101
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Joon HK, Thalor A, Gupta D. Machine learning analysis of lung squamous cell carcinoma gene expression datasets reveals novel prognostic signatures. Comput Biol Med 2023; 165:107430. [PMID: 37703712 DOI: 10.1016/j.compbiomed.2023.107430] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/06/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND Lung squamous cell carcinoma (LUSC) patients are often diagnosed at an advanced stage and have poor prognoses. Thus, identifying novel biomarkers for the LUSC is of utmost importance. METHODS Multiple datasets from the NCBI-GEO repository were obtained and merged to construct the complete dataset. We also constructed a subset from this complete dataset with only known cancer driver genes. Further, machine learning classifiers were employed to obtain the best features from both datasets. Simultaneously, we perform differential gene expression analysis. Furthermore, survival and enrichment analyses were performed. RESULTS The kNN classifier performed comparatively better on the complete and driver datasets' top 40 and 50 gene features, respectively. Out of these 90 gene features, 35 were found to be differentially regulated. Lasso-penalized Cox regression further reduced the number of genes to eight. The median risk score of these eight genes significantly stratified the patients, and low-risk patients have significantly better overall survival. We validated the robust performance of these eight genes on the TCGA dataset. Pathway enrichment analysis identified that these genes are associated with cell cycle, cell proliferation, and migration. CONCLUSION This study demonstrates that an integrated approach involving machine learning and system biology may effectively identify novel biomarkers for LUSC.
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Affiliation(s)
- Hemant Kumar Joon
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Anamika Thalor
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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102
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Desai A, Dimou A. Toxicity From Sotorasib After Immune Checkpoint Inhibitors: A Note of Caution and Reflections of Future Advancements in the Field. J Thorac Oncol 2023; 18:1265-1267. [PMID: 37758343 DOI: 10.1016/j.jtho.2023.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 10/03/2023]
Affiliation(s)
- Aakash Desai
- Division of Medical Oncology, Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Anastasios Dimou
- Department of Medical Oncology, Mayo Clinic, Rochester, Minnesota.
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103
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Watkins TBK, Colliver EC, Huska MR, Kaufmann TL, Lim EL, Duncan CB, Haase K, Van Loo P, Swanton C, McGranahan N, Schwarz RF. Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity. PLoS Comput Biol 2023; 19:e1011379. [PMID: 37871126 PMCID: PMC10621967 DOI: 10.1371/journal.pcbi.1011379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 11/02/2023] [Accepted: 07/22/2023] [Indexed: 10/25/2023] Open
Abstract
Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient's disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase's ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours.
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Affiliation(s)
- Thomas B. K. Watkins
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | | | - Matthew R. Huska
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
| | - Tom L. Kaufmann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
- Department of Electrical Engineering & Computer Science, Technische Universität Berlin, Berlin, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Emilia L. Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Cody B. Duncan
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kerstin Haase
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Van Loo
- The Francis Crick Institute, London, United Kingdom
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, United Kingdom
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
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104
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Karlow JA, Pehrsson EC, Xing X, Watson M, Devarakonda S, Govindan R, Wang T. Non-small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-smokers. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:991-1013. [PMID: 37742993 PMCID: PMC10928376 DOI: 10.1016/j.gpb.2023.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 02/11/2023] [Accepted: 03/14/2023] [Indexed: 09/26/2023]
Abstract
Epigenetic alterations are widespread in cancer and can complement genetic alterations to influence cancer progression and treatment outcome. To determine the potential contribution of DNAmethylation alterations to tumor phenotype in non-small cell lung cancer (NSCLC) in both smoker and never-smoker patients, we performed genome-wide profiling of DNA methylation in 17 primary NSCLC tumors and 10 matched normal lung samples using the complementary assays, methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation sensitive restriction enzyme sequencing (MRE-seq). We reported recurrent methylation changes in the promoters of several genes, many previously implicated in cancer, including FAM83A and SEPT9 (hypomethylation), as well as PCDH7, NKX2-1, and SOX17 (hypermethylation). Although many methylation changes between tumors and their paired normal samples were shared across patients, several were specific to a particular smoking status. For example, never-smokers displayed a greater proportion of hypomethylated differentially methylated regions (hypoDMRs) and a greater number of recurrently hypomethylated promoters, including those of ASPSCR1, TOP2A, DPP9, and USP39, all previously linked to cancer. Changes outside of promoters were also widespread and often recurrent, particularly methylation loss over repetitive elements, highly enriched for ERV1 subfamilies. Recurrent hypoDMRs were enriched for several transcription factor binding motifs, often for genes involved in signaling and cell proliferation. For example, 71% of recurrent promoter hypoDMRs contained a motif for NKX2-1. Finally, the majority of DMRs were located within an active chromatin state in tissues profiled using the Roadmap Epigenomics data, suggesting that methylation changes may contribute to altered regulatory programs through the adaptation of cell type-specific expression programs.
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Affiliation(s)
- Jennifer A Karlow
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erica C Pehrsson
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mark Watson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Siddhartha Devarakonda
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ramaswamy Govindan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
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105
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Sahu P, Donovan C, Paudel KR, Pickles S, Chimankar V, Kim RY, Horvart JC, Dua K, Ieni A, Nucera F, Bielefeldt-Ohmann H, Mazilli S, Caramori G, Lyons JG, Hansbro PM. Pre-clinical lung squamous cell carcinoma mouse models to identify novel biomarkers and therapeutic interventions. Front Oncol 2023; 13:1260411. [PMID: 37817767 PMCID: PMC10560855 DOI: 10.3389/fonc.2023.1260411] [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: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 10/12/2023] Open
Abstract
Primary lung carcinoma or lung cancer (LC) is classified into small-cell or non-small-cell (NSCLC) lung carcinoma. Lung squamous cell carcinoma (LSCC) is the second most common subtype of NSCLC responsible for 30% of all LCs, and its survival remains low with only 24% of patients living for five years or longer post-diagnosis primarily due to the advanced stage of tumors at the time of diagnosis. The pathogenesis of LSCC is still poorly understood and has hampered the development of effective diagnostics and therapies. This review highlights the known risk factors, genetic and epigenetic alterations, miRNA biomarkers linked to the development and diagnosis of LSCC and the lack of therapeutic strategies to target specifically LSCC. We will also discuss existing animal models of LSCC including carcinogen induced, transgenic and xenograft mouse models, and their advantages and limitations along with the chemopreventive studies and molecular studies conducted using them. The importance of developing new and improved mouse models will also be discussed that will provide further insights into the initiation and progression of LSCC, and enable the identification of new biomarkers and therapeutic targets.
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Affiliation(s)
- Priyanka Sahu
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
| | - Chantal Donovan
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Sophie Pickles
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Vrushali Chimankar
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Richard Y. Kim
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Jay C. Horvart
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Antonio Ieni
- Department of Human Pathology in Adult and Developmental Age “Gaetano Barresi”, Section of Anatomic Pathology, University of Messina, Messina, Italy
| | - Francesco Nucera
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Messina, Italy
| | - Helle Bielefeldt-Ohmann
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Sarah Mazilli
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Messina, Italy
| | - J. Guy Lyons
- Department of Dermatology, The University of Sydney at Royal Prince Alfred Hospital, Sydney, Australia, and Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Philip M. Hansbro
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
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106
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Bai X, Shao J, Duan T, Liu X, Wang M, Li X, You Q, Zhang Z, Pan J. Exo-miR-1290-induced by COX-2 overexpression promotes cancer-associated fibroblasts activation and tumor progression by CUL3-Nrf2 pathway in lung adenocarcinoma. Cell Commun Signal 2023; 21:242. [PMID: 37723559 PMCID: PMC10506250 DOI: 10.1186/s12964-023-01268-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/12/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) are critically involved in tumor progression by maintaining extracellular mesenchyma (ECM) production and improving tumor development. Cyclooxygenase-2 (COX-2) has been proved to promote ECM formation and tumor progression. However, the mechanisms of COX-2 mediated CAFs activation have not yet been elucidated. Therefore, we conducted this study to identify the effects and mechanisms of COX-2 underlying CAFs activation by tumor-derived exosomal miRNAs in lung adenocarcinoma (LUAD) progression. METHODS As measures of CAFs activation, the expressions of fibroblasts activated protein-1 (FAP-1) and α-smooth muscle actin (α-SMA), the main CAFs markers, were detected by Western blotting and Immunohistochemistry. And the expression of Fibronectin (FN1) was used to analyze ECM production by CAFs. The exosomes were extracted by ultracentrifugation and exo-miRNAs were detected by qRT-PCR. Herein, we further elucidated the implicated mechanisms using online prediction software, luciferase reporter assays, co-immunoprecipitation, and experimental animal models. RESULTS In vivo, a positive correlation was observed between the COX-2 expression levels in parenchyma and α-SMA/FN1 expression levels in mesenchyma in LUAD. However, PGE2, one of major product of COX-2, did not affect CAFs activation directly. COX-2 overexpression increased exo-miR-1290 expression, which promoted CAFs activation. Furthermore, Cullin3 (CUL3), a potential target of miR-1290, was found to suppress COX-2/exo-miR-1290-mediated CAFs activation and ECM production, consequently impeding tumor progression. CUL3 is identified to induce the Nuclear Factor Erythroid 2-Related Factor 2 (NFE2L2, Nrf2) ubiquitination and degradation, while exo-miR-1290 can prevent Nrf2 ubiquitination and increase its protein stability by targeting CUL3. Additionally, we identified that Nrf2 is direcctly bound with promoters of FAP-1 and FN1, which enhanced CAFs activation by promoting FAP-1 and FN1 transcription. CONCLUSIONS Our data identify a new CAFs activation mechanism by exosomes derived from cancer cells that overexpress COX-2. Specifically, COX-2/exo-miR-1290/CUL3 is suggested as a novel signaling pathway for mediating CAFs activation and tumor progression in LUAD. Consequently, this finding suggests a novel strategy for cancer treatment that may tackle tumor progression in the future. Video Abstract.
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Affiliation(s)
- Xiaoming Bai
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Jiaofang Shao
- Department of Bioinformatics, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Tinghong Duan
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Xue Liu
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Min Wang
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Xuanya Li
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Qiang You
- Department of Biotherapy, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, P.R. China
| | - Zhiyuan Zhang
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China.
| | - Jinshun Pan
- Department of Biotherapy, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, P.R. China.
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107
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Shen J, Sun N, Wang J, Zens P, Kunzke T, Buck A, Prade VM, Wang Q, Feuchtinger A, Hu R, Berezowska S, Walch A. Patterns of Carbon-Bound Exogenous Compounds Impact Disease Pathophysiology in Lung Cancer Subtypes in Different Ways. ACS NANO 2023; 17:16396-16411. [PMID: 37639684 PMCID: PMC10510585 DOI: 10.1021/acsnano.2c11161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Carbon-bound exogenous compounds, such as polycyclic aromatic hydrocarbons (PAHs), tobacco-specific nitrosamines, aromatic amines, and organohalogens, are known to affect both tumor characteristics and patient outcomes in lung squamous cell carcinoma (LUSC); however, the roles of these compounds in lung adenocarcinoma (LUAD) remain unclear. We analyzed 11 carbon-bound exogenous compounds in LUAD and LUSC samples using in situ high mass-resolution matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry imaging and performed a cluster analysis to compare the patterns of carbon-bound exogenous compounds between these two lung cancer subtypes. Correlation analyses were conducted to investigate associations among exogenous compounds, endogenous metabolites, and clinical data, including patient survival outcomes and smoking behaviors. Additionally, we examined differences in exogenous compound patterns between normal and tumor tissues. Our analyses revealed that PAHs, aromatic amines, and organohalogens were more abundant in LUAD than in LUSC, whereas the tobacco-specific nitrosamine nicotine-derived nitrosamine ketone was more abundant in LUSC. Patients with LUAD and LUSC could be separated according to carbon-bound exogenous compound patterns detected in the tumor compartment. The same compounds had differential impacts on patient outcomes, depending on the cancer subtype. Correlation and network analyses indicated substantial differences between LUAD and LUSC metabolomes, associated with substantial differences in the patterns of the carbon-bound exogenous compounds. These data suggest that the contributions of these carcinogenic compounds to cancer biology may differ according to the cancer subtypes.
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Affiliation(s)
- Jian Shen
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
- Nanxishan
Hospital of Guangxi Zhuang Autonomous Region, Institute of Pathology, Guilin 541002, People’s Republic of China
| | - Na Sun
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Jun Wang
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Philipp Zens
- Institute
of Tissue Medicine and Pathology, University
of Bern, Murtenstrasse 31, Bern 3008, Switzerland
- Graduate
School for Health Sciences, University of
Bern, Mittelstrasse 43, Bern 3012, Switzerland
| | - Thomas Kunzke
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Achim Buck
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Verena M. Prade
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Qian Wang
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Annette Feuchtinger
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Ronggui Hu
- Center
for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200030, People’s
Republic of China
| | - Sabina Berezowska
- Institute
of Tissue Medicine and Pathology, University
of Bern, Murtenstrasse 31, Bern 3008, Switzerland
- Department
of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Axel Walch
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
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108
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Luo Y, Yang Y, Yang C, Li C, Hu R, Geng W, Kang X, Lin H. UBE3A and MCM6 synergistically regulate the proliferation and migration of lung adenocarcinoma cells. FEBS Open Bio 2023; 13:1756-1771. [PMID: 37454373 PMCID: PMC10476561 DOI: 10.1002/2211-5463.13675] [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: 02/07/2023] [Revised: 05/16/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023] Open
Abstract
Lung cancer is a leading cause of mortality worldwide and shows substantial clinical and biomolecular heterogeneity. Currently, specific therapeutic strategies are lacking, so effective drug targets are urgently needed. E6AP/UBE3A is a multifaceted ubiquitin ligase that controls various signaling pathways implicated in neurological diseases and various cancers; however, its role in lung cancer is incompletely understood. Here, MCM6 was identified as an interacting partner of E6AP using the yeast two-hybrid assay. MCM2 and MCM4 were then shown to interact with E6AP. E6AP knockout enhanced the ubiquitination of MCM2/4/6, suggesting that E6AP was not the E3 ubiquitin ligase for these three MCM proteins. Ablation of E6AP inhibited proliferation and migration, but had no significant effect on apoptosis in A549 and H1975 cells, and proliferation and migration inhibition was also observed in MCM6 knockdown cells. Furthermore, ablation of MCM6 and E6AP synergistically suppressed the proliferation and migration of A549 and H1975 cells. To verify the above findings in vivo, we established tumor models in nude mice and identified that the tumorigenicity of human lung adenocarcinoma (LUAD) cells was synergistically regulated by MCM6 and E6AP. Moreover, the expression levels of MCM6 and E6AP were higher in LUAD tissues than in adjacent tissues. Furthermore, the expression levels of MCM6 and E6AP were positively correlated in human LUAD samples. Thus, our study suggests that the interaction of E6AP and MCM proteins plays an important role in the progression of LUAD, which might offer potential therapeutic targets for cancer treatment.
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Affiliation(s)
- Yanyan Luo
- Department of Pain, Wenzhou Key Laboratory of Perioperative MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityChina
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell Science, Chinese Academy of SciencesShanghaiChina
| | - Yun Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell Science, Chinese Academy of SciencesShanghaiChina
- School of MedicineGuizhou UniversityGuiyangChina
| | - Cong Yang
- Cancer Center, School of Medicine, Shanghai Tenth People's HospitalfTongji UniversityShanghaiChina
| | - Chuanyin Li
- Cancer Center, School of Medicine, Shanghai Tenth People's HospitalfTongji UniversityShanghaiChina
| | - Ronggui Hu
- Department of Pain, Wenzhou Key Laboratory of Perioperative MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityChina
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell Science, Chinese Academy of SciencesShanghaiChina
| | - Wujun Geng
- Department of Pain, Wenzhou Key Laboratory of Perioperative MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityChina
| | - Xianhui Kang
- Department of Pain, Wenzhou Key Laboratory of Perioperative MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityChina
- Department of Anesthesiology, The First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Hai Lin
- Department of Pain, Wenzhou Key Laboratory of Perioperative MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityChina
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109
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Mu D, Tang H, Teng G, Li X, Zhang Y, Gao G, Wang D, Bai L, Lian X, Wen M, Jiang L, Wu S, Jiang H, Zhu C. Differences of genomic alterations and heavy metals in non-small cell lung cancer with different histological subtypes. J Cancer Res Clin Oncol 2023; 149:9999-10013. [PMID: 37256381 PMCID: PMC10423170 DOI: 10.1007/s00432-023-04929-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
PURPOSE This study aimed to explore the correlations among heavy metals concentration, histologic subtypes and molecular characteristics in patients with non-small cell lung cancer (NSCLC). METHODS In this study, an NGS panel of 82 tumor-associated genes was used to identify genomic alternations in 180 newly diagnosed patients with NSCLC. The concentrations of 18 heavy metals in the serum samples were detected by inductively coupled plasma emission spectrometry (ICP-MS). RESULTS A total of 243 somatic mutations of 25 mutant genes were identified in 115 of 148 patients with LUAD and 45 somatic mutations of 15 mutant genes were found in 24 of 32 patients with LUSC. The genomic alternations, somatic interactions, traditional serum biomarkers, and heavy metals were markedly different between patients with LUAD and LUSC. Moreover, patients with LUSC were significantly positively correlated with Ba, but not LUAD. Lastly, patients with EGFR mutations presented significant negative correlations with Cd and Sr, whereas patients with TP53 mutations showed a significant positive correlation with Pb. CONCLUSION The genomic alternations, somatic interactions, traditional serum biomarkers, and heavy metals were different between patients with LUAC and LUSC, and heavy metals (e.g., Ba, Pb, and Cd) may contribute to the tumorigenesis of NSCLC with different histological and molecular subtypes.
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Affiliation(s)
- Die Mu
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Hui Tang
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, 200135, China
- Department of Interventional and Vascular Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Gen Teng
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Xinyang Li
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Yarui Zhang
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Ge Gao
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Dongjuan Wang
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Lu Bai
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Xiangyao Lian
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Ming Wen
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, 200135, China
| | - Lisha Jiang
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, 200135, China
| | - Shouxin Wu
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, 200135, China
| | - Huihui Jiang
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, 200135, China.
| | - Cuimin Zhu
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China.
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Cai R, Zhu H, Liu Y, Sha H, Peng W, Yin R, Zhou G, Fang Y. To be, or not to be: the dilemma of immunotherapy for non-small cell lung cancer harboring various driver mutations. J Cancer Res Clin Oncol 2023; 149:10027-10040. [PMID: 37261523 PMCID: PMC10423141 DOI: 10.1007/s00432-023-04919-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
INTRODUCTION Lung cancer is one of primary cancer type with high incidence and mortality, non-small cell lung cancer (NSCLC) is the most common type of lung cncer. For advanced lung cancer, traditional chemotherapy and targeted therapy become difficult to solve the dilemma of further progress. In recent years, with the clinical application of immunotherapy, the therapeutic strategy of lung cancer has changed dramatically. At present, immunotherapy has shown conspicuous efficacy in NSCLC patients with high expression of programmed death-ligand 1 (PD-L1) and high tumor mutational burden (TMB). The discovery of driver mutations brings delightful hope for targeted cancer therapy. However, it remains controversial whether immunotherapy can be used in NSCLC patients with these specific driver mutations. METHOD This article summarized the latest research progresses of immunotherapy in advanced NSCLC. We paid close attention to the relevance of various driver mutations and immunotherapy in NSCLC patients, and summarized the predictive effects of several driver mutations and immunotherapy. RESULTS The mutations of KRAS, KRAS+TP53, EPHA (especially EPHA5), ZFHX3, ZFHX3+TP53, NOTCH, BRAF and LRP1B+FAT3 have potential to be used as biomarkers to predict the positive effectiveness of immunotherapy. ZFHX3, ZFHX3+TP53, STKII/LKB1+KEAP1+SMARCA4+PBRM1 mutations in LUAD patients get more positive effect in immunotherapy. While the mutations of EGFR, KEAP1, STKII/LKB1+KRAS, EML4-ALK, MET exon 14 skipping mutation, PBRM1, STKII/LKB1+KEAP1+SMARCA4+PBRM1, ERBB2, PIK3CA and RET often indicate poor benefit from immunotherapy. CONCLUSION Many gene mutations have been shown to be associated with immunotherapy efficacy. Gene mutations should be combined with PD-L1, TMB, etc. to predict the effect of immunotherapy.
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Affiliation(s)
- Ruoxue Cai
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Baiziting 42, Nanjing, 210009, People's Republic of China
| | - Hongyu Zhu
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, 210009, People's Republic of China
| | - Ying Liu
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Baiziting 42, Nanjing, 210009, People's Republic of China
| | - Huanhuan Sha
- Department of Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
| | - Weiwei Peng
- Department of Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
| | - Rong Yin
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, 210009, People's Republic of China
| | - Guoren Zhou
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Baiziting 42, Nanjing, 210009, People's Republic of China.
| | - Ying Fang
- Department of Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
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111
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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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112
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Buscà R, Onesto C, Egensperger M, Pouysségur J, Pagès G, Lenormand P. N-terminal alanine-rich (NTAR) sequences drive precise start codon selection resulting in elevated translation of multiple proteins including ERK1/2. Nucleic Acids Res 2023; 51:7714-7735. [PMID: 37414542 PMCID: PMC10450180 DOI: 10.1093/nar/gkad528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
We report the discovery of N-terminal alanine-rich sequences, which we term NTARs, that act in concert with their native 5'-untranslated regions to promote selection of the proper start codon. NTARs also facilitate efficient translation initiation while limiting the production of non-functional polypeptides through leaky scanning. We first identified NTARs in the ERK1/2 kinases, which are among the most important signaling molecules in mammals. Analysis of the human proteome reveals that hundreds of proteins possess NTARs, with housekeeping proteins showing a particularly high prevalence. Our data indicate that several of these NTARs act in a manner similar to those found in the ERKs and suggest a mechanism involving some or all of the following features: alanine richness, codon rarity, a repeated amino acid stretch and a nearby second AUG. These features may help slow down the leading ribosome, causing trailing pre-initiation complexes (PICs) to pause near the native AUG, thereby facilitating accurate translation initiation. Amplification of erk genes is frequently observed in cancer, and we show that NTAR-dependent ERK protein levels are a rate-limiting step for signal output. Thus, NTAR-mediated control of translation may reflect a cellular need to precisely control translation of key transcripts such as potential oncogenes. By preventing translation in alternative reading frames, NTAR sequences may be useful in synthetic biology applications, e.g. translation from RNA vaccines.
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Affiliation(s)
- Roser Buscà
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
| | - Cercina Onesto
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
- Polytech’Nice Sophia, Bioengineering Department, Sophia-Antipolis, France
| | - Mylène Egensperger
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
| | - Jacques Pouysségur
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
- Centre Scientifique de Monaco, Biomedical Department, Principality of Monaco
| | - Gilles Pagès
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
- Centre Scientifique de Monaco, Biomedical Department, Principality of Monaco
| | - Philippe Lenormand
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
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Al-Hawary SIS, Alsalamy A, Gupta R, Alsaab HO, Hjazi A, Edilboyev U, Ramadan MF, Hussien BM, Ahmed M, Hosseini-Fard SR. VAV3 in human cancers: Mechanism and clinical implication. Pathol Res Pract 2023; 248:154681. [PMID: 37467637 DOI: 10.1016/j.prp.2023.154681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
Guanine nucleotide exchange factors (GEFs) are primarily involved in signal transmission between cell membrane receptors and intracellular mediators. Upon replacing GDP with GTP, GEFs can alter their conformation, resulting in their binding to downstream effectors, such as GTPases like Ras homologous (Rho). VAV GEF family are versatile proteins working as an adaptor mediator and GEF for Rho GTPase. They act as a phosphorylation-dependent molecular switcher, fluctuating between active (tyrosine phosphorylated) and inactive (non-phosphorylated) conformation in cell signaling. Accumulating data showed that VAV3 is implicated in cancer progression. The higher levels of VAV3 in human cancers proposed that it may have an oncogenic role in cancer progression. Available studies demonstrated that VAV3 promoted cell proliferation, epithelial-mesenchymal transition (EMT), colony formation, cell cycle, survival, migration and invasion, and suppressed cell apoptosis. In addition, other studies indicated that VAV3 may have a prognostic value in cancer as well as it may act as a mediator in cancer chemoresistance. Here, we aimed to investigate the underlying molecular mechanism of VAV3 in cancer progression as well as to review its value as a prognostic biomarker and chemoresistance mediator in human cancers.
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Affiliation(s)
| | - Ali Alsalamy
- College of Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
| | - Reena Gupta
- Institute of Pharmaceutical Research, GLA University, District-Mathura, U.P., 281406, India
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, Taif University, Taif 21944, Saudi Arabia
| | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Unarbek Edilboyev
- Department of Engineering Graphics and Design Theory, Tashkent Institute of Irrigation and Agricultural Mechanization Engineers, National Research University, Tashkent, Uzbekistan
| | | | - Beneen M Hussien
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Muhja Ahmed
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
| | - Seyed Reza Hosseini-Fard
- Biochemistry Department, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Timilsina M, Fey D, Buosi S, Janik A, Costabello L, Carcereny E, Abreu DR, Cobo M, Castro RL, Bernabé R, Minervini P, Torrente M, Provencio M, Nováček V. Synergy between imputed genetic pathway and clinical information for predicting recurrence in early stage non-small cell lung cancer. J Biomed Inform 2023; 144:104424. [PMID: 37352900 DOI: 10.1016/j.jbi.2023.104424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 06/25/2023]
Abstract
OBJECTIVE Lung cancer exhibits unpredictable recurrence in low-stage tumors and variable responses to different therapeutic interventions. Predicting relapse in early-stage lung cancer can facilitate precision medicine and improve patient survivability. While existing machine learning models rely on clinical data, incorporating genomic information could enhance their efficiency. This study aims to impute and integrate specific types of genomic data with clinical data to improve the accuracy of machine learning models for predicting relapse in early-stage, non-small cell lung cancer patients. METHODS The study utilized a publicly available TCGA lung cancer cohort and imputed genetic pathway scores into the Spanish Lung Cancer Group (SLCG) data, specifically in 1348 early-stage patients. Initially, tumor recurrence was predicted without imputed pathway scores. Subsequently, the SLCG data were augmented with pathway scores imputed from TCGA. The integrative approach aimed to enhance relapse risk prediction performance. RESULTS The integrative approach achieved improved relapse risk prediction with the following evaluation metrics: an area under the precision-recall curve (PR-AUC) score of 0.75, an area under the ROC (ROC-AUC) score of 0.80, an F1 score of 0.61, and a Precision of 0.80. The prediction explanation model SHAP (SHapley Additive exPlanations) was employed to explain the machine learning model's predictions. CONCLUSION We conclude that our explainable predictive model is a promising tool for oncologists that addresses an unmet clinical need of post-treatment patient stratification based on the relapse risk while also improving the predictive power by incorporating proxy genomic data not available for specific patients.
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Affiliation(s)
- Mohan Timilsina
- Data Science Institute, Insight Centre for Data Analytics, University of Galway, Ireland.
| | - Dirk Fey
- Systems Biology Ireland, University College Dublin, Ireland.
| | - Samuele Buosi
- Data Science Institute, Insight Centre for Data Analytics, University of Galway, Ireland.
| | | | | | - Enric Carcereny
- Catalan Institute of Oncology, Hospital Universitari Germans Trias i Pujol, B-ARGO, IGTP, Badalona, Spain.
| | | | - Manuel Cobo
- Medical Oncology Intercenter Unit. Regional and Virgen de la Victoria University Hospitals. IBIMA. Málaga., Spain.
| | | | - Reyes Bernabé
- Hospital Universitario Virgen del Rocio, Sevilla, Spain.
| | | | - Maria Torrente
- Medical Oncology Department, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain.
| | - Mariano Provencio
- Medical Oncology Department, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain.
| | - Vít Nováček
- Data Science Institute, Insight Centre for Data Analytics, University of Galway, Ireland; Faculty of Informatics, Masaryk University Brno, Czech Republic; Masaryk Memorial Cancer Institute, Brno, Czech Republic.
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115
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Hu F, Chen B, Wang Q, Yang Z, Chu M. Multi-omics data analysis reveals the biological implications of alternative splicing events in lung adenocarcinoma. J Bioinform Comput Biol 2023; 21:2350020. [PMID: 37694487 DOI: 10.1142/s0219720023500208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Cancer is characterized by the dysregulation of alternative splicing (AS). However, the comprehensive regulatory mechanisms of AS in lung adenocarcinoma (LUAD) are poorly understood. Here, we displayed the AS landscape in LUAD based on the integrated analyses of LUAD's multi-omics data. We identified 13,995 AS events in 6309 genes as differentially expressed alternative splicing events (DEASEs) mainly covering protein-coding genes. These DEASEs were strongly linked to "cancer hallmarks", such as apoptosis, DNA repair, cell cycle, cell proliferation, angiogenesis, immune response, generation of precursor metabolites and energy, p53 signaling pathway and PI3K-AKT signaling pathway. We further built a regulatory network connecting splicing factors (SFs) and DEASEs. In addition, RNA-binding protein (RBP) mutations that can affect DEASEs were investigated to find some potential cancer drivers. Further association analysis demonstrated that DNA methylation levels were highly correlated with DEASEs. In summary, our results can bring new insight into understanding the mechanism of AS and provide novel biomarkers for personalized medicine of LUAD.
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Affiliation(s)
- Fuyan Hu
- Department of Statistics, School of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, Hubei 430070, P. R. China
| | - Bifeng Chen
- Department of Biological Science and Technology, School of Chemistry Chemical Engineering and Life Sciences, Wuhan University of Technology Wuhan, Hubei, P. R. China
| | - Qing Wang
- Department of Traditional Chinese Medicine of Wuhan Puren Hospital, Affiliated Hospital of Wuhan University of Science and Technology, 1# Benxi Street, Qingshan District, Wuhan, Hubei, P. R. China
| | - Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, P. R. China
| | - Man Chu
- The Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, Shaanxi 712046, P. R. China
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116
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DuCote TJ, Naughton KJ, Skaggs EM, Bocklage TJ, Allison DB, Brainson CF. Using Artificial Intelligence to Identify Tumor Microenvironment Heterogeneity in Non-Small Cell Lung Cancers. J Transl Med 2023; 103:100176. [PMID: 37182840 PMCID: PMC10527157 DOI: 10.1016/j.labinv.2023.100176] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 05/16/2023] Open
Abstract
Lung cancer heterogeneity is a major barrier to effective treatments and encompasses not only the malignant epithelial cell phenotypes and genetics but also the diverse tumor-associated cell types. Current techniques used to investigate the tumor microenvironment can be time-consuming, expensive, complicated to interpret, and often involves destruction of the sample. Here we use standard hematoxylin and eosin-stained tumor sections and the HALO AI nuclear phenotyping software to characterize 6 distinct cell types (epithelial, mesenchymal, macrophage, neutrophil, lymphocyte, and plasma cells) in both murine lung cancer models and human lung cancer samples. CD3 immunohistochemistry and lymph node sections were used to validate lymphocyte calls, while F4/80 immunohistochemistry was used for macrophage validation. Consistent with numerous prior studies, we demonstrated that macrophages predominate the adenocarcinomas, whereas neutrophils predominate the squamous cell carcinomas in murine samples. In human samples, we showed a strong negative correlation between neutrophils and lymphocytes as well as between mesenchymal cells and lymphocytes and that higher percentages of mesenchymal cells correlate with poor prognosis. Taken together, we demonstrate the utility of this AI software to identify, quantify, and compare distributions of cell types on standard hematoxylin and eosin-stained slides. Given the simplicity and cost-effectiveness of this technique, it may be widely beneficial for researchers designing new therapies and clinicians working to select favorable treatments for their patients.
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Affiliation(s)
- Tanner J DuCote
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | - Kassandra J Naughton
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | - Erika M Skaggs
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | - Therese J Bocklage
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky; Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky
| | - Derek B Allison
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky; Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky
| | - Christine F Brainson
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky; Markey Cancer Center, University of Kentucky, Lexington, Kentucky.
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117
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Hong CS, Alanya H, DiStasio M, Boulware SD, Rimmer RA, Omay SB, Erson-Omay EZ. Sporadic pituitary adenoma with somatic double-hit loss of MEN1. Pituitary 2023; 26:488-494. [PMID: 37438451 DOI: 10.1007/s11102-023-01336-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2023] [Indexed: 07/14/2023]
Abstract
PURPOSE Pituitary adenomas commonly arise in patients with MEN1 syndrome, an autosomal dominant condition predisposing to neuroendocrine tumor formation, and typically diagnosed in patients with a relevant family cancer history. In these patients with existing germline loss of MEN1 on one allele, somatic loss of the second MEN1 allele leads to complete loss of the MEN1 protein, menin, and subsequent tumor formation. METHODS Whole exome sequencing was performed on the tumor and matching blood under an institutional board approved protocol. DNA extraction and analysis was conducted according to previously described methods. RESULTS We describe a 23 year-old patient with no significant past medical history or relevant family history who underwent surgical resection of a symptomatic and medically resistant prolactinoma. Whole exome sequencing of tumor and blood samples revealed somatic loss of MEN1 at both alleles, suggesting a double hit mechanism, with no underlying germline MEN1 mutation. CONCLUSION To our knowledge, this is the first case of pituitary adenoma to arise from somatic loss of MEN1 and in the absence of an underlying germline MEN1 mutation.
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Affiliation(s)
- Christopher S Hong
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Hasan Alanya
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Marcello DiStasio
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Susan D Boulware
- Department of Pediatrics, Section of Endocrinology and Diabetes, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Ryan A Rimmer
- Department of Surgery, Division of Otolaryngology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Sacit Bulent Omay
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, 06510, USA
| | - E Zeynep Erson-Omay
- Department of Neurosurgery, Yale School of Medicine, 300 Cedar Street, TAC S327, New Haven, CT, 06511, USA.
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Tang P, Sun D, Xu W, Li H, Chen L. Long non‑coding RNAs as potential therapeutic targets in non‑small cell lung cancer (Review). Int J Mol Med 2023; 52:68. [PMID: 37350412 PMCID: PMC10413047 DOI: 10.3892/ijmm.2023.5271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/02/2023] [Indexed: 06/24/2023] Open
Abstract
Non‑small cell lung cancer (NSCLC) is one of the most common malignancies with a high morbidity and mortality rate. Long non‑coding RNAs (lncRNAs) have been reported to be closely associated with the occurrence and progression of NSCLC. In addition, lncRNAs have been documented to participate in the development of drug resistance and radiation sensitivity in patients with NSCLC. Due to their extensive functional characterization, high tissue specificity and sex specificity, lncRNAs have been proposed to be novel biomarkers and therapeutic targets for NSCLC. Therefore, in the current review, the functional classification of lncRNAs were presented, whilst the potential roles of lncRNAs in NSCLC were also summarized. Various physiological aspects, including proliferation, invasion and drug resistance, were all discussed. It is anticipated that the present review will provide a perspective on lncRNAs as potential diagnostic molecular biomarkers and therapeutic targets for NSCLC.
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Affiliation(s)
- Peiyu Tang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
| | - Dejuan Sun
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
| | - Wei Xu
- Institute of Structural Pharmacology and TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
- Institute of Structural Pharmacology and TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
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119
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Xu D, Qian W, Yang Z, Zhang Z, Sun P, Wan Q, Yin Y, Hu Y, Gong L, Zhang B, Yang X, Pu Z, Lu P, Zou J. Acetylation halts missense mutant p53 aggregation and rescues tumor suppression in non-small cell lung cancers. iScience 2023; 26:107003. [PMID: 37534137 PMCID: PMC10391690 DOI: 10.1016/j.isci.2023.107003] [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: 02/13/2023] [Revised: 04/28/2023] [Accepted: 05/26/2023] [Indexed: 08/04/2023] Open
Abstract
TP53 mutations are ubiquitous with tumorigenesis in non-small cell lung cancers (NSCLC). By analyzing the TCGA database, we reported that TP53 missense mutations are correlated with chromosomal instability and tumor mutation burden in NSCLC. The inability of wild-type nor mutant p53 expression can't predict survival in lung cancer cohorts, however, an examination of primary NSCLC tissues found that acetylated p53 did yield an association with improved survival outcomes. Molecularly, we demonstrated that acetylation drove the ubiquitination and degradation of mutant p53 but enhanced stability of wild-type p53. Moreover, acetylation of a missense p53 mutation prevented the gain of oncogenic function observed in typical TP53 mutant-expressing cells and enhanced tumor suppressor functions. Consequently, acetylation inducer targeting of missense mutant p53 may be a viable therapeutic goal for NSCLC treatment and may improve the accuracy of current efforts to utilize p53 mutations in a prognostic manner.
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Affiliation(s)
- Daxing Xu
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Wei Qian
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Zhenkun Yang
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Zhenhao Zhang
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Ping Sun
- Department of Pathology, Jiangnan University Medical Center, Wuxi, Jiangsu 214023, China
| | - Quan Wan
- Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu 214023, China
| | - Ying Yin
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Yaling Hu
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Lingli Gong
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Bo Zhang
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Xusheng Yang
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Zhening Pu
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Peihua Lu
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Department of Medical Oncology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Jian Zou
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
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120
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Li Y, Slavik KM, Toyoda HC, Morehouse BR, de Oliveira Mann CC, Elek A, Levy S, Wang Z, Mears KS, Liu J, Kashin D, Guo X, Mass T, Sebé-Pedrós A, Schwede F, Kranzusch PJ. cGLRs are a diverse family of pattern recognition receptors in innate immunity. Cell 2023; 186:3261-3276.e20. [PMID: 37379839 PMCID: PMC10527820 DOI: 10.1016/j.cell.2023.05.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 04/03/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is an enzyme in human cells that controls an immune response to cytosolic DNA. Upon binding DNA, cGAS synthesizes a nucleotide signal 2'3'-cGAMP that activates STING-dependent downstream immunity. Here, we discover that cGAS-like receptors (cGLRs) constitute a major family of pattern recognition receptors in innate immunity. Building on recent analysis in Drosophila, we identify >3,000 cGLRs present in nearly all metazoan phyla. A forward biochemical screening of 150 animal cGLRs reveals a conserved mechanism of signaling including response to dsDNA and dsRNA ligands and synthesis of isomers of the nucleotide signals cGAMP, c-UMP-AMP, and c-di-AMP. Combining structural biology and in vivo analysis in coral and oyster animals, we explain how synthesis of distinct nucleotide signals enables cells to control discrete cGLR-STING signaling pathways. Our results reveal cGLRs as a widespread family of pattern recognition receptors and establish molecular rules that govern nucleotide signaling in animal immunity.
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Affiliation(s)
- Yao Li
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kailey M Slavik
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Hunter C Toyoda
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Benjamin R Morehouse
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shani Levy
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Zhenwei Wang
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08349, USA
| | - Kepler S Mears
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jingjing Liu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Dmitry Kashin
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08349, USA
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain
| | - Frank Schwede
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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121
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Sun Z, Chen X, Huang X, Wu Y, Shao L, Zhou S, Zheng Z, Lin Y, Chen S. Cuproptosis and Immune-Related Gene Signature Predicts Immunotherapy Response and Prognosis in Lung Adenocarcinoma. Life (Basel) 2023; 13:1583. [PMID: 37511958 PMCID: PMC10381686 DOI: 10.3390/life13071583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Cuproptosis and associated immune-related genes (IRG) have been implicated in tumorigenesis and tumor progression. However, their effects on lung adenocarcinoma (LUAD) have not been elucidated. Therefore, we investigated the impact of cuproptosis-associated IRGs on the immunotherapy response and prognosis of LUAD using a bioinformatical approach and in vitro experiments analyzing clinical samples. Using the cuproptosis-associated IRG signature, we classified LUAD into two subtypes, cluster 1 and cluster 2, and identified three key cuproptosis-associated IRGs, NRAS, TRAV38-2DV8, and SORT1. These three genes were employed to establish a risk model and nomogram, and to classify the LUAD cohort into low- and high-risk subgroups. Biofunctional annotation revealed that cluster 2, remarkably downregulating epigenetic, stemness, and proliferation pathways activity, had a higher overall survival (OS) and immunoinfiltration abundance compared to cluster 1. Real-time quantitative PCR (RT-qPCR) validated the differential expression of these three genes in both subgroups. scRNA-seq demonstrated elevated expression of NRAS and SORT1 in macrophages. Immunity and oncogenic and stromal activation pathways were dramatically enriched in the low-risk subgroup, and patients in this subgroup responded better to immunotherapy. Our data suggest that the cuproptosis-associated IRG signature can be used to effectively predict the immunotherapy response and prognosis in LUAD. Our work provides enlightenment for immunotherapy response assessment, prognosis prediction, and the development of potential prognostic biomarkers for LUAD patients.
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Affiliation(s)
- Zihao Sun
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Xiujing Chen
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Xiaoning Huang
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Yanfen Wu
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Lijuan Shao
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Key Laboratory of Cancer Immunotherapy of Guangdong Higher Education Institutes, Guangzhou 510080, China
| | - Suna Zhou
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Zhu Zheng
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Yiguang Lin
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Key Laboratory of Cancer Immunotherapy of Guangdong Higher Education Institutes, Guangzhou 510080, China
- Research & Development Division, Guangzhou Anjie Biomedical Technology Co., Ltd., Guangzhou 510535, China
| | - Size Chen
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Key Laboratory of Cancer Immunotherapy of Guangdong Higher Education Institutes, Guangzhou 510080, China
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122
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Attig J, Pape J, Doglio L, Kazachenka A, Ottina E, Young GR, Enfield KS, Aramburu IV, Ng KW, Faulkner N, Bolland W, Papayannopoulos V, Swanton C, Kassiotis G. Human endogenous retrovirus onco-exaptation counters cancer cell senescence through calbindin. J Clin Invest 2023; 133:e164397. [PMID: 37192000 PMCID: PMC10348765 DOI: 10.1172/jci164397] [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: 08/10/2022] [Accepted: 05/11/2023] [Indexed: 05/17/2023] Open
Abstract
Increased levels and diversity of human endogenous retrovirus (HERV) transcription characterize most cancer types and are linked with disease outcomes. However, the underlying processes are incompletely understood. Here, we show that elevated transcription of HERVH proviruses predicted survival of lung squamous cell carcinoma (LUSC) and identified an isoform of CALB1, encoding calbindin, ectopically driven by an upstream HERVH provirus under the control of KLF5, as the mediator of this effect. HERVH-CALB1 expression was initiated in preinvasive lesions and associated with their progression. Calbindin loss in LUSC cell lines impaired in vitro and in vivo growth and triggered senescence, consistent with a protumor effect. However, calbindin also directly controlled the senescence-associated secretory phenotype (SASP), marked by secretion of CXCL8 and other neutrophil chemoattractants. In established carcinomas, CALB1-negative cancer cells became the dominant source of CXCL8, correlating with neutrophil infiltration and worse prognosis. Thus, HERVH-CALB1 expression in LUSC may display antagonistic pleiotropy, whereby the benefits of escaping senescence early during cancer initiation and clonal competition were offset by the prevention of SASP and protumor inflammation at later stages.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - George Kassiotis
- Retroviral Immunology
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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Nowak P, Bil-Lula I, Śliwińska-Mossoń M. A Cross-Talk about Radioresistance in Lung Cancer-How to Improve Radiosensitivity According to Chinese Medicine and Medicaments That Commonly Occur in Pharmacies. Int J Mol Sci 2023; 24:11206. [PMID: 37446385 DOI: 10.3390/ijms241311206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Lung cancer is one of the most common cancers in the population and is characterized by non-specific symptoms that delay the diagnosis and reduce the effectiveness of oncological treatment. Due to the difficult placement of the tumor, one of the main methods of lung cancer treatment is radiotherapy, which damages the DNA of cancer cells, inducing their apoptosis. However, resistance to ionizing radiation may develop during radiotherapy cycles, leading to an increase in the number of DNA points of control that protect cells from apoptosis. Cancer stem cells are essential for radioresistance, and due to their ability to undergo epithelial-mesenchymal transition, they modify the phenotype, bypassing the genotoxic effect of radiotherapy. It is therefore necessary to search for new methods that could improve the cytotoxic effect of cells through new mechanisms of action. Chinese medicine, with several thousand years of tradition, offers a wide range of possibilities in the search for compounds that could be used in conventional medicine. This review introduces the potential candidates that may present a radiosensitizing effect on lung cancer cells, breaking their radioresistance. Additionally, it includes candidates taken from conventional medicine-drugs commonly available in pharmacies, which may also be significant candidates.
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Affiliation(s)
- Paulina Nowak
- Scientific Club of Specialized Biological Analyzes, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland
| | - Iwona Bil-Lula
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Hematology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland
| | - Mariola Śliwińska-Mossoń
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Hematology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland
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124
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Boiarsky D, Lydon CA, Chambers ES, Sholl LM, Nishino M, Skoulidis F, Heymach JV, Luo J, Awad MM, Janne PA, Van Allen EM, Barbie DA, Vokes NI. Molecular markers of metastatic disease in KRAS-mutant lung adenocarcinoma. Ann Oncol 2023; 34:589-604. [PMID: 37121400 PMCID: PMC10425882 DOI: 10.1016/j.annonc.2023.04.514] [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: 02/03/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND Prior studies characterized the association of molecular alterations with treatment-specific outcomes in KRAS-mutant (KRASMUT) lung adenocarcinoma (LUAD). Less is known about the prognostic role of molecular alterations and their associations with metastatic disease. PATIENTS AND METHODS We analyzed clinicogenomic data from 1817 patients with KRASMUT LUAD sequenced at the Dana-Farber Cancer Institute (DFCI) and Memorial Sloan Kettering Cancer Center (MSKCC). Patients with metastatic (M1) and nonmetastatic (M0) disease were compared. Transcriptomic data from The Cancer Genome Atlas (TCGA) were investigated to characterize the biology of differential associations with clinical outcomes. Organ-specific metastasis was associated with overall survival (OS). RESULTS KEAP1 (DFCI: OR = 2.3, q = 0.04; MSKCC: OR = 2.2, q = 0.00027) and SMARCA4 mutations (DFCI: OR = 2.5, q = 0.06; MSKCC: OR = 2.6, q = 0.0021) were enriched in M1 versus M0 tumors. On integrative modeling, NRF2 activation was the genomic feature most associated with OS. KEAP1 mutations were enriched in M1 versus M0 tumors independent of STK11 status (KEAP1MUT/STK11WT: DFCI OR = 3.0, P = 0.0064; MSKCC OR = 2.0, P = 0.041; KEAP1MUT/STK11MUT: DFCI OR = 2.3, P = 0.0063; MSKCC OR = 2.5, P = 3.6 × 10-05); STK11 mutations without KEAP1 loss were not associated with stage (KEAP1WT/STK11MUT: DFCI OR = 0.97, P = 1.0; MSKCC OR = 1.2, P = 0.33) or outcome. KEAP1/KRAS-mutated tumors with and without STK11 mutations exhibited high functional STK11 loss. The negative effects of KEAP1 were compounded in the presence of bone (HR = 2.3, P = 4.4 × 10-14) and negated in the presence of lymph node metastasis (HR = 1.0, P = 0.91). CONCLUSIONS Mutations in KEAP1 and SMARCA4, but not STK11, were associated with metastatic disease and poor OS. Functional STK11 loss, however, may contribute to poor outcomes in KEAP1MUT tumors. Integrating molecular data with clinical and metastatic-site annotations can more accurately risk stratify patients.
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Affiliation(s)
- D Boiarsky
- Department of Medicine, Tufts Medical Center, Boston
| | - C A Lydon
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston
| | - E S Chambers
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - L M Sholl
- Center for Advanced Molecular Diagnostics, Brigham & Women's Hospital & Harvard Medical School, Boston
| | - M Nishino
- Department of Radiology, Brigham and Women's Hospital, Boston
| | - F Skoulidis
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston
| | - J V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston
| | - J Luo
- Department of Medicine, Dana-Farber Cancer Institute, Boston
| | - M M Awad
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston
| | - P A Janne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - E M Van Allen
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston; Broad Institute of Harvard & MIT, Cambridge; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston
| | - D A Barbie
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - N I Vokes
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston; Department of Genomic Medicine, University of Texas M.D. Anderson Cancer Center, Houston, USA.
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125
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Tseng SC, Gagne S, Hatabu H, Lin G, Sholl L, Nishino M. Lung Cancer in Lung Transplant Recipients: Clinical, Radiologic, and Pathologic Characteristics and Treatment Outcome. J Comput Assist Tomogr 2023; 47:590-597. [PMID: 36944140 PMCID: PMC10363202 DOI: 10.1097/rct.0000000000001466] [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] [Indexed: 03/23/2023]
Abstract
OBJECTIVE This study aimed to investigate clinical and radiologic characteristics of lung cancer in lung transplant recipients and evaluate the treatment course and prognosis. METHODS The study included 448 patients who underwent lung transplant between 2005 and 2021. All patients had pretransplant chest computed tomography (CT), 429 patients had posttransplant CT, whereas 19 had no posttransplant CT (median number of posttransplant CT, 6; range, 0-24). Medical records of these patients were reviewed to identify patients who developed lung cancer after lung transplant. Computed tomography and positron emission tomography/CT at the time of lung cancer diagnoses were reviewed to obtain imaging features. Demographics, tumor histology, stages, and survival were compared using Fisher exact test and Wilcoxon rank sum test. RESULTS Among 448 lung transplant recipients with a median follow-up of 71.3 months after lung transplant, 15 patients (3.3%) developed posttransplant lung cancer (13 unilateral, 2 bilateral; 10 men, 5 women; median age, 63.1 years; median time from transplantation to cancer diagnosis, 3.1 years). Twelve cancers were in native lung, and 3 were in transplanted lung. The incidence of lung cancer was higher in single lung transplant recipients than in bilateral lung transplant recipients (10.3% vs 0.6%, respectively; P < 0.0001). Imaging manifestations varied according to tumor stages. Among 12 patients treated for lung cancer, 2 patients developed posttreatment acute respiratory distress syndrome. The median survival from cancer diagnosis of cancer was 6.2 months. CONCLUSIONS Posttransplant lung cancer was noted in 3% of lung transplant recipients and was more common in unilateral transplant recipients. The prognosis upon diagnosis was poor with rapid clinical deterioration and serious posttreatment complications.
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Affiliation(s)
- Shu-Chi Tseng
- Department of Imaging, Dana-Farber Cancer Institute 450 Brookline Ave. Boston MA, 02215, USA
- Department of Radiology, Brigham and Women’s Hospital 75 Francis St. Boston MA, 02215, USA
- Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital at Linkou and Chang Gung University, Taoyuan, Taiwan
| | - Staci Gagne
- Department of Imaging, Dana-Farber Cancer Institute 450 Brookline Ave. Boston MA, 02215, USA
- Department of Radiology, Brigham and Women’s Hospital 75 Francis St. Boston MA, 02215, USA
| | - Hiroto Hatabu
- Department of Imaging, Dana-Farber Cancer Institute 450 Brookline Ave. Boston MA, 02215, USA
- Department of Radiology, Brigham and Women’s Hospital 75 Francis St. Boston MA, 02215, USA
| | - Gigin Lin
- Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital at Linkou and Chang Gung University, Taoyuan, Taiwan
| | - Lynnette Sholl
- Department of Pathology, Brigham and Women’s Hospital 75 Francis St. Boston MA, 02215, USA
| | - Mizuki Nishino
- Department of Imaging, Dana-Farber Cancer Institute 450 Brookline Ave. Boston MA, 02215, USA
- Department of Radiology, Brigham and Women’s Hospital 75 Francis St. Boston MA, 02215, USA
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Theard PL, Linke AJ, Sealover NE, Daley BR, Yang J, Cox K, Kortum RL. SOS2 regulates the threshold of mutant EGFR-dependent oncogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524989. [PMID: 37425733 PMCID: PMC10327037 DOI: 10.1101/2023.01.20.524989] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Son of Sevenless 1 and 2 (SOS1 and SOS2) are RAS guanine nucleotide exchange factors (RasGEFs) that mediate physiologic and pathologic RTK-dependent RAS activation. Here, we show that SOS2 modulates the threshold of epidermal growth factor receptor (EGFR) signaling to regulate the efficacy of and resistance to the EGFR-TKI osimertinib in lung adenocarcinoma (LUAD). SOS2 deletion sensitized EGFR-mutated cells to perturbations in EGFR signaling caused by reduced serum and/or osimertinib treatment to inhibit PI3K/AKT pathway activation, oncogenic transformation, and survival. Bypass RTK reactivation of PI3K/AKT signaling represents a common resistance mechanism to EGFR-TKIs; SOS2 KO reduced PI3K/AKT reactivation to limit osimertinib resistance. In a forced HGF/MET-driven bypass model, SOS2 KO inhibited HGF-stimulated PI3K signaling to block HGF-driven osimertinib resistance. Using a long term in situ resistance assay, a majority of osimertinib resistant cultures exhibited a hybrid epithelial/mesenchymal phenotype associated with reactivated RTK/AKT signaling. In contrast, RTK/AKT-dependent osimertinib resistance was markedly reduced by SOS2 deletion; the few SOS2 KO cultures that became osimertinib resistant primarily underwent non-RTK dependent EMT. Since bypass RTK reactivation and/or tertiary EGFR mutations represent the majority of osimertinib-resistant cancers, these data suggest that targeting SOS2 has the potential to eliminate the majority of osimertinib resistance.
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Affiliation(s)
- Patricia L. Theard
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA 20814
| | - Amanda J. Linke
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA 20814
| | - Nancy E. Sealover
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA 20814
| | - Brianna R. Daley
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA 20814
| | - Johnny Yang
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA 20814
| | - Katherine Cox
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA 20814
| | - Robert L Kortum
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA 20814
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Malapelle U, Tabbò F, Muscarella LA. Editorial: Concomitant pathogenic mutations in oncogene-driven subgroups: when next generation biology meets targeted therapy in NSCLC. Front Oncol 2023; 13:1239304. [PMID: 37427122 PMCID: PMC10325716 DOI: 10.3389/fonc.2023.1239304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Fabrizio Tabbò
- SC Oncologia ASLCN2 Alba e BRA, PO Michele e Pietro Ferrero, Verduno, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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Jin X, Liu D, Kong D, Zhou X, Zheng L, Xu C. Dissecting the alternation landscape of mitochondrial metabolism-related genes in lung adenocarcinoma and their latent mechanisms. Aging (Albany NY) 2023; 15:5482-5496. [PMID: 37335087 PMCID: PMC10333067 DOI: 10.18632/aging.204803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Lung adenocarcinoma (LUAD) is the most common histological subtype of lung cancer with high incidence and unsatisfactory prognosis. The majority of LUAD patients eventually succumb to local and/or distinct metastatic recurrence. Genomic research of LUAD has broadened our understanding of this disease's biology and improved target therapies. However, the alternation landscape and characteristics of mitochondrial metabolism-related genes (MMRGs) in LUAD progression remain poorly understood. We performed a comprehensive analysis to identify the function and mechanism of MMRGs in LUAD based on the TCGA and GEO databases, which might offer therapeutic values for clinical researchers. Then, we figured out three hub prognosis-associated MMRGs (also termed as PMMRGs: ACOT11, ALDH2, and TXNRD1) that were engaged in the evolution of LUAD. To investigate the correlation between clinicopathological characteristics and MMRGs, we divided LUAD samples into two clusters (C1 and C2) based on key MMRGs. In addition, important pathways and the immune infiltration landscape affected by LUAD clusters were also delineated. Further, we nominated potential regulatory mechanisms underlying the MMRGs in LUAD development and progression. In conclusion, our integrative analysis enables a more comprehensive understanding of the mutation landscape of MMRGs in LUAD and provides an opportunity for more precise treatment.
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Affiliation(s)
- Xing Jin
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Di Liu
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Demiao Kong
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Xiaojiang Zhou
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Liken Zheng
- Genecast Biotechnology, Wuxi, Jiangsu Province, China
| | - Chuan Xu
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
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129
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Yoo H, La H, Park C, Yoo S, Lee H, Song H, Do JT, Choi Y, Hong K. Common and distinct functions of mouse Dot1l in the regulation of endothelial transcriptome. Front Cell Dev Biol 2023; 11:1176115. [PMID: 37397258 PMCID: PMC10311421 DOI: 10.3389/fcell.2023.1176115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/06/2023] [Indexed: 07/04/2023] Open
Abstract
Epigenetic mechanisms are mandatory for endothelial called lymphangioblasts during cardiovascular development. Dot1l-mediated gene transcription in mice is essential for the development and function of lymphatic ECs (LECs). The role of Dot1l in the development and function of blood ECs blood endothelial cells is unclear. RNA-seq datasets from Dot1l-depleted or -overexpressing BECs and LECs were used to comprehensively analyze regulatory networks of gene transcription and pathways. Dot1l depletion in BECs changed the expression of genes involved in cell-to-cell adhesion and immunity-related biological processes. Dot1l overexpression modified the expression of genes involved in different types of cell-to-cell adhesion and angiogenesis-related biological processes. Genes involved in specific tissue development-related biological pathways were altered in Dot1l-depleted BECs and LECs. Dot1l overexpression altered ion transportation-related genes in BECs and immune response regulation-related genes in LECs. Importantly, Dot1l overexpression in BECs led to the expression of genes related to the angiogenesis and increased expression of MAPK signaling pathways related was found in both Dot1l-overexpressing BECs and LECs. Therefore, our integrated analyses of transcriptomics in Dot1l-depleted and Dot1l-overexpressed ECs demonstrate the unique transcriptomic program of ECs and the differential functions of Dot1l in the regulation of gene transcription in BECs and LECs.
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Zhang J, Yang T, Han M, Wang X, Yang W, Guo N, Ren Y, Cui W, Li S, Zhao Y, Zhai X, Jia L, Yang J, Wu C, Wang L. Gain-of-function mutations in the catalytic domain of DOT1L promote lung cancer malignant phenotypes via the MAPK/ERK signaling pathway. SCIENCE ADVANCES 2023; 9:eadc9273. [PMID: 37256945 PMCID: PMC10413674 DOI: 10.1126/sciadv.adc9273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
Lung cancer is a lethal malignancy lacking effective therapies. Emerging evidence suggests that epigenetic enzyme mutations are closely related to the malignant phenotype of lung cancer. Here, we identified a series of gain-of-function mutations in the histone methyltransferase DOT1L. The strongest of them is R231Q, located in the catalytic DOT domain. R231Q can enhance the substrate binding ability of DOT1L. Moreover, R231Q promotes cell growth and drug resistance of lung cancer cells in vitro and in vivo. Mechanistic studies also revealed that the R231Q mutant specifically activates the MAPK/ERK signaling pathway by enriching H3K79me2 on the RAF1 promoter and epigenetically regulating the expression of downstream targets. The combination of a DOT1L inhibitor (SGC0946) and a MAPK/ERK axis inhibitor (binimetinib) can effectively reverse the R231Q-induced phenomena. Our results reveal gain-of-function mutations in an epigenetic enzyme and provide promising insights for the precise treatment of lung cancer patients.
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Affiliation(s)
- Jiayu Zhang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Ting Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Mei Han
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Xiaoxuan Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Weiming Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Ning Guo
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Yong Ren
- Department of Pathology, General Hospital of Central Theater Command of People's Liberation Army, Wuhan 430070, China
| | - Wei Cui
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shangxiao Li
- Department of Biochemistry and Molecular Biology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yongshan Zhao
- Department of Biochemistry and Molecular Biology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lina Jia
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jingyu Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Chunfu Wu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lihui Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
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131
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Liu C, Wei X. Unraveling the potential of senescence-related genes in guiding clinical therapy of lung adenocarcinoma patients. Funct Integr Genomics 2023; 23:188. [PMID: 37246190 DOI: 10.1007/s10142-023-01073-5] [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: 12/02/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/30/2023]
Abstract
Lung adenocarcinoma (LUAD) is the most common histological type of lung cancer. In recent years, cell senescence emerges as a potential therapeutic target of cancer therapy. However, the role of cell senescence in LUAD has not been comprehensively unveiled. One single cell RNA sequencing (scRNA-seq) dataset (GSE149655) and two bulk RNA-seq datasets (TCGA and GSE31210) of LUAD were included. Seurat R package was used to process scRNA-seq data and identify immune cell subgroups. Single sample gene set enrichment analysis (ssGSEA) was performed to calculate enrichment score of senescence-related pathways. Senescence-based molecular subtyping for LUAD samples was conducted through unsupervised consensus clustering. pRRophetic package was introduced to analysis drug sensitivity. The senescence-associated risk model was established using univariate regression and stepAIC methods. Western blot, RT-qPCR, immunofluorescence assay and CCK-8 were used to explore the effect of CYCS in LUAD cell lines. Malignant immune cells had remarkedly higher enrichment of senescence-related pathways than non-malignant cells. P53 signaling and DNA damage telomere stress induced senescence pathways were found to be significantly activated in LUAD samples compared with normal samples. We identified two clusters (clust1 and clust2) based on senescence-related genes. Clust1 had severe genomic instability, aggravated senescent features, and low immune and stromal infiltration. The senescence-associated risk model including CASP9, CHEK1, CYCS, SERPINE1, SESN2, TP53I3, LMNB1, RAD50 and TERF2IP, was effective to distinguish high- and low-risk groups. Moreover, low-risk group exhibited sensitive responses to immunotherapy and chemotherapeutic drugs. In vitro experiments results showed that CYCS expression was increased and promoted cell viability in LUAD cell lines. This study explored the important role of senescence in LUAD progression, and confirmed the potential of senescence-related genes in predicting LUAD prognosis and response to immunotherapy and chemotherapy.
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Affiliation(s)
- Chuan Liu
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 59, Haier RoadLaoshan DistrictShandong Province, 266001, Qingdao, China
| | - Xiaojuan Wei
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 59, Haier RoadLaoshan DistrictShandong Province, 266001, Qingdao, China.
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132
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Ouyang H, Li W, Hansen SH. p120 RasGAP and ZO-2 are essential for Hippo signaling and tumor suppressor function mediated by p190A RhoGAP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541483. [PMID: 37292741 PMCID: PMC10245842 DOI: 10.1101/2023.05.22.541483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
ARHGAP35 , which encodes p190A RhoGAP (p190A), is a major cancer gene. p190A is a tumor suppressor that activates the Hippo pathway. p190A was originally cloned via direct binding to p120 RasGAP (RasGAP). Here, we determine that a novel interaction of p190A with the tight junction-associated protein ZO-2 is dependent on RasGAP. We establish that both RasGAP and ZO-2 are necessary for p190A to activate LATS kinases, elicit mesenchymal-to-epithelial transition, promote contact inhibition of cell proliferation and suppress tumorigenesis. Moreover, RasGAP and ZO-2 are required for transcriptional modulation by p190A. Finally, we demonstrate that low ARHGAP35 expression is associated with shorter survival in patients with high, but not low, transcript levels of TJP2 encoding ZO-2. Hence, we define a tumor suppressor interactome of p190A that includes ZO-2, an established constituent of the Hippo pathway, and RasGAP, which despite strong association with Ras signaling, is essential for p190A to activate LATS kinases.
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133
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Yin G, Huang J, Petela J, Jiang H, Zhang Y, Gong S, Wu J, Liu B, Shi J, Gao Y. Targeting small GTPases: emerging grasps on previously untamable targets, pioneered by KRAS. Signal Transduct Target Ther 2023; 8:212. [PMID: 37221195 DOI: 10.1038/s41392-023-01441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 05/25/2023] Open
Abstract
Small GTPases including Ras, Rho, Rab, Arf, and Ran are omnipresent molecular switches in regulating key cellular functions. Their dysregulation is a therapeutic target for tumors, neurodegeneration, cardiomyopathies, and infection. However, small GTPases have been historically recognized as "undruggable". Targeting KRAS, one of the most frequently mutated oncogenes, has only come into reality in the last decade due to the development of breakthrough strategies such as fragment-based screening, covalent ligands, macromolecule inhibitors, and PROTACs. Two KRASG12C covalent inhibitors have obtained accelerated approval for treating KRASG12C mutant lung cancer, and allele-specific hotspot mutations on G12D/S/R have been demonstrated as viable targets. New methods of targeting KRAS are quickly evolving, including transcription, immunogenic neoepitopes, and combinatory targeting with immunotherapy. Nevertheless, the vast majority of small GTPases and hotspot mutations remain elusive, and clinical resistance to G12C inhibitors poses new challenges. In this article, we summarize diversified biological functions, shared structural properties, and complex regulatory mechanisms of small GTPases and their relationships with human diseases. Furthermore, we review the status of drug discovery for targeting small GTPases and the most recent strategic progress focused on targeting KRAS. The discovery of new regulatory mechanisms and development of targeting approaches will together promote drug discovery for small GTPases.
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Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Jing Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Johnny Petela
- Wake Forest University School of Medicine, Winston-Salem, NC, 27101, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Yuetong Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Siqi Gong
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jiaxin Wu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Bei Liu
- National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, 100871, China
| | - Jianyou Shi
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, 610072, China.
| | - Yijun Gao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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134
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Weeden CE, Gayevskiy V, Marceaux C, Batey D, Tan T, Yokote K, Ribera NT, Clatch A, Christo S, Teh CE, Mitchell AJ, Trussart M, Rankin L, Obers A, McDonald JA, Sutherland KD, Sharma VJ, Starkey G, D'Costa R, Antippa P, Leong T, Steinfort D, Irving L, Swanton C, Gordon CL, Mackay LK, Speed TP, Gray DHD, Asselin-Labat ML. Early immune pressure initiated by tissue-resident memory T cells sculpts tumor evolution in non-small cell lung cancer. Cancer Cell 2023; 41:837-852.e6. [PMID: 37086716 DOI: 10.1016/j.ccell.2023.03.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/05/2023] [Accepted: 03/24/2023] [Indexed: 04/24/2023]
Abstract
Tissue-resident memory T (TRM) cells provide immune defense against local infection and can inhibit cancer progression. However, it is unclear to what extent chronic inflammation impacts TRM activation and whether TRM cells existing in tissues before tumor onset influence cancer evolution in humans. We performed deep profiling of healthy lungs and lung cancers in never-smokers (NSs) and ever-smokers (ESs), finding evidence of enhanced immunosurveillance by cells with a TRM-like phenotype in ES lungs. In preclinical models, tumor-specific or bystander TRM-like cells present prior to tumor onset boosted immune cell recruitment, causing tumor immune evasion through loss of MHC class I protein expression and resistance to immune checkpoint inhibitors. In humans, only tumors arising in ES patients underwent clonal immune evasion, unrelated to tobacco-associated mutagenic signatures or oncogenic drivers. These data demonstrate that enhanced TRM-like activity prior to tumor development shapes the evolution of tumor immunogenicity and can impact immunotherapy outcomes.
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Affiliation(s)
- Clare E Weeden
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Velimir Gayevskiy
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Claire Marceaux
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Daniel Batey
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Tania Tan
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Kenta Yokote
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Nina Tubau Ribera
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Allison Clatch
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Susan Christo
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Charis E Teh
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Andrew J Mitchell
- Materials Characterisation and Fabrication Platform, Department of Chemical Engineering, the University of Melbourne, Parkville, VIC, Australia
| | - Marie Trussart
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Lucille Rankin
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Andreas Obers
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jackson A McDonald
- ACRF Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Kate D Sutherland
- ACRF Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Varun J Sharma
- Department of Surgery, the University of Melbourne, Parkville, VIC, Australia; Liver and Intestinal Transplant Unit, Austin Health, Heidelberg, VIC, Australia; Department of Cardiothoracic Surgery, Austin Health, Heidelberg, VIC, Australia
| | - Graham Starkey
- Department of Surgery, the University of Melbourne, Parkville, VIC, Australia; Liver and Intestinal Transplant Unit, Austin Health, Heidelberg, VIC, Australia
| | - Rohit D'Costa
- DonateLife Victoria, Carlton, VIC, Australia; Department of Intensive Care Medicine, Melbourne Health, Melbourne, VIC, Australia
| | - Phillip Antippa
- Department of Surgery, the University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Tracy Leong
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia; Department of Respiratory and Sleep Medicine, Austin Health, Heidelberg, VIC, Australia
| | - Daniel Steinfort
- Department of Medicine, the University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Louis Irving
- Department of Medicine, the University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, UK; University College London Hospitals, London, UK
| | - Claire L Gordon
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia; North Eastern Public Health Unit, Austin Health, Heidelberg, VIC, Australia
| | - Laura K Mackay
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Terence P Speed
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; School of Mathematics and Statistics, the University of Melbourne, Parkville, VIC, Australia
| | - Daniel H D Gray
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia.
| | - Marie-Liesse Asselin-Labat
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia.
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135
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Yang Y, Bhargava D, Chen X, Zhou T, Dursuk G, Jiang W, Wang J, Zong Z, Katz SI, Lomberk GA, Urrutia RA, Katz JP. KLF5 and p53 comprise an incoherent feed-forward loop directing cell-fate decisions following stress. Cell Death Dis 2023; 14:299. [PMID: 37130837 PMCID: PMC10154356 DOI: 10.1038/s41419-023-05731-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 03/01/2023] [Accepted: 03/13/2023] [Indexed: 05/04/2023]
Abstract
In response to stress, cells make a critical decision to arrest or undergo apoptosis, mediated in large part by the tumor suppressor p53. Yet the mechanisms of these cell fate decisions remain largely unknown, particularly in normal cells. Here, we define an incoherent feed-forward loop in non-transformed human squamous epithelial cells involving p53 and the zinc-finger transcription factor KLF5 that dictates responses to differing levels of cellular stress from UV irradiation or oxidative stress. In normal unstressed human squamous epithelial cells, KLF5 complexes with SIN3A and HDAC2 repress TP53, allowing cells to proliferate. With moderate stress, this complex is disrupted, and TP53 is induced; KLF5 then acts as a molecular switch for p53 function by transactivating AKT1 and AKT3, which direct cells toward survival. By contrast, severe stress results in KLF5 loss, such that AKT1 and AKT3 are not induced, and cells preferentially undergo apoptosis. Thus, in human squamous epithelial cells, KLF5 gates the response to UV or oxidative stress to determine the p53 output of growth arrest or apoptosis.
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Affiliation(s)
- Yizeng Yang
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Dharmendra Bhargava
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Xiao Chen
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Taicheng Zhou
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Gizem Dursuk
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Wenpeng Jiang
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Jinshen Wang
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Zhen Zong
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Sharyn I Katz
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Gwen A Lomberk
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Raul A Urrutia
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Jonathan P Katz
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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136
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Härkönen J, Pölönen P, Deen AJ, Selvarajan I, Teppo HR, Dimova EY, Kietzmann T, Ahtiainen M, Väyrynen JP, Väyrynen SA, Elomaa H, Tynkkynen N, Eklund T, Kuopio T, Talvitie EM, Taimen P, Kallajoki M, Kaikkonen MU, Heinäniemi M, Levonen AL. A pan-cancer analysis shows immunoevasive characteristics in NRF2 hyperactive squamous malignancies. Redox Biol 2023; 61:102644. [PMID: 36867945 PMCID: PMC10011429 DOI: 10.1016/j.redox.2023.102644] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
The NRF2 pathway is frequently activated in various cancer types, yet a comprehensive analysis of its effects across different malignancies is currently lacking. We developed a NRF2 activity metric and utilized it to conduct a pan-cancer analysis of oncogenic NRF2 signaling. We identified an immunoevasive phenotype where high NRF2 activity is associated with low interferon-gamma (IFNγ), HLA-I expression and T cell and macrophage infiltration in squamous malignancies of the lung, head and neck area, cervix and esophagus. Squamous NRF2 overactive tumors comprise a molecular phenotype with SOX2/TP63 amplification, TP53 mutation and CDKN2A loss. These immune cold NRF2 hyperactive diseases are associated with upregulation of immunomodulatory NAMPT, WNT5A, SPP1, SLC7A11, SLC2A1 and PD-L1. Based on our functional genomics analyses, these genes represent candidate NRF2 targets, suggesting direct modulation of the tumor immune milieu. Single-cell mRNA data shows that cancer cells of this subtype exhibit decreased expression of IFNγ responsive ligands, and increased expression of immunosuppressive ligands NAMPT, SPP1 and WNT5A that mediate signaling in intercellular crosstalk. In addition, we discovered that the negative relationship of NRF2 and immune cells are explained by stromal populations of lung squamous cell carcinoma, and this effect spans multiple squamous malignancies based on our molecular subtyping and deconvolution data.
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Affiliation(s)
- Jouni Härkönen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland; Department of Pathology, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland
| | - Petri Pölönen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland; Faculty of Health Sciences, Institute of Biomedicine, University of Eastern Finland, Kuopio, 70210, Finland
| | - Ashik Jawahar Deen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland
| | - Ilakya Selvarajan
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland
| | - Hanna-Riikka Teppo
- Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, 90220, Finland; Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, 90570, Finland; Department of Pathology, Oulu University Hospital, Oulu, 90220, Finland
| | - Elitsa Y Dimova
- Faculty of Biochemistry and Molecular Medicine, University of Oulu and Biocenter Oulu, Oulu, 90570, Finland
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, University of Oulu and Biocenter Oulu, Oulu, 90570, Finland
| | - Maarit Ahtiainen
- Department of Education and Research, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland
| | - Juha P Väyrynen
- Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, 90220, Finland; Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, 90570, Finland; Department of Pathology, Oulu University Hospital, Oulu, 90220, Finland
| | - Sara A Väyrynen
- Department of Internal Medicine, Oulu University Hospital, Oulu, 90220, Finland
| | - Hanna Elomaa
- Department of Education and Research, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland; Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40100, Finland
| | - Niko Tynkkynen
- Gerontology Research Center (GEREC), Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Tiia Eklund
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40100, Finland
| | - Teijo Kuopio
- Department of Pathology, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland; Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40100, Finland
| | - Eva-Maria Talvitie
- Department of Genomics, Turku University Hospital and University of Turku, Turku, 20520, Finland
| | - Pekka Taimen
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, 20520, Finland; Department of Pathology, Turku University Hospital, Turku, 20521, Finland
| | - Markku Kallajoki
- Department of Pathology, Turku University Hospital, Turku, 20521, Finland
| | - Minna U Kaikkonen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland
| | - Merja Heinäniemi
- Faculty of Health Sciences, Institute of Biomedicine, University of Eastern Finland, Kuopio, 70210, Finland
| | - Anna-Liisa Levonen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland.
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137
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Adinolfi S, Patinen T, Jawahar Deen A, Pitkänen S, Härkönen J, Kansanen E, Küblbeck J, Levonen AL. The KEAP1-NRF2 pathway: Targets for therapy and role in cancer. Redox Biol 2023; 63:102726. [PMID: 37146513 DOI: 10.1016/j.redox.2023.102726] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023] Open
Abstract
The KEAP1-NRF2 pathway is the key regulator of cellular defense against both extrinsic and intrinsic oxidative and electrophilic stimuli. Since its discovery in the 1990s, its seminal role in various disease pathologies has become well appreciated, motivating research to elucidate the intricacies of NRF2 signaling and its downstream effects to identify novel targets for therapy. In this graphical review, we present an updated overview of the KEAP1-NRF2 signaling, focusing on the progress made within the past ten years. Specifically, we highlight the advances made in understanding the mechanism of activation of NRF2, resulting in novel discoveries in its therapeutic targeting. Furthermore, we will summarize new findings in the rapidly expanding field of NRF2 in cancer, with important implications for its diagnostics and treatment.
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Affiliation(s)
- Simone Adinolfi
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Tommi Patinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Ashik Jawahar Deen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Sini Pitkänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Jouni Härkönen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland; Department of Pathology, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland
| | - Emilia Kansanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland; Science Service Center, Kuopio University Hospital, Kuopio, Finland
| | - Jenni Küblbeck
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland
| | - Anna-Liisa Levonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70210, Kuopio, Finland.
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138
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Shalom B, Salaymeh Y, Risling M, Katzav S. Unraveling the Oncogenic Potential of VAV1 in Human Cancer: Lessons from Mouse Models. Cells 2023; 12:cells12091276. [PMID: 37174676 PMCID: PMC10177506 DOI: 10.3390/cells12091276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
VAV1 is a hematopoietic signal transducer that possesses a GDP/GTP nucleotide exchange factor (GEF) that is tightly regulated by tyrosine phosphorylation, along with adapter protein domains, such as SH2 and SH3. Research on VAV1 has advanced over the years since its discovery as an in vitro activated oncogene in an NIH3T3 screen for oncogenes. Although the oncogenic form of VAV1 first identified in the screen has not been detected in human clinical tumors, its wild-type and mutant forms have been implicated in mammalian malignancies of various tissue origins, as well as those of the hematopoietic system. This review article addresses the activity of human VAV1 as an overexpressed or mutated gene and also describes the differences in the distribution of VAV1 mutations in the hematopoietic system and in other tissues. The knowledge accumulated thus far from GEMMs expressing VAV1 is described, with the conclusion that GEMMs of both wild-type VAV1 and mutant VAV1 do not form tumors, yet these will be generated when additional molecular insults, such as loss of p53 or KRAS mutation, occur.
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Affiliation(s)
- Batel Shalom
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Yaser Salaymeh
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Matan Risling
- Department of Military Medicine and "Tzameret", Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
- Medical Corps, Israel Defense Forces, Tel-Hashomer 02149, Israel
| | - Shulamit Katzav
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
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139
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Amézquita EJ, Nasrin F, Storey KM, Yoshizawa M. Genomics data analysis via spectral shape and topology. PLoS One 2023; 18:e0284820. [PMID: 37099525 PMCID: PMC10132553 DOI: 10.1371/journal.pone.0284820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/09/2023] [Indexed: 04/27/2023] Open
Abstract
Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and to retain information that may be lost using standard dimension-reduction algorithms. We propose a novel workflow to process and analyze RNA-seq data from tumor and healthy subjects integrating Mapper, differential gene expression, and spectral shape analysis. Precisely, we show that a Gaussian mixture approximation method can be used to produce graphical structures that successfully separate tumor and healthy subjects, and produce two subgroups of tumor subjects. A further analysis using DESeq2, a popular tool for the detection of differentially expressed genes, shows that these two subgroups of tumor cells bear two distinct gene regulations, suggesting two discrete paths for forming lung cancer, which could not be highlighted by other popular clustering methods, including t-distributed stochastic neighbor embedding (t-SNE). Although Mapper shows promise in analyzing high-dimensional data, tools to statistically analyze Mapper graphical structures are limited in the existing literature. In this paper, we develop a scoring method using heat kernel signatures that provides an empirical setting for statistical inferences such as hypothesis testing, sensitivity analysis, and correlation analysis.
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Affiliation(s)
- Erik J. Amézquita
- Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, United States of America
| | - Farzana Nasrin
- Department of Mathematics, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Kathleen M. Storey
- Department of Mathematics, Lafayette College, Easton, PA, United States of America
| | - Masato Yoshizawa
- School of Life Sciences, University of Hawaii at Manoa, Honolulu, HI, United States of America
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140
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Hagopian G, Grant C, Nagasaka M. Proteolysis targeting chimeras in non-small cell lung cancer. Cancer Treat Rev 2023; 117:102561. [PMID: 37178629 DOI: 10.1016/j.ctrv.2023.102561] [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: 02/19/2023] [Revised: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023]
Abstract
Non-small cell lung cancer (NSCLC) has very poor prognosis in advanced stages. Discovery and application of therapies targeting specific oncogenic driver mutations has greatly improved overall survival. However, targeted therapies are limited in their efficacy due to resistance mutations that may arise with long term use. Proteolysis targeting Chimeras (PROTACs) are a promising approach to combating resistance mutations. PROTACs commandeer innate ubiquitination machinery to degrade oncogenic proteins. Here we review the PROTACs that have been developed for targeting common EGFR, KRAS, and ALK mutations.
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Affiliation(s)
- Garo Hagopian
- Department of Medicine, University of California Irvine Medical Center, Orange CA, United States
| | - Christopher Grant
- Department of Medicine, University of California Irvine Medical Center, Orange CA, United States
| | - Misako Nagasaka
- Division of Hematology and Oncology, Department of Medicine, University of California Irvine Medical Center, Orange, CA, United States; St. Marianna University School of Medicine, Kawasaki, JAPAN.
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141
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Alizadeh J, Kavoosi M, Singh N, Lorzadeh S, Ravandi A, Kidane B, Ahmed N, Mraiche F, Mowat MR, Ghavami S. Regulation of Autophagy via Carbohydrate and Lipid Metabolism in Cancer. Cancers (Basel) 2023; 15:2195. [PMID: 37190124 PMCID: PMC10136996 DOI: 10.3390/cancers15082195] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 05/17/2023] Open
Abstract
Metabolic changes are an important component of tumor cell progression. Tumor cells adapt to environmental stresses via changes to carbohydrate and lipid metabolism. Autophagy, a physiological process in mammalian cells that digests damaged organelles and misfolded proteins via lysosomal degradation, is closely associated with metabolism in mammalian cells, acting as a meter of cellular ATP levels. In this review, we discuss the changes in glycolytic and lipid biosynthetic pathways in mammalian cells and their impact on carcinogenesis via the autophagy pathway. In addition, we discuss the impact of these metabolic pathways on autophagy in lung cancer.
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Affiliation(s)
- Javad Alizadeh
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada (S.L.)
| | - Mahboubeh Kavoosi
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada (S.L.)
| | - Navjit Singh
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada (S.L.)
| | - Shahrokh Lorzadeh
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada (S.L.)
| | - Amir Ravandi
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St. Boniface Hospital, Winnipeg, MB R2H 2A6, Canada;
| | - Biniam Kidane
- Section of Thoracic Surgery, Department of Surgery, Health Sciences Centre, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 6C5, Canada;
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada; (N.A.)
| | - Naseer Ahmed
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada; (N.A.)
- Department of Radiology, Section of Radiation Oncology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Fatima Mraiche
- College of Pharmacy, QU Health, Qatar University, Doha 2713, Qatar;
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Michael R. Mowat
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada; (N.A.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada (S.L.)
- Research Institute of Oncology and Hematology, Winnipeg, MB R3E 0V9, Canada
- Faculty of Medicine in Zabrze, Academia of Silesia, 41-800 Zabrze, Poland
- Biology of Breathing Theme, Children Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
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142
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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: 71] [Impact Index Per Article: 71.0] [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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Martínez-Ruiz C, Black JRM, Puttick C, Hill MS, Demeulemeester J, Larose Cadieux E, Thol K, Jones TP, Veeriah S, Naceur-Lombardelli C, Toncheva A, Prymas P, Rowan A, Ward S, Cubitt L, Athanasopoulou F, Pich O, Karasaki T, Moore DA, Salgado R, Colliver E, Castignani C, Dietzen M, Huebner A, Al Bakir M, Tanić M, Watkins TBK, Lim EL, Al-Rashed AM, Lang D, Clements J, Cook DE, Rosenthal R, Wilson GA, Frankell AM, de Carné Trécesson S, East P, Kanu N, Litchfield K, Birkbak NJ, Hackshaw A, Beck S, Van Loo P, Jamal-Hanjani M, Swanton C, McGranahan N. Genomic-transcriptomic evolution in lung cancer and metastasis. Nature 2023; 616:543-552. [PMID: 37046093 PMCID: PMC10115639 DOI: 10.1038/s41586-023-05706-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/04/2023] [Indexed: 04/14/2023]
Abstract
Intratumour heterogeneity (ITH) fuels lung cancer evolution, which leads to immune evasion and resistance to therapy1. Here, using paired whole-exome and RNA sequencing data, we investigate intratumour transcriptomic diversity in 354 non-small cell lung cancer tumours from 347 out of the first 421 patients prospectively recruited into the TRACERx study2,3. Analyses of 947 tumour regions, representing both primary and metastatic disease, alongside 96 tumour-adjacent normal tissue samples implicate the transcriptome as a major source of phenotypic variation. Gene expression levels and ITH relate to patterns of positive and negative selection during tumour evolution. We observe frequent copy number-independent allele-specific expression that is linked to epigenomic dysfunction. Allele-specific expression can also result in genomic-transcriptomic parallel evolution, which converges on cancer gene disruption. We extract signatures of RNA single-base substitutions and link their aetiology to the activity of the RNA-editing enzymes ADAR and APOBEC3A, thereby revealing otherwise undetected ongoing APOBEC activity in tumours. Characterizing the transcriptomes of primary-metastatic tumour pairs, we combine multiple machine-learning approaches that leverage genomic and transcriptomic variables to link metastasis-seeding potential to the evolutionary context of mutations and increased proliferation within primary tumour regions. These results highlight the interplay between the genome and transcriptome in influencing ITH, lung cancer evolution and metastasis.
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Affiliation(s)
- 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
| | - 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
| | - Clare Puttick
- 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
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Integrative Cancer Genomics Laboratory, Department of Oncology, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
| | - Elizabeth Larose Cadieux
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Medical Genomics, 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
| | - Thomas P Jones
- 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
| | - Selvaraju Veeriah
- 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
| | - Paulina Prymas
- 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 and 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 and University College London Cancer Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Laura Cubitt
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Foteini Athanasopoulou
- 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 and University College London Cancer Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer 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 and University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer 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 and University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Carla Castignani
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Medical Genomics, 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 Genome Evolution Research Group, 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 and University College London Cancer Institute, London, UK
| | - Ariana Huebner
- 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
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and 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 and University College London Cancer Institute, London, UK
| | - Miljana Tanić
- Medical Genomics, University College London Cancer Institute, London, UK
- Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and 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 and University College London Cancer Institute, London, UK
| | - Ali M Al-Rashed
- Centre for Nephrology, Division of Medicine, University College London, London, UK
| | - Danny Lang
- Scientific Computing STP, Francis Crick Institute, London, UK
| | - James Clements
- Scientific Computing STP, Francis Crick Institute, London, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer 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 and University College London Cancer Institute, London, UK
| | | | - Philip East
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Nnennaya Kanu
- 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
| | - 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 and 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
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Stephan Beck
- Medical Genomics, 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
| | - 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 Medical Oncology, University College London Hospitals, 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 and University College London Cancer Institute, London, UK.
- Department of Medical 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.
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144
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Hayashi T, Kishi M, Takamochi K, Hosoya M, Kohsaka S, Kishikawa S, Ura A, Sano K, Sasahara N, Suehara Y, Takahashi F, Saito T, Suzuki K, Yao T. Expression of paired box 9 defines an aggressive subset of lung adenocarcinoma preferentially occurring in smokers. Histopathology 2023; 82:672-683. [PMID: 36527228 DOI: 10.1111/his.14853] [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: 07/18/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
AIMS A distinct subset of lung adenocarcinomas (LADs), arising from a series of peripheral lung cells defined as the terminal respiratory unit (TRU), is characterised by thyroid transcription factor 1 (TTF-1) expression. The clinical relevance of transcription factors (TFs) other than TTF-1 remains unknown in LAD and was explored in the present study. METHODS AND RESULTS Seventy-one LAD samples were subjected to high-throughput transcriptome screening of LAD using cap analysis gene expression (CAGE) sequencing data; CAGE provides genome-wide expression levels of the transcription start sites (TSSs). In total, 1083 invasive LAD samples were subjected to immunohistochemical examination for paired box 9 (PAX9) and TTF-1 expression levels. PAX9 is an endoderm development-associated TF that most strongly and inversely correlates with the expression of TTF-1 TSS subsets. Immunohistochemically, PAX9 expression was restricted to the nuclei of ciliated epithelial and basal cells in the bronchi and bronchioles and the nuclei of epithelial cells of the bronchial glands; moreover, PAX9 expression was observed in 304 LADs (28%). PAX9-positive LADs were significantly associated with heavy smoking, non-lepidic subtype, EGFR wild-type tumours and PD-L1 expression (all P < 0.0001). All these characteristics were opposite to those of TRU-type LADs with TTF-1 expression. PAX9 expression was an independent prognostic factor for decreased overall survival (P = 0.022). CONCLUSIONS Our results revealed that PAX9 expression defines an aggressive subset of LADs preferentially occurring in smokers that may arise from bronchial or bronchiolar cells.
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Affiliation(s)
- Takuo Hayashi
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Monami Kishi
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Kazuya Takamochi
- Department of General Thoracic Surgery, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Masaki Hosoya
- Department of Medical Oncology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo
| | - Satsuki Kishikawa
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Ayako Ura
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Kei Sano
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo.,Department of Medicine for Orthopaedics and Motor Organ, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Noriko Sasahara
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Yoshiyuki Suehara
- Department of Medicine for Orthopaedics and Motor Organ, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Fumiyuki Takahashi
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Kenji Suzuki
- Department of General Thoracic Surgery, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Takashi Yao
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
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145
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Guo J, Zhao Y, Wu X, Li G, Zhang Y, Song Y, Du Q. Mechanism exploration and prognosis study of Astragali Radix-Spreading hedyotis herb for the treatment of lung adenocarcinoma based on bioinformatics approaches and molecular dynamics simulation. Front Chem 2023; 11:1128671. [PMID: 37065830 PMCID: PMC10090857 DOI: 10.3389/fchem.2023.1128671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Background: Herb pair of Astragali Radix (AR) and Spreading Hedyotis Herb (SH) has been frequently prescribed in clinical for the treatment of lung cancer owing to its favorable efficacy. Yet, the mechanism under the therapeutic effects remained unveiled, which has limited its clinical applications, and new drug development for lung cancer.Methods: The bioactive ingredients of AR and SH were retrieved from the Traditional Chinese Medicine System Pharmacology Database, with the targets of obtained components predicted by Swiss Target Prediction. Genes related to lung adenocarcinoma (LUAD) were acquired from GeneCards, OMIM and CTD databases, with the hub genes of LUAD screened by CTD database. The intersected targets of LUAD and AR-SH were obtained by Venn, with David Database employed to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Survival analysis of the hub genes of LUAD was carried out using TCGA-LUAD dataset. Molecular docking of core proteins and active ingredients was performed by Auto-Dock Vina software, followed by molecular dynamics simulations of protein-ligand complexes with well-docked conformations.Results: 29 active ingredients were screened out with 422 corresponding targets predicted. It is revealed that AR-SH can act on various targets such as EGFR, MAPK1, and KARS by ursolic acid (UA), Astragaloside IV(ASIV), and Isomucronulatol 7,2′-di-O-glucoside (IDOG) to alleviate the symptoms of LUAD. Biological processes involved are protein phosphorylation, negative regulation of apoptotic process, and pathways involved are endocrine resistance, EGFR tyrosine kinase inhibitor resistance, PI3K-Akt, and HIF-1 pathway. Molecular docking analysis indicated that the binding energy of most of the screened active ingredients to proteins encoded by core genes was less than −5.6 kcal/mol, with some active ingredients showing even lower binding energy to EGFR than Gefitinib. Three ligand-receptor complexes including EGFR-UA, MAPK1-ASIV, and KRAS-IDOG were found to bind relatively stable by molecular dynamics simulation, which was consistent with the results of molecule docking.Conclusion: We suggested that the herb pair of AR-SH can act on targets like EGFR, MAPK1 and KRAS by UA, ASIV and IDOG, to play a vital role in the treatment and the enhancement of prognosis of LUAD.
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Affiliation(s)
- Junfeng Guo
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuting Zhao
- Laboratory of Metabolomics and Drug-Induced Liver Injury, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xuanyu Wu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ganggang Li
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuwei Zhang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yang Song
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Correspondence: Yang Song, ; Quanyu Du,
| | - Quanyu Du
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Correspondence: Yang Song, ; Quanyu Du,
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146
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Wang Z, Yuan X, Jiang G, Li Y, Yang F, Wang J, Chen K. Towards the molecular era of discriminating multiple lung cancers. EBioMedicine 2023; 90:104508. [PMID: 36958271 PMCID: PMC10040518 DOI: 10.1016/j.ebiom.2023.104508] [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: 10/22/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
In the era of histopathology-based diagnosis, the discrimination between multiple lung cancers (MLCs) poses significant uncertainties and has thus become a clinical dilemma. However, recent significant advances and increased application of molecular technologies in clonal relatedness assessment have led to more precision in distinguishing between multiple primary lung cancers (MPLCs) and intrapulmonary metastasis (IPMs). This review summarizes recent advances in the molecular identification of MLCs and compares various methods based on somatic mutations, chromosome alterations, microRNAs, and tumor microenvironment markers. The paper also discusses current challenges at the forefront of genomics-based discrimination, including the selection of detection technology, application of next-generation sequencing, and intratumoral heterogeneity (ITH). In summary, this paper highlights an entrance into the primary stage of molecule-based diagnostics.
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Affiliation(s)
- Ziyang Wang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Xiaoqiu Yuan
- Peking University Health Science Center, Beijing, 100191, China
| | - Guanchao Jiang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Yun Li
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Fan Yang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Jun Wang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Kezhong Chen
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
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147
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Spella M, Ntaliarda G, Skiadas G, Lamort AS, Vreka M, Marazioti A, Lilis I, Bouloukou E, Giotopoulou GA, Pepe MAA, Weiss SAI, Petrera A, Hauck SM, Koch I, Lindner M, Hatz RA, Behr J, Arendt KAM, Giopanou I, Brunn D, Savai R, Jenne DE, de Château M, Yull FE, Blackwell TS, Stathopoulos GT. Non-Oncogene Addiction of KRAS-Mutant Cancers to IL-1β via Versican and Mononuclear IKKβ. Cancers (Basel) 2023; 15:1866. [PMID: 36980752 PMCID: PMC10047096 DOI: 10.3390/cancers15061866] [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: 02/16/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Kirsten rat sarcoma virus (KRAS)-mutant cancers are frequent, metastatic, lethal, and largely undruggable. While interleukin (IL)-1β and nuclear factor (NF)-κB inhibition hold promise against cancer, untargeted treatments are not effective. Here, we show that human KRAS-mutant cancers are addicted to IL-1β via inflammatory versican signaling to macrophage inhibitor of NF-κB kinase (IKK) β. Human pan-cancer and experimental NF-κB reporter, transcriptome, and proteome screens reveal that KRAS-mutant tumors trigger macrophage IKKβ activation and IL-1β release via secretory versican. Tumor-specific versican silencing and macrophage-restricted IKKβ deletion prevents myeloid NF-κB activation and metastasis. Versican and IKKβ are mutually addicted and/or overexpressed in human cancers and possess diagnostic and prognostic power. Non-oncogene KRAS/IL-1β addiction is abolished by IL-1β and TLR1/2 inhibition, indicating cardinal and actionable roles for versican and IKKβ in metastasis.
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Affiliation(s)
- Magda Spella
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Giannoula Ntaliarda
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Georgios Skiadas
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Anne-Sophie Lamort
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Malamati Vreka
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Antonia Marazioti
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Ioannis Lilis
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Eleni Bouloukou
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Georgia A. Giotopoulou
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Mario A. A. Pepe
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Stefanie A. I. Weiss
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Agnese Petrera
- Research Unit Protein Science-Core Facility Proteomics, Helmholtz Center Munich–German Research Center for Environmental Health, 80939 Munich, Germany
| | - Stefanie M. Hauck
- Research Unit Protein Science-Core Facility Proteomics, Helmholtz Center Munich–German Research Center for Environmental Health, 80939 Munich, Germany
| | - Ina Koch
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich and Asklepios Medical Center, 82131 Gauting, Germany
| | - Michael Lindner
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich and Asklepios Medical Center, 82131 Gauting, Germany
| | - Rudolph A. Hatz
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich and Asklepios Medical Center, 82131 Gauting, Germany
| | - Juergen Behr
- Department of Internal Medicine V, Ludwig-Maximilian-University of Munich, 81377 Munich, Germany
| | - Kristina A. M. Arendt
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - Ioanna Giopanou
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
| | - David Brunn
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- Frankfurt Cancer Institute (FCI), Goethe University, 60596 Frankfurt am Main, Germany
- Department of Internal Medicine and Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
| | - Dieter E. Jenne
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
- Max-Planck-Institute of Neurobiology, 82152 Planegg, Germany
| | | | - Fiona E. Yull
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Timothy S. Blackwell
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Georgios T. Stathopoulos
- Department of Physiology, Faculty of Medicine, University of Patras, 26504 Rio, Greece
- Comprehensive Pneumology Center and Institute for Lung Biology and Disease, Helmholtz Center Munich-German Research Center for Environmental Health, 81377 Munich, Germany
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
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148
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Eichner LJ, Curtis SD, Brun SN, McGuire CK, Gushterova I, Baumgart JT, Trefts E, Ross DS, Rymoff TJ, Shaw RJ. HDAC3 is critical in tumor development and therapeutic resistance in Kras-mutant non-small cell lung cancer. SCIENCE ADVANCES 2023; 9:eadd3243. [PMID: 36930718 PMCID: PMC10022903 DOI: 10.1126/sciadv.add3243] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
HDAC3 is one of the main targets of histone deacetylase (HDAC) inhibitors in clinical development as cancer therapies, yet the in vivo role of HDAC3 in solid tumors is unknown. We identified a critical role for HDAC3 in Kras-mutant lung cancer. Using genetically engineered mouse models (GEMMs), we found that HDAC3 is required for lung tumor growth in vivo. HDAC3 was found to direct and enhance the transcription effects of the lung cancer lineage transcription factor NKX2-1 to mediate expression of a common set of target genes. We identified FGFR1 as a critical previously unidentified target of HDAC3. Leveraging this, we identified that an HDAC3-dependent transcriptional cassette becomes hyperactivated as Kras/LKB1-mutant cells develop resistance to the MEK inhibitor trametinib, and this can be reversed by treatment with the HDAC1/HDAC3 inhibitor entinostat. We found that the combination of entinostat plus trametinib treatment elicits therapeutic benefit in the Kras/LKB1 GEMM.
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Affiliation(s)
- Lillian J. Eichner
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 E. Superior Street, Chicago, IL USA
| | - Stephanie D. Curtis
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA USA
| | - Sonja N. Brun
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA USA
| | - Caroline K. McGuire
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 E. Superior Street, Chicago, IL USA
| | - Irena Gushterova
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 E. Superior Street, Chicago, IL USA
| | - Joshua T. Baumgart
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA USA
| | - Elijah Trefts
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA USA
| | - Debbie S. Ross
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA USA
| | - Tammy J. Rymoff
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA USA
| | - Reuben J. Shaw
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA USA
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149
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Roberts M, Ogden J, Hossain ASM, Chaturvedi A, Kerr ARW, Dive C, Beane JE, Lopez-Garcia C. Interrogating the precancerous evolution of pathway dysfunction in lung squamous cell carcinoma using XTABLE. eLife 2023; 12:e77507. [PMID: 36892933 PMCID: PMC10038660 DOI: 10.7554/elife.77507] [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: 02/02/2022] [Accepted: 03/09/2023] [Indexed: 03/10/2023] Open
Abstract
Lung squamous cell carcinoma (LUSC) is a type of lung cancer with a dismal prognosis that lacks adequate therapies and actionable targets. This disease is characterized by a sequence of low- and high-grade preinvasive stages with increasing probability of malignant progression. Increasing our knowledge about the biology of these premalignant lesions (PMLs) is necessary to design new methods of early detection and prevention, and to identify the molecular processes that are key for malignant progression. To facilitate this research, we have designed XTABLE (Exploring Transcriptomes of Bronchial Lesions), an open-source application that integrates the most extensive transcriptomic databases of PMLs published so far. With this tool, users can stratify samples using multiple parameters and interrogate PML biology in multiple manners, such as two- and multiple-group comparisons, interrogation of genes of interests, and transcriptional signatures. Using XTABLE, we have carried out a comparative study of the potential role of chromosomal instability scores as biomarkers of PML progression and mapped the onset of the most relevant LUSC pathways to the sequence of LUSC developmental stages. XTABLE will critically facilitate new research for the identification of early detection biomarkers and acquire a better understanding of the LUSC precancerous stages.
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Affiliation(s)
- Matthew Roberts
- Cancer Biomarker Centre, Cancer Research UK Manchester Institute, The University of ManchesterMacclesfieldUnited Kingdom
- Cancer Research UK Lung Cancer Centre of ExcellenceAlderley ParkUnited Kingdom
| | - Julia Ogden
- Cancer Research UK Lung Cancer Centre of ExcellenceAlderley ParkUnited Kingdom
- Translational Lung Cancer Biology Laboratory, Cancer Research UK Manchester Institute, University of ManchesterMacclesfieldUnited Kingdom
| | - AS Mukarram Hossain
- Cancer Biomarker Centre, Cancer Research UK Manchester Institute, The University of ManchesterMacclesfieldUnited Kingdom
- Cancer Research UK Lung Cancer Centre of ExcellenceAlderley ParkUnited Kingdom
| | - Anshuman Chaturvedi
- Cancer Research UK Lung Cancer Centre of ExcellenceAlderley ParkUnited Kingdom
- Department of Histopathology, The Christie HospitalManchesterUnited Kingdom
| | - Alastair RW Kerr
- Cancer Biomarker Centre, Cancer Research UK Manchester Institute, The University of ManchesterMacclesfieldUnited Kingdom
- Cancer Research UK Lung Cancer Centre of ExcellenceAlderley ParkUnited Kingdom
| | - Caroline Dive
- Cancer Biomarker Centre, Cancer Research UK Manchester Institute, The University of ManchesterMacclesfieldUnited Kingdom
- Cancer Research UK Lung Cancer Centre of ExcellenceAlderley ParkUnited Kingdom
| | | | - Carlos Lopez-Garcia
- Cancer Research UK Lung Cancer Centre of ExcellenceAlderley ParkUnited Kingdom
- Translational Lung Cancer Biology Laboratory, Cancer Research UK Manchester Institute, University of ManchesterMacclesfieldUnited Kingdom
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150
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Wang H, Chi L, Yu F, Dai H, Gao C, Si X, Wang Z, Liu L, Zheng J, Shan L, Liu H, Zhang Q. Annual review of KRAS inhibitors in 2022. Eur J Med Chem 2023; 249:115124. [PMID: 36680986 DOI: 10.1016/j.ejmech.2023.115124] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/17/2023]
Abstract
Kirsten rat sarcoma viral (KRAS) oncogene is the most commonly mutated isoform of RAS, accounting for 85% of RAS-driven human cancers. KRAS functioning as a signaling hub participates in multiple cellular signaling pathways and regulates a variety of critical processes such as cell proliferation, differentiation, growth, metabolism and migration. Over the past decades, KRAS oncoprotein has been considered as an "undruggable" target due to its smooth surface and high GTP/GDP affinity. The breakthrough in directly targeting G12C mutated-KRAS and recently approved covalent KRASG12C inhibitors sotorasib and adagrasib broke the myth of KRAS undruggable and confirmed the directly targeting KRAS as one of the most promising strategies for the treatment of cancers. Targeting KRASG12C successfully enriched the understanding of KRAS and brought opportunities for the development of inhibitors to directly target other KRAS mutations. With the stage now set for a new era in the treatment of KRAS-driven cancers, the development of KRAS inhibitors also enters a booming epoch. In this review, we overviewed the research progress of KRAS inhibitors with the potential to treat cancers covering articles published in 2022. The design strategies, discovery processes, structure-activity relationship (SAR) studies, cocrystal structure analysis as well as in vitro and in vivo activity were highlighted with the aim of providing updated sight to accelerate the further development of more potent inhibitors targeting various mutated-KRAS with favorable drug-like properties.
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Affiliation(s)
- Hao Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China
| | - Lingling Chi
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China
| | - Fuqiang Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China
| | - Honglin Dai
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China
| | - Chao Gao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China
| | - Xiaojie Si
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China
| | - Zhengjie Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China
| | - Limin Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China
| | - Jiaxin Zheng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China
| | - Lihong Shan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China.
| | - Hongmin Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, 450052, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China.
| | - Qiurong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province, Zhengzhou, 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China.
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