1
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He Q, Qu M, Xu C, Wu L, Xu Y, Su J, Bao H, Shen T, He Y, Cai J, Xu D, Zeng LH, Wu X. Smoking-induced CCNA2 expression promotes lung adenocarcinoma tumorigenesis by boosting AT2/AT2-like cell differentiation. Cancer Lett 2024; 592:216922. [PMID: 38704137 DOI: 10.1016/j.canlet.2024.216922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024]
Abstract
Lung adenocarcinoma (LUAD), a type of non-small cell lung cancer (NSCLC), originates from not only bronchial epithelial cells but also alveolar type 2 (AT2) cells, which could differentiate into AT2-like cells. AT2-like cells function as cancer stem cells (CSCs) of LUAD tumorigenesis to give rise to adenocarcinoma. However, the mechanism underlying AT2 cell differentiation into AT2-like cells in LUAD remains unknown. We analyze genes differentially expressed and genes with significantly different survival curves in LUAD, and the combination of these two analyses yields 147 differential genes, in which 14 differentially expressed genes were enriched in cell cycle pathway. We next analyze the protein levels of these genes in LUAD and find that Cyclin-A2 (CCNA2) is closely associated with LUAD tumorigenesis. Unexpectedly, high CCNA2 expression in LUAD is restrictedly associated with smoking and independent of other driver mutations. Single-cell sequencing analyses reveal that CCNA2 is predominantly involved in AT2-like cell differentiation, while inhibition of CCNA2 significantly reverses smoking-induced AT2-like cell differentiation. Mechanistically, CCNA2 binding to CDK2 phosphorylates the AXIN1 complex, which in turn induces ubiquitination-dependent degradation of β-catenin and inhibits the WNT signaling pathway, thereby failing AT2 cell maintenance. These results uncover smoking-induced CCNA2 overexpression and subsequent WNT/β-catenin signaling inactivation as a hitherto uncharacterized mechanism controlling AT2 cell differentiation and LUAD tumorigenesis.
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Affiliation(s)
- Qiangqiang He
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Meiyu Qu
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chengyun Xu
- Department of Pharmacology, Hangzhou City University, Hangzhou 310015, China
| | - Lichao Wu
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yana Xu
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jiakun Su
- Technology Center, China Tobacco Jiangxi Industrial Co. Ltd., Nanchang 330096, China
| | - Hangyang Bao
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Tingyu Shen
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yangxun He
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jibao Cai
- Technology Center, China Tobacco Jiangxi Industrial Co. Ltd., Nanchang 330096, China
| | - Da Xu
- Technology Center, China Tobacco Jiangxi Industrial Co. Ltd., Nanchang 330096, China
| | - Ling-Hui Zeng
- Department of Pharmacology, Hangzhou City University, Hangzhou 310015, China.
| | - Ximei Wu
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China; Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China.
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2
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Borja NA, Silva-Smith R, Calfa C, Sussman DA, Tekin M. Triple Primary Cancers: An Analysis of Genetic and Environmental Factors. Cancer Prev Res (Phila) 2024; 17:209-215. [PMID: 38361103 DOI: 10.1158/1940-6207.capr-23-0395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/07/2023] [Accepted: 02/14/2024] [Indexed: 02/17/2024]
Abstract
The occurrence of multiple primary cancers (MPC) is thought to reflect increased cancer susceptibility in patients due to a combination of genetic and environmental factors. Here we conducted a retrospective review of 2,894 consecutive patients evaluated at a single institution and identified 31 (1.14%) individuals with a history of three or more primary cancers, then analyzed the genetic and environmental influences associated with their propensity for developing malignancies. We found that 35.5% of patients had a hereditary cancer syndrome (HCS), with high penetrance HCS in 72.7% of cases, suggesting that monogenic causes underly a significant proportion of triple primary cancer risk. Analysis of cancer frequencies found that the diagnosis of breast cancer was associated with a significantly lower likelihood of HCS, while the diagnosis of colorectal, prostate, and pancreas cancer was associated with a significantly higher likelihood of HCS. Comparison of HCS-positive and HCS-negative patients revealed similar demographic characteristics, mean age at first diagnosis, and family history of cancer. Moreover, no significant differences in lifestyle behaviors, occupational exposures, chronic health conditions, or treatment with chemotherapy and radiation were observed between HCS-positive and -negative groups, though outliers in tobacco smoking, as well as systemic treatment after both first and second primary cancers were observed. These findings indicate a robust contribution of HCS to cancer susceptibility among patients with triple primary cancers while environmental influences were less evident. This emphasizes the need for larger MPC cohorts incorporating additional genetic and environmental factors to more comprehensively characterize drivers of cancer risk. PREVENTION RELEVANCE In patients with three or more primary cancers, genetic predisposition explained a significant proportion of cases; however, treatment history, lifestyle habits, and other exposures appeared to play a less significant role. This highlights the value of early genetic screening and the need to develop more sensitive markers of cancer susceptibility. See related Spotlight, p. 193.
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Affiliation(s)
- Nicholas A Borja
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Rachel Silva-Smith
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Carmen Calfa
- Division of Medical Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Daniel A Sussman
- Division of Digestive Health and Liver Diseases, Miller School of Medicine, University of Miami, Miami, Florida
| | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida
- John P. Hussmann Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
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3
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Hofman P, Berezowska S, Kazdal D, Mograbi B, Ilié M, Stenzinger A, Hofman V. Current challenges and practical aspects of molecular pathology for non-small cell lung cancers. Virchows Arch 2024; 484:233-246. [PMID: 37801103 PMCID: PMC10948551 DOI: 10.1007/s00428-023-03651-1] [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: 08/11/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023]
Abstract
The continuing evolution of treatment options in thoracic oncology requires the pathologist to regularly update diagnostic algorithms for management of tumor samples. It is essential to decide on the best way to use tissue biopsies, cytological samples, as well as liquid biopsies to identify the different mandatory predictive biomarkers of lung cancers in a short turnaround time. However, biological resources and laboratory member workforce are limited and may be not sufficient for the increased complexity of molecular pathological analyses and for complementary translational research development. In this context, the surgical pathologist is the only one who makes the decisions whether or not to send specimens to immunohistochemical and molecular pathology platforms. Moreover, the pathologist can rapidly contact the oncologist to obtain a new tissue biopsy and/or a liquid biopsy if he/she considers that the biological material is not sufficient in quantity or quality for assessment of predictive biomarkers. Inadequate control of algorithms and sampling workflow may lead to false negative, inconclusive, and incomplete findings, resulting in inappropriate choice of therapeutic strategy and potentially poor outcome for patients. International guidelines for lung cancer treatment are based on the results of the expression of different proteins and on genomic alterations. These guidelines have been established taking into consideration the best practices to be set up in clinical and molecular pathology laboratories. This review addresses the current predictive biomarkers and algorithms for use in thoracic oncology molecular pathology as well as the central role of the pathologist, notably in the molecular tumor board and her/his participation in the treatment decision-making. The perspectives in this setting will be discussed.
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Affiliation(s)
- Paul Hofman
- Côte d'Azur University, FHU OncoAge, IHU RespirERA, Laboratory of Clinical and Experimental Pathology, BB-0033-00025, Louis Pasteur Hospital, 30 avenue de la voie romaine, BP69, 06001, Nice cedex 01, France.
- Côte d'Azur University, IRCAN, Inserm, CNRS 7284, U1081, Nice, France.
| | - Sabina Berezowska
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Daniel Kazdal
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Centers for Personalized Medicine (ZPM), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Baharia Mograbi
- Côte d'Azur University, FHU OncoAge, IHU RespirERA, Laboratory of Clinical and Experimental Pathology, BB-0033-00025, Louis Pasteur Hospital, 30 avenue de la voie romaine, BP69, 06001, Nice cedex 01, France
- Côte d'Azur University, IRCAN, Inserm, CNRS 7284, U1081, Nice, France
| | - Marius Ilié
- Côte d'Azur University, FHU OncoAge, IHU RespirERA, Laboratory of Clinical and Experimental Pathology, BB-0033-00025, Louis Pasteur Hospital, 30 avenue de la voie romaine, BP69, 06001, Nice cedex 01, France
- Côte d'Azur University, IRCAN, Inserm, CNRS 7284, U1081, Nice, France
| | - Albrecht Stenzinger
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Centers for Personalized Medicine (ZPM), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Véronique Hofman
- Côte d'Azur University, FHU OncoAge, IHU RespirERA, Laboratory of Clinical and Experimental Pathology, BB-0033-00025, Louis Pasteur Hospital, 30 avenue de la voie romaine, BP69, 06001, Nice cedex 01, France
- Côte d'Azur University, IRCAN, Inserm, CNRS 7284, U1081, Nice, France
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LoPiccolo J, Gusev A, Christiani DC, Jänne PA. Lung cancer in patients who have never smoked - an emerging disease. Nat Rev Clin Oncol 2024; 21:121-146. [PMID: 38195910 PMCID: PMC11014425 DOI: 10.1038/s41571-023-00844-0] [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] [Accepted: 11/28/2023] [Indexed: 01/11/2024]
Abstract
Lung cancer is the most common cause of cancer-related deaths globally. Although smoking-related lung cancers continue to account for the majority of diagnoses, smoking rates have been decreasing for several decades. Lung cancer in individuals who have never smoked (LCINS) is estimated to be the fifth most common cause of cancer-related deaths worldwide in 2023, preferentially occurring in women and Asian populations. As smoking rates continue to decline, understanding the aetiology and features of this disease, which necessitate unique diagnostic and treatment paradigms, will be imperative. New data have provided important insights into the molecular and genomic characteristics of LCINS, which are distinct from those of smoking-associated lung cancers and directly affect treatment decisions and outcomes. Herein, we review the emerging data regarding the aetiology and features of LCINS, particularly the genetic and environmental underpinnings of this disease as well as their implications for treatment. In addition, we outline the unique diagnostic and therapeutic paradigms of LCINS and discuss future directions in identifying individuals at high risk of this disease for potential screening efforts.
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Affiliation(s)
- Jaclyn LoPiccolo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - David C Christiani
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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5
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Daylan AEC, Miao E, Tang K, Chiu G, Cheng H. Lung Cancer in Never Smokers: Delving into Epidemiology, Genomic and Immune Landscape, Prognosis, Treatment, and Screening. Lung 2023; 201:521-529. [PMID: 37973682 DOI: 10.1007/s00408-023-00661-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/19/2023]
Abstract
Lung cancer in never smokers (LCINS) represents a growing and distinct entity within the broader landscape of lung malignancies. This review provides a comprehensive overview of LCINS, encompassing its epidemiologic trends, risk factors, distinct genomic alterations, clinical outcomes and the ongoing initiative aimed at formulating screening guidelines tailored to this unique population. As LCINS continues to gain prominence, understanding its intricate genomic landscape has become pivotal for tailoring effective therapeutic strategies. Moreover, LCINS does not meet the criteria for lung cancer screening as per the current guidelines. Hence, there is an urgent need to explore its heterogeneity in order to devise optimal screening guidelines conducive to early-stage detection. This review underscores the vital importance of detailed research to elucidate the multifaceted nature of LCINS, with the potential to shape future clinical management and screening recommendations for this unique and growing patient cohort.
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Affiliation(s)
- Ayse Ece Cali Daylan
- Department of Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Emily Miao
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kevin Tang
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Grace Chiu
- Scarsdale High School, Scarsdale, NY, USA
| | - Haiying Cheng
- Department of Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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6
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Dong F, Davies KD. Mutational Signatures in Cancer: Laboratory Considerations and Emerging Applications. J Mol Diagn 2023; 25:790-795. [PMID: 37633594 DOI: 10.1016/j.jmoldx.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/29/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023] Open
Abstract
Patterns of somatic mutations have emerged from the broad sequencing of human cancer genomes. These mutational signatures reflect mechanisms of mutagenesis and DNA repair defects and represent an emerging class of cancer biomarkers. The appropriate interpretation of mutational signatures from sequencing assays holds implications in the reporting of molecular diagnostic results for patients with cancer. This brief review describes the scientific principles, laboratory considerations, and emerging clinical applications of mutational signature analysis from clinical cancer genomes.
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Affiliation(s)
- Fei Dong
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
| | - Kurtis D Davies
- Emerging and Evolving Biomarker Content Committee, A Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado-Anschutz Medical Campus, Aurora, Colorado
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7
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Liu C, Li K, Sui Y, Liu H, Zhang Y, Lu Y, Lu W, Chen Y, Wang G, Xu S, Xiang T, Cai Y, Huang K. Different gene alterations in patients with non-small-cell lung cancer between the eastern and southern China. Heliyon 2023; 9:e20171. [PMID: 37767514 PMCID: PMC10520317 DOI: 10.1016/j.heliyon.2023.e20171] [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: 05/05/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Geographical differences are conspicuous in lung cancer, and the distinct molecular features of lung tumor between Western patients and Asian patients have been demonstrated. However, the etiology of non-small-cell lung cancer (NSCLC) and the distribution of associated molecular aberrations in China have not been fully elucidated. The mutational profiles of 12 lung cancer-related genes were investigated in 85 patients from eastern China and 88 patients from southern China who had been histologically confirmed NSCLC. Overall, 93.6% (162/173) of tumor samples harbored at least one somatic alteration. The most frequently mutated genes were TP53 (56.1%), EGFR (50.3%), and KRAS (14.5%). We found that EGFR mutated much more frequently (60.0% vs 40.9%, P = 0.012) and TP53 mutations had significantly lower incidence (47.1% vs 64.8%, P = 0.019) in eastern cohort than that in southern cohort. Mutational signature analysis revealed a region-related mutagenesis mechanism characterized by a high prevalence of C to T transitions mainly occurring at CpG dinucleotides in southern patients. This study reveals the difference in the mutational features between NSCLC patients in eastern and southern China. The distinct patterns of gene mutation could provide clues for the mechanism of carcinogenesis of lung cancer, offering opportunities to stratify patients into optimal treatment plans based on genomic profiles.
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Affiliation(s)
- Chengdong Liu
- Department of thoracic surgery, Naval Medical Center of PLA, 338 Huaihai Road, Changning District, Shanghai 200052, China
| | - Kangbao Li
- Department of Geriatrics, Gastroenterology Ward, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
| | - Yi Sui
- Singlera Genomics Inc., Shanghai 201318, China
| | - Hongmei Liu
- Singlera Genomics Inc., Shanghai 201318, China
| | | | - Yuan Lu
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Wei Lu
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Yongfeng Chen
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Gehui Wang
- Singlera Genomics Inc., Shanghai 201318, China
| | - Suqian Xu
- Singlera Genomics Inc., Shanghai 201318, China
| | | | - Yongguang Cai
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Kenan Huang
- Department of Thoracic Surgery, Shanghai Changzheng Hospital, Navy Military Medical University, 415 Fengyang Road, Huangpu District, Shanghai 200003, China
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
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8
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Shehata SA, Toraih EA, Ismail EA, Hagras AM, Elmorsy E, Fawzy MS. Vaping, Environmental Toxicants Exposure, and Lung Cancer Risk. Cancers (Basel) 2023; 15:4525. [PMID: 37760496 PMCID: PMC10526315 DOI: 10.3390/cancers15184525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/18/2023] [Accepted: 06/22/2023] [Indexed: 09/29/2023] Open
Abstract
Lung cancer (LC) is the second-most prevalent tumor worldwide. According to the most recent GLOBOCAN data, over 2.2 million LC cases were reported in 2020, with an estimated new death incident of 1,796,144 lung cancer cases. Genetic, lifestyle, and environmental exposure play an important role as risk factors for LC. E-cigarette, or vaping, products (EVPs) use has been dramatically increasing world-wide. There is growing concern that EVPs consumption may increase the risk of LC because EVPs contain several proven carcinogenic compounds. However, the relationship between EVPs and LC is not well established. E-cigarette contains nicotine derivatives (e.g., nitrosnornicotine, nitrosamine ketone), heavy metals (including organometal compounds), polycyclic aromatic hydrocarbons, and flavorings (aldehydes and complex organics). Several environmental toxicants have been proven to contribute to LC. Proven and plausible environmental carcinogens could be physical (ionizing and non-ionizing radiation), chemicals (such as asbestos, formaldehyde, and dioxins), and heavy metals (such as cobalt, arsenic, cadmium, chromium, and nickel). Air pollution, especially particulate matter (PM) emitted from vehicles and industrial exhausts, is linked with LC. Although extensive environmental exposure prevention policies and smoking reduction strategies have been adopted globally, the dangers remain. Combined, both EVPs and toxic environmental exposures may demonstrate significant synergistic oncogenicity. This review aims to analyze the current publications on the importance of the relationship between EVPs consumption and environmental toxicants in the pathogenesis of LC.
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Affiliation(s)
- Shaimaa A. Shehata
- Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (S.A.S.); (A.M.H.)
| | - Eman A. Toraih
- Division of Endocrine and Oncologic Surgery, Department of Surgery, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Ezzat A. Ismail
- Department of Urology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
| | - Abeer M. Hagras
- Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (S.A.S.); (A.M.H.)
| | - Ekramy Elmorsy
- Department of Pathology, Faculty of Medicine, Northern Border University, Arar 73213, Saudi Arabia;
- Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Manal S. Fawzy
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar 73213, Saudi Arabia
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Spisak N, de Manuel M, Milligan W, Sella G, Przeworski M. Disentangling sources of clock-like mutations in germline and soma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.07.556720. [PMID: 37745549 PMCID: PMC10515775 DOI: 10.1101/2023.09.07.556720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The rates of mutations vary across cell types. To identify causes of this variation, mutations are often decomposed into a combination of the single base substitution (SBS) "signatures" observed in germline, soma and tumors, with the idea that each signature corresponds to one or a small number of underlying mutagenic processes. Two such signatures turn out to be ubiquitous across cell types: SBS signature 1, which consists primarily of transitions at methylated CpG sites caused by spontaneous deamination, and the more diffuse SBS signature 5, which is of unknown etiology. In cancers, the number of mutations attributed to these two signatures accumulates linearly with age of diagnosis, and thus the signatures have been termed "clock-like." To better understand this clock-like behavior, we develop a mathematical model that includes DNA replication errors, unrepaired damage, and damage repaired incorrectly. We show that mutational signatures can exhibit clock-like behavior because cell divisions occur at a constant rate and/or because damage rates remain constant over time, and that these distinct sources can be teased apart by comparing cell lineages that divide at different rates. With this goal in mind, we analyze the rate of accumulation of mutations in multiple cell types, including soma as well as male and female germline. We find no detectable increase in SBS signature 1 mutations in neurons and only a very weak increase in mutations assigned to the female germline, but a significant increase with time in rapidly-dividing cells, suggesting that SBS signature 1 is driven by rounds of DNA replication occurring at a relatively fixed rate. In contrast, SBS signature 5 increases with time in all cell types, including post-mitotic ones, indicating that it accumulates independently of cell divisions; this observation points to errors in DNA repair as the key underlying mechanism. Thus, the two "clock-like" signatures observed across cell types likely have distinct origins, one set by rates of cell division, the other by damage rates.
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Affiliation(s)
- Natanael Spisak
- Department of Biological Sciences, Columbia University, New York, United States
| | - Marc de Manuel
- Department of Biological Sciences, Columbia University, New York, United States
| | - William Milligan
- Department of Biological Sciences, Columbia University, New York, United States
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, United States
- Department of Systems Biology, Columbia University, New York, United States
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10
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Wang P, Sun S, Lam S, Lockwood WW. New insights into the biology and development of lung cancer in never smokers-implications for early detection and treatment. J Transl Med 2023; 21:585. [PMID: 37653450 PMCID: PMC10472682 DOI: 10.1186/s12967-023-04430-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths worldwide. Despite never smokers comprising between 10 and 25% of all cases, lung cancer in never smokers (LCNS) is relatively under characterized from an etiological and biological perspective. The application of multi-omics techniques on large patient cohorts has significantly advanced the current understanding of LCNS tumor biology. By synthesizing the findings of multi-omics studies on LCNS from a clinical perspective, we can directly translate knowledge regarding tumor biology into implications for patient care. Primarily focused on never smokers with lung adenocarcinoma, this review details the predominance of driver mutations, particularly in East Asian patients, as well as the frequency and importance of germline variants in LCNS. The mutational patterns present in LCNS tumors are thoroughly explored, highlighting the high abundance of the APOBEC signature. Moreover, this review recognizes the spectrum of immune profiles present in LCNS tumors and posits how it can be translated to treatment selection. The recurring and novel insights from multi-omics studies on LCNS tumor biology have a wide range of clinical implications. Risk factors such as exposure to outdoor air pollution, second hand smoke, and potentially diet have a genomic imprint in LCNS at varying degrees, and although they do not encompass all LCNS cases, they can be leveraged to stratify risk. Germline variants similarly contribute to a notable proportion of LCNS, which warrants detailed documentation of family history of lung cancer among never smokers and demonstrates value in developing testing for pathogenic variants in never smokers for early detection in the future. Molecular driver subtypes and specific co-mutations and mutational signatures have prognostic value in LCNS and can guide treatment selection. LCNS tumors with no known driver alterations tend to be stem-like and genes contributing to this state may serve as potential therapeutic targets. Overall, the comprehensive findings of multi-omics studies exert a wide influence on clinical management and future research directions in the realm of LCNS.
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Affiliation(s)
- Peiyao Wang
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Sophie Sun
- Department of Medical Oncology, British Columbia Cancer Agency Vancouver, Vancouver, BC, Canada
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - William W Lockwood
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada.
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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11
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Donker HC, Cuppens K, Froyen G, Groen HJM, Hiltermann TJN, Maes B, Schuuring E, Volders PJ, Lunter GA, van Es B. Reliability of panel-based mutational signatures for immune-checkpoint-inhibition efficacy prediction in non-small cell lung cancer. Lung Cancer 2023; 182:107286. [PMID: 37421934 DOI: 10.1016/j.lungcan.2023.107286] [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: 05/09/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/10/2023]
Abstract
OBJECTIVES Mutational signatures (MS) are gaining traction for deriving therapeutic insights for immune checkpoint inhibition (ICI). We asked if MS attributions from comprehensive targeted sequencing assays are reliable enough for predicting ICI efficacy in non-small cell lung cancer (NSCLC). METHODS Somatic mutations of m = 126 patients were assayed using panel-based sequencing of 523 cancer-related genes. In silico simulations of MS attributions for various panels were performed on a separate dataset of m = 101 whole genome sequenced patients. Non-synonymous mutations were deconvoluted using COSMIC v3.3 signatures and used to test a previously published machine learning classifier. RESULTS The ICI efficacy predictor performed poorly with an accuracy of 0.51-0.09+0.09, average precision of 0.52-0.11+0.11, and an area under the receiver operating characteristic curve of 0.50-0.09+0.10. Theoretical arguments, experimental data, and in silico simulations pointed to false negative rates (FNR) related to panel size. A secondary effect was observed, where deconvolution of small ensembles of point mutations lead to reconstruction errors and misattributions. CONCLUSION MS attributions from current targeted panel sequencing are not reliable enough to predict ICI efficacy. We suggest that, for downstream classification tasks in NSCLC, signature attributions be based on whole exome or genome sequencing instead.
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Affiliation(s)
- H C Donker
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany.
| | - K Cuppens
- Department of Pulmonology and Thoracic Oncology, Jessa Hospital, Hasselt, Belgium; Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Faculty of Medicine and Life Sciences - LCRC, Hasselt University, Diepenbeek, Belgium.
| | - G Froyen
- Faculty of Medicine and Life Sciences - LCRC, Hasselt University, Diepenbeek, Belgium; Laboratory of Molecular Diagnostics, Dept Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - H J M Groen
- Department of Pulmonary Diseases, University of Groningen and University Medical Center Groningen, the Netherlands.
| | - T J N Hiltermann
- Department of Pulmonary Diseases, University of Groningen and University Medical Center Groningen, the Netherlands.
| | - B Maes
- Faculty of Medicine and Life Sciences - LCRC, Hasselt University, Diepenbeek, Belgium; Laboratory of Molecular Diagnostics, Dept Clinical Biology, Jessa Hospital, Hasselt, Belgium.
| | - E Schuuring
- Department of Pathology, University of Groningen and University Medical Center Groningen, the Netherlands.
| | - P-J Volders
- Laboratory of Molecular Diagnostics, Dept Clinical Biology, Jessa Hospital, Hasselt, Belgium.
| | - G A Lunter
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK.
| | - B van Es
- Central Diagnostic Laboratory, University Medical Centre Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA Utrecht, the Netherlands; MedxAI, Theophile de Bockstraat 77-1, 1058VA Amsterdam, the Netherlands.
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Cha YJ, Kim EY, Choi YJ, Kim CY, Park MK, Chang YS. Accumulation of plasmacytoid dendritic cell is associated with a treatment response to DNA-damaging treatment and favorable prognosis in lung adenocarcinoma. Front Immunol 2023; 14:1154881. [PMID: 37435086 PMCID: PMC10330699 DOI: 10.3389/fimmu.2023.1154881] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/08/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Favorable responses to the treatment including immune checkpoint inhibitors (ICIs) have been consistently reported in lung cancer with smoking history. As the tumor microenvironment (TME) may be involved in the treatment response to ICIs, we aimed to investigate the TME of lung cancer with different smoking status. Methods Lung adenocarcinoma (LUAD) tissue (Tu) and adjacent normal-appearing lung tissue (NL) from current and never smokers were investigated by single-cell RNA sequencing and immunofluorescence and immunohistochemical staining. The clinical implications of identified biomarkers were validated using open-source datasets. Results The lungs of smokers had an increased proportion of innate immune cells in NL tissues, whereas Tu tissues had a lower proportion of these cells than those of non-smokers. Monocyte-derived macrophages (mono-Mc), CD163-LGMN macrophages, monocyte-derived dendritic cells (DCs), and plasmacytoid DCs (pDCs) were significantly enriched in smokers' Tu. Among these clusters, pDCs, specifically enriched in the Tu of smokers. The expression of representative pDC markers, leukocyte immunoglobulin-like receptor A4 (LILRA4) and Toll-like receptor 9 (TLR9), was increased in the stromal cells of LUAD in patients with a smoking history. In an animal model of lung cancer, ionizing radiation induced robust TLR9 expressing immune cells in peritumoral area. Survival analysis using a TCGA-LUAD dataset indicated that patients overexpressing pDC markers exhibited superior clinical outcomes to age-, sex-, and smoking-matched control groups. Top 25% patients with high TLR9 expression exhibited significantly higher tumor mutational burden than that of low TLR9 expression group (bottom 25% patients) (5.81 mutations/Mb vs 4.36 mutations/Mb; P = 0.0059, Welch's two-sample t-test). Conclusion There is an increased pDC in the TME of smokers' lung cancer, and the response of pDC to DNA damaging treatment would lead a conducive environment to ICIs containing regimens. These findings suggest that R&D that induces an increase in the activated pDC population is continuously required to enhance therapeutic effectiveness of ICIs-containing therapies in lung cancer.
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Affiliation(s)
- Yoon Jin Cha
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eun Young Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yong Jun Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Chi Young Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Min Kyung Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yoon Soo Chang
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
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Moreira AL, Sabari JK. Seeing Beyond the Smoke: Reclassifying Lung Cancer by Smoking-Related Mutational Signatures. J Thorac Oncol 2023; 18:396-398. [PMID: 36990571 DOI: 10.1016/j.jtho.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 03/29/2023]
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