1
|
Liu Z, Zheng Y, Yuan M, Zhang G, Yang G. Association of CTACK, IL-2, and IL-13 with increased risk of lung cancer: A Mendelian randomization study. Cytokine 2024; 181:156680. [PMID: 38885591 DOI: 10.1016/j.cyto.2024.156680] [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: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND In recent years, relevant studies have reported that inflammatory cytokines are related to the occurrence of cancer. However, the correlation with lung cancer is not clear. This study used the Mendelian random grouping method to investigate the correlation between inflammatory factors and lung cancer in different populations. METHODS We obtained the single nucleotide polymorphisms (SNPs) of inflammatory cytokines through the open database and the SNPs of lung cancer (European and East Asian) through the IEU OpenGWAS project. Inverse variance-weighted (IVW) MR analyses were used to determine the causalities of exposures and outcomes. Supplementary analyses were also performed using weighted median and MR-Egger regressions. Afterward, sensitivity analyses were performed to test the robustness. Search the ChEMBL database for target drugs and indications for CTACK, IL-2, and IL-13. RESULTS By IVW method, we found that CTACK, IL-2, and IL-13 were associated with an increased risk of lung cancer in the European population (CTACK, OR = 1.098, 95 % CI 1.001-1.204, P = 0.047; IL-2, OR = 1.112, 95 % CI 1.009-1.225, P = 0.032; IL-13, OR = 1.068, 95 % CI 1.007-1.132, P = 0.029), while only IL-13 was associated with an increased risk of lung cancer in the East Asian population (IL-13, OR = 1.110, 95 % CI 1.010-1.220, P = 0.030). The weighted median and MR-Egger regression methods were in the same direction as the IVW effect sizes. Furthermore, no evidence of multidirectionality was detected using the MR-Egger intercept as a sensitivity analysis. Currently, there are no approved or phase III studied indications for CTACK, IL-2, and IL-13 targets in lung cancer. CONCLUSION The study outcomes supported that the inflammatory cytokines CTACK, IL-2, and IL-13 increase the risk of lung cancer. There is a lack of indications for drugs in these three targets. We explored the causal relationship between inflammatory cytokines and lung cancer, providing a basis for future cancer prediction models and targets for anti-tumor therapy.
Collapse
Affiliation(s)
- Zishen Liu
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yingying Zheng
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Mengqi Yuan
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Ganlin Zhang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.
| | - Guowang Yang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.
| |
Collapse
|
2
|
Lahmadi M, Beddar L, Ketit S, Makhbouche T, Laouar N, Filali T. Clinicopathological characteristics and prognosis of non-small cell lung cancer in Algeria: a single-center retrospective study. BMC Cancer 2024; 24:946. [PMID: 39095812 PMCID: PMC11297703 DOI: 10.1186/s12885-024-12709-5] [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: 11/28/2023] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Lung cancer is the most commonly diagnosed cancer and the leading cause of cancer-related death in men in Algeria. Little is known about the characteristics of lung cancer in Algeria. This study aimed to determine the clinicopathological characteristics and prognosis of non-small cell lung cancer (NSCLC) patients in Algeria. METHODS This retrospective study was performed on 269 pathologically confirmed cases of NSCLC at the Benbadis University Hospital of Constantine (2015-2023). Of these, 95 patients were included in the survival analysis. The clinicopathological and outcome data were investigated based on the patients' medical records. RESULTS This study showed male predominance with sex ratio of 5.7, with a mean age of 61.8 years. Histologically, 67.3% of cases had adenocarcinoma (ADC) and 22.7% squamous cell carcinoma (SCC). ADC and SCC occurred more frequently in female (p = 0.02) and male (p = 0.003) patients, respectively. Smoking was estimated at 82.2% in men. Over 28% were non-smokers, of which 50.7% were women, and presented at younger age (p = 0.04). Most of our patients (75.5%) have an advanced stage at diagnosis. Around 70% of patients underwent chemotherapy (CT) as first-line treatment, with medians diagnostic and treatment delays of 4 and 1 months, respectively. The median overall survival (mOS) was estimated at 10.3 and 6.7 months in I-III and IV stages, respectively. Other factors that negatively impact OS were age > 65 years (p = 0.01), and the presence of symptoms (p = 0.005) and comorbidity (p = 0.004) in stage IV, and delayed treatment (p = 0.03) and receiving CT alone (p = 0.03) in stages I-III cases. Medians progression free survival (mPFS) in stage IV, III, and II patients were 4.1, 5.2, and 8.3 months, respectively, and negatively affected by the comorbidity (stage IV, p = 0.03) and receiving CT alone (stages II-III, p = 0.03). CONCLUSIONS NSCLC presents at an early age and advanced stage in Algerian patients. ADC is the most frequent histological subtype and smoking remains the most important risk factor in men. Furthermore, the prognostic factors affecting survival are stage, age, comorbidity, symptoms, and treatment. Thus, tobacco control, early detection program, and access to novel therapies may be the best strategies to reduce NSCLC morbidity and mortality.
Collapse
Affiliation(s)
- Mohamed Lahmadi
- Division of Biotechnology and Health, Biotechnology Research Centre (CRBt), Constantine, Algeria.
| | - Leila Beddar
- Department of Anatomical Pathology, Benbadis Hospital, University Constantine 3, Constantine, Algeria
| | - Souad Ketit
- Department of Anatomical Pathology, Benbadis Hospital, University Constantine 3, Constantine, Algeria
| | - Tarek Makhbouche
- Department of Thoracic Surgery, Benbadis Hospital, University Constantine 3, Constantine, Algeria
| | - Narriman Laouar
- Department of Medical Oncology, Benbadis Hospital, University Constantine 3, Constantine, Algeria
| | - Taha Filali
- Department of Medical Oncology, Benbadis Hospital, University Constantine 3, Constantine, Algeria
| |
Collapse
|
3
|
Leong TL, Steinfort DP. Contemporary Concise Review 2023: Advances in lung cancer and interventional pulmonology. Respirology 2024; 29:665-673. [PMID: 38960450 DOI: 10.1111/resp.14789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
Eligibility criteria for lung cancer screening increasingly need to consider family history of lung cancer, as well as age and smoking status. Lung cancer screening will reveal a multitude of incidental findings, of variable clinical significance, and with a need for clear pathways of management. Pulmonary nodule sampling is enhanced by intra-procedural imaging and cutting-edge robotic technology. Systematic thoracic lymph node sampling has implications for treatment efficacy. Bronchoscopic ablative techniques are feasible for peripheral lung cancers. Bronchoscopic sampling continues to have a high yield for lung cancer molecular characterization. Immunotherapy indications have expanded to include early stage and resectable lung cancer.
Collapse
Affiliation(s)
- Tracy L Leong
- Department of Respiratory Medicine, Austin Health, Heidelberg, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- Melbourne Medical School, University of Melbourne, Parkville, Victoria, Australia
| | - Daniel P Steinfort
- Melbourne Medical School, University of Melbourne, Parkville, Victoria, Australia
- Department of Respiratory Medicine, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| |
Collapse
|
4
|
Patel AJ, Hemead H, Jesani H, Bille A, Taniere P, Middleton G. Squamous Cell Carcinoma in Never Smokers: An Insight into SMARCB1 Loss. Int J Mol Sci 2024; 25:8165. [PMID: 39125735 PMCID: PMC11311737 DOI: 10.3390/ijms25158165] [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: 07/09/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
Lung cancer remains the leading cause of cancer-related mortality worldwide, with non-small cell lung cancer (NSCLC) constituting 85% of cases. Among NSCLCs, squamous cell carcinoma (SqCC) is strongly associated with smoking. However, lung cancer in never smokers (LCINS) represents approximately 25% of lung cancer cases globally and shows increasing incidence, particularly in East Asia. LCINS-SqCC is less well-characterized, especially regarding its genomic alterations and their impact on clinical outcomes. We conducted a retrospective analysis over a 20-year period (July 2003-July 2023) at two major tertiary centers in the UK. The cohort included 59 patients with LCINS-SqCC who underwent radical surgical resection. Data collected included demographic information, comorbidities, histopathological details, and outcome metrics such as disease-free and overall survival. Molecular sequencing of tumor specimens was performed to identify genomic aberrations. The cohort had a median age of 71 years (IQR 62-77) and a median BMI of 25.4 (IQR 22.8-27.8), with a slight male predominance (53%). The majority of patients (93%) had a preoperative MRC of 1-2. Recurrent disease was observed in 23 patients (39%), and 32 patients (54%) had died at a median follow-up of 3 years. Median disease-free survival was 545 days (IQR 132-1496), and overall survival was 888 days (IQR 443-2071). Preoperative creatinine levels were higher in patients who experienced recurrence (p = 0.037). Molecular analysis identified biallelic SMARCB1 loss in two younger patients, associated with rapid disease progression despite R0 resection. These patients' tumors were PDL1-negative, TTF-1-negative, and positive for cytokeratin, CD56, and p40. SMARCB1-deficient SqCC in never smokers represents a highly aggressive variant with poor disease-free survival, highlighting the importance of integrating advanced molecular diagnostics in clinical practice. This study underscores the necessity for personalized treatment strategies, including targeted therapies such as EZH2 inhibitors and immune checkpoint blockade, to address the unique molecular pathways in SMARCB1-deficient cancers. Further clinical trials are essential to optimize therapeutic approaches for this challenging subgroup of lung cancer.
Collapse
Affiliation(s)
- Akshay J. Patel
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK;
- Department of Thoracic Surgery, University Hospitals Birmingham, Birmingham B15 2GW, UK; (H.H.); (H.J.)
| | - Hanan Hemead
- Department of Thoracic Surgery, University Hospitals Birmingham, Birmingham B15 2GW, UK; (H.H.); (H.J.)
| | - Hannah Jesani
- Department of Thoracic Surgery, University Hospitals Birmingham, Birmingham B15 2GW, UK; (H.H.); (H.J.)
| | - Andrea Bille
- Department of Thoracic Surgery, Guy’s Hospital, Guy’s and St. Thomas’ NHS Foundation Trust, London SE1 9RT, UK;
| | - Philippe Taniere
- Department of Cellular Histopathology, University Hospitals Birmingham, Birmingham B15 2GW, UK;
| | - Gary Middleton
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK;
| |
Collapse
|
5
|
Zandwijk NV, Frank AL, Reid G, Dimitri Røe O, Amos CI. Asbestos-Related lung Cancer: An underappreciated oncological issue. Lung Cancer 2024; 194:107861. [PMID: 39003938 DOI: 10.1016/j.lungcan.2024.107861] [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: 12/11/2023] [Revised: 06/19/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024]
Abstract
Asbestos, a group of class I (WHO) carcinogenic fibers, is the main cause of mesothelioma. Asbestos inhalation also increases the risk to develop other solid tumours with lung cancer as the most prominent example [91]. The incidence of asbestos-related lung cancer (ARLC) is estimated to be to six times larger than the mesothelioma incidence thereby becoming an important health issue [86]. Although the pivotal role of asbestos in inducing lung cancer is well established, the precise causal relationships between exposures to asbestos, tobacco smoke, radon and 'particulate' (PM2.5) air pollution remain obscure and new knowledge is needed to establish appropriate preventive measures and to tailor existing screening practices[22,61,65]. We hypothesize that a part of the increasing numbers of lung cancer diagnoses in never-smokers can be explained by (historic and current) exposures to asbestos as well as combinations of different forms of air pollution (PM2.5, asbestos and silica).
Collapse
Affiliation(s)
- Nico van Zandwijk
- Sydney Local Health District (SLHD), Department of Cell and Molecular Therapies, Royal, Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia.
| | - Arthur L Frank
- School of Public Health of Drexel, University, Philadelphia, PA, USA
| | - Glen Reid
- Department of Pathology, Otago Medical, School, University of Otago, Dunedin, New Zealand
| | - Oluf Dimitri Røe
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | |
Collapse
|
6
|
Mochizuki A, Shiraishi K, Honda T, Higashiyama RI, Sunami K, Matsuda M, Shimada Y, Miyazaki Y, Yoshida Y, Watanabe SI, Yatabe Y, Hamamoto R, Kohno T. Passive Smoking-Induced Mutagenesis as a Promoter of Lung Carcinogenesis. J Thorac Oncol 2024; 19:984-994. [PMID: 38382595 DOI: 10.1016/j.jtho.2024.02.006] [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: 09/01/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/23/2024]
Abstract
INTRODUCTION The International Agency for Research on Cancer has classified passive smoking (PS) or secondhand smoke exposure as a group 1 carcinogen linked to lung cancer. However, in contrast to active smoking, the mutagenic properties of PS remain unclear. METHODS A consecutive cohort of 564 lung adenocarcinoma samples from female never-smokers, who provided detailed information about their exposure to PS during adolescence and in their thirties through a questionnaire, was prepared. Of these, all 291 cases for whom frozen tumor tissues were available were subjected to whole exome sequencing to estimate tumor mutational burden, and the top 84 cases who were exposed daily, or not, to PS during adolescence, in their thirties or in both periods, were further subjected to whole genome sequencing. RESULTS A modest yet statistically significant increase in tumor mutational burden was observed in the group exposed to PS compared with the group not exposed to PS (median values = 1.44 versus 1.29 per megabase, respectively; p = 0.020). Instead of inducing driver oncogene mutations, PS-induced substantial subclonal mutations exhibiting APOBEC-type signatures, including SMAD4 and ADGRG6 hotspot mutations. A polymorphic APOBEC3A/3B allele-specific to the Asian population that leads to up-regulated expression of APOBEC3A accentuated the mutational load in individuals exposed daily to PS during adolescence. CONCLUSIONS This study reveals that PS-induced mutagenesis can promote lung carcinogenesis. The APOBEC3A/3B polymorphism may serve as a biomarker for identifying passive nonsmoking individuals at high risk of developing lung cancer.
Collapse
Affiliation(s)
- Akifumi Mochizuki
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan; Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Takayuki Honda
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Kuniko Sunami
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Maiko Matsuda
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoko Shimada
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yukihiro Yoshida
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Yatabe
- Department of Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan.
| |
Collapse
|
7
|
Cavagna RDO, Escremim de Paula F, Berardinelli GN, Bonatelli M, Santana I, Albino da Silva EC, Teixeira GR, Zaniolo BG, Mourão Dias J, Ferreira da Silva FA, Baston Silva CE, Guimarães MGB, Barone CP, Jacinto AA, Noleto da Nóbrega Oliveira RE, Miziara JE, De Marchi P, Molina-Vila MA, Leal LF, Reis RM. Molecular profile of driver genes in lung adenocarcinomas of Brazilian patients who have never smoked: implications for targeted therapies. Oncologist 2024:oyae129. [PMID: 38944844 DOI: 10.1093/oncolo/oyae129] [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: 10/20/2023] [Accepted: 05/10/2024] [Indexed: 07/02/2024] Open
Abstract
INTRODUCTION Lung cancer in never-smoker (LCINS) patients accounts for 20% of lung cancer cases, and its biology remains poorly understood, particularly in genetically admixed populations. We elucidated the molecular profile of driver genes in Brazilian LCINS. METHODS The mutational and gene fusion status of 119 lung adenocarcinomas from self-reported never-smoker patients, was assessed using targeted sequencing (NGS), nCounter, and immunohistochemistry. A panel of 46 ancestry-informative markers determined patients' genetic ancestry. RESULTS The most frequently mutated gene was EGFR (49.6%), followed by TP53 (39.5%), ALK (12.6%), ERBB2 (7.6%), KRAS (5.9%), PIK3CA (1.7%), and less than 1% alterations in RET, NTRK1, MET∆ex14, PDGFRA, and BRAF. Except for TP53 and PIK3CA, all other alterations were mutually exclusive. Genetic ancestry analysis revealed a predominance of European (71.1%), and a higher African ancestry was associated with TP53 mutations. CONCLUSION Brazilian LCINS exhibited a similar molecular profile to other populations, except the increased ALK and TP53 alterations. Importantly, 73% of these patients have actionable alterations that are suitable for targeted treatments.
Collapse
Affiliation(s)
| | | | | | - Murilo Bonatelli
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
| | - Iara Santana
- Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Gustavo Ramos Teixeira
- Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
- Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - Beatriz Garbe Zaniolo
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, Brazil
| | | | | | | | | | | | | | | | - José Elias Miziara
- Deparment of Thoracic Surgery, Barretos Cancer Hospital, Barretos, Brazil
| | - Pedro De Marchi
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Oncoclinicas, Rio de Janeiro, Brazil
| | - Miguel A Molina-Vila
- Laboratory of Oncology/Pangaea Oncology, Dexeus University Hospital, Barcelona, Spain
| | - Letícia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| |
Collapse
|
8
|
Jayakrishnan R, Kwiatkowski DJ, Rose MG, Nassar AH. Topography of mutational signatures in non-small cell lung cancer: emerging concepts, clinical applications, and limitations. Oncologist 2024:oyae091. [PMID: 38907669 DOI: 10.1093/oncolo/oyae091] [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: 12/08/2023] [Accepted: 04/16/2024] [Indexed: 06/24/2024] Open
Abstract
The genome of a cell is continuously battered by a plethora of exogenous and endogenous processes that can lead to damaged DNA. Repair mechanisms correct this damage most of the time, but failure to do so leaves mutations. Mutations do not occur in random manner, but rather typically follow a more or less specific pattern due to known or imputed mutational processes. Mutational signature analysis is the process by which the predominant mutational process can be inferred for a cancer and can be used in several contexts to study both the genesis of cancer and its response to therapy. Recent pan-cancer genomic efforts such as "The Cancer Genome Atlas" have identified numerous mutational signatures that can be categorized into single base substitutions, doublet base substitutions, or small insertions/deletions. Understanding these mutational signatures as they occur in non-small lung cancer could improve efforts at prevention, predict treatment response to personalized treatments, and guide the development of therapies targeting tumor evolution. For non-small cell lung cancer, several mutational signatures have been identified that correlate with exposures such as tobacco smoking and radon and can also reflect endogenous processes such as aging, APOBEC activity, and loss of mismatch repair. Herein, we provide an overview of the current knowledge of mutational signatures in non-small lung cancer.
Collapse
Affiliation(s)
- Ritujith Jayakrishnan
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - David J Kwiatkowski
- Department of Pulmonary Medicine, Brigham and Women's Hospital, Boston, MA, 02115, United States
| | - Michal G Rose
- Yale University School of Medicine and Cancer Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516, United States
- Department of Medicine, Medical Oncology Division, Yale Cancer Center, New Haven, CT, United States
| | - Amin H Nassar
- Yale University School of Medicine and Cancer Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516, United States
| |
Collapse
|
9
|
Li Y, Zhu R, Jin J, Guo H, Zhang J, He Z, Liang T, Guo L. Exploring the Role of Clustered Mutations in Carcinogenesis and Their Potential Clinical Implications in Cancer. Int J Mol Sci 2024; 25:6744. [PMID: 38928450 PMCID: PMC11203652 DOI: 10.3390/ijms25126744] [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: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Abnormal cell proliferation and growth leading to cancer primarily result from cumulative genome mutations. Single gene mutations alone do not fully explain cancer onset and progression; instead, clustered mutations-simultaneous occurrences of multiple mutations-are considered to be pivotal in cancer development and advancement. These mutations can affect different genes and pathways, resulting in cells undergoing malignant transformation with multiple functional abnormalities. Clustered mutations influence cancer growth rates, metastatic potential, and drug treatment sensitivity. This summary highlights the various types and characteristics of clustered mutations to understand their associations with carcinogenesis and discusses their potential clinical significance in cancer. As a unique mutation type, clustered mutations may involve genomic instability, DNA repair mechanism defects, and environmental exposures, potentially correlating with responsiveness to immunotherapy. Understanding the characteristics and underlying processes of clustered mutations enhances our comprehension of carcinogenesis and cancer progression, providing new diagnostic and therapeutic approaches for cancer.
Collapse
Affiliation(s)
- Yi Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Rui Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Haochuan Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaxi Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Zhiheng He
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| |
Collapse
|
10
|
Huang CY, Jiang N, Shen M, Lai GG, Tan AC, Jain A, Saw SP, Ang MK, Ng QS, Lim DW, Kanesvaran R, Tan EH, Tan WL, Ong BH, Chua KL, Anantham D, Takano AM, Lim KH, Tam WL, Sim NL, Skanderup AJ, Tan DS, Rozen SG. Oncogene-Driven Non-Small Cell Lung Cancers in Patients with a History of Smoking Lack Smoking-Induced Mutations. Cancer Res 2024; 84:2009-2020. [PMID: 38587551 DOI: 10.1158/0008-5472.can-23-2551] [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: 09/01/2023] [Revised: 12/29/2023] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
Non-small cell lung cancers (NSCLC) in nonsmokers are mostly driven by mutations in the oncogenes EGFR, ERBB2, and MET and fusions involving ALK and RET. In addition to occurring in nonsmokers, alterations in these "nonsmoking-related oncogenes" (NSRO) also occur in smokers. To better understand the clonal architecture and genomic landscape of NSRO-driven tumors in smokers compared with typical-smoking NSCLCs, we investigated genomic and transcriptomic alterations in 173 tumor sectors from 48 NSCLC patients. NSRO-driven NSCLCs in smokers and nonsmokers had similar genomic landscapes. Surprisingly, even in patients with prominent smoking histories, the mutational signature caused by tobacco smoking was essentially absent in NSRO-driven NSCLCs, which was confirmed in two large NSCLC data sets from other geographic regions. However, NSRO-driven NSCLCs in smokers had higher transcriptomic activities related to the regulation of the cell cycle. These findings suggest that, whereas the genomic landscape is similar between NSRO-driven NSCLC in smokers and nonsmokers, smoking still affects the tumor phenotype independently of genomic alterations. SIGNIFICANCE Non-small cell lung cancers driven by nonsmoking-related oncogenes do not harbor genomic scars caused by smoking regardless of smoking history, indicating that the impact of smoking on these tumors is mainly nongenomic.
Collapse
Affiliation(s)
- Chen-Yang Huang
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Division of Hematology-Oncology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Nanhai Jiang
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Meixin Shen
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Gillianne G Lai
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Aaron C Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Amit Jain
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Stephanie P Saw
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Mei Kim Ang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Quan Sing Ng
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Darren W Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ravindran Kanesvaran
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Eng Huat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Wan Ling Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Boon-Hean Ong
- Department of Cardiothoracic Surgery, National Heart Centre Singapore, Singapore, Singapore
| | - Kevin L Chua
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Devanand Anantham
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Angela M Takano
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ngak Leng Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Anders J Skanderup
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Daniel S Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Duke-NUS Medical School Singapore, Singapore, Singapore
- Cancer Therapeutics Research Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Steven G Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina
| |
Collapse
|
11
|
Zhao W, Chen W, Li G, Lei D, Yang J, Chen Y, Jiang Y, Wu J, Ni B, Sun Y, Wang S, Sun Y, Li M, Liu J. GMILT: A Novel Transformer Network That Can Noninvasively Predict EGFR Mutation Status. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2024; 35:7324-7338. [PMID: 35862326 DOI: 10.1109/tnnls.2022.3190671] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Noninvasively and accurately predicting the epidermal growth factor receptor (EGFR) mutation status is a clinically vital problem. Moreover, further identifying the most suspicious area related to the EGFR mutation status can guide the biopsy to avoid false negatives. Deep learning methods based on computed tomography (CT) images may improve the noninvasive prediction of EGFR mutation status and potentially help clinicians guide biopsies by visual methods. Inspired by the potential inherent links between EGFR mutation status and invasiveness information, we hypothesized that the predictive performance of a deep learning network can be improved through extra utilization of the invasiveness information. Here, we created a novel explainable transformer network for EGFR classification named gated multiple instance learning transformer (GMILT) by integrating multi-instance learning and discriminative weakly supervised feature learning. Pathological invasiveness information was first introduced into the multitask model as embeddings. GMILT was trained and validated on a total of 512 patients with adenocarcinoma and tested on three datasets (the internal test dataset, the external test dataset, and The Cancer Imaging Archive (TCIA) public dataset). The performance (area under the curve (AUC) =0.772 on the internal test dataset) of GMILT exceeded that of previously published methods and radiomics-based methods (i.e., random forest and support vector machine) and attained a preferable generalization ability (AUC =0.856 in the TCIA test dataset and AUC =0.756 in the external dataset). A diameter-based subgroup analysis further verified the efficiency of our model (most of the AUCs exceeded 0.772) to noninvasively predict EGFR mutation status from computed tomography (CT) images. In addition, because our method also identified the "core area" of the most suspicious area related to the EGFR mutation status, it has the potential ability to guide biopsies.
Collapse
|
12
|
Xu Y, Jia L, Zhang L, Wang H, Jiang L, Feng X, Wei R, Yao Q, Ren M, Xue T, Li Y, Zhu X, Zhou X, Bai Q. Comprehensive analysis of next generation sequencing and ARMS-PCR for detecting EGFR exon 20 insertion (ex20ins) mutations in Chinese non-small cell lung cancer patients. Transl Lung Cancer Res 2024; 13:986-997. [PMID: 38854943 PMCID: PMC11157361 DOI: 10.21037/tlcr-23-848] [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: 12/25/2023] [Accepted: 04/22/2024] [Indexed: 06/11/2024]
Abstract
Background Amivantamab (JNJ-372) and mobocertinib (TAK-788) have been reported to have favorable therapeutic effect for non-small cell lung cancer (NSCLC) patients with epidermal growth factor receptor (EGFR) exon 20 insertion (ex20ins) mutations. Thus, accurate detection of EGFR ex20ins mutations is crucial for subsequent individualized therapy. The aim of this study was to compare the two common methods of next generation sequencing (NGS) and amplification refractory mutation system polymerase chain reaction (ARMS-PCR) for detecting EGFR ex20ins mutations in Chinese NSCLC patients. Methods We retrospectively analyzed EGFR mutations, especially for ex20ins, in 3,606 NSCLC patients detected by NGS and 1,785 patients by ARMS. Results Among the 3,606 NGS patients, a total of 2,077 EGFR mutations and 95 EGFR ex20ins were identified, accounting for 57.6% and 2.6%, respectively. While 48.4% of EGFR mutations and 1.1% of ex20ins were detected in 1,785 ARMS patients, which were significantly lower than those of NGS (P<0.01). Thirty-four unique ex20ins variants were identified by NGS, and eight of them was reported for the first time. However, ARMS was designed to detect only several known EGFR ex20ins variants, and even did not include the most common variants in Chinese NSCLC patients. Conclusions NGS is more advantageous and strongly recommended for the detection of EGFR ex20ins mutations. Considering the fast and cost-effective ARMS detection method, it is suggested that the primers design should be updated according to the characteristics of EGFR ex20ins mutations in Chinese NSCLC patients.
Collapse
Affiliation(s)
- Yuyin Xu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Liqing Jia
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Ling Zhang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Haochen Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Lin Jiang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xu Feng
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Ran Wei
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Qianlan Yao
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Min Ren
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Tian Xue
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Yuan Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xiaoli Zhu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Qianming Bai
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| |
Collapse
|
13
|
Díaz-Gay M, Zhang T, Hoang PH, Khandekar A, Zhao W, Steele CD, Otlu B, Nandi SP, Vangara R, Bergstrom EN, Kazachkova M, Pich O, Swanton C, Hsiung CA, Chang IS, Wong MP, Leung KC, Sang J, McElderry J, Yang L, Nowak MA, Shi J, Rothman N, Wedge DC, Homer R, Yang SR, Lan Q, Zhu B, Chanock SJ, Alexandrov LB, Landi MT. The mutagenic forces shaping the genomic landscape of lung cancer in never smokers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307318. [PMID: 38798417 PMCID: PMC11118654 DOI: 10.1101/2024.05.15.24307318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Lung cancer in never smokers (LCINS) accounts for up to 25% of all lung cancers and has been associated with exposure to secondhand tobacco smoke and air pollution in observational studies. Here, we evaluate the mutagenic exposures in LCINS by examining deep whole-genome sequencing data from a large international cohort of 871 treatment-naïve LCINS recruited from 28 geographical locations within the Sherlock-Lung study. KRAS mutations were 3.8-fold more common in adenocarcinomas of never smokers from North America and Europe, while a 1.6-fold higher prevalence of EGFR and TP53 mutations was observed in adenocarcinomas from East Asia. Signature SBS40a, with unknown cause, was found in most samples and accounted for the largest proportion of single base substitutions in adenocarcinomas, being enriched in EGFR-mutated cases. Conversely, the aristolochic acid signature SBS22a was almost exclusively observed in patients from Taipei. Even though LCINS exposed to secondhand smoke had an 8.3% higher mutational burden and 5.4% shorter telomeres, passive smoking was not associated with driver mutations in cancer driver genes or the activities of individual mutational signatures. In contrast, patients from regions with high levels of air pollution were more likely to have TP53 mutations while exhibiting shorter telomeres and an increase in most types of somatic mutations, including a 3.9-fold elevation of signature SBS4 (q-value=3.1 × 10-5), previously linked mainly to tobacco smoking, and a 76% increase of clock-like signature SBS5 (q-value=5.0 × 10-5). A positive dose-response effect was observed with air pollution levels, which correlated with both a decrease in telomere length and an elevation in somatic mutations, notably attributed to signatures SBS4 and SBS5. Our results elucidate the diversity of mutational processes shaping the genomic landscape of lung cancer in never smokers.
Collapse
Affiliation(s)
- Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher D. Steele
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Shuvro P. Nandi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Mariya Kazachkova
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick 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
| | - Chao Agnes Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Maria Pik Wong
- Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Kin Chung Leung
- Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - John McElderry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, Department of Human Genetics, Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
| | - Martin A Nowak
- Department of Mathematics, Harvard University, Cambridge, MA, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C. Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
- Manchester NIHR Biomedical Research Centre, Manchester, UK
| | - Robert Homer
- Yale Surgery Pathology Department, Yale University, New Haven, CT, USA
| | - Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| |
Collapse
|
14
|
Hu X, Zhu B, Vokes N, Fujimoto J, Rojas Alvarez FR, Heeke S, Moreira AL, Solis LM, Haymaker C, Velcheti V, Sterman DH, Pass HI, Cheng C, Lee JJ, Zhang J, Wei Z, Wu J, Le X, Ostrin E, Toumazis I, Gibbons D, Su D, Fukuoka J, Antonoff MB, Gerber DE, Li C, Kadara H, Wang L, Davis M, Heymach JV, Hannash S, Wistuba I, Dubinett S, Alexandrov L, Lippman S, Spira A, Futreal AP, Reuben A, Zhang J. The evolution of lung adenocarcinoma precursors is associated with chromosomal instability and transition from innate to adaptive immune response/evasion. RESEARCH SQUARE 2024:rs.3.rs-4396272. [PMID: 38798564 PMCID: PMC11118701 DOI: 10.21203/rs.3.rs-4396272/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Studying lung adenocarcinoma (LUAD) early carcinogenesis is challenging, primarily due to the lack of LUAD precursors specimens. We amassed multi-omics data from 213 LUAD and LUAD precursors to identify molecular features underlying LUAD precancer evolution. We observed progressively increasing mutations, chromosomal aberrations, whole genome doubling and genomic instability from precancer to invasive LUAD, indicating aggravating chromosomal instability (CIN). Telomere shortening, a crucial genomic alteration linked to CIN, emerged at precancer stage. Moreover, later-stage lesions demonstrated increasing cancer stemness and decreasing alveolar identity, suggesting epithelial de-differentiation during early LUAD carcinogenesis. The innate immune cells progressively diminished from precancer to invasive LUAD, concomitant with a gradual recruitment of adaptive immune cells (except CD8+ and gamma-delta T cells that decreased in later stages) and upregulation of numerous immune checkpoints, suggesting LUAD precancer evolution is associated with a shift from innate to adaptive immune response and immune evasion mediated by various mechanisms.
Collapse
Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bo Zhu
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Natalie Vokes
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - Frank R. Rojas Alvarez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Simon Heeke
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Andre L. Moreira
- Department of Pathology, New York University Langone Medical Center, New York, 10012, USA
| | - Luisa M. Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vamsidhar Velcheti
- Department of Medical oncology, New York University, New York, 10012, USA
| | | | - Harvey I. Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, 10016, USA
| | - Chao Cheng
- Department of Medicine, Epidemiology and Population Science, Baylor College of Medicine. Houston, TX, 77030, USA
| | - Jack J. Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Zhubo Wei
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiuning Le
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Edwin Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Iakovos Toumazis
- Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Don Gibbons
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dan Su
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Mara B. Antonoff
- Department of Thoracic & Cardiovasc Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David E. Gerber
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chenyang Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark Davis
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - John V. Heymach
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Samir Hannash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Steven Dubinett
- Departments of Medicine and Pathology, University of California Los Angeles and Greater Los Angeles Healthcare System, Los Angeles, CA, 90095, USA
| | - Ludmil Alexandrov
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - Scott Lippman
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - Avrum Spira
- Pathology & Laboratory Medicine, and Bioinformatics, Boston University, Boston, MA, 02215, USA
| | - Andrew P. Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexandre Reuben
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Lead contact
| |
Collapse
|
15
|
Shiels MS, Graubard BI, McNeel TS, Kahle L, Freedman ND. Trends in smoking-attributable and smoking-unrelated lung cancer death rates in the United States, 1991-2018. J Natl Cancer Inst 2024; 116:711-716. [PMID: 38070489 PMCID: PMC11077306 DOI: 10.1093/jnci/djad256] [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: 09/13/2023] [Revised: 11/14/2023] [Accepted: 12/05/2023] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND In the United States, lung cancer death rates have been declining for decades, primarily as a result of pronounced decreases in cigarette smoking. It is unclear, however, whether there have been similar declines in mortality rates of lung cancer unrelated to smoking. We estimated trends in US lung cancer death rates attributable and not attributable to smoking from 1991 to 2018. METHODS The study included 30- to 79-year-olds in the National Health Interview Survey who were linked to the National Death Index, 1991-2014. Adjusted hazard ratios for smoking status and lung cancer death were estimated, and age-specific population attributable fractions were calculated. Annual population attributable fractions were multiplied by annual US national lung cancer mortality, partitioning rates into smoking-attributable and smoking-unrelated lung cancer deaths. All statistical tests were 2-sided. RESULTS During 1991-2018, the proportion of never smokers increased among both men (35.1%-54.6%) and women (54.0%-65.4%). Compared with those who had ever smoked, those who had never smoked had 86% lower risk (hazard ratio = 0.14; 95% confidence interval [CI] = 0.12 to 0.16) of lung cancer death. The fraction of lung cancer deaths attributable to smoking decreased from 81.4% (95% CI = 78.9 to 81.4) to 74.7% (95% CI = 78.1 to 71.4). Smoking-attributable lung cancer death rates declined 2.7% per year (95% CI = ‒2.9% to ‒2.5%) and smoking-unrelated lung cancer death rates declined 1.8% per year (95% CI = ‒2.0% to ‒1.5%); these declines have accelerated in recent years. CONCLUSIONS An increasing proportion of lung cancer deaths are unrelated to smoking based on declines in smoking prevalence. Smoking-unrelated lung cancer death rates have declined, however, perhaps because of decreases in secondhand smoke and air pollution exposure as well as treatment improvements.
Collapse
Affiliation(s)
- Meredith S Shiels
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Barry I Graubard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Lisa Kahle
- Information Management Services, Calverton, MD, USA
| | - Neal D Freedman
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD, USA
| |
Collapse
|
16
|
Collins JC, Magaziner SJ, English M, Hassan B, Chen X, Balanda N, Anderson M, Lam A, Fernandez-Pol S, Kwong B, Greenberg PL, Terrier B, Likhite ME, Kosmider O, Wang Y, Samara NL, Walters KJ, Beck DB, Werner A. Shared and distinct mechanisms of UBA1 inactivation across different diseases. EMBO J 2024; 43:1919-1946. [PMID: 38360993 PMCID: PMC11099125 DOI: 10.1038/s44318-024-00046-z] [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: 09/22/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Most cellular ubiquitin signaling is initiated by UBA1, which activates and transfers ubiquitin to tens of E2 enzymes. Clonally acquired UBA1 missense mutations cause an inflammatory-hematologic overlap disease called VEXAS (vacuoles, E1, X-linked, autoinflammatory, somatic) syndrome. Despite extensive clinical investigation into this lethal disease, little is known about the underlying molecular mechanisms. Here, by dissecting VEXAS-causing UBA1 mutations, we discovered that p.Met41 mutations alter cytoplasmic isoform expression, whereas other mutations reduce catalytic activity of nuclear and cytoplasmic isoforms by diverse mechanisms, including aberrant oxyester formation. Strikingly, non-p.Met41 mutations most prominently affect transthioesterification, revealing ubiquitin transfer to cytoplasmic E2 enzymes as a shared property of pathogenesis amongst different VEXAS syndrome genotypes. A similar E2 charging bottleneck exists in some lung cancer-associated UBA1 mutations, but not in spinal muscular atrophy-causing UBA1 mutations, which instead, render UBA1 thermolabile. Collectively, our results highlight the precision of conformational changes required for faithful ubiquitin transfer, define distinct and shared mechanisms of UBA1 inactivation in diverse diseases, and suggest that specific E1-E2 modules control different aspects of tissue differentiation and maintenance.
Collapse
Affiliation(s)
- Jason C Collins
- Stem Cell Biochemistry Section, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD, USA
| | - Samuel J Magaziner
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Maya English
- Stem Cell Biochemistry Section, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD, USA
| | - Bakar Hassan
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Xiang Chen
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Nicholas Balanda
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Meghan Anderson
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Athena Lam
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | | | - Bernice Kwong
- Department of Dermatology, Stanford University Cancer Center, Stanford, CA, USA
| | - Peter L Greenberg
- Division of Hematology, Stanford University Cancer Center, Stanford, CA, USA
| | - Benjamin Terrier
- Department of Internal Medicine, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Mary E Likhite
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Olivier Kosmider
- Laboratory of Hematology, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Yan Wang
- Mass Spectrometry Facility, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Nadine L Samara
- Structural Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - David B Beck
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Achim Werner
- Stem Cell Biochemistry Section, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
17
|
Peng H, Wu X, Cui X, Liu S, Liang Y, Cai X, Shi M, Zhong R, Li C, Liu J, Wu D, Gao Z, Lu X, Luo H, He J, Liang W. Molecular and immune characterization of Chinese early-stage non-squamous non-small cell lung cancer: a multi-omics cohort study. Transl Lung Cancer Res 2024; 13:763-784. [PMID: 38736486 PMCID: PMC11082711 DOI: 10.21037/tlcr-23-800] [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: 12/02/2023] [Accepted: 03/15/2024] [Indexed: 05/14/2024]
Abstract
Background Albeit considered with superior survival, around 30% of the early-stage non-squamous non-small cell lung cancer (Ns-NSCLC) patients relapse within 5 years, suggesting unique biology. However, the biological characteristics of early-stage Ns-NSCLC, especially in the Chinese population, are still unclear. Methods Multi-omics interrogation of early-stage Ns-NSCLC (stage I-III), paired blood samples and normal lung tissues (n=76) by whole-exome sequencing (WES), RNA sequencing, and T-cell receptor (TCR) sequencing were conducted. Results An average of 128 exonic mutations were identified, and the most frequently mutant gene was EGFR (55%), followed by TP53 (37%) and TTN (26%). Mutations in MUC17, ABCA2, PDE4DIP, and MYO18B predicted significantly unfavorable disease-free survival (DFS). Moreover, cytobands amplifications in 8q24.3, 14q13.1, 14q11.2, and deletion in 3p21.1 were highlighted in recurrent cases. Higher incidence of human leukocyte antigen loss of heterozygosity (HLA-LOH), higher tumor mutational burden (TMB) and tumor neoantigen burden (TNB) were identified in ever-smokers than never-smokers. HLA-LOH also correlated with higher TMB, TNB, intratumoral heterogeneity (ITH), and whole chromosomal instability (wCIN) scores. Interestingly, higher ITH was an independent predictor of better DFS in early-stage Ns-NSCLC. Up-regulation of immune-related genes, including CRABP2, ULBP2, IL31RA, and IL1A, independently portended a dismal prognosis. Enhanced TCR diversity of peripheral blood mononuclear cells (PBMCs) predicted better prognosis, indicative of a noninvasive method for relapse surveillance. Eventually, seven machine-learning (ML) algorithms were employed to evaluate the predictive accuracy of clinical, genomic, transcriptomic, and TCR repertoire data on DFS, showing that clinical and RNA features combination in the random forest (RF) algorithm, with area under the curve (AUC) of 97.5% and 83.3% in the training and testing cohort, respectively, significantly outperformed other methods. Conclusions This study comprehensively profiled the genomic, transcriptomic, and TCR repertoire spectrums of Chinese early-stage Ns-NSCLC, shedding light on biological underpinnings and candidate biomarkers for prognosis development.
Collapse
Affiliation(s)
- Haoxin Peng
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Clinical Medicine, Nanshan School, Guangzhou Medical University, Guangzhou, China
| | - Xiangrong Wu
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Clinical Medicine, Nanshan School, Guangzhou Medical University, Guangzhou, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoli Cui
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Shaopeng Liu
- Department of Computer Science, Guangdong Polytechnic Normal University, Guangzhou, China
- Department of Artificial Intelligence Research, Pazhou Lab, Guangzhou, China
| | - Yueting Liang
- Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiuyu Cai
- Department of General Internal Medicine, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Cener for Cancer Medicine, Guangzhou, China
| | - Mengping Shi
- Department of Computer Science, Guangdong Polytechnic Normal University, Guangzhou, China
| | - Ran Zhong
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Caichen Li
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun Liu
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dongfang Wu
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Zhibo Gao
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Xu Lu
- Department of Computer Science, Guangdong Polytechnic Normal University, Guangzhou, China
- Department of Artificial Intelligence Research, Pazhou Lab, Guangzhou, China
| | - Haitao Luo
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Jianxing He
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenhua Liang
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Medical Oncology, The First People’s Hospital of Zhaoqing, Zhaoqing, China
| |
Collapse
|
18
|
Ramos R, Moura CS, Costa M, Lamas NJ, Correia R, Garcez D, Pereira JM, Sousa C, Vale N. Enhancing Lung Cancer Care in Portugal: Bridging Gaps for Improved Patient Outcomes. J Pers Med 2024; 14:446. [PMID: 38793028 PMCID: PMC11121920 DOI: 10.3390/jpm14050446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Lung cancer has the highest incidence and cancer-related mortality worldwide. In Portugal, it ranks as the fourth most common cancer, with nearly 6000 new cases being diagnosed every year. Lung cancer is the main cause of cancer-related death among males and the third cause of cancer-related death in females. Despite the globally accepted guidelines and recommendations for what would be the ideal path for a lung cancer patient, several challenges occur in real clinical management across the world. The recommendations emphasize the importance of adequate screening of high-risk individuals, a precise tumour biopsy, and an accurate final diagnosis to confirm the neoplastic nature of the nodule. A detailed histological classification of the lung tumour type and a comprehensive molecular characterization are of utmost importance for the selection of an efficacious and patient-directed therapeutic approach. However, in the context of the Portuguese clinical organization and the national healthcare system, there are still several gaps in the ideal pathway for a lung cancer patient, involving aspects ranging from the absence of a national lung cancer screening programme through difficulties in histological diagnosis and molecular characterization to challenges in therapeutic approaches. In this manuscript, we address the most relevant weaknesses, presenting several proposals for potential solutions to improve the management of lung cancer patients, helping to decisively improve their overall survival and quality of life.
Collapse
Affiliation(s)
- Raquel Ramos
- PerMed Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal; (R.R.); (C.S.)
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Molecular Diagnostics Laboratory, Unilabs Portugal, Centro Empresarial Lionesa Porto, Rua Lionesa, 4465-671 Leça do Balio, Portugal; (M.C.); (N.J.L.)
| | - Conceição Souto Moura
- Pathology Laboratory, Unilabs Portugal, Rua Manuel Pinto de Azevedo 173, 4100-321 Porto, Portugal;
| | - Mariana Costa
- Molecular Diagnostics Laboratory, Unilabs Portugal, Centro Empresarial Lionesa Porto, Rua Lionesa, 4465-671 Leça do Balio, Portugal; (M.C.); (N.J.L.)
| | - Nuno Jorge Lamas
- Molecular Diagnostics Laboratory, Unilabs Portugal, Centro Empresarial Lionesa Porto, Rua Lionesa, 4465-671 Leça do Balio, Portugal; (M.C.); (N.J.L.)
- Anatomic Pathology Service, Pathology Department, Centro Hospitalar Universitário de Santo António (CHUdSA), Largo Professor Abel Salazar, 4099-001 Porto, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Campus de Gualtar, University of Minho, Rua da Universidade, 4710-057 Braga, Portugal
| | - Renato Correia
- Technology & Innovation Department, Unilabs Portugal, Rua Manuel Pinto de Azevedo 173, 4100-321 Porto, Portugal; (R.C.); (D.G.)
| | - Diogo Garcez
- Technology & Innovation Department, Unilabs Portugal, Rua Manuel Pinto de Azevedo 173, 4100-321 Porto, Portugal; (R.C.); (D.G.)
| | - José Miguel Pereira
- Radiology Department, Unilabs Portugal, Rua de Diogo Botelho 485, 4150-255 Porto, Portugal;
| | - Carlos Sousa
- PerMed Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal; (R.R.); (C.S.)
- Molecular Diagnostics Laboratory, Unilabs Portugal, Centro Empresarial Lionesa Porto, Rua Lionesa, 4465-671 Leça do Balio, Portugal; (M.C.); (N.J.L.)
| | - Nuno Vale
- PerMed Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal; (R.R.); (C.S.)
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Health Information and Decision (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal
| |
Collapse
|
19
|
Zhang Y, Yang Y, Ma Y, Liu Y, Ye Z. Development and validation of an interpretable radiomic signature for preoperative estimation of tumor mutational burden in lung adenocarcinoma. Front Genet 2024; 15:1367434. [PMID: 38660677 PMCID: PMC11039798 DOI: 10.3389/fgene.2024.1367434] [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: 01/08/2024] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
Background Tumor mutational burden (TMB) is a promising biomarker for immunotherapy. The challenge of spatial and temporal heterogeneity and high costs weaken its power in clinical routine. The aim of this study is to estimate TMB preoperatively using a volumetric CT-based radiomic signature (rMB). Methods Seventy-one patients with resectable lung adenocarcinoma (LUAD) who underwent whole-exome sequencing (WXS) from 2011 to 2014 were enrolled from the institutional biobank of Tianjin Medical University Cancer Institute and Hospital (TMUCIH). Forty-nine LUAD patients with WXS from the Cancer Genome Atlas Program (TCGA) served as the external validation cohort. Computed tomography (CT) volumes were resampled to 1-mm isotropic, semi-automatically segmented, and manually adjusted by two radiologists. A total of 3,108 radiomic features were extracted via PyRadiomics and then harmonized across cohorts by ComBat. Features with inter-segmentation intra-class correlation coefficient (ICC) > 0.8, low collinearity, and significant univariate power were passed to the least absolute shrinkage and selection operator (LASSO)-logistic classifier to discriminate TMB-high/TMB-low at a threshold of 10 mut/Mb. The receiver operating characteristic (ROC) curve analysis and calibration curve were used to determine its efficiency. Shapley values (SHAP) attributed individual predictions to feature contributions. Clinical variables and circulating biomarkers were collected to find potential associations with TMB and rMB. Results The top frequently mutated genes significantly differed between the Chinese and TCGA cohorts, with a median TMB of 2.20 and 3.46 mut/Mb and 15 (21.12%) and 9 (18.37%) cases of TMB-high, respectively. After dimensionality reduction, rMB comprised 21 features, which reached an AUC of 0.895 (sensitivity = 0.867, specificity = 0.875, and accuracy = 0.873) in the discovery cohort and 0.878 (sensitivity = 1.0, specificity = 0.825, and accuracy = 0.857 in a consist cutoff) in the validation cohort. rMB of TMB-high patients was significantly higher than rMB of TMB-low patients in both cohorts (p < 0.01). rMB was well-calibrated in the discovery cohort and validation cohort (p = 0.27 and 0.74, respectively). The square-filtered gray-level concurrence matrix (GLCM) correlation was of significant importance in prediction. The proportion of circulating monocytes and the monocyte-to-lymphocyte ratio were associated with TMB, whereas the circulating neutrophils and lymphocyte percentage, original and derived neutrophil-to-lymphocyte ratio, and platelet-to-lymphocyte ratio were associated with rMB. Conclusion rMB, an intra-tumor radiomic signature, could predict lung adenocarcinoma patients with higher TMB. Insights from the Shapley values may enhance persuasiveness of the purposed signature for further clinical application. rMB could become a promising tool to triage patients who might benefit from a next-generation sequencing test.
Collapse
Affiliation(s)
- Yuwei Zhang
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Key Laboratory of Cancer Immunology and Biotherapy of Tianjin, Tianjin, China
| | - Yichen Yang
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin, China
| | - Yue Ma
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Key Laboratory of Cancer Immunology and Biotherapy of Tianjin, Tianjin, China
| | - Ying Liu
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Key Laboratory of Cancer Immunology and Biotherapy of Tianjin, Tianjin, China
| | - Zhaoxiang Ye
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Key Laboratory of Cancer Immunology and Biotherapy of Tianjin, Tianjin, China
| |
Collapse
|
20
|
Zhang T, Sang J, Hoang PH, Zhao W, Rosenbaum J, Johnson KE, Klimczak LJ, McElderry J, Klein A, Wirth C, Bergstrom EN, Díaz-Gay M, Vangara R, Colon-Matos F, Hutchinson A, Lawrence SM, Cole N, Zhu B, Przytycka TM, Shi J, Caporaso NE, Homer R, Pesatori AC, Consonni D, Imielinski M, Chanock SJ, Wedge DC, Gordenin DA, Alexandrov LB, Harris RS, Landi MT. APOBEC shapes tumor evolution and age at onset of lung cancer in smokers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587805. [PMID: 38617360 PMCID: PMC11014539 DOI: 10.1101/2024.04.02.587805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues1,2. Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B)3-6. However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations, whereas HAS for A3A-like mutagenesis and TP53 mutations. Unlike APOBEC3A, APOBEC3B expression is strongly associated with an upregulation of the base excision repair pathway. Hypermutation by unrepaired A3A and tobacco smoking mutagenesis combined with TP53-induced genomic instability can trigger senescence7, apoptosis8, and cell regeneration9, as indicated by high expression of pulmonary healing signaling pathway, stemness markers and distal cell-of-origin in HAS. The expected association of tobacco smoking variables (e.g., time to first cigarette) with genomic/epigenomic changes are not observed in HAS, a plausible consequence of frequent cell senescence or apoptosis. HAS have more neoantigens, slower clonal expansion, and older age at onset compared to LAS, particularly in heavy smokers, consistent with high proportions of newly generated, unmutated cells and frequent immuno-editing. These findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development, with important clinical implications.
Collapse
Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - John McElderry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alyssa Klein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher Wirth
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Frank Colon-Matos
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M. Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Angela C. Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Dario Consonni
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C. Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| |
Collapse
|
21
|
Feng C, Li N, Gao G, He Q, Kwok LY, Zhang H. Dynamic Changes of the Gut Microbiota and Its Functional Metagenomic Potential during the Development of Non-Small Cell Lung Cancer. Int J Mol Sci 2024; 25:3768. [PMID: 38612577 PMCID: PMC11011768 DOI: 10.3390/ijms25073768] [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: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
The gut microbiota plays a significant role in tumor pathogenesis by regulating the host metabolism and immune response, and there are few studies focused on tracking changes in the gut microbiota from the onset of lung cancer. Therefore, the aim of our study is combining preclinical and clinical research to thoroughly analyze the signatures of fecal microbiota in lung cancer, which will be useful for early diagnosis and predicting the therapeutic efficacy of lung cancer. The first part of this study analyzed the fecal metagenomic differences between patients with non-small cell lung cancer and healthy subjects, and the second part of this work constructed a murine lung cancer model to monitor changes in mouse fecal metagenomics and T cell immunology during lung cancer progression. We found that the fecal microbiota was altered in both humans and mice with lung cancer, characterized by a significantly reduced microbial diversity and number of beneficial microbes, with increases in potential pathogens. The fecal level of Akkermansia muciniphila and the gut metabolic module of the secondary bile acid metabolism were diminished in both humans and mice with lung cancer compared with healthy subjects. Splenomegaly was observed in the lung cancer mice. Flow cytometer analysis of the splenocytes revealed substantial alterations in the proportions of T cell subsets in the lung cancer mice, characterized by significant increases in CD4+Foxp3+CD25+ T regulatory cells (p < 0.05) while significant decreases in CD3+ T cells (p < 0.001), CD4+ T cells (p < 0.001), and the CD4+/CD8+ ratio (p < 0.01). Vertical and longitudinal analyses of the fecal microbiota of the two mouse groups identified some lung cancer biomarkers (including Acutalibacter timonensis, Lachnospiraceae bacterium NSJ-38 sp014337195, etc.). The fecal microbiota of the lung cancer mice had a reduced metagenomic potential for neurotransmitters (melatonin, γ-aminobutyric acid, and histamine) compared with healthy mice. In summary, this study found that the diversity, structure, and composition of gut microbiota vary between cancer and healthy conditions, ultimately leading to changes in the potential for functional metagenomics.
Collapse
Affiliation(s)
- Cuijiao Feng
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.F.); (N.L.); (G.G.); (Q.H.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Na Li
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.F.); (N.L.); (G.G.); (Q.H.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Guangqi Gao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.F.); (N.L.); (G.G.); (Q.H.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Qiuwen He
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.F.); (N.L.); (G.G.); (Q.H.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.F.); (N.L.); (G.G.); (Q.H.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.F.); (N.L.); (G.G.); (Q.H.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| |
Collapse
|
22
|
Chang E, An JY. Whole-genome doubling is a double-edged sword: the heterogeneous role of whole-genome doubling in various cancer types. BMB Rep 2024; 57:125-134. [PMID: 38449300 PMCID: PMC10979346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 03/08/2024] Open
Abstract
Whole-genome doubling (WGD), characterized by the duplication of an entire set of chromosomes, is commonly observed in various tumors, occurring in approximately 30-40% of patients with different cancer types. The effect of WGD on tumorigenesis varies depending on the context, either promoting or suppressing tumor progression. Recent advances in genomic technologies and large-scale clinical investigations have led to the identification of the complex patterns of genomic alterations underlying WGD and their functional consequences on tumorigenesis progression and prognosis. Our comprehensive review aims to summarize the causes and effects of WGD on tumorigenesis, highlighting its dualistic influence on cancer cells. We then introduce recent findings on WGD-associated molecular signatures and genetic aberrations and a novel subtype related to WGD. Finally, we discuss the clinical implications of WGD in cancer subtype classification and future therapeutic interventions. Overall, a comprehensive understanding of WGD in cancer biology is crucial to unraveling its complex role in tumorigenesis and identifying novel therapeutic strategies. [BMB Reports 2024; 57(3): 125-134].
Collapse
Affiliation(s)
- Eunhyong Chang
- Department of Integrated Biomedical and Life Science, Korea University, Seoul 02841, Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul 02841, Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul 02841, Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul 02841, Korea
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul 02841, Korea
| |
Collapse
|
23
|
Desai S, Ahmad S, Bawaskar B, Rashmi S, Mishra R, Lakhwani D, Dutt A. Singleton mutations in large-scale cancer genome studies: uncovering the tail of cancer genome. NAR Cancer 2024; 6:zcae010. [PMID: 38487301 PMCID: PMC10939354 DOI: 10.1093/narcan/zcae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Singleton or low-frequency driver mutations are challenging to identify. We present a domain driver mutation estimator (DOME) to identify rare candidate driver mutations. DOME analyzes positions analogous to known statistical hotspots and resistant mutations in combination with their functional and biochemical residue context as determined by protein structures and somatic mutation propensity within conserved PFAM domains, integrating the CADD scoring scheme. Benchmarked against seven other tools, DOME exhibited superior or comparable accuracy compared to all evaluated tools in the prediction of functional cancer drivers, with the exception of one tool. DOME identified a unique set of 32 917 high-confidence predicted driver mutations from the analysis of whole proteome missense variants within domain boundaries across 1331 genes, including 1192 noncancer gene census genes, emphasizing its unique place in cancer genome analysis. Additionally, analysis of 8799 TCGA (The Cancer Genome Atlas) and in-house tumor samples revealed 847 potential driver mutations, with mutations in tyrosine kinase members forming the dominant burden, underscoring its higher significance in cancer. Overall, DOME complements current approaches for identifying novel, low-frequency drivers and resistant mutations in personalized therapy.
Collapse
Affiliation(s)
- Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Suhail Ahmad
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Bhargavi Bawaskar
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Sonal Rashmi
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Rohit Mishra
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Deepika Lakhwani
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
- Department of Genetics, University of Delhi, South Campus, New Delhi 110021, India
| |
Collapse
|
24
|
Ankudavicius V, Nikitina D, Lukosevicius R, Tilinde D, Salteniene V, Poskiene L, Miliauskas S, Skieceviciene J, Zemaitis M, Kupcinskas J. Detailed Characterization of the Lung-Gut Microbiome Axis Reveals the Link between PD-L1 and the Microbiome in Non-Small-Cell Lung Cancer Patients. Int J Mol Sci 2024; 25:2323. [PMID: 38396998 PMCID: PMC10889071 DOI: 10.3390/ijms25042323] [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: 12/11/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Next-generation sequencing technologies have started a new era of respiratory tract research in recent years. Alterations in the respiratory microbiome between healthy and malignant conditions have been revealed. However, the composition of the microbiome varies among studies, even in similar medical conditions. Also, there is a lack of complete knowledge about lung-gut microbiome interactions in lung cancer patients. The aim of this study was to explore the lung-gut axis in non-small-cell lung cancer (NSCLC) patients and the associations between lung-gut axis microbiota and clinical parameters (CRP, NLR, LPS, CD8, and PD-L1). Lung tissue and fecal samples were used for bacterial 16S rRNA sequencing. The results revealed, for the first time, that the bacterial richness in lung tumor tissue gradually decreased with an increase in the level of PD-L1 expression (p < 0.05). An analysis of β-diversity indicated a significant positive correlation between the genera Romboutsia and Alistipes in both the lung tumor biopsies and stool samples from NSCLC patients (p < 0.05). Survival analysis showed that NSCLC patients with higher bacterial richness in their stool samples had prolonged overall survival (HR: 2.06, 95% CI: 1.025-4.17, p = 0.0426).
Collapse
Affiliation(s)
- Vytautas Ankudavicius
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Darja Nikitina
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Deimante Tilinde
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Violeta Salteniene
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Skaidrius Miliauskas
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Marius Zemaitis
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Krutz M, Acharya P, Elliott J, Zhao D, Mhawej R, Queimado L. Tobacco Cessation Following Laryngeal Cancer Diagnosis Predicts Response to Treatment and Laryngectomy-Free Survival. Otolaryngol Head Neck Surg 2024; 170:438-446. [PMID: 37890055 PMCID: PMC10872773 DOI: 10.1002/ohn.567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/19/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023]
Abstract
OBJECTIVE To determine the effect of tobacco cessation following laryngeal cancer diagnosis on response to first-line therapy, laryngectomy-free survival, and overall survival in patients who were current smokers at the time of diagnosis. STUDY DESIGN Retrospective, case-control study. SETTING OU Stephenson Cancer Center, National Cancer Institute-Designated Cancer Center. METHODS We included 140 patients diagnosed with laryngeal squamous cell carcinoma, who were current smokers at the time of diagnosis, and were treated with first-line definitive radiation or chemo/radiation with the intent to cure. The association between patient characteristics and treatment response was assessed using the χ2 test and logistic regression analysis. Survival outcomes were analyzed using Kaplan-Meier methods and Cox proportional-hazards models. RESULTS Of the 140 current smokers, 61 patients (45%) quit smoking prior to treatment initiation. In adjusted logistic regression analysis, quitters had 3.7 times higher odds of achieving a complete response to first-line therapy than active smokers (odds ratio: 3.694 [1.575-8.661]; P = .003). In the adjusted Cox proportional-hazards model, quitters were 54% less likely to require salvage laryngectomy within 7 years of diagnosis than active smokers (hazard ratio: 0.456 [0.246-0.848]; P = .013). Quitters had a statistically significant increase in 7-year overall survival compared to active smokers (P = .02). CONCLUSION This is the first study to show that in newly diagnosed laryngeal cancer patients who are current smokers at the time of diagnosis, tobacco cessation significantly increases therapy response, laryngectomy-free survival, and overall survival. These data stress the importance of systematically incorporating tobacco cessation programs into laryngeal cancer treatment plans.
Collapse
Affiliation(s)
- Matthew Krutz
- Department of Otolaryngology Head and Neck Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City OK, USA
| | - Pawan Acharya
- Department of Biostatistics & Epidemiology, The University of Oklahoma Health Sciences Center, Oklahoma City OK, USA
| | - Jacey Elliott
- Department of Otolaryngology Head and Neck Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City OK, USA
| | - Daniel Zhao
- Department of Biostatistics & Epidemiology, The University of Oklahoma Health Sciences Center, Oklahoma City OK, USA
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Rachad Mhawej
- Department of Otolaryngology Head and Neck Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City OK, USA
| | - Lurdes Queimado
- Department of Otolaryngology Head and Neck Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City OK, USA
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City OK, USA
- TSET Health Promotion Research Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| |
Collapse
|
27
|
Okawa Y, Sasagawa S, Kato H, Johnson TA, Nagaoka K, Kobayashi Y, Hayashi A, Shibayama T, Maejima K, Tanaka H, Miyano S, Shibahara J, Nishizuka S, Hirano S, Seto Y, Iwaya T, Kakimi K, Yasuda T, Nakagawa H. Immuno-genomic analysis reveals eosinophilic feature and favorable prognosis of female non-smoking esophageal squamous cell carcinomas. Cancer Lett 2024; 581:216499. [PMID: 38013050 DOI: 10.1016/j.canlet.2023.216499] [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: 09/12/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Most of esophageal squamous cell carcinoma (ESCC) develop in smoking males in Japan, but the genomic etiology and immunological characteristics of rare non-smoking female ECSS remain unclear. To elucidate the genomic and immunological features of ESCC in non-smoking females, we analyzed whole-genome or transcriptome sequencing data from 94 ESCCs, including 20 rare non-smoking female cases. In addition, 31,611 immune cells were extracted from four ESCC tissues and subject to single-cell RNA-seq. We compared their immuno-genomic and microbiome profiles between non-smoking female and smoking ESCCs. Non-smoking females showed much better prognosis. Whole-genome sequencing analysis showed no significant differences in driver genes or copy number alterations depending on smoking status. The mutational signatures specifically observed in non-smoking females ESCC could be attributed to aging. Immune profiling from RNA-seq revealed that ESCC in non-smoking females had high tumor microenvironment signatures and a high abundance of eosinophils with a favorable prognosis. Single-cell RNA-sequencing of intratumor immune cells revealed gender differences of eosinophils and their activation in female cases. ESCCs in non-smoking females have age-related mutational signatures and gender-specific tumor immune environment with eosinophils, which is likely to contribute to their favorable prognosis.
Collapse
Affiliation(s)
- Yuki Okawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroaki Kato
- Department of Surgery, Graduate School of Medicine, Kindai University, Osaka, Japan
| | - Todd A Johnson
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Koji Nagaoka
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan
| | - Yukari Kobayashi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan
| | - Akimasa Hayashi
- Department of Pathology, Kyorin University Faculty of Medicine, Mitaka, Japan
| | - Takahiro Shibayama
- Department of Pathology, Kyorin University Faculty of Medicine, Mitaka, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroko Tanaka
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University Faculty of Medicine, Mitaka, Japan
| | - Satoshi Nishizuka
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
| | - Satoshi Hirano
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Yasuyuki Seto
- Department of GI Surgery, Graduate of School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Iwaya
- Department of Clinical Oncology, Iwate Medical University School of Medicine, Yahaba, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan; Department of Immunology, Graduate School of Medicine, Kindai University, Osaka, Japan
| | - Takushi Yasuda
- Department of Surgery, Graduate School of Medicine, Kindai University, Osaka, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| |
Collapse
|
28
|
Yamaguchi T, Masago K, Sasaki E, Kuroda H, Matsushita H, Horio Y. EML4-ALK Variant 3a/b as a mechanism of osimertinib resistance in a patient with EGFR L858R positive NSCLC. Cancer Genet 2024; 280-281:13-16. [PMID: 38128381 DOI: 10.1016/j.cancergen.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/08/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Affiliation(s)
- Teppei Yamaguchi
- Department of Thoracic Oncology, Aichi Cancer Center Hospital, Japan
| | - Katsuhiro Masago
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Japan; Division of Translational Oncoimmunology, Aichi Cancer Research Institute, Nagoya, Japan.
| | - Eiichi Sasaki
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Japan
| | - Hiroaki Kuroda
- Department of Respiratory Surgery, Aichi Cancer Center Hospital, Nagoya, Japan; Department of Thoracic Surgery, Teikyo University Mizonokuchi Hospital, Tokyo, Japan; Division of Translational Oncoimmunology, Aichi Cancer Research Institute, Nagoya, Japan
| | - Hirokazu Matsushita
- Division of Translational Oncoimmunology, Aichi Cancer Research Institute, Nagoya, Japan
| | - Yoshitsugu Horio
- Department of Thoracic Oncology, Aichi Cancer Center Hospital, Japan; Division of Translational Oncoimmunology, Aichi Cancer Research Institute, Nagoya, Japan
| |
Collapse
|
29
|
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: 3] [Impact Index Per Article: 3.0] [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.
Collapse
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.
| |
Collapse
|
30
|
Chu X, Wang Q, Su C. Indoor air pollution: An important risk factor for lung cancer among Asian women without a history of smoking. CHINESE MEDICAL JOURNAL PULMONARY AND CRITICAL CARE MEDICINE 2023; 1:198-199. [PMID: 39171281 PMCID: PMC11332901 DOI: 10.1016/j.pccm.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Indexed: 08/23/2024]
Affiliation(s)
- Xiangling Chu
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Qi Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Chunxia Su
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| |
Collapse
|
31
|
Stephens EKH, Guayco Sigcha J, Lopez-Loo K, Yang IA, Marshall HM, Fong KM. Biomarkers of lung cancer for screening and in never-smokers-a narrative review. Transl Lung Cancer Res 2023; 12:2129-2145. [PMID: 38025810 PMCID: PMC10654441 DOI: 10.21037/tlcr-23-291] [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: 05/10/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
Background and Objective Lung cancer is the leading cause of cancer-related mortality worldwide, partially attributed to late-stage diagnoses. In order to mitigate this, lung cancer screening (LCS) of high-risk patients is performed using low dose computed tomography (CT) scans, however this method is burdened by high false-positive rates and radiation exposure for patients. Further, screening programs focus on individuals with heavy smoking histories, and as such, never-smokers who may otherwise be at risk of lung cancer are often overlooked. To resolve these limitations, biomarkers have been posited as potential supplements or replacements to low-dose CT, and as such, a large body of research in this area has been produced. However, comparatively little information exists on their clinical efficacy and how this compares to current LCS strategies. Methods Here we conduct a search and narrative review of current literature surrounding biomarkers of lung cancer to supplement LCS, and biomarkers of lung cancer in never-smokers (LCINS). Key Content and Findings Many potential biomarkers of lung cancer have been identified with varying levels of sensitivity, specificity, clinical efficacy, and supporting evidence. Of the markers identified, multi-target panels of circulating microRNAs, lipids, and metabolites are likely the most clinically efficacious markers to aid current screening programs, as these provide the highest sensitivity and specificity for lung cancer detection. However, circulating lipid and metabolite levels are known to vary in numerous systemic pathologies, highlighting the need for further validation in large cohort randomised studies. Conclusions Lung cancer biomarkers is a fast-expanding area of research and numerous biomarkers with potential clinical applications have been identified. However, in all cases the level of evidence supporting clinical efficacy is not yet at a level at which it can be translated to clinical practice. The priority now should be to validate existing candidate markers in appropriate clinical contexts and work to integrating these into clinical practice.
Collapse
Affiliation(s)
- Edward K. H. Stephens
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Jazmin Guayco Sigcha
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Kenneth Lopez-Loo
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Ian A. Yang
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia
| | - Henry M. Marshall
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia
| | - Kwun M. Fong
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia
| |
Collapse
|
32
|
Pulice JL, Meyerson M. Dosage amplification dictates oncogenic regulation by the NKX2-1 lineage factor in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.563996. [PMID: 37994369 PMCID: PMC10664179 DOI: 10.1101/2023.10.26.563996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Amplified oncogene expression is a critical and widespread driver event in cancer, yet our understanding of how amplification-mediated elevated dosage mediates oncogenic regulation is limited. Here, we find that the most significant focal amplification event in lung adenocarcinoma (LUAD) targets a lineage super-enhancer near the NKX2-1 lineage transcription factor. The NKX2-1 super-enhancer is targeted by focal and co-amplification with NKX2-1, and activation or repression controls NKX2-1 expression. We find that NKX2-1 is a widespread dependency in LUAD cell lines, where NKX2-1 pioneers enhancer accessibility to drive a lineage addicted state in LUAD, and NKX2-1 confers persistence to EGFR inhibitors. Notably, we find that oncogenic NKX2-1 regulation requires expression above a minimum dosage threshold-NKX2-1 dosage below this threshold is insufficient for cell viability, enhancer remodeling, and TKI persistence. Our data suggest that copy-number amplification can be a gain-of-function alteration, wherein amplification elevates oncogene expression above a critical dosage required for oncogenic regulation and cancer cell survival.
Collapse
Affiliation(s)
- John L. Pulice
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Lead contact
| |
Collapse
|
33
|
Collins JC, Magaziner SJ, English M, Hassan B, Chen X, Balanda N, Anderson M, Lam A, Fernandez-Pol S, Kwong B, Greenberg PL, Terrier B, Likhite ME, Kosmider O, Wang Y, Samara NL, Walters KJ, Beck DB, Werner A. Shared and Distinct Mechanisms of UBA1 Inactivation Across Different Diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561769. [PMID: 37873213 PMCID: PMC10592724 DOI: 10.1101/2023.10.10.561769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Most cellular ubiquitin signaling is initiated by UBA1, which activates and transfers ubiquitin to tens of E2 enzymes. Clonally acquired UBA1 missense mutations cause an inflammatory-hematologic overlap disease called VEXAS (vacuoles, E1, X-linked, autoinflammatory, somatic) syndrome. Despite extensive clinical investigation into this lethal disease, little is known about the underlying molecular mechanisms. Here, by dissecting VEXAS-causing UBA1 mutations, we discovered that p.Met41 mutations alter cytoplasmic isoform expression, whereas other mutations reduce catalytic activity of nuclear and cytoplasmic isoforms by diverse mechanisms, including aberrant oxyester formation. Strikingly, non-p.Met41 mutations most prominently affect transthioesterification, revealing ubiquitin transfer to cytoplasmic E2 enzymes as a shared property of pathogenesis amongst different VEXAS syndrome genotypes. A similar E2 charging bottleneck exists in some lung cancer-associated UBA1 mutations, but not in spinal muscular atrophy-causing UBA1 mutations, which instead, render UBA1 thermolabile. Collectively, our results highlight the precision of conformational changes required for faithful ubiquitin transfer, define distinct and shared mechanisms of UBA1 inactivation in diverse diseases, and suggest that specific E1-E2 modules control different aspects of tissue differentiation and maintenance.
Collapse
Affiliation(s)
- Jason C. Collins
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD
| | - Samuel J. Magaziner
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
| | - Maya English
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD
| | - Bakar Hassan
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Xiang Chen
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Nicholas Balanda
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
| | - Meghan Anderson
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
| | - Athena Lam
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
| | | | - Bernice Kwong
- Department of Dermatology, Stanford University Cancer Center, Stanford, CA, USA
| | - Peter L. Greenberg
- Division of Hematology, Stanford University Cancer Center, Stanford, California, USA
| | - Benjamin Terrier
- Department of Internal Medicine, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris
| | - Mary E. Likhite
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
| | - Olivier Kosmider
- Laboratory of Hematology, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris
| | - Yan Wang
- Mass Spectrometry Facility, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD
| | - Nadine L. Samara
- Structural Biochemistry Unit, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD
| | - Kylie J. Walters
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - David B. Beck
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD
| |
Collapse
|
34
|
Holme JA, Vondráček J, Machala M, Lagadic-Gossmann D, Vogel CFA, Le Ferrec E, Sparfel L, Øvrevik J. Lung cancer associated with combustion particles and fine particulate matter (PM 2.5) - The roles of polycyclic aromatic hydrocarbons (PAHs) and the aryl hydrocarbon receptor (AhR). Biochem Pharmacol 2023; 216:115801. [PMID: 37696458 PMCID: PMC10543654 DOI: 10.1016/j.bcp.2023.115801] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Air pollution is the leading cause of lung cancer after tobacco smoking, contributing to 20% of all lung cancer deaths. Increased risk associated with living near trafficked roads, occupational exposure to diesel exhaust, indoor coal combustion and cigarette smoking, suggest that combustion components in ambient fine particulate matter (PM2.5), such as polycyclic aromatic hydrocarbons (PAHs), may be central drivers of lung cancer. Activation of the aryl hydrocarbon receptor (AhR) induces expression of xenobiotic-metabolizing enzymes (XMEs) and increase PAH metabolism, formation of reactive metabolites, oxidative stress, DNA damage and mutagenesis. Lung cancer tissues from smokers and workers exposed to high combustion PM levels contain mutagenic signatures derived from PAHs. However, recent findings suggest that ambient air PM2.5 exposure primarily induces lung cancer development through tumor promotion of cells harboring naturally acquired oncogenic mutations, thus lacking typical PAH-induced mutations. On this background, we discuss the role of AhR and PAHs in lung cancer development caused by air pollution focusing on the tumor promoting properties including metabolism, immune system, cell proliferation and survival, tumor microenvironment, cell-to-cell communication, tumor growth and metastasis. We suggest that the dichotomy in lung cancer patterns observed between smoking and outdoor air PM2.5 represent the two ends of a dose-response continuum of combustion PM exposure, where tumor promotion in the peripheral lung appears to be the driving factor at the relatively low-dose exposures from ambient air PM2.5, whereas genotoxicity in the central airways becomes increasingly more important at the higher combustion PM levels encountered through smoking and occupational exposure.
Collapse
Affiliation(s)
- Jørn A Holme
- Department of Air Quality and Noise, Division of Climate and Environmental Health, Norwegian Institute of Public Health, PO Box PO Box 222 Skøyen, 0213 Oslo, Norway
| | - Jan Vondráček
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic
| | - Miroslav Machala
- Department of Pharmacology and Toxicology, Veterinary Research Institute, 62100 Brno, Czech Republic
| | - Dominique Lagadic-Gossmann
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Christoph F A Vogel
- Department of Environmental Toxicology and Center for Health and the Environment, University of California, Davis, CA 95616, USA
| | - Eric Le Ferrec
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Lydie Sparfel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Johan Øvrevik
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway; Division of Climate and Environmental Health, Norwegian Institute of Public Health, PO Box 222 Skøyen, 0213 Oslo, Norway.
| |
Collapse
|
35
|
Fontana D, Crespiatico I, Crippa V, Malighetti F, Villa M, Angaroni F, De Sano L, Aroldi A, Antoniotti M, Caravagna G, Piazza R, Graudenzi A, Mologni L, Ramazzotti D. Evolutionary signatures of human cancers revealed via genomic analysis of over 35,000 patients. Nat Commun 2023; 14:5982. [PMID: 37749078 PMCID: PMC10519956 DOI: 10.1038/s41467-023-41670-3] [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: 03/29/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
Recurring sequences of genomic alterations occurring across patients can highlight repeated evolutionary processes with significant implications for predicting cancer progression. Leveraging the ever-increasing availability of cancer omics data, here we unveil cancer's evolutionary signatures tied to distinct disease outcomes, representing "favored trajectories" of acquisition of driver mutations detected in patients with similar prognosis. We present a framework named ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) to extract such signatures from sequencing experiments generated by different technologies such as bulk and single-cell sequencing data. We apply ASCETIC to (i) single-cell data from 146 myeloid malignancy patients and bulk sequencing from 366 acute myeloid leukemia patients, (ii) multi-region sequencing from 100 early-stage lung cancer patients, (iii) exome/genome data from 10,000+ Pan-Cancer Atlas samples, and (iv) targeted sequencing from 25,000+ MSK-MET metastatic patients, revealing subtype-specific single-nucleotide variant signatures associated with distinct prognostic clusters. Validations on several datasets underscore the robustness and generalizability of the extracted signatures.
Collapse
Affiliation(s)
- Diletta Fontana
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Ilaria Crespiatico
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Valentina Crippa
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Federica Malighetti
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Matteo Villa
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Fabrizio Angaroni
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
- Center of Computational Biology, Human Technopole, Milano, Italy
| | - Luca De Sano
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
| | - Andrea Aroldi
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- Hematology and Clinical Research Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Marco Antoniotti
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre-B4, Milan, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Alex Graudenzi
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy.
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre-B4, Milan, Italy.
- Institute of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche (IBFM-CNR), Segrate, Milan, Italy.
| | - Luca Mologni
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
| |
Collapse
|
36
|
Hudson KM, Klimczak LJ, Sterling JF, Burkholder AB, Kazanov M, Saini N, Mieczkowski PA, Gordenin DA. Glycidamide-induced hypermutation in yeast single-stranded DNA reveals a ubiquitous clock-like mutational motif in humans. Nucleic Acids Res 2023; 51:9075-9100. [PMID: 37471042 PMCID: PMC10516655 DOI: 10.1093/nar/gkad611] [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: 03/19/2023] [Revised: 06/28/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
Mutagens often prefer specific nucleotides or oligonucleotide motifs that can be revealed by studying the hypermutation spectra in single-stranded (ss) DNA. We utilized a yeast model to explore mutagenesis by glycidamide, a simple epoxide formed endogenously in humans from the environmental toxicant acrylamide. Glycidamide caused ssDNA hypermutation in yeast predominantly in cytosines and adenines. The most frequent mutations in adenines occurred in the nAt→nGt trinucleotide motif. Base substitutions A→G in this motif relied on Rev1 translesion polymerase activity. Inactivating Rev1 did not alter the nAt trinucleotide preference, suggesting it may be an intrinsic specificity of the chemical reaction between glycidamide and adenine in the ssDNA. We found this mutational motif enriched in published sequencing data from glycidamide-treated mouse cells and ubiquitous in human cancers. In cancers, this motif was positively correlated with the single base substitution (SBS) smoking-associated SBS4 signature, with the clock-like signatures SBS1, SBS5, and was strongly correlated with smoking history and with age of tumor donors. Clock-like feature of the motif was also revealed in cells of human skin and brain. Given its pervasiveness, we propose that this mutational motif reflects mutagenic lesions to adenines in ssDNA from a potentially broad range of endogenous and exogenous agents.
Collapse
Affiliation(s)
- Kathleen M Hudson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Joan F Sterling
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Adam B Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, 34956, Turkey
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Natalie Saini
- Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Piotr A Mieczkowski
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| |
Collapse
|
37
|
Zhang T, Hoang PH, Wong JYY, Yang K, Chen K, Wong MP, Vermeulen RCH, Huang Y, Chanock SJ, Rothman N, Lan Q, Landi MT. Distinct Genomic Landscape of Lung Adenocarcinoma from Household Use of Smoky Coal. Am J Respir Crit Care Med 2023; 208:733-736. [PMID: 37406454 PMCID: PMC10515572 DOI: 10.1164/rccm.202302-0340le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023] Open
Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Jason Y. Y. Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Kaiyun Yang
- The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, Yunnan, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China; and
| | - Maria Pik Wong
- Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Roel C. H. Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Xuanwei study team
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
- The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, Yunnan, China
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China; and
- Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Yunchao Huang
- The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, Yunnan, China
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| |
Collapse
|
38
|
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.
Collapse
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.
| |
Collapse
|
39
|
Otlu B, Díaz-Gay M, Vermes I, Bergstrom EN, Zhivagui M, Barnes M, Alexandrov LB. Topography of mutational signatures in human cancer. Cell Rep 2023; 42:112930. [PMID: 37540596 PMCID: PMC10507738 DOI: 10.1016/j.celrep.2023.112930] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 05/09/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023] Open
Abstract
The somatic mutations found in a cancer genome are imprinted by different mutational processes. Each process exhibits a characteristic mutational signature, which can be affected by the genome architecture. However, the interplay between mutational signatures and topographical genomic features has not been extensively explored. Here, we integrate mutations from 5,120 whole-genome-sequenced tumors from 40 cancer types with 516 topographical features from ENCODE to evaluate the effect of nucleosome occupancy, histone modifications, CTCF binding, replication timing, and transcription/replication strand asymmetries on the cancer-specific accumulation of mutations from distinct mutagenic processes. Most mutational signatures are affected by topographical features, with signatures of related etiologies being similarly affected. Certain signatures exhibit periodic behaviors or cancer-type-specific enrichments/depletions near topographical features, revealing further information about the processes that imprinted them. Our findings, disseminated via the COSMIC (Catalog of Somatic Mutations in Cancer) signatures database, provide a comprehensive online resource for exploring the interactions between mutational signatures and topographical features across human cancer.
Collapse
Affiliation(s)
- Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA; Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara 06800, Turkey
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ian Vermes
- COSMIC, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Maria Zhivagui
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA.
| |
Collapse
|
40
|
Hamouz M, Hammouz RY, Bajwa MA, Alsayed AW, Orzechowska M, Bednarek AK. A Functional Genomics Review of Non-Small-Cell Lung Cancer in Never Smokers. Int J Mol Sci 2023; 24:13314. [PMID: 37686122 PMCID: PMC10488233 DOI: 10.3390/ijms241713314] [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: 08/04/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023] Open
Abstract
There is currently a dearth of information regarding lung cancer in never smokers (LCINS). Additionally, there is a difference in somatic mutations, tumour mutational burden, and chromosomal aberrations between smokers and never smokers (NS), insinuating a different disease entity in LCINS. A better understanding of actionable driver alterations prevalent in LCINS and the genomic landscape will contribute to identifying new molecular targets of relevance for NS that will drastically improve outcomes. Differences in treatment outcomes between NS and smokers, as well as sexes, with NSCLC suggest unique tumour characteristics. Epidermal growth factor receptor (EGFR) tyrosine kinase mutations and echinoderm microtubule-associated protein-like 4 anaplastic lymphoma kinase (EML4-ALK) gene rearrangements are more common in NS and have been associated with chemotherapy resistance. Moreover, NS are less likely to benefit from immune mediators including PD-L1. Unravelling the genomic and epigenomic underpinnings of LCINS will aid in the development of not only novel targeted therapies but also more refined approaches. This review encompasses driver genes and pathways involved in the pathogenesis of LCINS and a deeper exploration of the genomic landscape and tumour microenvironment. We highlight the dire need to define the genetic and environmental aspects entailing the development of lung cancer in NS.
Collapse
|
41
|
Yan W, Zhong Y, Hu X, Xu T, Zhang Y, Kales S, Qu Y, Talley DC, Baljinnyam B, LeClair CA, Simeonov A, Polster BM, Huang R, Ye Y, Rai G, Henderson MJ, Tao D, Fang S. Auranofin targets UBA1 and enhances UBA1 activity by facilitating ubiquitin trans-thioesterification to E2 ubiquitin-conjugating enzymes. Nat Commun 2023; 14:4798. [PMID: 37558718 PMCID: PMC10412574 DOI: 10.1038/s41467-023-40537-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: 01/09/2023] [Accepted: 07/25/2023] [Indexed: 08/11/2023] Open
Abstract
UBA1 is the primary E1 ubiquitin-activating enzyme responsible for generation of activated ubiquitin required for ubiquitination, a process that regulates stability and function of numerous proteins. Decreased or insufficient ubiquitination can cause or drive aging and many diseases. Therefore, a small-molecule enhancing UBA1 activity could have broad therapeutic potential. Here we report that auranofin, a drug approved for the treatment of rheumatoid arthritis, is a potent UBA1 activity enhancer. Auranofin binds to the UBA1's ubiquitin fold domain and conjugates to Cys1039 residue. The binding enhances UBA1 interactions with at least 20 different E2 ubiquitin-conjugating enzymes, facilitating ubiquitin charging to E2 and increasing the activities of seven representative E3s in vitro. Auranofin promotes ubiquitination and degradation of misfolded ER proteins during ER-associated degradation in cells at low nanomolar concentrations. It also facilitates outer mitochondrial membrane-associated degradation. These findings suggest that auranofin can serve as a much-needed tool for UBA1 research and therapeutic exploration.
Collapse
Affiliation(s)
- Wenjing Yan
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Yongwang Zhong
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Tuan Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Yinghua Zhang
- Center for Innovative Biomedical Resources, Biosensor Core, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Stephen Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Yanyan Qu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Daniel C Talley
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Bolormaa Baljinnyam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Brian M Polster
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA.
| | - Shengyun Fang
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Program in Oncology, UM Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| |
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
Zhang J, Ma Q, Yu Q, Xiao F, Zhang Z, Feng H, Liang C. PSMD3-ILF3 signaling cascade drives lung cancer cell proliferation and migration. Biol Direct 2023; 18:33. [PMID: 37337223 DOI: 10.1186/s13062-023-00389-3] [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: 04/12/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Proteasome 26S subunit, non-ATPase 3 (PSMD3) has been reported to participate in various human cancers. Nevertheless, the function of PSMD3 in lung cancer (LC) remains unclear. METHODS RT-qPCR and western blot were used to detect the expression of PSMD3 in LC tissues form TCGA database and clinical samples, and LC cell lines. To study the effect of PSMD3 on LC cell proliferation, migration, invasion, and apoptosis, siRNAs targeting PSMD3 were synthesized and overexpressed plasmids were constructed. CCK-8 assay, Transwell assay, and etc. were used to evaluate the results. Tumor xenograft model was used to evaluate the function of PSMD3 on tumor growth. CO-IP and MS were used to scan the proteins that bind with PSMD3. The interaction between PSMD3 and ILF3 in lung cancer cells were studied using IF staining, CHX protein stability, and ubiquitination assay. Additionally, the effect of ILF3 on cell progression and LC tumor growth was demonstrated by conducting a recovery assay using siILF3 and an ILF3 inhibitor YM155. RESULTS We observed that PSMD3 was significantly overexpressed in LC tissues and cells, which indicated a poor prognosis. Meanwhile, we found that PSMD3 promoted cell proliferation, migration, and invasion of LC cells. We also determined that PSMD3 stabilized the protein expression of ILF3 and the deubiquitination of ILF3 in lung cancer cells. Furthermore, animal experiments showed that the ILF3 inhibitor YM155 could suppress tumor growth with the presence of PSMD3. CONCLUSIONS PSMD3 collectively regulated the stability of ILF3 protein and facilitated the ubiquitination of endogenous ILF3 in LC, which ultimately promoted the progression of LC cells. The PSMD3/ ILF3 axis could potentially be used as a novel strategy for both diagnosis and treatment of LC.
Collapse
Affiliation(s)
- Jin Zhang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Number 2, Yinghua East Street, Chaoyang District, Beijing, 100029, China
| | - Qianli Ma
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Number 2, Yinghua East Street, Chaoyang District, Beijing, 100029, China
| | - Qiduo Yu
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Number 2, Yinghua East Street, Chaoyang District, Beijing, 100029, China
| | - Fei Xiao
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Number 2, Yinghua East Street, Chaoyang District, Beijing, 100029, China
| | - Zhenrong Zhang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Number 2, Yinghua East Street, Chaoyang District, Beijing, 100029, China
| | - Hongxiang Feng
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Number 2, Yinghua East Street, Chaoyang District, Beijing, 100029, China
| | - Chaoyang Liang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Number 2, Yinghua East Street, Chaoyang District, Beijing, 100029, China.
| |
Collapse
|
44
|
Allegra A, Caserta S, Genovese S, Pioggia G, Gangemi S. Gender Differences in Oxidative Stress in Relation to Cancer Susceptibility and Survival. Antioxidants (Basel) 2023; 12:1255. [PMID: 37371985 DOI: 10.3390/antiox12061255] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Genetic, developmental, biochemical, and environmental variables interact intricately to produce sex differences. The significance of sex differences in cancer susceptibility is being clarified by numerous studies. Epidemiological research and cancer registries have revealed over the past few years that there are definite sex variations in cancer incidence, progression, and survival. However, oxidative stress and mitochondrial dysfunction also have a significant impact on the response to treatment of neoplastic diseases. Young women may be more protected from cancer than men because most of the proteins implicated in the regulation of redox state and mitochondrial function are under the control of sexual hormones. In this review, we describe how sexual hormones control the activity of antioxidant enzymes and mitochondria, as well as how they affect several neoplastic diseases. The molecular pathways that underlie the gender-related discrepancies in cancer that have been identified may be better understood, which may lead to more effective precision medicine and vital information on treatment options for both males and females with neoplastic illnesses.
Collapse
Affiliation(s)
- Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood 'Gaetano Barresi', University of Messina, 98125 Messina, Italy
| | - Santino Caserta
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood 'Gaetano Barresi', University of Messina, 98125 Messina, Italy
| | - Sara Genovese
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, Italy
| | - Giovanni Pioggia
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, Italy
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, 98100 Messina, Italy
| |
Collapse
|
45
|
Luo W, Zeng Z, Jin Y, Yang L, Fan T, Wang Z, Pan Y, Yang Y, Yao M, Li Y, Xiao X, Wang G, Wang C, Chang S, Che G, Zhang L, Li Y, Peng Y, Li W. Distinct immune microenvironment of lung adenocarcinoma in never-smokers from smokers. Cell Rep Med 2023:101078. [PMID: 37301197 DOI: 10.1016/j.xcrm.2023.101078] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/19/2023] [Accepted: 05/15/2023] [Indexed: 06/12/2023]
Abstract
Lung cancer in never-smokers (LCINS) presents clinicopathological and molecular features distinct from that in smokers. Tumor microenvironment (TME) plays important roles in cancer progression and therapeutic response. To decipher the difference in TME between never-smoker and smoker lung cancers, we conduct single-cell RNA sequencing on 165,753 cells from 22 treatment-naive lung adenocarcinoma (LUAD) patients. We find that the dysfunction of alveolar cells induced by cigarette smoking contributes more to the aggressiveness of smoker LUADs, while the immunosuppressive microenvironment exerts more effects on never-smoker LUADs' aggressiveness. Moreover, the SPP1hi pro macrophage is identified to be another independent source of monocyte-derived macrophage. Importantly, higher expression of immune checkpoint CD47 and lower expression of major histocompatibility complex (MHC)-I in cancer cells of never-smoker LUADs imply that CD47 may be a better immunotherapy target for LCINS. Therefore, this study reveals the difference of tumorigenesis between never-smoker and smoker LUADs and provides a potential immunotherapy strategy for LCINS.
Collapse
Affiliation(s)
- Wenxin Luo
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhen Zeng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Jin
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lan Yang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ting Fan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhoufeng Wang
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yitong Pan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ying Yang
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Menglin Yao
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yangqian Li
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xue Xiao
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Gang Wang
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chengdi Wang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shuai Chang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Guowei Che
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Li Zhang
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yalun Li
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| |
Collapse
|
46
|
Woodard GA, Ding V, Cho C, Brand NR, Kratz JR, Jones KD, Jablons DM. Comparative genomics between matched solid and lepidic portions of semi-solid lung adenocarcinomas. Lung Cancer 2023; 180:107211. [PMID: 37121213 PMCID: PMC10900430 DOI: 10.1016/j.lungcan.2023.107211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
BACKGROUND Genetic changes that drive the transition from lepidic to invasive cancer development within a radiographic ground glass or semi-solid lung lesion (SSL) are not well understood. Biomarkers to predict the transition to solid, invasive cancer within SSL are needed. METHODS Patients with surgically resected SSL were identified retrospectively from a surgical database. Clinical characteristics and survival were compared between stage I SSL (n = 65) and solid adenocarcinomas (n = 120) resected during the same time period. Areas of normal lung, in situ lepidic, and invasive solid tumor were microdissected from within the same SSL specimens and next generation sequencing (NGS) and Affymetrix microarray of gene expression were performed. RESULTS There were more never smokers, Asian patients, and sub-lobar resections among SSL but no difference in 5-year survival between SSL and solid adenocarcinoma. Driver mutations found in both lepidic and solid invasive portion were EGFR (43%), KRAS (21%), and DNMT3A (5%). CEACAM5 was the most upregulated gene found in solid, invasive portions of SSL. Lepidic and invasive solid areas had many similarities in gene expression, however there were some significant differences with the gene SPP1 being a unique biomarker for the invasive component of a SSL. CONCLUSIONS Common lung cancer driver mutations are present in in situ lepidic as well as invasive solid portions of a SSL, suggesting early development of driver mutations. CEACAM5 and SPP1 emerged as promising biomarkers of invasive potential in semi-solid lesions. Other studies have shown both genes to correlate with poor prognosis in lung cancer and their role in evolution of semi-solid lung lesions warrants further study.
Collapse
Affiliation(s)
- Gavitt A Woodard
- University of California, San Francisco, Department of Surgery, Division of Adult Cardiothoracic Surgery, 500 Parnassus Avenue, Room MUW-424, San Francisco, CA 94143-1724, United States.
| | - Vivianne Ding
- University of California, San Francisco, Department of Surgery, Division of Adult Cardiothoracic Surgery, 500 Parnassus Avenue, Room MUW-424, San Francisco, CA 94143-1724, United States
| | - Christina Cho
- Yale Cancer Center, Department of Immunobiology, 333 Cedar Street, New Haven, CT 06520, United States
| | - Nathan R Brand
- University of California, San Francisco, Department of Surgery, Division of Adult Cardiothoracic Surgery, 500 Parnassus Avenue, Room MUW-424, San Francisco, CA 94143-1724, United States
| | - Johannes R Kratz
- University of California, San Francisco, Department of Surgery, Division of Adult Cardiothoracic Surgery, 500 Parnassus Avenue, Room MUW-424, San Francisco, CA 94143-1724, United States
| | - Kirk D Jones
- University of California, San Francisco, Department of Pathology, 505 Parnassus Avenue Suite M590, Box 0511, San Francisco, CA 94143, United States
| | - David M Jablons
- University of California, San Francisco, Department of Surgery, Division of Adult Cardiothoracic Surgery, 500 Parnassus Avenue, Room MUW-424, San Francisco, CA 94143-1724, United States
| |
Collapse
|
47
|
Triphuridet N, Zhang SS, Nagasaka M, Gao Y, Zhao JJ, Syn NL, Hanaoka T, Ou SHI, Shum E. Low-Dose Computed Tomography (LDCT) Lung Cancer Screening in Asian Female Never-Smokers Is as Efficacious in Detecting Lung Cancer as in Asian Male Ever-Smokers: A Systematic Review and Meta-Analysis. J Thorac Oncol 2023; 18:698-717. [PMID: 36775191 DOI: 10.1016/j.jtho.2023.01.094] [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: 12/11/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023]
Abstract
INTRODUCTION Lung cancer in never-smokers is the major cancer cause of death globally. We compared the efficacy of low-dose computed tomography (LDCT) lung cancer screening among never-smokers versus ever-smokers using systematic review and meta-analysis. METHODS LDCT lung cancer screening studies that simultaneously included both ever-smoker and never-smoker participants published by April 30, 2021, were searched through PubMed and Scopus. Primary outcome measure was relative risk (RR) of lung cancer diagnosed among never-smokers versus ever-smokers. RESULTS A total of 14 studies (13 from Asia) were included (141,396 ever-smokers, 109,251 never-smokers, 1961 lung cancer cases diagnosed). RR of lung cancer diagnosed between ever-smokers versus never-smokers overall was 1.21 (95% confidence interval [CI]: 0.89-1.65), 1.37 (95% CI: 1.08-1.75) among males, and 0.88 (95% CI: 0.59-1.31) among females. RR was 1.78 (95% CI: 1.41-2.24) and 1.22 (95% CI: 0.89-1.68) for Asian female never-smokers versus male never-smokers and versus male ever-smokers, respectively, and 0.99 (95% CI: 0.65-1.50) versus high-risk ever-smokers (≥30 pack-years). Proportional meta-analysis revealed significantly more lung cancers diagnosed at first scan (95.4% [95% CI: 84.9-100.0] versus 70.9% [95% CI: 54.6-84.9], p = 0.010) and at stage 1 (88.5% [95% CI: 79.3-95.4] versus 79.7% [95% CI: 71.1-87.4], p = 0.071) among never-smokers versus ever-smokers, respectively. RR of lung cancer death and 5-year all-cause mortality in never-smokers versus ever-smokers was 0.27 (95% CI: 0.1-0.55, p < 0.001) and 0.13 (95% CI: 0.05-0.33, p < 0.001), respectively. CONCLUSIONS The RR of lung cancer detected by LDCT screening among female never-smokers and male ever-smokers in Asia was statistically similar. Overall and lung cancer specific mortality from the lung cancer diagnosed from LDCT screening was significantly reduced among never-smokers compared to ever-smokers.
Collapse
Affiliation(s)
- Natthaya Triphuridet
- Department of Medicine, Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Shannon S Zhang
- Department of Medicine, Division of Hematology-Oncology, University of California Irvine School of Medicine, Orange, California
| | - Misako Nagasaka
- Department of Medicine, Division of Hematology-Oncology, University of California Irvine School of Medicine, Orange, California; Chao Family Comprehensive Cancer Center, Orange, California; Dalian Best Biotechnology Ltd., Beijing, People's Republic of China
| | - Yanfei Gao
- Division of Neurology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Joseph J Zhao
- National University of Singapore Yong Loo Lin School of Medicine, Singapore
| | - Nicholas L Syn
- National University of Singapore Yong Loo Lin School of Medicine, Singapore
| | - Takaomi Hanaoka
- Department of Thoracic Surgery, JA Nagano North Alps Medical Center Azumi Hospital, Nagano, Japan
| | - Sai-Hong Ignatius Ou
- Department of Medicine, Division of Hematology-Oncology, University of California Irvine School of Medicine, Orange, California; Chao Family Comprehensive Cancer Center, Orange, California.
| | - Elaine Shum
- Division of Medical Oncology, Department of Medicine, NYU Perlmutter Cancer Center/NYU Langone Health, New York, New York
| |
Collapse
|
48
|
Malyla V, Paudel KR, De Rubis G, Hansbro NG, Hansbro PM, Dua K. Cigarette smoking induces lung cancer tumorigenesis via upregulation of the WNT/β-catenin signaling pathway. Life Sci 2023; 326:121787. [PMID: 37209867 DOI: 10.1016/j.lfs.2023.121787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023]
Abstract
Lung cancer has the highest mortality rate compared to any other cancer worldwide, and cigarette smoking is one of the major etiological factors. How cigarette smoke (CS) induces tumorigenesis in healthy cells is still not completely understood. In this study, we treated healthy human bronchial epithelial cells (16HBE14o) with 1 % cigarette smoke extract (CSE) for one week. The CSE exposed cells showed upregulation of WNT/β-catenin pathway genes like WNT3, DLV3, AXIN and β-catenin, 30 oncology proteins were found to be upregulated after CSE treatment. Further, we explored whether the role of extracellular vesicles (EVs) obtained from CSE exposed cells can induce tumorigenesis. We observed that CSE EVs induced migration of healthy 16HBE14o cells by upregulation of various oncology proteins in recipient cells like AXL, EGFR, DKK1, ENG, FGF2, ICAM1, HMOX1, HIF1a, SERPINE1, SNAIL, HGFR, PLAU which are related to WNT signaling, epithelial mesenchymal transition (EMT) and Inflammation, whereas inflammatory marker, GAL-3 and EMT marker, VIM were downregulated. Moreover, β-catenin RNA was found in CSE EVs, upon treatment of these EVs to healthy cells, the β-catenin gene level was decreased in recipient cells compared to healthy 16HBE14o cells, indicating the utilisation of β-catenin RNA in healthy cells. Overall, our study suggests that CS treatment can induce tumorigenesis of healthy cells by upregulating WNT/β-catenin signaling in vitro and human lung cancer patients. Therefore targeting the WNT/β-catenin signaling pathway is involved in tumorigenesis inhibition of this pathway could be a potential therapeutic approach for cigarette smoke induced lung cancer.
Collapse
Affiliation(s)
- Vamshikrishna Malyla
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Centre for Inflammation, Faculty of Science, School of Life Sciences, Centenary Institute and University of Technology Sydney, Sydney, NSW 2007, Australia; Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Faculty of Science, School of Life Sciences, Centenary Institute and University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Gabriele De Rubis
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Nicole G Hansbro
- Centre for Inflammation, Faculty of Science, School of Life Sciences, Centenary Institute and University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Faculty of Science, School of Life Sciences, Centenary Institute and University of Technology Sydney, Sydney, NSW 2007, Australia.
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Centre for Inflammation, Faculty of Science, School of Life Sciences, Centenary Institute and University of Technology Sydney, Sydney, NSW 2007, Australia; Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia.
| |
Collapse
|
49
|
Pagadala M, Sears TJ, Wu VH, Pérez-Guijarro E, Kim H, Castro A, Talwar JV, Gonzalez-Colin C, Cao S, Schmiedel BJ, Goudarzi S, Kirani D, Au J, Zhang T, Landi T, Salem RM, Morris GP, Harismendy O, Patel SP, Alexandrov LB, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind JS, Vijayanand P, Carter H. Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. Nat Commun 2023; 14:2744. [PMID: 37173324 PMCID: PMC10182072 DOI: 10.1038/s41467-023-38271-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
With the continued promise of immunotherapy for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer screening and treatment strategies. Here, we study 1084 eQTLs affecting the TIME found through analysis of The Cancer Genome Atlas and literature curation. These TIME eQTLs are enriched in areas of active transcription, and associate with gene expression in specific immune cell subsets, such as macrophages and dendritic cells. Polygenic score models built with TIME eQTLs reproducibly stratify cancer risk, survival and immune checkpoint blockade (ICB) response across independent cohorts. To assess whether an eQTL-informed approach could reveal potential cancer immunotherapy targets, we inhibit CTSS, a gene implicated by cancer risk and ICB response-associated polygenic models; CTSS inhibition results in slowed tumor growth and extended survival in vivo. These results validate the potential of integrating germline variation and TIME characteristics for uncovering potential targets for immunotherapy.
Collapse
Affiliation(s)
- Meghana Pagadala
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Timothy J Sears
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Victoria H Wu
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | - Eva Pérez-Guijarro
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Hyo Kim
- Undergraduate Bioengineering Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrea Castro
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - James V Talwar
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Steven Cao
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Divya Kirani
- Undergraduate Biology and Bioinformatics Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jessica Au
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Olivier Harismendy
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Sandip Pravin Patel
- Center for Personalized Cancer Therapy, Division of Hematology and Oncology, UC San Diego Moores Cancer Center, San Diego, CA, 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jill P Mesirov
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- The Laboratory of Immunology and Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Chun Chieh Fan
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK, 74136, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wesley K Thompson
- Division of Biostatistics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - J Silvio Gutkind
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | | | - Hannah Carter
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
50
|
Dragani TA, Muley T, Schneider MA, Kobinger S, Eichhorn M, Winter H, Hoffmann H, Kriegsmann M, Noci S, Incarbone M, Tosi D, Franzi S, Colombo F. Lung Adenocarcinoma Diagnosed at a Younger Age Is Associated with Advanced Stage, Female Sex, and Ever-Smoker Status, in Patients Treated with Lung Resection. Cancers (Basel) 2023; 15:cancers15082395. [PMID: 37190323 DOI: 10.3390/cancers15082395] [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: 01/31/2023] [Revised: 04/06/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
To date, the factors which affect the age at diagnosis of lung adenocarcinoma are not fully understood. In our study, we examined the relationships of age at diagnosis with smoking, pathological stage, sex, and year of diagnosis in a discovery (n = 1694) and validation (n = 1384) series of lung adenocarcinoma patients who had undergone pulmonary resection at hospitals in the Milan area and at Thoraxklinik (Heidelberg), respectively. In the discovery series, younger age at diagnosis was associated with ever-smoker status (OR = 1.5, p = 0.0035) and advanced stage (taking stage I as reference: stage III OR = 1.4, p = 0.0067; stage IV OR = 1.7, p = 0.0080), whereas older age at diagnosis was associated with male sex (OR = 0.57, p < 0.001). Analysis in the validation series confirmed the ever versus never smokers' association (OR = 2.9, p < 0.001), the association with highest stages (stage III versus stage I OR = 1.4, p = 0.0066; stage IV versus stage I OR = 2.0, p = 0.0022), and the male versus female sex association (OR = 0.78, p = 0.032). These data suggest the role of smoking in affecting the natural history of the disease. Moreover, aggressive tumours seem to have shorter latency from initiation to clinical detection. Finally, younger age at diagnosis is associated with the female sex, suggesting that hormonal status of young women confers risk to develop lung adenocarcinoma. Overall, this study provided novel findings on the mechanisms underlying age at diagnosis of lung adenocarcinoma.
Collapse
Affiliation(s)
- Tommaso A Dragani
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Thomas Muley
- Translational Research Unit (STF), Thoraxklinik, Heidelberg University Hospital, 69126 Heidelberg, Germany
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Marc A Schneider
- Translational Research Unit (STF), Thoraxklinik, Heidelberg University Hospital, 69126 Heidelberg, Germany
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Sonja Kobinger
- Department of Thoracic Surgery, Thoraxklinik, Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Martin Eichhorn
- Department of Thoracic Surgery, Thoraxklinik, Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Hauke Winter
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Department of Thoracic Surgery, Thoraxklinik, Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Hans Hoffmann
- Department of Thoracic Surgery, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Mark Kriegsmann
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Sara Noci
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Matteo Incarbone
- Department of Surgery, IRCCS Multimedica, 20099 Sesto San Giovanni, Italy
| | - Davide Tosi
- Thoracic Surgery and Lung Transplantation, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Sara Franzi
- Thoracic Surgery and Lung Transplantation, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Francesca Colombo
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
- Institute for Biomedical Technologies, CNR, 20054 Segrate, Italy
| |
Collapse
|