in sensitivity to Aurora A inhibition. In addition, we observe synergy between mutant RIT1 and activation of YAP1 in multiple models and frequent nuclear overexpression of YAP1 in human primary RIT1-mutant lung tumors. These results provide a genome-wide atlas of oncogenic RIT1 functional interactions and identify components of the RAS pathway, spindle assembly checkpoint, and Hippo/YAP1 network as candidate therapeutic targets in RIT1-mutant lung cancer.
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Affiliation(s)
- Athea Vichas
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda K Riley
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Naomi T Nkinsi
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Shriya Kamlapurkar
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phoebe C R Parrish
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - April Lo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Fujiko Duke
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Jennifer Chen
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Iris Fung
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | | | - Matthew Rees
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Austin M Gabel
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James D Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert K Bradley
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John K Lee
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emily M Hatch
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marina K Baine
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Federica Piccioni
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Merck Research Laboratories, Boston, MA, USA
| | - Alice H Berger
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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47
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Sonkar A, Kumar P, Gautam A, Maity B, Saha S. New Scope of Targeted Therapies in Lung Carcinoma. Mini Rev Med Chem 2021; 22:629-639. [PMID: 34353252 DOI: 10.2174/1389557521666210805104714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/30/2020] [Accepted: 04/27/2021] [Indexed: 11/22/2022]
Abstract
Lung cancer (LC) is the leading cause of cancer deaths worldwide. Recent research has also shown LC as a genomic disease, causing somatic mutations in patients. Tests related to mutational analysis and genome profiles have lately expanded significantly in the genetics/genomics field of LC. This review summarizes the current knowledge about different signalling pathways of LC based on the clinical impact of molecular targets. It describes the main molecular pathways and changes involved in the development, progression, and cellular breakdown of LC and the molecular changes. This review focuses on approved and targeted experimental therapies such as immunotherapy and clinical trials that examine the different targeted approaches to treating LC. We aimto clarify the differences in the extent of various genetic mutations in several areas for LC patients. Targeted molecular therapies for LC can be continued with advanced racial differences in genetic changes, which have a significant impact on the choice of drug treatment and our understanding of the profile of drug susceptibility/resistance. The most relevant genes described in this review are EGFR, KRAS, MET, BRAF, PIK3CA, STK11, ERBB3, PTEN, and RB1. Combined research efforts in this field are required to understand the genetic difference in LC outcomes in the future.
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Affiliation(s)
- Archana Sonkar
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raibareli Road, Lucknow 226025. India
| | - Pranesh Kumar
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raibareli Road, Lucknow 226025. India
| | - Anurag Gautam
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raibareli Road, Lucknow 226025. India
| | - Biswanath Maity
- Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh. India
| | - Sudipta Saha
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raibareli Road, Lucknow 226025. India
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48
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Muiños F, Martínez-Jiménez F, Pich O, Gonzalez-Perez A, Lopez-Bigas N. In silico saturation mutagenesis of cancer genes. Nature 2021; 596:428-432. [PMID: 34321661 DOI: 10.1038/s41586-021-03771-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 06/25/2021] [Indexed: 12/24/2022]
Abstract
Despite the existence of good catalogues of cancer genes1,2, identifying the specific mutations of those genes that drive tumorigenesis across tumour types is still a largely unsolved problem. As a result, most mutations identified in cancer genes across tumours are of unknown significance to tumorigenesis3. We propose that the mutations observed in thousands of tumours-natural experiments testing their oncogenic potential replicated across individuals and tissues-can be exploited to solve this problem. From these mutations, features that describe the mechanism of tumorigenesis of each cancer gene and tissue may be computed and used to build machine learning models that encapsulate these mechanisms. Here we demonstrate the feasibility of this solution by building and validating 185 gene-tissue-specific machine learning models that outperform experimental saturation mutagenesis in the identification of driver and passenger mutations. The models and their assessment of each mutation are designed to be interpretable, thus avoiding a black-box prediction device. Using these models, we outline the blueprints of potential driver mutations in cancer genes, and demonstrate the role of mutation probability in shaping the landscape of observed driver mutations. These blueprints will support the interpretation of newly sequenced tumours in patients and the study of the mechanisms of tumorigenesis of cancer genes across tissues.
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Affiliation(s)
- Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Francisco Martínez-Jiménez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain.
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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49
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Dräger O, Metz K, Busch M, Dünker N. Role of L1CAM in retinoblastoma tumorigenesis: identification of novel therapeutic targets. Mol Oncol 2021; 16:957-981. [PMID: 34228897 PMCID: PMC8847994 DOI: 10.1002/1878-0261.13054] [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: 03/11/2021] [Revised: 05/11/2021] [Accepted: 07/05/2021] [Indexed: 11/08/2022] Open
Abstract
The study presented focuses on the role of the neuronal cell adhesion molecule L1 cell adhesion molecule (L1CAM) in retinoblastoma (RB), the most common malignant intraocular childhood tumor. L1CAM is differentially expressed in a variety of human cancers and has been suggested as a promising therapeutic target. We likewise observed differential expression patterns for L1CAM in RB cell lines and patient samples. The two proteases involved in ectodomain shedding of L1CAM (L1CAM sheddases: ADAM10 and ADAM17) were likewise differentially expressed in the RB cell lines investigated, and an involvement in L1CAM processing in RB cells could be verified. We also identified ezrin, galectin-3, and fibroblast growth factor basic as L1CAM signaling target genes in RB cells. Lentiviral L1CAM knockdown induced apoptosis and reduced cell viability, proliferation, growth, and colony formation capacity of RB cells, whereas L1CAM-overexpressing RB cells displayed the opposite effects. Chicken chorioallantoic membrane assays revealed that L1CAM depletion decreases the tumorigenic and migration potential of RB cells in vivo. Moreover, L1CAM depletion decreased viability and tumor growth of etoposide-resistant RB cell lines upon etoposide treatment in vitro and in vivo. Thus, L1CAM and its processing sheddases are potential novel targets for future therapeutic RB approaches.
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Affiliation(s)
- Oliver Dräger
- Institute of Anatomy II, Department of Neuroanatomy, University of Duisburg-Essen, Medical Faculty, Germany
| | - Klaus Metz
- Institute of Pathology, University of Duisburg-Essen, Medical Faculty, Germany
| | - Maike Busch
- Institute of Anatomy II, Department of Neuroanatomy, University of Duisburg-Essen, Medical Faculty, Germany
| | - Nicole Dünker
- Institute of Anatomy II, Department of Neuroanatomy, University of Duisburg-Essen, Medical Faculty, Germany
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50
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Gao L, Liu Y, Du X, Ma S, Ge M, Tang H, Han C, Zhao X, Liu Y, Shao Y, Wu Z, Zhang L, Meng F, Xiao-Feng Qin F. The intrinsic role and mechanism of tumor expressed-CD38 on lung adenocarcinoma progression. Cell Death Dis 2021; 12:680. [PMID: 34226519 PMCID: PMC8256983 DOI: 10.1038/s41419-021-03968-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022]
Abstract
It has been recently reported that CD38 expressed on tumor cells of multiple murine and human origins could be upregulated in response to PD-L1 antibody therapy, which led to dysfunction of tumor-infiltrating CD8+ T immune cells due to increasing the production of adenosine. However, the role of tumor expressed-CD38 on neoplastic formation and progression remains elusive. In the present study, we aimed to delineate the molecular and biochemical function of the tumor-associated CD38 in lung adenocarcinoma progression. Our clinical data showed that the upregulation of tumor-originated CD38 was correlated with poor survival of lung cancer patients. Using multiple in vitro assays we found that the enzymatic activity of tumor expressed-CD38 facilitated lung cancer cell migration, proliferation, colony formation, and tumor development. Consistently, our in vivo results showed that inhibition of the enzymatic activity or antagonizing the enzymatic product of CD38 resulted in the similar inhibition of tumor proliferation and metastasis as CD38 gene knock-out or mutation. At biochemical level, we further identified that cADPR, the mainly hydrolytic product of CD38, was responsible for inducing the opening of TRPM2 iron channel leading to the influx of intracellular Ca2+ and then led to increasing levels of NRF2 while decreasing expression of KEAP1 in lung cancer cells. These findings suggested that malignant lung cancer cells were capable of using cADPR catalyzed by CD38 to facilitate tumor progression, and blocking the enzymatic activity of CD38 could be represented as an important strategy for preventing tumor progression.
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Affiliation(s)
- Long Gao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Yuan Liu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Xiaohong Du
- Institute of Clinical Medicine Research, the Affiliated Suzhou Hospital of Nanjing Medical University; Suzhou Science and Technology Town Hospital, Suzhou, China
| | - Sai Ma
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Minmin Ge
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Haijun Tang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Chenfeng Han
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Xin Zhao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Yanbin Liu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Yun Shao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Zhao Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Lianjun Zhang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Fang Meng
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China.
| | - F Xiao-Feng Qin
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China.
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