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Wong LY, Elliott IA, Liou DZ, Backhus LM, Lui NS, Shrager JB, Berry MF. Lepidic-Type Lung Adenocarcinomas: Is It Safe to Observe for Growth Before Treating? Ann Thorac Surg 2024; 118:817-823. [PMID: 38490310 DOI: 10.1016/j.athoracsur.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/23/2024] [Accepted: 03/04/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND Lepidic-type adenocarcinomas (LPAs) can be multifocal, and treatment is often deferred until growth is observed. This study investigated the potential downside of that strategy by evaluating the relationship of nodal involvement with tumor size and survival. METHODS The impact of tumor size on lymph node involvement and survival was evaluated for National Cancer Database patients who underwent surgery without induction therapy as primary treatment for cT1-3 N0 M0 histologically confirmed LPA from 2006 to 2019 by using logistic regression, Kaplan-Meier, and Cox analyses. RESULTS Positive nodes occurred in 442 of 8286 patients (5.3%). The incidence of having positive nodes approximately doubled with each 1-cm increment increase in size. Patients with positive nodes were more likely to have larger tumors (27 mm vs 20 mm, P < .001) and clinical ≥T2 disease (40.7% vs 26.8%, P < .001) compared with node-negative patients. However, tumor size was the only significant independent predictor of having positive nodal disease in logistic regression analysis, and this association grew stronger with each incremental centimeter increase in size. Patients with positive nodes were more likely to undergo adjuvant radiotherapy (23.5% vs 1.1%, P < .001) and chemotherapy (72.9% vs 7.9%, P < .001), and expectedly, had worse survival compared with the node-negative group in univariate (5-year overall survival, 50.9% vs 81.1%, P < .001) and multivariable (hazard ratio, 2.56; 95% CI, 2.14-3.05; P < .001) analyses. CONCLUSIONS Nodal involvement is relatively uncommon in early-stage LPAs but steadily increases with tumor size and is associated with dramatically worse survival. These data can be used to inform treatment decisions when evaluating LPA patients.
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Affiliation(s)
- Lye-Yeng Wong
- Department of Cardiothoracic Surgery, Stanford University Medical Center, Palo Alto, California.
| | - Irmina A Elliott
- Department of Cardiothoracic Surgery, Stanford University Medical Center, Palo Alto, California; Department of Cardiothoracic Surgery, Veterans Affairs Palo Alto Health Care System, Palo Alto, California
| | - Douglas Z Liou
- Department of Cardiothoracic Surgery, Stanford University Medical Center, Palo Alto, California
| | - Leah M Backhus
- Department of Cardiothoracic Surgery, Stanford University Medical Center, Palo Alto, California; Department of Cardiothoracic Surgery, Veterans Affairs Palo Alto Health Care System, Palo Alto, California
| | - Natalie S Lui
- Department of Cardiothoracic Surgery, Stanford University Medical Center, Palo Alto, California
| | - Joseph B Shrager
- Department of Cardiothoracic Surgery, Stanford University Medical Center, Palo Alto, California; Department of Cardiothoracic Surgery, Veterans Affairs Palo Alto Health Care System, Palo Alto, California
| | - Mark F Berry
- Department of Cardiothoracic Surgery, Stanford University Medical Center, Palo Alto, California
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Chen G, Yu Y, Qi Y, Li G, Li N, Meng F, Wang W, Shen R. Comparative analysis of PD-L1 expression and molecular alterations in primary versus metastatic lung adenocarcinoma: a real-world study in China. Front Oncol 2024; 14:1393686. [PMID: 39323996 PMCID: PMC11422015 DOI: 10.3389/fonc.2024.1393686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 08/26/2024] [Indexed: 09/27/2024] Open
Abstract
Objectives Programmed death-ligand 1 (PD-L1) is the only Food and Drug Administration-approved biomarker for monitoring response to immune checkpoint inhibitor (ICI) therapy in patients with lung adenocarcinoma. Understanding the nuances of molecular phenotypes, clinical attributes, and PD-L1 expression levels in primary and metastatic lung adenocarcinoma may help predict response to therapy and assist in the clinical management of lung adenocarcinoma. Methods A total of 235 primary and metastatic lesion specimens from patients with non-small cell lung cancer (NSCLC) an institution in Shandong, China were analyzed. PD-L1 expression was assessed by immunohistochemistry using the 22C3 antibody, and the molecular phenotype was determined by next-generation sequencing of 450 genes. The molecular phenotypes of the primary and metastatic lesions were compared. Results Elevated PD-L1 expression was significantly associated with advanced and metastatic disease (P = 0.001). The distribution of PD-L1 expression varied based on the anatomical location, showing a higher frequency of elevated PD-L1 expression in distal metastases than in the primary tumor. Metastatic lesions exhibited a higher proportion of carcinogenic pathway gene alterations and a greater number of DNA damage-repair pathway gene alterations than the primary lesions. Notably, CDKN2A copy number deletions were more prevalent in metastatic lesions than in primary lesions. Clinical data stemming from research conducted at the Memorial Sloan Kettering Cancer Center revealed an association between the absence of CDKN2A expression and a poorer prognosis in stage I lung adenocarcinoma. Conclusion Samples of metastatic tumors exhibited a higher proportion of elevated PD-L1 expression, a greater number of pathway alterations, and a higher occurrence of CDKN2A copy number deletions than primary samples. This highlights the importance of reinforcing the clinical management and follow-up of patients with CDKN2A deficiency, particularly within the subset of stage I lung adenocarcinoma.
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Affiliation(s)
- Gang Chen
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yang Yu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Youchao Qi
- Department of Thoracic Surgery, The Second People's Hospital of Dezhou City, Dezhou, Shandong, China
| | - Guangxu Li
- Department of Thoracic Surgery, The Second People's Hospital of Dezhou City, Dezhou, Shandong, China
| | - Ning Li
- Department of Radiotherapy, The Second People's Hospital of Dezhou City, Dezhou, Shandong, China
| | - Fande Meng
- Department of Internal Medicine, Changle County Traditional Chinese Medicine (TMC) Hospital, Weifang, Shandong, China
| | - Wujie Wang
- Department of Interventional Medicine, The Second Hospital, Cheeloo College of Medicine, Institute of Tumor Intervention, Shandong University, Jinan, Shandong, China
| | - Rong Shen
- Department of Minimally Invasive Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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Krishnamurthy K, Chai J, Liu X, Elsayad M, Goldstein DY. Intratumoral heterogeneity of oncogenic drivers in mixed histology lung adenocarcinomas: How tissue selection impacts molecular testing? Pathol Res Pract 2024; 263:155577. [PMID: 39265501 DOI: 10.1016/j.prp.2024.155577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/21/2024] [Accepted: 08/31/2024] [Indexed: 09/14/2024]
Abstract
Majority of the lung adenocarcinomas show a mixture of different histological patterns. The possibility of histologically heterogeneous areas of the adenocarcinoma showing genetic heterogeneity and harboring different driver mutations, with potentially significant clinical impact, has not been adequately addressed. Currently, there are no guidelines to suggest how to submit tumor tissue in adenocarcinomas with mixed histological features for molecular testing. The objective of this study is to assess intra-tumoral heterogeneity in prominent driver mutations among different morphological patterns of lung adenocarcinoma, its implications on the future of molecular testing as well as its potential impact on patient management. Twenty-three cases of mixed histology lung adenocarcinoma resected between 2018 and 2023 were retrieved from the archives. H&E slides were reviewed to identify the predominant and second most predominant histological patterns. The morphologically different tumor areas were manually macro-dissected for DNA extraction. Next-Generation Sequencing with Ion AmpliSeq™ Cancer Hotspot Panel v2 (Thermo Fisher Scientific, USA). Thirteen cases showed the same pathological variant in both histological components tested. Three cases (13 %) exhibited disparities in the variants detected across the different histological patterns tested (p=0.025). The discrepant findings had a direct therapeutic impact in 4.3 % cases. Seven cases showed no pathogenic variants detected on either of the histological components tested. This study elucidates the presence of infrequent yet significant intra-tumoral heterogeneity in the molecular profiles of mixed histology adenocarcinomas, highlighting the need for guidelines directing tissue selection for molecular testing to avoid missed therapeutic opportunities and mitigate disease relapse.
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Affiliation(s)
| | - Jiani Chai
- Montefiore medical Center, Bronx, NY, USA
| | | | | | - Doctor Y Goldstein
- Montefiore medical Center, Bronx, NY, USA; Albert Einstein College of Medicine, Bronx, NY, USA
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4
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Budczies J, Romanovsky E, Kirchner M, Neumann O, Blasi M, Schnorbach J, Shah R, Bozorgmehr F, Savai R, Stiewe T, Peters S, Schirmacher P, Thomas M, Kazdal D, Christopoulos P, Stenzinger A. KRAS and TP53 co-mutation predicts benefit of immune checkpoint blockade in lung adenocarcinoma. Br J Cancer 2024; 131:524-533. [PMID: 38866964 PMCID: PMC11300455 DOI: 10.1038/s41416-024-02746-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: 11/10/2023] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Predictive biomarkers in use for immunotherapy in advanced non-small cell lung cancer are of limited sensitivity and specificity. We analysed the potential of activating KRAS and pathogenic TP53 mutations to provide additional predictive information. METHODS The study cohort included 713 consecutive immunotherapy patients with advanced lung adenocarcinomas, negative for actionable genetic alterations. Additionally, two previously published immunotherapy and two surgical patient cohorts were analyzed. Therapy benefit was stratified by KRAS and TP53 mutations. Molecular characteristics underlying KRASmut/TP53mut tumours were revealed by the analysis of TCGA data. RESULTS An interaction between KRAS and TP53 mutations was observed in univariate and multivariate analyses of overall survival (Hazard ratio [HR] = 0.56, p = 0.0044 and HR = 0.53, p = 0.0021) resulting in a stronger benefit for KRASmut/TP53mut tumours (HR = 0.71, CI 0.55-0.92). This observation was confirmed in immunotherapy cohorts but not observed in surgical cohorts. Tumour mutational burden, proliferation, and PD-L1 mRNA were significantly higher in TP53-mutated tumours, regardless of KRAS status. Genome-wide expression analysis revealed 64 genes, including CX3CL1 (fractalkine), as specific transcriptomic characteristic of KRASmut/TP53mut tumours. CONCLUSIONS KRAS/TP53 co-mutation predicts ICI benefit in univariate and multivariate survival analyses and is associated with unique molecular tumour features. Mutation testing of the two genes can be easily implemented using small NGS panels.
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Affiliation(s)
- Jan Budczies
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Center for Personalized Medicine (ZPM), Heidelberg, Germany.
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
| | - Eva Romanovsky
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martina Kirchner
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Miriam Blasi
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Thoracic Oncology, Thoraxklinik, Heidelberg University Hospital and National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Johannes Schnorbach
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Thoracic Oncology, Thoraxklinik, Heidelberg University Hospital and National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Rajiv Shah
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Thoracic Oncology, Thoraxklinik, Heidelberg University Hospital and National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Farastuk Bozorgmehr
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Thoracic Oncology, Thoraxklinik, Heidelberg University Hospital and National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Rajkumar Savai
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, Marburg, Germany
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne University, Lausanne, Switzerland
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Michael Thomas
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Thoracic Oncology, Thoraxklinik, Heidelberg University Hospital and National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Petros Christopoulos
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Thoracic Oncology, Thoraxklinik, Heidelberg University Hospital and National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
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5
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Li J, Xiong S, He P, Liang P, Li C, Zhong R, Cai X, Xie Z, Liu J, Cheng B, Chen Z, Liang H, Lao S, Chen Z, Shi J, Li F, Feng Y, Huo Z, Deng H, Yu Z, Wang H, Zhan S, Xiang Y, Wang H, Zheng Y, Lin X, He J, Liang W. Spatial whole exome sequencing reveals the genetic features of highly-aggressive components in lung adenocarcinoma. Neoplasia 2024; 54:101013. [PMID: 38850835 PMCID: PMC11208950 DOI: 10.1016/j.neo.2024.101013] [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: 01/07/2024] [Revised: 05/22/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024]
Abstract
In invasive lung adenocarcinoma (LUAD), patients with micropapillary (MIP) or solid (SOL) components had a significantly poorer prognosis than those with only lepidic (LEP), acinar (ACI) or papillary (PAP) components. It is interesting to explore the genetic features of different histologic subtypes, especially the highly aggressive components. Based on a cohort of 5,933 patients, this study observed that in different tumor size groups, LUAD with MIP/SOL components showed a different prevalence, and patients with ALK alteration or TP53 mutations had a higher probability of developing MIP/SOL components. To control individual differences, this research used spatial whole-exome sequencing (WES) via laser-capture microdissection of five patients harboring these five coexistent components and identified genetic features among different histologic components of the same tumor. In tracing the evolution of components, we found that titin (TTN) mutation might serve as a crucial intratumor potential driver for MIP/SOL components, which was validated by a cohort of 146 LUAD patients undergoing bulk WES. Functional analysis revealed that TTN mutations enriched the complement and coagulation cascades, which correlated with the pathway of cell adhesion, migration, and proliferation. Collectively, the histologic subtypes of invasive LUAD were genetically different, and certain trunk genotypes might synergize with branching TTN mutation to develop highly aggressive components.
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Affiliation(s)
- Jianfu Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Shan Xiong
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Ping He
- Department of pathology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Peng Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Caichen Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Ran Zhong
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Xiuyu Cai
- Department of General Internal Medicine, Sun Yat-sen University Cancer Centre, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou, China
| | - Zhanhong Xie
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou 510120, China
| | - Jun Liu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Bo Cheng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Zhuxing Chen
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Hengrui Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Shen Lao
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Zisheng Chen
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Jiang Shi
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Feng Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Yi Feng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Zhenyu Huo
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Hongsheng Deng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Ziwen Yu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Haixuan Wang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Shuting Zhan
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Yang Xiang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Huiting Wang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Yongmin Zheng
- Department of pathology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Xiaodong Lin
- Department of pathology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Jianxing He
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China; Southern Medical University, Guangzhou 510120, China.
| | - Wenhua Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China.
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6
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Moorthi S, Paguirigan A, Itagi P, Ko M, Pettinger M, Hoge AC, Nag A, Patel NA, Wu F, Sather C, Levine KM, Fitzgibbon MP, Thorner AR, Anderson GL, Ha G, Berger AH. The genomic landscape of lung cancer in never-smokers from the Women's Health Initiative. JCI Insight 2024; 9:e174643. [PMID: 39052387 PMCID: PMC11385083 DOI: 10.1172/jci.insight.174643] [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: 08/14/2023] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
Over 200,000 individuals are diagnosed with lung cancer in the United States every year, with a growing proportion of cases, especially lung adenocarcinoma, occurring in individuals who have never smoked. Women over the age of 50 comprise the largest affected demographic. To understand the genomic drivers of lung adenocarcinoma and therapeutic response in this population, we performed whole genome and/or whole exome sequencing on 73 matched lung tumor/normal pairs from postmenopausal women who participated in the Women's Health Initiative. Somatic copy number alterations showed little variation by smoking status, suggesting that aneuploidy may be a general characteristic of lung cancer regardless of smoke exposure. Similarly, clock-like and APOBEC mutation signatures were prevalent but did not differ in tumors from smokers and never-smokers. However, mutations in both EGFR and KRAS showed unique allelic differences determined by smoking status that are known to alter tumor response to targeted therapy. Mutations in the MYC-network member MGA were more prevalent in tumors from smokers. Fusion events in ALK, RET, and ROS1 were absent, likely due to age-related differences in fusion prevalence. Our work underscores the profound effect of smoking status, age, and sex on the tumor mutational landscape and identifies areas of unmet medical need.
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Affiliation(s)
| | | | - Pushpa Itagi
- Human Biology Division
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Minjeong Ko
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Mary Pettinger
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Anna Ch Hoge
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Anwesha Nag
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Neil A Patel
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Feinan Wu
- Genomics and Bioinformatics Shared Resource, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Cassie Sather
- Genomics and Bioinformatics Shared Resource, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Kevin M Levine
- Human Biology Division
- Division of Hematology and Oncology, Department of Medicine and
| | - Matthew P Fitzgibbon
- Genomics and Bioinformatics Shared Resource, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Aaron R Thorner
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Garnet L Anderson
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Gavin Ha
- Human Biology Division
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Alice H Berger
- Human Biology Division
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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7
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Xia W, Zhang S, Ye Y, Xiao H, Zhang Y, Ning G, Zhang Y, Wang W, Fei GH. Clinicopathological and molecular characterization of resected lung adenocarcinoma: Correlations with histopathological grading systems in Chinese patients. Pathol Res Pract 2024; 259:155359. [PMID: 38810376 DOI: 10.1016/j.prp.2024.155359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/04/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
PURPOSE Driver mutations inform lung adenocarcinoma (LUAD) targeted therapy. Association of histopathological attributes and molecular profiles facilitates clinically viable testing platforms. We assessed correlations between LUAD clinicopathological features, mutational landscapes, and two grading systems among Chinese cases. METHODS 79 Chinese LUAD patients undergoing resection were subjected to targeted sequencing. 68 were invasive nonmucinous adenocarcinoma (INMA), graded via: predominant histologic pattern-based grading system (P-GS) or novel IASLC grading system (I-GS). Driver mutation distributions were appraised and correlated with clinical and pathological data. RESULTS Compared to INMA, non-INMA exhibited smaller, well-differentiated tumors with higher mucin content. INMA grade correlated with size, lymph invasion (P-GS), and driver/EGFR mutations. Mutational spectra varied markedly between grades, with EGFR p.L858R and exon 19 deletion mutations predominating in lower grades; while high-grade P-GS tumors often harbored EGFR copy number variants and complex alterations alongside wild-type cases. I-GS upgrade of P-GS grade 2 to grade 3 was underpinned by ≥20 % high-grade regions bearing p.L858R or ALK fusions. Both systems defined tumors of distinctive phenotypic attributes and molecular genotypes. CONCLUSIONS INMA represent larger, mucin-poor, molecularly heterogeneous LUAD with divergent grade-specific mutation profiles. Stronger predictor of clinicopathological attributes and driver mutations, P-GS stratification offers greater accuracy for molecular testing. A small panel encompassing EGFR and ALK captures the majority of P-GS grade 1/2 mutations whereas expanded panels are optimal for grade 3.
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Affiliation(s)
- Wanli Xia
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Siyuan Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Yuanzi Ye
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China.
| | - Han Xiao
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Ying Zhang
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Guangyao Ning
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Yanbei Zhang
- Department of Geriatric Respiratory and Critical Care, Anhui Geriatric Institute, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Wei Wang
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China; Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China.
| | - Guang-He Fei
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China; Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, PR China.
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8
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Thomas PA, Seguin-Givelet A, Pages PB, Alifano M, Brouchet L, Falcoz PE, Baste JM, Glorion M, Belaroussi Y, Filaire M, Heyndrickx M, Loundou A, Fourdrain A, Dahan M, Boyer L. Real-world outcomes of lobectomy, segmentectomy and wedge resection for the treatment of stage c-IA lung carcinoma. Eur J Cardiothorac Surg 2024; 66:ezae251. [PMID: 38917411 DOI: 10.1093/ejcts/ezae251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 06/01/2024] [Accepted: 06/23/2024] [Indexed: 06/27/2024] Open
Abstract
OBJECTIVES To determine safety and survival outcomes associated with lobectomy, segmentectomy and wedge resection for early-stage lung cancer by quiring the French population-based registry EPIdemiology in THORacic surgery (EPITHOR). METHODS Retrospective analysis of 19 452 patients with stage c IA lung carcinoma who underwent lobectomy, segmentectomy or wedge resection between 2016 and 2022 with curative-intent. Main outcome measures were 90-day mortality and 5-year overall survival estimates. Proportional hazards regression and propensity score matching were used to adjust outcomes for key patient, tumour and practice environment factors. RESULTS The treatment distribution was 72.2% for lobectomy, 21.5% for segmentectomy and 6.3% for wedge. Unadjusted 90-day mortality rates were 1.6%, 1.2% and 1.1%, respectively (P = 0.10). Unadjusted 5-year overall survival estimates were 80%, 78% and 70%, with significant inter-group survival curves differences (P < 0.0001). Multivariable proportional hazards regression showed that wedge was associated with worse overall survival [adjusted hazard ratio (AHR), 1.23 (95% confidence interval 1.03-1.47); P = 0.021] compared with lobectomy, while no significant difference was disclosed when comparing segmentectomy to lobectomy (1.08 [0.97-1.20]; P = 0.162). The three-way propensity score analyses confirmed similar 90-day mortality rate for wedge resection and segmentectomy compared with lobectomy (hazard ratio: 0.43; 95% confidence interval 0.16-1.11; P = 0.081 and 0.99; 0.48-2.10; P = 0.998, respectively), but poorer overall survival (1.45; 1.13-1.86; P = 0.003 and 1.31; 1-1.71; P = 0.048, respectively). CONCLUSIONS Wedge resection was associated with comparable 90-day mortality but lower overall survival when compared to lobectomy. Overall, all types of sublobar resections may not offer equivalent oncologic effectiveness in real-world settings.
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Affiliation(s)
- Pascal Alexandre Thomas
- Department of Thoracic Surgery, Diseases of the Esophagus & Lung Transplantation, Hôpital Nord & CRCM, Inserm UMR 1068, CNRS, UMR 7258, Assistance Publique-Hôpitaux de Marseille & Aix-Marseille University, Marseille, France
| | - Agathe Seguin-Givelet
- Department of Thoracic Surgery, Institut Mutualiste Montsouris, Thorax Institute-Curie-Montsouris, Paris, France
| | - Pierre-Benoît Pages
- Department of Thoracic and Cardiovascular Surgery, Hôpital François Mitterrand, CHU Dijon Bourgogne, Dijon, France
| | - Marco Alifano
- Thoracic Surgery Department, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris & University of Paris Cité, Paris, France
| | - Laurent Brouchet
- Department of Thoracic Surgery, Hôpital Larrey, Toulouse University Hospitals, Toulouse, France
| | - Pierre-Emmanuel Falcoz
- Department of Thoracic Surgery, Nouvel Hôpital Civil, Strasbourg University Hospitals, Strasbourg, France
| | - Jean-Marc Baste
- Department of Thoracic and Cardiovascular Surgery, Hôpital Charles-Nicolle & U1096, Rouen University Hospitals, Rouen, France
| | - Matthieu Glorion
- Department of Thoracic Surgery and Lung Transplantation, Hôpital Foch & Paris-Saclay University, Suresnes, France
| | - Yaniss Belaroussi
- Department of Thoracic Surgery, Hôpital Haut Lévêque, Bordeaux University Hospitals, Bordeaux, France
| | - Marc Filaire
- Department of Thoracic and Endocrine Surgery, Centre Jean Perrin Unicancer Clermont Auvergne Métropole, Clermont-Ferrand, France
| | - Maxime Heyndrickx
- Department of Thoracic Surgery, Hôpital Universitaire de la Côte de Nacre, University Hospitals of Caen Normandie, Caen, France
| | - Anderson Loundou
- Public Health Department Research, Unit EA3279, Aix-Marseille University, Marseille, France
| | - Alex Fourdrain
- Department of Thoracic Surgery, Diseases of the Esophagus & Lung Transplantation, Hôpital Nord & CRCM, Inserm UMR 1068, CNRS, UMR 7258, Assistance Publique-Hôpitaux de Marseille & Aix-Marseille University, Marseille, France
| | - Marcel Dahan
- Department of Thoracic Surgery, Hôpital Larrey, Toulouse University Hospitals, Toulouse, France
| | - Laurent Boyer
- Public Health Department Research, Unit EA3279, Aix-Marseille University, Marseille, France
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Han T, Bai Y, Liu Y, Dong Y, Liang C, Gao L, Zhou J, Guo J, Wu J, Hu D. Integrated multi-omics analysis and machine learning to refine molecular subtypes, prognosis, and immunotherapy in lung adenocarcinoma. Funct Integr Genomics 2024; 24:118. [PMID: 38935217 DOI: 10.1007/s10142-024-01388-x] [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: 12/23/2023] [Revised: 04/01/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024]
Abstract
Lung adenocarcinoma (LUAD) has a malignant characteristic that is highly aggressive and prone to metastasis. There is still a lack of suitable biomarkers to facilitate the refinement of precision-based therapeutic regimens. We used a combination of 10 known clustering algorithms and the omics data from 4 dimensions to identify high-resolution molecular subtypes of LUAD. Subsequently, consensus machine learning-related prognostic signature (CMRS) was developed based on subtypes related genes and an integrated program framework containing 10 machine learning algorithms. The efficiency of CMRS was analyzed from the perspectives of tumor microenvironment, genomic landscape, immunotherapy, drug sensitivity, and single-cell analysis. In terms of results, through multi-omics clustering, we identified 2 comprehensive omics subtypes (CSs) in which CS1 patients had worse survival outcomes, higher aggressiveness, mRNAsi and mutation frequency. Subsequently, we developed CMRS based on 13 key genes up-regulated in CS1. The prognostic predictive efficiency of CMRS was superior to most established LUAD prognostic signatures. CMRS demonstrated a strong correlation with tumor microenvironmental feature variants and genomic instability generation. Regarding clinical performance, patients in the high CMRS group were more likely to benefit from immunotherapy, whereas low CMRS were more likely to benefit from chemotherapy and targeted drug therapy. In addition, we evaluated that drugs such as neratinib, oligomycin A, and others may be candidates for patients in the high CMRS group. Single-cell analysis revealed that CMRS-related genes were mainly expressed in epithelial cells. The novel molecular subtypes identified in this study based on multi-omics data could provide new insights into the stratified treatment of LUAD, while the development of CMRS could serve as a candidate indicator of the degree of benefit of precision therapy and immunotherapy for LUAD.
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Affiliation(s)
- Tao Han
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China
- Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Ying Bai
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China.
- Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China.
| | - Yafeng Liu
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China
- Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Yunjia Dong
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China
- Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Chao Liang
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China
- Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Lu Gao
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China
- Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Jiawei Zhou
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China
- Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Jianqiang Guo
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China
- Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Jing Wu
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China.
- Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China.
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institute, Huainan, Anhui, China.
- Key Laboratory of Industrial Dust Prevention and Control & Occupational Safety and Health of the Ministry of Education, Anhui University of Science and Technology, Huainan, Anhui, China.
| | - Dong Hu
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China.
- Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China.
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institute, Huainan, Anhui, China.
- Key Laboratory of Industrial Dust Prevention and Control & Occupational Safety and Health of the Ministry of Education, Anhui University of Science and Technology, Huainan, Anhui, China.
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10
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Lee Y, Lee B, Choi YL, Kang DW, Han J. Clinicopathologic and Molecular Characteristics of HER2 (ERBB2)-Altered Non-Small Cell Lung Cancer: Implications for Precision Medicine. Mod Pathol 2024; 37:100490. [PMID: 38588887 DOI: 10.1016/j.modpat.2024.100490] [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: 09/30/2023] [Revised: 03/18/2024] [Accepted: 03/30/2024] [Indexed: 04/10/2024]
Abstract
The heterogeneous relationship between protein expression, amplification, and mutations in human epidermal growth factor receptor 2 (HER2) in non-small cell lung cancer (NSCLC) and the optimal methods for detecting these alterations remain unclear. We aimed to elucidate the clinicopathological and molecular characteristics of HER2-altered NSCLC and investigate practical approaches for identifying patients who might benefit from HER2-targeted therapies. Using next-generation sequencing data from 1680 individuals, we searched for patients with HER2-altered NSCLCs, including amplifications and mutations. Clinicopathological data and tissue slides were reviewed. Immunohistochemistry (IHC) and silver in situ hybridization were performed according to the American Society of Clinical Oncology/College of American Pathologists guidelines. Our analysis identified 89 (5.3%) patients with HER2-altered NSCLCs, comprising 30 (1.8%) with amplification and 59 (3.6%) mutations, and they were compared with 165 control patients. Of the 59 HER2-mutated cases, 52 harbored tyrosine kinase domain (TKD) mutations, primarily HER2 exon 20 insertions. HER2 TKD alterations were associated with younger age, female sex, nonsmoking status, adenocarcinoma with a micropapillary pattern, lung-to-lung metastasis, and poor overall survival. The 33 patients with TKD mutations and 3 with non-TKD point mutations showed incomplete or complete membranous HER2 immunoreactivity (1+ and 2+, 61.07%). Six patients exhibiting amplifications had an IHC score of ≤2+ despite their high copy numbers and concomitantly displayed other actionable EGFR, KRAS, SMARCA4, and other HER2 mutations. These HER2-altered NSCLCs with molecular coalterations showed heterogeneous patterns through HER2 IHC and silver in situ hybridization. Therefore, next-generation sequencing should be used to identify HER2 mutations in patients with NSCLC who present with concomitant alterations. In addition, the above clinicopathological characteristics and HER2 IHC results can be valuable determinants for identifying patients with HER2-altered NSCLC. These insights hold promise for the development of more effective diagnostic and therapeutic strategies for this complex subset of NSCLC patients.
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Affiliation(s)
- Yurimi Lee
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea; Department of Pathology, Chungnam National University College of Medicine, Daejeon, South Korea
| | - Boram Lee
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea; Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, South Korea.
| | - Dong-Wook Kang
- Department of Pathology, Chungnam National University College of Medicine, Daejeon, South Korea
| | - Joungho Han
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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11
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Zhou J, Wu D, Zheng Q, Wang T, Mei J. Development of a predictive model to predict postoperative bone metastasis in pathological I-II non-small cell lung cancer. Transl Lung Cancer Res 2024; 13:998-1009. [PMID: 38854951 PMCID: PMC11157370 DOI: 10.21037/tlcr-23-866] [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: 01/02/2024] [Accepted: 04/14/2024] [Indexed: 06/11/2024]
Abstract
Background Bone is a common metastatic site in postoperative metastasis, but related risk factors for early-stage non-small cell lung cancer (NSCLC) remain insufficiently investigated. Thus, the study aimed to identify risk factors for postoperative bone metastasis in early-stage NSCLC and construct a nomogram to identify high-risk individuals. Methods Between January 2015 and January 2021, we included patients with resected stage I-II NSCLC at the Department of Thoracic Surgery, West China Hospital. Univariable and multivariable Cox regression analyses were used to identify related risk factors. Additionally, we developed a visual nomogram to forecast the likelihood of bone metastasis. Evaluation of the model involved metrics such as the area under the curve (AUC), C-index, and calibration curves. To ensure reliability, internal validation was performed through bootstrap resampling. Results Our analyses included 2,106 eligible patients, with 54 (2.56%) developing bone metastasis. Multivariable Cox analyses showed that tumor nodules with solid component, higher pT stage, higher pN stage, and histologic subtypes especially solid/micropapillary predominant types were considered as independent risk factors of bone metastasis. In the training set, the developed model demonstrated AUCs of 0.807, 0.769, and 0.761 for 1-, 3-, and 5-year follow-ups, respectively. The C-index, derived from 1,000 bootstrap resampling, showed values of 0.820, 0.793, and 0.777 for 1-, 3-, and 5-year follow-ups. The calibration curve showed that the model was well calibrated. Conclusions The predictive model is proven to be valuable in estimating the probability of bone metastasis in early-stage NSCLC following surgery. Leveraging four easy-to-acquire clinical parameters, this model effectively identifies high-risk patients and enables individualized surveillance strategies for better patient care.
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Affiliation(s)
- Jian Zhou
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Dongsheng Wu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Quan Zheng
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Tengyong Wang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Jiandong Mei
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
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12
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Fick CN, Dunne EG, Vanstraelen S, Toumbacaris N, Tan KS, Rocco G, Molena D, Huang J, Park BJ, Rekhtman N, Travis WD, Chaft JE, Bott MJ, Rusch VW, Adusumilli PS, Sihag S, Isbell JM, Jones DR. High-risk features associated with recurrence in stage I lung adenocarcinoma. J Thorac Cardiovasc Surg 2024:S0022-5223(24)00440-9. [PMID: 38788834 DOI: 10.1016/j.jtcvs.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
OBJECTIVE There is a lack of knowledge regarding the use of prognostic features in stage I lung adenocarcinoma (LUAD). Thus, we investigated clinicopathologic features associated with recurrence after complete resection for stage I LUAD. METHODS We performed a retrospective analysis of patients with pathologic stage I LUAD who underwent R0 resection from 2010 to 2020. Exclusion criteria included history of lung cancer, induction or adjuvant therapy, noninvasive or mucinous LUAD, and death within 90 days of surgery. Fine and Gray competing-risk regression assessed associations between clinicopathologic features and disease recurrence. RESULTS In total, 1912 patients met inclusion criteria. Most patients (1565 [82%]) had stage IA LUAD, and 250 developed recurrence: 141 (56%) distant and 109 (44%) locoregional only. The 5-year cumulative incidence of recurrence was 12% (95% CI, 11%-14%). Higher maximum standardized uptake value of the primary tumor (hazard ratio [HR], 1.04), sublobar resection (HR, 2.04), higher International Association for the Study of Lung Cancer grade (HR, 5.32 [grade 2]; HR, 7.93 [grade 3]), lymphovascular invasion (HR, 1.70), visceral pleural invasion (HR, 1.54), and tumor size (HR, 1.30) were independently associated with a hazard of recurrence. Tumors with 3 to 4 high-risk features had a higher cumulative incidence of recurrence at 5 years than tumors without these features (30% vs 4%; P < .001). CONCLUSIONS Recurrence after resection for stage I LUAD remains an issue for select patients. Commonly reported clinicopathologic features can be used to define patients at high risk of recurrence and should be considered when assessing the prognosis of patients with stage I disease.
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Affiliation(s)
- Cameron N Fick
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth G Dunne
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stijn Vanstraelen
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicolas Toumbacaris
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gaetano Rocco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniela Molena
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - James Huang
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bernard J Park
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Natasha Rekhtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - William D Travis
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jamie E Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY; Weill Cornell Medical College, New York, NY
| | - Matthew J Bott
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Valerie W Rusch
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Prasad S Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Smita Sihag
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - James M Isbell
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David R Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY.
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Lin Y, Li D, Hui H, Miao H, Luo M, Roy B, Chen B, Zhang W, Shao D, Ma D, Jie Y, Qiu F, Li H, Jiang B. Genomic landscape and tumor mutational features of resected preinvasive to invasive lung adenocarcinoma. Front Oncol 2024; 14:1389618. [PMID: 38803537 PMCID: PMC11128541 DOI: 10.3389/fonc.2024.1389618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) are considered pre-invasive forms of lung adenocarcinoma (LUAD) with a 5-year recurrence-free survival of 100%. We investigated genomic profiles in early tumorigenesis and distinguished mutational features of preinvasive to invasive adenocarcinoma (IAC) for early diagnosis. Methods Molecular information was obtained from a 689-gene panel in the 90 early-stage LUAD Chinese patients using next-generation sequencing. Gene signatures were identified between pathology subtypes, including AIS/MIA (n=31) and IAC (n=59) in this cohort. Mutational and clinicopathological information was also obtained from the Cancer Genome Atlas (TCGA) as a comparison cohort. Results A higher mutation frequency of TP53, RBM10, MUC1, CSMD, MED1, LRP1B, GLI1, MAP3K, and RYR2 was observed in the IAC than in the AIS/MIA group. The AIS/MIA group showed higher mutation frequencies of ERBB2, BRAF, GRIN2A, and RB1. Comparable mutation rates for mutually exclusive genes (EGFR and KRAS) across cohorts highlight the critical transition to invasive LUAD. Compared with the TCGA cohort, EGFR, KRAS, TP53, and RBM10 were frequently mutated in both cohorts. Despite limited gene mutation overlap between cohorts, we observed variant mutation types in invasive LUAD. Additionally, the tumor mutation burden (TMB) values were significantly lower in the AIS/MIA group than in the IAC group in both the Chinese cohort (P=0.0053) and TCGA cohort (P<0.01). Conclusion These findings highlight the importance of distinguishing preinvasive from invasive LUAD in the early stages of LUAD and both pathology and molecular features in clinical practice, revealing genomic tumor heterogeneity and population differences.
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Affiliation(s)
- Yangui Lin
- Department of Thoracic Cardiovascular Surgery, The Eighth Affiliated Hospital of Sun Yat−sen University, Shenzhen, Guangdong, China
| | - Dan Li
- Community Health Center, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Hongliang Hui
- Department of Thoracic Cardiovascular Surgery, The Eighth Affiliated Hospital of Sun Yat−sen University, Shenzhen, Guangdong, China
| | - Haoran Miao
- Department of Thoracic Cardiovascular Surgery, The Eighth Affiliated Hospital of Sun Yat−sen University, Shenzhen, Guangdong, China
| | - Min Luo
- Department of Thoracic Cardiovascular Surgery, The Eighth Affiliated Hospital of Sun Yat−sen University, Shenzhen, Guangdong, China
| | - Bhaskar Roy
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | | | - Wei Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Di Shao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Di Ma
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Fan Qiu
- Department of Thoracic Cardiovascular Surgery, The Eighth Affiliated Hospital of Sun Yat−sen University, Shenzhen, Guangdong, China
| | - Huaming Li
- Department of Thoracic Cardiovascular Surgery, The Eighth Affiliated Hospital of Sun Yat−sen University, Shenzhen, Guangdong, China
| | - Bo Jiang
- Department of Thoracic Cardiovascular Surgery, The Eighth Affiliated Hospital of Sun Yat−sen University, Shenzhen, Guangdong, China
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14
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Liu X, Mei W, Zhang P, Zeng C. PIK3CA mutation as an acquired resistance driver to EGFR-TKIs in non-small cell lung cancer: Clinical challenges and opportunities. Pharmacol Res 2024; 202:107123. [PMID: 38432445 DOI: 10.1016/j.phrs.2024.107123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
Epithelial growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have significantly enhanced the treatment outcomes in non-small cell lung cancer (NSCLC) patients harboring EGFR mutations. However, the occurrence of acquired resistance to EGFR-TKIs is an unavoidable outcome observed in these patients. Disruption of the PI3K/AKT/mTOR signaling pathway can contribute to the emergence of resistance to EGFR TKIs in lung cancer. The emergence of PIK3CA mutations following treatment with EGFR-TKIs can lead to resistance against EGFR-TKIs. This review provides an overview of the current perspectives regarding the involvement of PI3K/AKT/mTOR signaling in the development of lung cancer. Furthermore, we outline the state-of-the-art therapeutic strategies targeting the PI3K/AKT/mTOR signaling pathway in lung cancer. We highlight the role of PIK3CA mutation as an acquired resistance mechanism against EGFR-TKIs in EGFR-mutant NSCLC. Crucially, we explore therapeutic strategies targeting PIK3CA-mediated resistance to EGFR TKIs in lung cancer, aiming to optimize the effectiveness of treatment.
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Affiliation(s)
- Xiaohong Liu
- Department of Medical Oncology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, China
| | - Wuxuan Mei
- Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Pengfei Zhang
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Shenzhen 518110, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Shenzhen 518110, China.
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15
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Zheng X, Qiu L, Huang Y, Cheng R, Huang S, Xu K, Cai W, Deng Y, Wang W, Zhong X, Cui F, Hao Z, Liu J. Exploring the molecular and immune-landscape of lung cancer associated with cystic airspaces. Mol Immunol 2024; 168:75-88. [PMID: 38430689 DOI: 10.1016/j.molimm.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 03/05/2024]
Abstract
To explore the molecular biological characteristics of lung cancer associated with cystic airspaces (LCCA) and its potential roles on prognosis. A total of 165 LCCAs and 201 non-LCCAs were enrolled in this study. Bulk RNA sequencing was implemented in eight LCCAs and nine non-LCCAs to explore the differentially expressed genes. TCGA data were used to analyze LCCA-specific genes that associated with overall survival (OS). The median age was 60 (IQR 53 to 65) years in LCCA cohort. We found LCCA were predominant in men and had less visceral pleura invasion (VPI) or lympho-vascular invasion (LVI). Moreover, LCCA presented with higher histological heterogeneity. Kaplan-Meier analysis showed that patients of age more than 60 and positive VPI had significantly less PFS in LCCA. Cox regression suggested that LCCA, micropapillary subtype proportion and VPI were the independent risk factors for PFS. LCCA had up-regulated pathways associated with EMT, angiogenesis and cell migration. In addition, LCCA displayed higher levels of immunosuppressor infiltration (M2 macrophages, CAFs and MDSCs) and distinct cell death and metabolic patterns. BCR/TCR repertoire analysis revealed less BCR richness, clonality and high-abundance shared clonotypes in LCCA. Finally, Cox regression analysis identified that four cystic-specific genes, KCNK3, NRN1, PARVB and TRHDE-AS1, were associated with OS of lung adenocarcinoma (LUAD). And cystic-specific risk scores (CSRSs) were calculated to construct a nomogram, which performance well. Our study for the first time indicated significantly distinct molecular biological and immune characteristics between LCCA and non-LCCA, which provide complementary prognostic values in early-stage non-small cell lung cancer (NSCLC).
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Affiliation(s)
- Xiang Zheng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China; Department of Oncology, The First Clinical Medical College of Henan University, Kaifeng, China
| | - Li Qiu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ying Huang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ran Cheng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Sihe Huang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ke Xu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Weipeng Cai
- Department of Thoracic Surgery, Shantou Central Hospital, Shantou, China
| | - Yu Deng
- Department of Radiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Wang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Xi Zhong
- Department of Medical Imaging, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Fei Cui
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Zhexue Hao
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Jun Liu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China.
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Li X, Gao Z, Diao H, Guo C, Yu Y, Liu S, Feng Z, Peng Z. Lung adenocarcinoma: selection of surgical approaches in solid adenocarcinoma from the viewpoint of clinicopathologic features and tumor microenvironmental heterogeneity. Front Oncol 2024; 14:1326626. [PMID: 38505588 PMCID: PMC10949368 DOI: 10.3389/fonc.2024.1326626] [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: 10/23/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Introduction Solid adenocarcinoma represents a notably aggressive subtype of lung adenocarcinoma. Amidst the prevailing inclination towards conservative surgical interventions for diminutive lung cancer lesions, the critical evaluation of this subtype's malignancy and heterogeneity stands as imperative for the formulation of surgical approaches and the prognostication of long-term patient survival. Methods A retrospective dataset, encompassing 2406 instances of non-solid adenocarcinoma (comprising lepidic, acinar, and papillary adenocarcinoma) and 326 instances of solid adenocarcinoma, was analyzed to ascertain the risk factors concomitant with diverse histological variants of lung adenocarcinoma. Concurrently, RNA-sequencing data delineating explicit pathological subtypes were extracted from 261 cases in the TCGA database and 188 cases in the OncoSG database. This data served to illuminate the heterogeneity across lung adenocarcinoma (LUAD) specimens characterized by differential histological features. Results Solid adenocarcinoma is associated with an elevated incidence of pleural invasion, microscopic vessel invasion, and lymph node metastasis, relative to other subtypes of lung adenocarcinoma. Furthermore, the tumor microenvironment (TME) in solid pattern adenocarcinoma displayed suboptimal oxygenation and acidic conditions, concomitant with augmented tumor cell proliferation and invasion capacities. Energy and metabolic activities were significantly upregulated in tumor cells of the solid pattern subtype. This subtype manifested robust immune tolerance and capabilities for immune evasion. Conclusion This present investigation identifies multiple potential metrics for evaluating the invasive propensity, metastatic likelihood, and immune resistance of solid pattern adenocarcinoma. These insights may prove instrumental in devising surgical interventions that are tailored to patients diagnosed with disparate histological subtypes of LUAD, thereby offering valuable directional guidance.
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Affiliation(s)
- Xiao Li
- Department of Thoracic Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Zhen Gao
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong First Medical University, Jinan, Shandong, China
| | - Haixiao Diao
- Department of Thoracic Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Chenran Guo
- Department of Thoracic Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Yue Yu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong First Medical University, Jinan, Shandong, China
| | - Shang Liu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong First Medical University, Jinan, Shandong, China
| | - Zhen Feng
- Department of Thoracic Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Zhongmin Peng
- Department of Thoracic Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
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Ma S, Wang R, Peng Q, Liu Y, Qian J, Li M, Li K, Huang Z, Wu L, Xie D. Is there a prognostic difference among stage I lung adenocarcinoma patients with different BRAF-mutation status? Thorac Cancer 2024; 15:715-721. [PMID: 38362771 PMCID: PMC10961218 DOI: 10.1111/1759-7714.15248] [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: 01/02/2024] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND The data of the prognostic role of V-Raf murine sarcoma viral oncogene homolog B1 (BRAF) mutations in early-stage lung adenocarcinoma (LUAD) patients is scarce. This study aimed to investigate the proportion, clinicopathological features, and prognostic significance of patients with stage I LUAD carrying BRAF mutations. METHODS We collected 431 patients with pathological stage I LUAD from cBioPortal for Cancer Genomics and 1604 LUAD patients tested for BRAF V600E and epidermal growth factor receptor (EGFR) mutations from Shanghai Pulmonary Hospital. Survival curves were drawn by the Kaplan-Meier method and compared by log-rank test. Cox proportional hazard models, propensity-score matching (PSM), and overlap weighting (OW) were performed in this study. The primary endpoint was recurrence-free survival (RFS). RESULTS The proportion of BRAF mutations was estimated at 5.6% in a Caucasian cohort. BRAF V600E mutations were detected in six (1.4%) patients in Caucasian populations and 16 (1.0%) patients in Chinese populations. Two BRAF V600E-mutant patients were detected to have concurrent EGFR mutations, one for 19-del and one for L858R. For pathological stage I LUAD patients, BRAF mutations were not significantly associated with worse RFS than wild-type BRAF patients (HR = 1.111; p = 0.885). After PSM and OW, similar results were presented (HR = 1.352; p = 0.742 and HR = 1.246; p = 0.764, respectively). BRAF V600E mutation status also lacked predictive significance for RFS (HR, 1.844; p = 0.226; HR = 1.144; p = 0.831 and HR = 1.466; p = 0.450, respectively). CONCLUSIONS In this study, we demonstrated that BRAF status may not be capable of predicting prognosis in stage I LUAD patients. There is a need for more data to validate our findings.
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Affiliation(s)
- Shang‐Shang Ma
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiP. R. China
| | - Rang‐Rang Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiP. R. China
| | - Qiao Peng
- School of MedicineTongji UniversityShanghaiP. R. China
| | - Yu'e Liu
- School of MedicineTongji UniversityShanghaiP. R. China
| | - Jia‐Yi Qian
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiP. R. China
| | - Ming‐Jun Li
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiP. R. China
| | - Kun Li
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiP. R. China
| | - Zhi‐Ye Huang
- School of MedicineTongji UniversityShanghaiP. R. China
| | - Lei‐Lei Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiP. R. China
| | - Dong Xie
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiP. R. China
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Nishimura T, Végvári Á, Nakamura H, Fujii K, Sakai H, Naruki S, Furuya N, Saji H. Cancer cell immunity-related protein co-expression networks are associated with early-stage solid-predominant lung adenocarcinoma. Front Oncol 2024; 14:1273780. [PMID: 38450191 PMCID: PMC10915646 DOI: 10.3389/fonc.2024.1273780] [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: 08/07/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024] Open
Abstract
Background Solid-predominant lung adenocarcinoma (SPA), which is one of the high-risk subtypes with poor prognosis and unsatisfactory response to chemotherapy and targeted therapy in lung adenocarcinoma, remains molecular profile unclarified. Weighted correlation network analysis (WGCNA) was used for data mining, especially for studying biological networks based on pairwise correlations between variables. This study aimed to identify disease-related protein co-expression networks associated with early-stage SPA. Methods We assessed cancerous cells laser-microdissected from formalin-fixed paraffin-embedded (FFPE) tissues of a SPA group (n = 5), referencing a low-risk subtype, a lepidic predominant subtype group (LPA) (n = 4), and another high-risk subtype, micropapillary predominant subtype (MPA) group (n = 3) and performed mass spectrometry-based proteomic analysis. Disease-related co-expression networks associated with the SPA subtype were identified by WGCNA and their upstream regulators and causal networks were predicted by Ingenuity Pathway Analysis. Results Among the forty WGCNA network modules identified, two network modules were found to be associated significantly with the SPA subtype. Canonical enriched pathways were highly associated with cellular growth, proliferation, and immune response. Upregulated HLA class I molecules HLA-G and HLA-B implicated high mutation burden and T cell activation in the SPA subtype. Upstream analysis implicated the involvement of highly activated oncogenic regulators, MYC, MLXIPL, MYCN, the redox master regulator NFE2L2, and the highly inhibited LARP1, leading to oncogenic IRES-dependent translation, and also regulators of the adaptive immune response, including highly activated IFNG, TCRD, CD3-TCR, CD8A, CD8B, CD3, CD80/CD86, and highly inhibited LILRB2. Interestingly, the immune checkpoint molecule HLA-G, which is the counterpart of LILRB2, was highly expressed characteristically in the SPA subtype and might be associated with antitumor immunity. Conclusion Our findings provide a disease molecular profile based on protein co-expression networks identified for the high-risk solid predominant adenocarcinoma, which will help develop future therapeutic strategies.
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Affiliation(s)
- Toshihide Nishimura
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Haruhiko Nakamura
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Kiyonaga Fujii
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
- Laboratory of Analytical Chemistry, Daiichi University of Pharmacy, Fukuoka, Japan
| | - Hiroki Sakai
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Saeko Naruki
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Naoki Furuya
- Division of Respiratory Medicine, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hisashi Saji
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
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Xie L, Kong H, Yu J, Sun M, Lu S, Zhang Y, Hu J, Du F, Lian Q, Xin H, Zhou J, Wang X, Powell CA, Hirsch FR, Bai C, Song Y, Yin J, Yang D. Spatial transcriptomics reveals heterogeneity of histological subtypes between lepidic and acinar lung adenocarcinoma. Clin Transl Med 2024; 14:e1573. [PMID: 38318637 PMCID: PMC10844893 DOI: 10.1002/ctm2.1573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/15/2024] [Accepted: 01/21/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Patients who possess various histological subtypes of early-stage lung adenocarcinoma (LUAD) have considerably diverse prognoses. The simultaneous existence of several histological subtypes reduces the clinical accuracy of the diagnosis and prognosis of early-stage LUAD due to intratumour intricacy. METHODS We included 11 postoperative LUAD patients pathologically confirmed to be stage IA. Single-cell RNA sequencing (scRNA-seq) was carried out on matched tumour and normal tissue. Three formalin-fixed and paraffin-embedded cases were randomly selected for 10× Genomics Visium analysis, one of which was analysed by digital spatial profiler (DSP). RESULTS Using DSP and 10× Genomics Visium analysis, signature gene profiles for lepidic and acinar histological subtypes were acquired. The percentage of histological subtypes predicted for the patients from samples of 11 LUAD fresh tissues by scRNA-seq showed a degree of concordance with the clinicopathologic findings assessed by visual examination. DSP proteomics and 10× Genomics Visium transcriptomics analyses revealed that a negative correlation (Spearman correlation analysis: r = -.886; p = .033) between the expression levels of CD8 and the expression trend of programmed cell death 1(PD-L1) on tumour endothelial cells. The percentage of CD8+ T cells in the acinar region was lower than in the lepidic region. CONCLUSIONS These findings illustrate that assessing patient histological subtypes at the single-cell level is feasible. Additionally, tumour endothelial cells that express PD-L1 in stage IA LUAD suppress immune-responsive CD8+ T cells.
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Affiliation(s)
- Linshan Xie
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalFudan UniversityShanghaiChina
| | - Hui Kong
- Department of PathologyZhongshan HospitalFudan UniversityShanghaiChina
| | - Jinjie Yu
- Department of Thoracic SurgeryZhongshan HospitalFudan UniversityShanghaiChina
- Department of Thoracic SurgeryShanghai Geriatric Medical CenterShanghaiChina
| | - Mengting Sun
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalFudan UniversityShanghaiChina
| | - Shaohua Lu
- Department of PathologyZhongshan HospitalFudan UniversityShanghaiChina
| | - Yong Zhang
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalFudan UniversityShanghaiChina
| | - Jie Hu
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalFudan UniversityShanghaiChina
| | - Fang Du
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghaiChina
| | - Qiuyu Lian
- Gurdon InstituteUniversity of CambridgeCambridgeUK
| | - Hongyi Xin
- Global Institute of Future TechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Jian Zhou
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Engineer and Technology Research Center of Internet of Things for Respiratory MedicineShanghaiChina
- Shanghai Key Laboratory of Lung Inflammation and InjuryShanghaiChina
- Shanghai Respiratory Research InstitutionShanghaiChina
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Institute of Clinical BioinformaticsShanghaiChina
- Shanghai Engineering Research for AI Technology for Cardiopulmonary DiseasesFudan University Shanghai Medical CollegeShanghaiChina
| | - Charles A. Powell
- Pulmonary, Critical Care and Sleep MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Fred R. Hirsch
- Tisch Cancer Institute, Center for Thoracic Oncology, Mount Sinai Health SystemNew YorkNew YorkUSA
| | - Chunxue Bai
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Engineer and Technology Research Center of Internet of Things for Respiratory MedicineShanghaiChina
- Shanghai Key Laboratory of Lung Inflammation and InjuryShanghaiChina
- Shanghai Respiratory Research InstitutionShanghaiChina
| | - Yuanlin Song
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Engineer and Technology Research Center of Internet of Things for Respiratory MedicineShanghaiChina
- Shanghai Key Laboratory of Lung Inflammation and InjuryShanghaiChina
- Shanghai Respiratory Research InstitutionShanghaiChina
| | - Jun Yin
- Department of Thoracic SurgeryZhongshan HospitalFudan UniversityShanghaiChina
| | - Dawei Yang
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Engineer and Technology Research Center of Internet of Things for Respiratory MedicineShanghaiChina
- Shanghai Key Laboratory of Lung Inflammation and InjuryShanghaiChina
- Shanghai Respiratory Research InstitutionShanghaiChina
- Department of Pulmonary and Critical Care MedicineZhongshan Hospital (Xiamen)Fudan UniversityXiamenChina
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Han T, Liu Y, Zhou J, Guo J, Xing Y, Xie J, Bai Y, Wu J, Hu D. Development of an invasion score based on metastasis-related pathway activity profiles for identifying invasive molecular subtypes of lung adenocarcinoma. Sci Rep 2024; 14:1692. [PMID: 38243040 PMCID: PMC10799059 DOI: 10.1038/s41598-024-51681-9] [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: 09/09/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024] Open
Abstract
The invasive capacity of lung adenocarcinoma (LUAD) is an important factor influencing patients' metastatic status and survival outcomes. However, there is still a lack of suitable biomarkers to evaluate tumor invasiveness. LUAD molecular subtypes were identified by unsupervised consistent clustering of LUAD. The differences in prognosis, tumor microenvironment (TME), and mutation were assessed among different subtypes. After that, the invasion-related gene score (IRGS) was constructed by genetic differential analysis, WGCNA analysis, and LASSO analysis, then we evaluated the relationship between IRGS and invasive characteristics, TME, and prognosis. The predictive ability of the IRGS was verified by in vitro experiments. Next, the "oncoPredict" R package and CMap were used to assess the potential value of IRGS in drug therapy. The results showed that LUAD was clustered into two molecular subtypes. And the C1 subtype exhibited a worse prognosis, higher stemness enrichment activity, less immune infiltration, and higher mutation frequency. Subsequently, IRGS developed based on molecular subtypes demonstrated a strong association with malignant characteristics such as invasive features, higher stemness scores, less immune infiltration, and worse survival. In vitro experiments showed that the higher IRGS LUAD cell had a stronger invasive capacity than the lower IRGS LUAD cell. Predictive analysis based on the "oncoPredict" R package showed that the high IRGS group was more sensitive to docetaxel, erlotinib, paclitaxel, and gefitinib. Among them, in vitro experiments verified the greater killing effect of paclitaxel on high IRGS cell lines. In addition, CMap showed that purvalanol-a, angiogenesis-inhibitor, and masitinib have potential therapeutic effects in the high IRGS group. In summary we identified and analyzed the molecular subtypes associated with the invasiveness of LUAD and developed IRGS that can efficiently predict the prognosis and invasive ability of the tumor. IRGS may be able to facilitate the precision treatment of LUAD to some extent.
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Affiliation(s)
- Tao Han
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China
| | - Yafeng Liu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China
- Affiliated Cancer Hospital, Anhui University of Science and Technology, Huainan, 232035, China
| | - Jiawei Zhou
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China
| | - Jianqiang Guo
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China
| | - Yingru Xing
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China
- Department of Clinical Laboratory, Anhui Zhongke Gengjiu Hospital, Hefei, China
| | - Jun Xie
- Affiliated Cancer Hospital, Anhui University of Science and Technology, Huainan, 232035, China
| | - Ying Bai
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China.
| | - Jing Wu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China.
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institutes, Anhui University of Science and Technology, Huainan, 232001, China.
| | - Dong Hu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China.
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institutes, Anhui University of Science and Technology, Huainan, 232001, China.
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Zhang Y, Fu F, Zhang Q, Li L, Liu H, Deng C, Xue Q, Zhao Y, Sun W, Han H, Gao Z, Guo C, Zheng Q, Hu H, Sun Y, Li Y, Ding C, Chen H. Evolutionary proteogenomic landscape from pre-invasive to invasive lung adenocarcinoma. Cell Rep Med 2024; 5:101358. [PMID: 38183982 PMCID: PMC10829798 DOI: 10.1016/j.xcrm.2023.101358] [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: 01/24/2023] [Revised: 08/29/2023] [Accepted: 12/11/2023] [Indexed: 01/08/2024]
Abstract
Lung adenocarcinoma follows a stepwise progression from pre-invasive to invasive. However, there remains a knowledge gap regarding molecular events from pre-invasive to invasive. Here, we conduct a comprehensive proteogenomic analysis comprising whole-exon sequencing, RNA sequencing, and proteomic and phosphoproteomic profiling on 98 pre-invasive and 99 invasive lung adenocarcinomas. The deletion of chr4q12 contributes to the progression from pre-invasive to invasive adenocarcinoma by downregulating SPATA18, thus suppressing mitophagy and promoting cell invasion. Proteomics reveals diverse enriched pathways in normal lung tissues and pre-invasive and invasive adenocarcinoma. Proteomic analyses identify three proteomic subtypes, which represent different stages of tumor progression. We also illustrate the molecular characterization of four immune clusters, including endothelial cells, B cells, DCs, and immune depression subtype. In conclusion, this comprehensive proteogenomic study characterizes the molecular architecture and hallmarks from pre-invasive to invasive lung adenocarcinoma, guiding the way to a deeper understanding of the tumorigenesis and progression of this disease.
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Affiliation(s)
- Yang Zhang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Fangqiu Fu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Qiao Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Lingling Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Hui Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China; State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Chaoqiang Deng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qianqian Xue
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Wenrui Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Han Han
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhendong Gao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chunmei Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Qiang Zheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Hong Hu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yihua Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuan Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China.
| | - Haiquan Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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Yan HJ, Lin SC, Xu SH, Gao YB, Zhou BJ, Zhou R, Chen FM, Li FR. Proteomic analysis reveals LRPAP1 as a key player in the micropapillary pattern metastasis of lung adenocarcinoma. Heliyon 2024; 10:e23913. [PMID: 38226250 PMCID: PMC10788494 DOI: 10.1016/j.heliyon.2023.e23913] [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: 08/04/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/17/2024] Open
Abstract
Objectives Lung adenocarcinomas have different prognoses depending on their histological growth patterns. Micropapillary growth within lung adenocarcinoma, particularly metastasis, is related to dismal prognostic outcome. Metastasis accounts for a major factor leading to mortality among lung cancer patients. Understanding the mechanisms underlying early stage metastasis can help develop novel treatments for improving patient survival. Methods Here, quantitative mass spectrometry was conducted for comparing protein expression profiles among various histological subtypes, including adenocarcinoma in situ, minimally invasive adenocarcinoma, and invasive adenocarcinoma (including acinar and micropapillary [MIP] types). To determine the mechanism of MIP-associated metastasis, we identified a protein that was highly expressed in MIP. The expression of the selected highly expressed MIP protein was verified via immunohistochemical (IHC) analysis and its function was validated by an in vitro migration assay. Results Proteomic data revealed that low-density lipoprotein receptor-related protein-associated protein 1 (LRPAP1) was highly expressed in MIP group, which was confirmed by IHC. The co-expressed proteins in this study, PSMD1 and HSP90AB1, have been reported to be highly expressed in different cancers and play an essential role in metastasis. We observed that LRPAP1 promoted lung cancer progression, including metastasis, invasion and proliferation in vitro and in vivo. Conclusion LRPAP1 is necessary for MIP-associated metastasis and is the candidate novel anti-metastasis therapeutic target.
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Affiliation(s)
- Hao-jie Yan
- Translational Medicine Collaborative Innovation Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
- Post-doctoral Scientific Research Station of Basic Medicine, Jinan University, 510632, Guangzhou, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, 518020, Shenzhen, China
| | - Sheng-cheng Lin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 518172, Shenzhen, China
| | | | - Yu-biao Gao
- Translational Medicine Collaborative Innovation Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, 518020, Shenzhen, China
| | - Bao-jin Zhou
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, China
| | - Ruo Zhou
- Deepxomics Co., Ltd, 518112, Shenzhen, China
| | - Fu-ming Chen
- Translational Medicine Collaborative Innovation Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, 518020, Shenzhen, China
| | - Fu-rong Li
- Translational Medicine Collaborative Innovation Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, 518020, Shenzhen, China
- Institute of Health Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
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Huang Y, Ma S, Xu JY, Qian K, Wang Y, Zhang Y, Tan M, Xiao T. Prognostic biomarker discovery based on proteome landscape of Chinese lung adenocarcinoma. Clin Proteomics 2024; 21:2. [PMID: 38182978 PMCID: PMC10768252 DOI: 10.1186/s12014-023-09449-2] [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: 06/26/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
Despite recent innovations in imaging and genomic screening promotes advance in diagnosis and treatment of lung adenocarcinoma (LUAD), there remains high mortality of LUAD and insufficient understanding of LUAD biology. Our previous study performed an integrative multi-omic analysis of LUAD, filling the gap between genomic alterations and their biological proteome effects. However, more detailed molecular characterization and biomarker resources at proteome level still need to be uncovered. In this study, a quantitative proteomic experiment of patient-derived benign lung disease samples was carried out. After that, we integrated the proteomic data with previous dataset of 103 paired LUAD samples. We depicted the proteomic differences between non-cancerous and tumor samples and among diverse pathological subtypes. We also found that up-regulated mitophagy was a significant characteristic of early-stage LUAD. Additionally, our integrative analysis filtered out 75 potential prognostic biomarkers and validated two of them in an independent LUAD serum cohort. This study provided insights for improved understanding proteome abnormalities of LUAD and the novel prognostic biomarker discovery offered an opportunity for LUAD precise management.
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Affiliation(s)
- Yuqi Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sheng Ma
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jun-Yu Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, 528400, China.
| | - Kun Qian
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Yaru Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yi Zhang
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong, 528400, China.
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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24
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Willner J, Narula N, Moreira AL. Updates on lung adenocarcinoma: invasive size, grading and STAS. Histopathology 2024; 84:6-17. [PMID: 37872108 DOI: 10.1111/his.15077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
Advancements in the classification of lung adenocarcinoma have resulted in significant changes in pathological reporting. The eighth edition of the tumour-node-metastasis (TNM) staging guidelines calls for the use of invasive size in staging in place of total tumour size. This shift improves prognostic stratification and requires a more nuanced approach to tumour measurements in challenging situations. Similarly, the adoption of new grading criteria based on the predominant and highest-grade pattern proposed by the International Association for the Study of Lung Cancer (IASLC) shows improved prognostication, and therefore clinical utility, relative to previous grading systems. Spread through airspaces (STAS) is a form of tumour invasion involving tumour cells spreading through the airspaces, which has been highly researched in recent years. This review discusses updates in pathological T staging, adenocarcinoma grading and STAS and illustrates the utility and limitations of current concepts in lung adenocarcinoma.
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Affiliation(s)
- Jonathan Willner
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Navneet Narula
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Andre L Moreira
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
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25
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Rusch VW. Commentary: Lobectomy, segmentectomy, or wedge resection for stage IA lung cancer: Several choices, many questions. J Thorac Cardiovasc Surg 2024; 167:348-349. [PMID: 37527725 DOI: 10.1016/j.jtcvs.2023.07.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/03/2023]
Affiliation(s)
- Valerie W Rusch
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY.
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26
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Kang H, Lv H, Tung TH, Ma D, Wang Z, Du J, Zhou K, Pan J, Zhang Y, Peng S, Yu Z, Shen B, Ye M. EGFR co-mutation is associated with the risk of recurrence in invasive lung adenocarcinoma with the micropapillary component. Asian J Surg 2024; 47:201-207. [PMID: 37574361 DOI: 10.1016/j.asjsur.2023.07.066] [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: 01/30/2023] [Revised: 06/06/2023] [Accepted: 07/09/2023] [Indexed: 08/15/2023] Open
Abstract
BACKGROUND Invasive lung adenocarcinoma (LUAD) patients with the micropapillary (MPP) component tend to have extremely poor prognosis. To optimize clinical outcomes, a better understanding of specific concurrent gene alterations and their impact on the prognosis of patients with the MPP component is necessary. METHOD A total of 621 Chinese patients with surgically resected invasive LUAD who underwent genetic testing for lung cancer were enrolled in this retrospective study. The genomic profiling of major lung cancer-related genes based on next-generation sequencing (NGS) was carried out on formalin-fixed paraffin-embedded tumor samples. RESULT Among 621 patients with invasive LUAD, 154 (24.8%, 154/621) had the MPP component. We found that PIK3CA (4.5% vs 1.3%), KRAS (9.1% vs 4.7%), and ROS1 (2.6% vs 0.4%) were more frequent in patients with the MPP component than those without the MPP component (P < 0.05). The co-mutation occurred in 66 patients (10.6%, 66/621), of which 19 patients with the MPP component. Most of them were EGFR co-mutations (89.5%, 17/19), including EGFR and PIK3CA, EGFR and ERBB2, and other types. Patients with the MPP component who harbored EGFR co-mutations showed significantly worse recurrence-free survival (RFS) than single EGFR mutation (median RFS 20.1 vs 30.5 months; hazard ratio [HR]: 8.008; 95% confidence interval [CI]: 1.322-48.508). CONCLUSIONS Patients with the MPP component harbored the co-mutation of driver genes had a higher risk of recurrence after surgery, especially in patients with EGFR co-mutation. EGFR co-mutation was a significant prognostic factor for RFS in patients with the MPP component.
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Affiliation(s)
- Haixin Kang
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, 317000, China
| | - Haiyan Lv
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, 317000, China
| | - Tao-Hsin Tung
- Evidence-based Medicine Center, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, 317000, China
| | - Dehua Ma
- Department of Thoracic Surgery, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, 317000, China
| | - Zheng Wang
- Department of Thoracic Surgery, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, 317000, China
| | - Juping Du
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, 317000, China
| | - Kai Zhou
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, 317000, China
| | - Juan Pan
- Department of Clinical Laboratory, Taizhou Hospital, Zhejiang University, Linhai, Zhejiang, 317000, China
| | - Yanjie Zhang
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, 317000, China
| | - Shuotao Peng
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, 317000, China
| | - Zhaonan Yu
- Hangzhou D.A. Medical Laboratory, Hangzhou, Zhejiang, 310000, China
| | - Bo Shen
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, 317000, China.
| | - Minhua Ye
- Department of Thoracic Surgery, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, 317000, China.
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Sharma R, Kamireddy AP, Hussaini SM, Chatterjee S, Hasan Q, Jain J. The landscape of actionable genomic alterations in lung adenocarcinomas in India. Front Genet 2023; 14:1256756. [PMID: 38155717 PMCID: PMC10754624 DOI: 10.3389/fgene.2023.1256756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/05/2023] [Indexed: 12/30/2023] Open
Abstract
Lung adenocarcinoma (LUAD), the most prevalent form of non-small cell lung cancer (NSCLC), remains a leading cause of cancer-related death globally, including in India, with a 5-year survival rate below 10%. Despite these grim statistics, recent advances in the use of next-generation sequencing (NGS) for identifying genetic alterations and the emergence of targeted therapies have opened new possibilities for personalized treatment based on distinct molecular signatures. To understand the molecular pattern of NSCLC, a retrospective study was conducted with 53 Indian LUAD patient samples, using a targeted NGS panel of 46 cancer-relevant oncogenes to identify clinically relevant variants. Pathogenic or likely pathogenic variants were detected in 94% of the 53 cases. Non-synonymous mutations, rearrangements, copy number alterations, insertions, and deletions of functional relevance were observed in 31 out of 46 genes. The most frequently mutated genes included TP53 (52.8%) and EGFR (50.9%), followed by RET, PIK3CA and ERBB2; some patients had multiple alterations in the same gene. Gender-based enrichment analysis indicated that ALK and IDH2 alterations were more prevalent in females, while TP53 and PTEN were more common in males. No significant correlation was found between mutations and other clinicopathological attributes, such as age, stage, and subtype. A higher prevalence of EGFR, RET, PIK3CA, ERBB2 and ALK mutations were observed compared to previous LUAD genetic studies coupled with a lower frequency of KRAS mutations. Clinically actionable variants were annotated using OncoKB and categorized into the four therapeutic levels based on their clinical evidence. Seventy-nine percent of cases had at least one clinically actionable alteration. Most patients (39.6%) had the highest level of actionability (Level 1) wherein an FDA-approved drug is available specifically for the observed mutation in lung cancer patients. EGFR Exon19 in-frame deletions and EGFR L858R were the most frequent among targetable variants (20.7%). These findings emphasize the importance of a selective NGS panel in enabling personalized medicine approaches by identifying actionable molecular alterations and informing the choice of targeted therapy for more effective treatment options in Indian NSCLC patients.
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Affiliation(s)
- Rakesh Sharma
- Sapien Biosciences Private Limited, Hyderabad, Telangana, India
| | - Aruna Priya Kamireddy
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, Telangana, India
| | | | - Soma Chatterjee
- Sapien Biosciences Private Limited, Hyderabad, Telangana, India
| | - Qurratulain Hasan
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, Telangana, India
| | - Jugnu Jain
- Sapien Biosciences Private Limited, Hyderabad, Telangana, India
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28
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Fick CN, Dunne EG, Lankadasari MB, Mastrogiacomo B, Asao T, Vanstraelen S, Liu Y, Sanchez-Vega F, Jones DR. Genomic profiling and metastatic risk in early-stage non-small cell lung cancer. JTCVS OPEN 2023; 16:9-16. [PMID: 38204702 PMCID: PMC10775106 DOI: 10.1016/j.xjon.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 01/12/2024]
Affiliation(s)
- Cameron N. Fick
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth G. Dunne
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manendra B. Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brooke Mastrogiacomo
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tetsuhiko Asao
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stijn Vanstraelen
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yuan Liu
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Francisco Sanchez-Vega
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David R. Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
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29
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Zhang S, Dong P, Pan Z, Chen Q, Zhu J, Mao Z. Comparison of gene mutation profile in different lung adenocarcinoma subtypes by targeted next-generation sequencing. Med Oncol 2023; 40:349. [PMID: 37935925 DOI: 10.1007/s12032-023-02206-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 09/28/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Disease prognosis after resection of lung cancer could be affected by pathological subtypes. In this study, we investigated the difference of gene variation and significantly altered pathways between adenocarcinoma in situ (AIS)/microinvasive adenocarcinoma (MIA) and invasive adenocarcinoma (IAC) subtypes to reveal the molecular mechanism of prognosis differences. METHODS Sixty one tumor tissues were subjected to DNA extraction and customized 136 gene targeted next-generation sequencing. Comparisons between groups were performed with two-sided Fisher's exact test for categorical variables and two-tailed unpaired t test for numerical variables. RESULTS A total of 402 somatic mutations involved in 70 genes were detected in all these samples, and 74.29% of these genes were mutated in at least two samples. PMS2, ARID1A, EGFR, and POLE were the most frequently mutated genes. ALK_EML4 fusion was observed in one IAC patient and RET_ KIF5B fusion in one AIS patient. A significant higher proportion of patients with TP53 gene mutation was observed in the IAC group (P = 0.0057). The average onset age in IAC group is 62.48 years, which is greater than other subtypes (P = 0.0166). It revealed that mutations in genes involved in the mTOR signaling pathway (56.52% vs 26.32%, P = 0.0288) and Hippo signaling pathway (34.78% vs 10.53%, P = 0.0427) were significantly enriched in IAC subtypes, suggesting the key involvement of mTOR and Hippo signaling pathways in lung tumor development and malignant progression. CONCLUSIONS This study revealed the heterogeneity of gene mutations and significantly altered pathways between different lung cancer subtypes, suggesting the potential mechanism of different prognosis.
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Affiliation(s)
- Shaowen Zhang
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, People's Republic of China
| | - Ping Dong
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, People's Republic of China
| | - Zongwei Pan
- Department of Medical Equipment, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, People's Republic of China
| | - Qian Chen
- Thorgene Co., Ltd, Beijing, 100176, China
| | - Junqi Zhu
- Thorgene Co., Ltd, Beijing, 100176, China
| | - Zhangfan Mao
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, People's Republic of China.
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30
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Fei W, Yan Y, Liu G, Peng B, Liu Y, Chen Q. High-risk histological subtype-related FAM83A hijacked FOXM1 transcriptional regulation to promote malignant progression in lung adenocarcinoma. PeerJ 2023; 11:e16306. [PMID: 37904848 PMCID: PMC10613442 DOI: 10.7717/peerj.16306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/26/2023] [Indexed: 11/01/2023] Open
Abstract
Background According to the histopathology, lung adenocarcinoma (LUAD) could be divided into five distinct pathological subtypes, categorized as high-risk (micropapillary and solid) group, intermediate-risk (acinar and papillary) group, and low-risk (lepidic) group. Despite this classification, there is limited knowledge regarding the role of transcription factors (TFs) in the molecular regulation of LUAD histology patterns. Methods Publish data was mined to explore the candidate TFs associated with high-risk histopathology in LUAD, which was validated in tissue samples. Colony formation, CCK8, EdU, transwell, and matrigel assays were performed to determine the biological function of FAM83A in vitro. Subcutaneous tumor-bearing in BALB/c nude mice and xenograft perivitelline injection in zebrafish were utilized to unreal the function of FAM83A in vivo. We also performed chromatin immunoprecipitation (ChIP), dual-luciferase reporter, and rescue assays to uncover the underline mechanism of FAM83A. Immunohistochemistry (IHC) was performed to confirm the oncogenic role of FAM83A in clinical LUAD tissues. Results Screening the transcriptional expression data from TCGA-LUAD, we focus on the differentially expressed TFs across the divergent pathological subtypes, and identified that the expression of FAM83A is higher in patients with high-risk groups compared with those with intermediate or low-risk groups. The FAM83A expression is positively correlated with worse overall survival, progression-free survival, and advanced stages. Gain- and loss-of-function assays revealed that FAM83A promoted cell proliferation, invasion, and migration of tumor cell lines both in vivo and in vitro. Pathway enrichment analysis shows that FAM83A expression is significantly enriched in cell cycle-related pathways. The ChIP and luciferase reporter assays revealed that FAM83A hijacks the promoter of FOXM1 to progress the malignant LUAD, and the rescue assay uncovered that the function of FAM83A is partly dependent on FOXM1 regulation. Additionally, patients with high FAM83A expression positively correlated with higher IHC scores of Ki-67 and FOXM1, and patients with active FAM83A/FOXM1 axis had poor prognoses in LUAD. Conclusions Taken together, our study revealed that the high-risk histological subtype-related FAM83A hijacks FOXM1 transcriptional regulation to promote malignant progression in lung adenocarcinoma, which implies targeting FAM83A/FOXM1 is the therapeutic vulnerability.
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Affiliation(s)
- Wei Fei
- Department of Clinical College, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yan Yan
- Department of Cardiovascular Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Guangjun Liu
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Bo Peng
- Department of Clinical College, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Yuanyuan Liu
- Department of Respiratory and Critical Care Medicine, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Qiang Chen
- Department of Clinical College, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
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31
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Karihtala P, Kilpivaara O, Porvari K. Mutational signatures and their association with survival and gene expression in urological carcinomas. Neoplasia 2023; 44:100933. [PMID: 37678146 PMCID: PMC10495641 DOI: 10.1016/j.neo.2023.100933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/31/2023] [Indexed: 09/09/2023]
Abstract
Different sources of mutagenesis cause consistently identifiable patterns of mutations and mutational signatures that mirror the various carcinogenetic processes. We used publicly available data from the Cancer Genome Atlas to evaluate the associations between the activity of the mutational signatures and various survival endpoints in six types of urological cancers after adjusting for established prognostic factors. The predictive power of the signatures was evaluated with dynamic area under curve models. In addition, links between mutational signature activities and differences in gene expression patterns were analysed. APOBEC-related signature SBS2 was associated with improved overall survival (OS) and disease-specific survival (DSS) in bladder carcinomas in the multivariate analysis, while clock-like signature SBS1 predicted shortened DSS and progression-free interval (PFI) in clear cell renal cell carcinomas (ccRCC). In papillary renal cell carcinomas (pRCC), SBS45 was a predictor of improved outcomes, and APOBEC-related SBS13 was a predictor of worse outcomes. Gene expression analyses revealed various enriched pathways between the low- and high-signature groups. Interestingly, in both the ccRCC and pRCC cohorts, the genes of several members of the melanoma antigen (MAGE) family were highly upregulated in the signatures, which predicted poor outcomes, and downregulated in signatures, which were associated with improved survival. To summarize, SBS signatures provide substantial prognostic value compared with just the traditional prognostic factors in certain cancer types. APOBEC-related SBS2 and SBS13 seem to provide robust prognostic information for particular urological cancers, maybe driven by the expression of specific groups of genes, including the MAGE gene family.
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Affiliation(s)
- Peeter Karihtala
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center and University of Helsinki, Helsinki FI-00290, Finland.
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki FI-00014, Finland; Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland; HUSLAB Laboratory of Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki FI-00014, Finland
| | - Katja Porvari
- Department of Pathology, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu FI-90220, Finland
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32
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Durham M, Vadde S, Brooks AN. MET exon 14 skipping is overexpressed in an allele-specific manner in lung adenocarcinoma primary samples. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000957. [PMID: 37829573 PMCID: PMC10565573 DOI: 10.17912/micropub.biology.000957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
MET exon 14 skipping ( METΔ14 ) is a well-characterized oncogene in the Ras-MAPK pathway driving lung adenocarcinoma (LUAD). Previous studies on METΔ14 revealed this aberrantly spliced oncogene is expressed in LUAD primary samples and is associated with heterozygous somatic mutations and deletions near exon 14 splice sites. Upon further examination of DNA and RNA sequencing data from primary samples, we highlight that METΔ14 is overexpressed in an allele-specific manner. These data suggest that dose-dependence of METΔ14 may be critical to oncogenesis.
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Affiliation(s)
- Megan Durham
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - Swetha Vadde
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States
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33
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Ohtani-Kim SJY, Taki T, Tane K, Miyoshi T, Samejima J, Aokage K, Nagasaki Y, Kojima M, Sakashita S, Watanabe R, Sakamoto N, Goto K, Tsuboi M, Ishii G. Efficacy of Preoperative Biopsy in Predicting the Newly Proposed Histologic Grade of Resected Lung Adenocarcinoma. Mod Pathol 2023; 36:100209. [PMID: 37149221 DOI: 10.1016/j.modpat.2023.100209] [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: 12/27/2022] [Revised: 04/05/2023] [Accepted: 04/25/2023] [Indexed: 05/08/2023]
Abstract
A novel histologic grading system for invasive lung adenocarcinomas (LUAD) has been newly proposed and adopted by the World Health Organization (WHO) classification. We aimed to evaluate the concordance of newly established grades between preoperative biopsy and surgically resected LUAD samples. Additionally, factors affecting the concordance rate and its prognostic impact were also analyzed. In this study, surgically resected specimens of 222 patients with invasive LUAD and their preoperative biopsies collected between January 2013 and December 2020 were used. We determined the histologic subtypes of preoperative biopsy and surgically resected specimens and classified them separately according to the novel WHO grading system. The overall concordance rate of the novel WHO grades between preoperative biopsy and surgically resected samples was 81.5%, which was higher than that of the predominant subtype. When stratified by grades, the concordance rate of grades 1 (well-differentiated, 84.2%) and 3 (poorly differentiated, 89.1%) was found to be superior compared to grade 2 (moderately differentiated, 66.2%). Overall, the concordance rate was not significantly different from biopsy characteristics, including the number of biopsy samples, biopsy sample size, and tumor area size. On the other hand, the concordance rate of grades 1 and 2 was significantly higher in tumors with smaller invasive diameters, and that of grade 3 was significantly higher in tumors with larger invasive diameters. Preoperative biopsy specimens can predict the novel WHO grades, especially grades 1 and 3 of surgically resected specimens, more accurately than the former grading system, regardless of preoperative biopsy or clinicopathologic characteristics.
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Affiliation(s)
- Seiyu Jeong-Yoo Ohtani-Kim
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Chiba, Japan; Department of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Chiba, Japan; Course of Advanced Clinical Research of Cancer, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tetsuro Taki
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Chiba, Japan.
| | - Kenta Tane
- Department of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Tomohiro Miyoshi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Joji Samejima
- Department of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Keiju Aokage
- Department of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Yusuke Nagasaki
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Chiba, Japan; Department of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Chiba, Japan; Course of Advanced Clinical Research of Cancer, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Motohiro Kojima
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Shingo Sakashita
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Reiko Watanabe
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Naoya Sakamoto
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Genichiro Ishii
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Chiba, Japan; Course of Advanced Clinical Research of Cancer, Juntendo University Graduate School of Medicine, Tokyo, Japan
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34
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Jin F, Yang Z, Shao J, Tao J, Reißfelder C, Loges S, Zhu L, Schölch S. ARID1A mutations in lung cancer: biology, prognostic role, and therapeutic implications. Trends Mol Med 2023; 29:646-658. [PMID: 37179132 DOI: 10.1016/j.molmed.2023.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Mutations in the AT-interacting domain-rich protein 1A (ARID1A) gene, a critical component of the switch/sucrose nonfermentable (SWI/SNF) complex, are frequently found in most human cancers. Approximately 5-10% of lung cancers carry ARID1A mutations. ARID1A loss in lung cancer correlates with clinicopathological features and poor prognosis. Co-mutation of ARID1A and epidermal growth factor receptor (EGFR) results in the limited efficacy of EGFR tyrosine kinase inhibitors (EGFR-TKIs) but increases the clinical benefit of immune checkpoint inhibitors (ICIs). ARID1A gene mutation plays a role in cell cycle regulation, metabolic reprogramming, and epithelial-mesenchymal transition. We present the first comprehensive review of the relationship between ARID1A gene mutations and lung cancer and discuss the potential of ARID1A as a new molecular target.
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Affiliation(s)
- Fukang Jin
- JCCU Translational Surgical Oncology (A430), German Cancer Research Center (DKFZ), Heidelberg, Germany; DKFZ-Hector Cancer Institute, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Zhiguang Yang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Jilin, China
| | - Jingbo Shao
- Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jianxin Tao
- JCCU Translational Surgical Oncology (A430), German Cancer Research Center (DKFZ), Heidelberg, Germany; DKFZ-Hector Cancer Institute, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Christoph Reißfelder
- DKFZ-Hector Cancer Institute, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Sonja Loges
- DKFZ-Hector Cancer Institute, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Division of Personalized Medical Oncology (A420), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Personalized Oncology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Lei Zhu
- JCCU Translational Surgical Oncology (A430), German Cancer Research Center (DKFZ), Heidelberg, Germany; DKFZ-Hector Cancer Institute, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
| | - Sebastian Schölch
- JCCU Translational Surgical Oncology (A430), German Cancer Research Center (DKFZ), Heidelberg, Germany; DKFZ-Hector Cancer Institute, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
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35
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Connolly JG, Kalchiem-Dekel O, Tan KS, Dycoco J, Chawla M, Rocco G, Park BJ, Lee RP, Beattie JA, Solomon SB, Ziv E, Adusumilli PS, Buonocore DJ, Husta BC, Jones DR, Baine MK, Bott MJ. Feasibility of shape-sensing robotic-assisted bronchoscopy for biomarker identification in patients with thoracic malignancies. J Thorac Cardiovasc Surg 2023; 166:231-240.e2. [PMID: 36621452 PMCID: PMC10209350 DOI: 10.1016/j.jtcvs.2022.10.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/11/2022] [Accepted: 10/29/2022] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Molecular diagnostic assays require samples with high nucleic acid content to generate reliable data. Similarly, programmed death-ligand 1 (PD-L1) immunohistochemistry (IHC) requires samples with adequate tumor content. We investigated whether shape-sensing robotic-assisted bronchoscopy (ssRAB) provides adequate samples for molecular and predictive testing. METHODS We retrospectively identified diagnostic samples from a prospectively collected database. Pathologic reports were reviewed to assess adequacy of samples for molecular testing and feasibility of PD-L1 IHC. Tumor cellularity was quantified by an independent pathologist using paraffin-embedded sections. Univariable and multivariable linear regression models were constructed to assess associations between lesion- and procedure-related variables and tumor cellularity. RESULTS In total, 128 samples were analyzed: 104 primary lung cancers and 24 metastatic lesions. On initial pathologic assessment, ssRAB samples were deemed to be adequate for molecular testing in 84% of cases; on independent review of cellular blocks, median tumor cellularity was 60% (interquartile range, 25%-80%). Hybrid capture-based next-generation sequencing was successful for 25 of 26 samples (96%), polymerase chain reaction-based molecular testing (Idylla; Biocartis) was successful for 49 of 52 samples (94%), and PD-L1 IHC was successful for 61 of 67 samples (91%). Carcinoid and small cell carcinoma histologic subtype and adequacy on rapid on-site evaluation were associated with higher tumor cellularity. CONCLUSIONS The ssRAB platform provided adequate tissue for next-generation sequencing, polymerase chain reaction-based molecular testing, and PD-L1 IHC in >80% of cases. Tumor histology and adequacy on intraoperative cytologic assessment might be associated with sample quality and suitability for downstream assays.
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Affiliation(s)
- James G Connolly
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Or Kalchiem-Dekel
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kay See Tan
- Biostatistics Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joe Dycoco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mohit Chawla
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gaetano Rocco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bernard J Park
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert P Lee
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jason A Beattie
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stephen B Solomon
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Etay Ziv
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Prasad S Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Darren J Buonocore
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bryan C Husta
- Section of Interventional Pulmonology, Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David R Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marina K Baine
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Matthew J Bott
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY.
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Juul NH, Yoon JK, Martinez MC, Rishi N, Kazadaeva YI, Morri M, Neff NF, Trope WL, Shrager JB, Sinha R, Desai TJ. KRAS(G12D) drives lepidic adenocarcinoma through stem-cell reprogramming. Nature 2023; 619:860-867. [PMID: 37468622 PMCID: PMC10423036 DOI: 10.1038/s41586-023-06324-w] [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: 09/18/2022] [Accepted: 06/14/2023] [Indexed: 07/21/2023]
Abstract
Many cancers originate from stem or progenitor cells hijacked by somatic mutations that drive replication, exemplified by adenomatous transformation of pulmonary alveolar epithelial type II (AT2) cells1. Here we demonstrate a different scenario: expression of KRAS(G12D) in differentiated AT1 cells reprograms them slowly and asynchronously back into AT2 stem cells that go on to generate indolent tumours. Like human lepidic adenocarcinoma, the tumour cells slowly spread along alveolar walls in a non-destructive manner and have low ERK activity. We find that AT1 and AT2 cells act as distinct cells of origin and manifest divergent responses to concomitant WNT activation and KRAS(G12D) induction, which accelerates AT2-derived but inhibits AT1-derived adenoma proliferation. Augmentation of ERK activity in KRAS(G12D)-induced AT1 cells increases transformation efficiency, proliferation and progression from lepidic to mixed tumour histology. Overall, we have identified a new cell of origin for lung adenocarcinoma, the AT1 cell, which recapitulates features of human lepidic cancer. In so doing, we also uncover a capacity for oncogenic KRAS to reprogram a differentiated and quiescent cell back into its parent stem cell en route to adenomatous transformation. Our work further reveals that irrespective of a given cancer's current molecular profile and driver oncogene, the cell of origin exerts a pervasive and perduring influence on its subsequent behaviour.
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Affiliation(s)
- Nicholas H Juul
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jung-Ki Yoon
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Marina C Martinez
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Neha Rishi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Yana I Kazadaeva
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Winston L Trope
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph B Shrager
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tushar J Desai
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Paniagua-Herranz L, Doger B, Díaz-Tejeiro C, Sanvicente A, Nieto-Jiménez C, Moreno V, Pérez Segura P, Gyorffy B, Calvo E, Ocana A. Genomic Mapping of Epidermal Growth Factor Receptor and Mesenchymal-Epithelial Transition-Up-Regulated Tumors Identifies Novel Therapeutic Opportunities. Cancers (Basel) 2023; 15:3250. [PMID: 37370859 DOI: 10.3390/cancers15123250] [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: 05/24/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND The identification of proteins in the cellular membrane of the tumoral cell is a key to the design of therapeutic agents. Recently, the bi-specific antibody amivantamab, targeting the oncogenic membrane proteins EGFR and MET, received regulatory approval for the treatment of adult patients with locally advanced or metastatic NSCLC. METHODS The authors interrogated several publicly available genomic datasets to evaluate the expression of both receptors and PD-L1 in most of the solid and hematologic malignancies and focused on prostate adenocarcinoma (PRAD) and pancreatic adenocarcinoma (PAAD). RESULTS In PAAD, EGFR highly correlated with PD-L1 and MET, and MET showed a moderate correlation with PD-L1, while in PRAD, EGFR, MET and PD-L1 showed a strong correlation. In addition, in tumors treated with immune checkpoint inhibitors, including anti-PD(L)1 and anti-CTLA4, a high expression of EGFR and MET predicted detrimental survival. When exploring the relationship of immune populations with these receptors, the authors observed that in PAAD and PRAD, EGFR moderately correlated with CD8+ T cells. Furthermore, EGFR and MET correlated with neutrophils in PRAD. CONCLUSIONS The authors identified tumor types where EGFR and MET were highly expressed and correlated with a high expression of PD-L1, opening the door for the future combination of bi-specific EGFR/MET antibodies with anti-PD(L)1 inhibitors.
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Affiliation(s)
- Lucía Paniagua-Herranz
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC) and CIBERONC, 28040 Madrid, Spain
| | - Bernard Doger
- START Madrid-HM Centro Integral Oncológico Clara Campal (CIOCC), Early Phase Program, HM Sanchinarro University Hospital, 28050 Madrid, Spain
| | - Cristina Díaz-Tejeiro
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC) and CIBERONC, 28040 Madrid, Spain
| | - Adrián Sanvicente
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC) and CIBERONC, 28040 Madrid, Spain
- Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Cristina Nieto-Jiménez
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC) and CIBERONC, 28040 Madrid, Spain
| | - Víctor Moreno
- START Madrid-Fundación Jiménez Díaz (FJD), Early Phase Program, Fundación Jiménez Díaz Hospital, 28040 Madrid, Spain
| | - Pedro Pérez Segura
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC) and CIBERONC, 28040 Madrid, Spain
| | - Balazs Gyorffy
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary
- Department of Pediatrics, Semmelweis University, 1094 Budapest, Hungary
- TTK Cancer Biomarker Research Group, Institute of Enzymology, 1117 Budapest, Hungary
| | - Emiliano Calvo
- START Madrid-HM Centro Integral Oncológico Clara Campal (CIOCC), Early Phase Program, HM Sanchinarro University Hospital, 28050 Madrid, Spain
| | - Alberto Ocana
- Experimental Therapeutics in Cancer Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC) and CIBERONC, 28040 Madrid, Spain
- START Madrid-Fundación Jiménez Díaz (FJD), Early Phase Program, Fundación Jiménez Díaz Hospital, 28040 Madrid, Spain
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Xu L, Su H, Zhao S, Si H, Xie H, Ren Y, Gao J, Wang F, Xie X, Dai C, Wu C, Zhao D, Chen C. Development of the semi-dry dot-blot method for intraoperative detecting micropapillary component in lung adenocarcinoma based on proteomics analysis. Br J Cancer 2023; 128:2116-2125. [PMID: 37016102 PMCID: PMC10206083 DOI: 10.1038/s41416-023-02241-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/06/2023] [Accepted: 03/16/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Micropapillary (MIP) component was a major concern in determining surgical strategy in lung adenocarcinoma (LUAD). We sought to develop a novel method for detecting MIP component during surgery. METHODS Differentially expressed proteins between MIP-positive and MIP-negative LUAD were identified through proteomics analysis. The semi-dry dot-blot (SDB) method which visualises the targeted protein was developed to detect MIP component. RESULTS Cellular retinoic acid-binding protein 2 (CRABP2) was significantly upregulated in MIP-positive LUAD (P < 0.001), and the high CRABP2 expression zone showed spatial consistency with MIP component. CRABP2 expression was also associated with decreased recurrence-free survival (P < 0.001). In the prospective cohort, the accuracy and sensitivity of detecting MIP component using SDB method by visualising CRABP2 were 82.2% and 72.7%, which were comparable to these of pathologist. Pathologist with the aid of SDB method would improve greatly in diagnostic accuracy (86.4%) and sensitivity (78.2%). In patients with minor MIP component (≤5%), the sensitivity of SDB method (63.6%) was significantly higher than pathologist (45.4%). CONCLUSIONS Intraoperative examination of CRABP2 using SDB method to detect MIP component reached comparable performance to pathologist, and SDB method had notable superiority than pathologist in detecting minor MIP component.
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Affiliation(s)
- Long Xu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Hang Su
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Shengnan Zhao
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Haojie Si
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Huikang Xie
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Yijiu Ren
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Jiani Gao
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Fang Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Xiaofeng Xie
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Chenyang Dai
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Deping Zhao
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China.
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Clinical Center for Thoracic Surgery Research, Tongji University, Shanghai, People's Republic of China.
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Gallina FT, Marinelli D, Melis E, Forcella D, Taje R, Buglioni S, Visca P, Torchia A, Cecere FL, Botticelli A, Santini D, Ciliberto G, Cappuzzo F, Facciolo F. KRAS G12C mutation and risk of disease recurrence in stage I surgically resected lung adenocarcinoma. Lung Cancer 2023; 181:107254. [PMID: 37253296 DOI: 10.1016/j.lungcan.2023.107254] [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: 03/26/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023]
Abstract
KRAS G12C mutations are found in about 12-13% of LUAD samples and it is unclear whether they are associated with worse survival outcomes in resected, stage I LUAD. We assessed whether KRAS-G12C mutated tumours had worse DFS when compared to KRAS-nonG12C mutated tumours and to KRAS wild-type tumours in a cohort of resected, stage I LUAD (IRE cohort). We then leveraged on publicly available datasets (TCGA-LUAD, MSK-LUAD604) to further test the hypothesis in external cohorts. In the stage I IRE cohort we found a significant association between the KRAS-G12C mutation and worse DFS in multivariable analysis (HR: 2.47). In the TCGA-LUAD stage I cohort we did not find statistically significant associations between the KRAS-G12C mutation and DFS. In the MSK-LUAD604 stage I cohort we found that KRAS-G12C mutated tumours had worse RFS when compared to KRAS-nonG12C mutated tumours in univariable analysis (HR 3.5). In the pooled stage I cohort we found that KRAS-G12C mutated tumours had worse DFS when compared to KRAS-nonG12C mutated tumours (HR 2.6), to KRAS wild-type tumours (HR 1.6) and to any other tumours (HR 1.8); in multivariable analysis, the KRAS-G12C mutation was associated with worse DFS (HR 1.61). Our results suggest that patients with resected, stage I LUAD with a KRAS-G12C mutation may have inferior survival outcomes..
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Affiliation(s)
- F T Gallina
- Thoracic Surgery Unit, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - D Marinelli
- Department of Experimental Medicine, Sapienza University, Viale Regina Elena 324, 00161 Roma RM, Italy.
| | - E Melis
- Thoracic Surgery Unit, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - D Forcella
- Thoracic Surgery Unit, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - R Taje
- Thoracic Surgery Unit, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - S Buglioni
- Department of Pathology, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - P Visca
- Department of Pathology, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - A Torchia
- Department of Radiological, Oncological and Anatomopathological Sciences, Sapienza University, Viale Regina Elena 324, 00161 Roma RM, Italy
| | - F L Cecere
- Medical Oncology Unit 2, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - A Botticelli
- Department of Radiological, Oncological and Anatomopathological Sciences, Sapienza University, Viale Regina Elena 324, 00161 Roma RM, Italy
| | - D Santini
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University, Corso della Repubblica 79, 04100 Latina, Italy
| | - G Ciliberto
- Scientific Direction, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - F Cappuzzo
- Medical Oncology Unit 2, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - F Facciolo
- Thoracic Surgery Unit, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
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40
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Lengel HB, Mastrogiacomo B, Connolly JG, Tan KS, Liu Y, Fick CN, Dunne EG, He D, Lankadasari MB, Satravada BA, Sun Y, Kundra R, Fong C, Smith S, Riely GJ, Rudin CM, Gomez DR, Solit DB, Berger MF, Li BT, Mayo MW, Matei I, Lyden DC, Adusumilli PS, Schultz N, Sanchez-Vega F, Jones DR. Genomic mapping of metastatic organotropism in lung adenocarcinoma. Cancer Cell 2023; 41:970-985.e3. [PMID: 37084736 PMCID: PMC10391526 DOI: 10.1016/j.ccell.2023.03.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/02/2023] [Accepted: 03/22/2023] [Indexed: 04/23/2023]
Abstract
We analyzed 2,532 lung adenocarcinomas (LUAD) to identify the clinicopathological and genomic features associated with metastasis, metastatic burden, organotropism, and metastasis-free survival. Patients who develop metastasis are younger and male, with primary tumors enriched in micropapillary or solid histological subtypes and with a higher mutational burden, chromosomal instability, and fraction of genome doublings. Inactivation of TP53, SMARCA4, and CDKN2A are correlated with a site-specific shorter time to metastasis. The APOBEC mutational signature is more prevalent among metastases, particularly liver lesions. Analyses of matched specimens show that oncogenic and actionable alterations are frequently shared between primary tumors and metastases, whereas copy number alterations of unknown significance are more often private to metastases. Only 4% of metastases harbor therapeutically actionable alterations undetected in their matched primaries. Key clinicopathological and genomic alterations in our cohort were externally validated. In summary, our analysis highlights the complexity of clinicopathological features and tumor genomics in LUAD organotropism.
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Affiliation(s)
- Harry B Lengel
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brooke Mastrogiacomo
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James G Connolly
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuan Liu
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cameron N Fick
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth G Dunne
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Di He
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manendra B Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Baby Anusha Satravada
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yichao Sun
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chris Fong
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shaleigh Smith
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel R Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T Li
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marty W Mayo
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Irina Matei
- Department of Pediatrics, Meyer Cancer Center, Weill Cornell Medicine of Cornell University, New York, NY, USA
| | - David C Lyden
- Department of Pediatrics, Meyer Cancer Center, Weill Cornell Medicine of Cornell University, New York, NY, USA
| | - Prasad S Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco Sanchez-Vega
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - David R Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Li Y, Byun AJ, Choe JK, Lu S, Restle D, Eguchi T, Tan KS, Saini J, Huang J, Rocco G, Jones DR, Travis WD, Adusumilli PS. Micropapillary and Solid Histologic Patterns in N1 and N2 Lymph Node Metastases Are Independent Factors of Poor Prognosis in Patients With Stages II to III Lung Adenocarcinoma. J Thorac Oncol 2023; 18:608-619. [PMID: 36681298 PMCID: PMC10122702 DOI: 10.1016/j.jtho.2023.01.002] [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: 10/03/2022] [Revised: 12/15/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023]
Abstract
INTRODUCTION High-grade histologic patterns are associated with poor prognosis in patients with primary nonmucinous lung adenocarcinoma (ADC). We investigated whether the presence of micropapillary (MIP), solid (SOL), or both patterns in lymph node (LN) metastases has prognostic value. METHODS Patients who underwent lobectomy for pathologic stages II to III lung ADC with N1 or N2 LN metastases (N = 360; 2000-2012) were analyzed. We assessed overall survival (OS), lung cancer-specific cumulative incidence of death (LC-CID), and cumulative incidence of recurrence (CIR) between patients with and without MIP/SOL patterns in LN metastases. Multivariable Cox regression analysis was used to quantify the association between MIP/SOL patterns and outcomes. RESULTS MIP and SOL in LN metastases were associated with a higher incidence of smoking history (p = 0.004), tumor necrosis (p = 0.013), and spread of tumor through air spaces (p < 0.0001), a higher prevalence of MIP or SOL in the primary tumor (p < 0.0001), shorter OS (5-y OS, 40% [95% confidence interval or CI: 29%-56%] versus 63% [48%-83%] for no MIP/SOL in LNs, p = 0.03), higher LC-CID (5-y, 43% [29%-56%] versus 14% [4%-29%], p = 0.013), and higher CIR (5-y, 65% [50%-77%] versus 43% [25%-60%], p = 0.057). MIP and SOL in LN metastases were independently associated with poor outcomes: OS (hazard ratio [HR] = 1.81 [95% CI: 1.00-3.29], p = 0.05), LC-CID (HR = 3.10 [1.30-7.37], p = 0.01), and CIR (HR = 2.06 [1.09-3.90], p = 0.026). CONCLUSIONS MIP/SOL histologic patterns in N1 or N2 LN metastases are associated with worse outcomes in patients with stages II to III lung ADC. MIP/SOL histologic patterns in LN metastases can stratify patients with high-risk stages II to III lung ADC.
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Affiliation(s)
- Yan Li
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science & Technology, Hubei, People's Republic of China
| | - Alexander J Byun
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jennie K Choe
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shaohua Lu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - David Restle
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Takashi Eguchi
- Division of Thoracic Surgery, Department of Surgery, Shinshu University, Matsumoto, Japan
| | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jasmeen Saini
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James Huang
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gaetano Rocco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Prasad S Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York; Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, New York.
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42
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Ito Y, Usui G, Seki M, Fukuyo M, Matsusaka K, Hoshii T, Sata Y, Morimoto J, Hata A, Nakajima T, Rahmutulla B, Kaiho T, Inage T, Tanaka K, Sakairi Y, Suzuki H, Yoshino I, Kaneda A. Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma. Cancer Sci 2023. [PMID: 37082886 DOI: 10.1111/cas.15817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/22/2023] Open
Abstract
Lung adenocarcinoma is classified morphologically into five histological subtypes according to the WHO classification. While each histological subtype correlates with a distinct prognosis, the molecular basis has not been fully elucidated. Here we conducted DNA methylation analysis of 30 lung adenocarcinoma cases annotated with the predominant histological subtypes and three normal lung cases using the Infinium BeadChip. Unsupervised hierarchical clustering analysis revealed three subgroups with different methylation levels: high-, intermediate-, and low-methylation epigenotypes (HME, IME, and LME). Micropapillary pattern (MPP)-predominant cases and those with MPP components were significantly enriched in HME (p = 0.02 and p = 0.03, respectively). HME cases showed a significantly poor prognosis for recurrence-free survival (p < 0.001) and overall survival (p = 0.006). We identified 365 HME marker genes specifically hypermethylated in HME cases with enrichment of "cell morphogenesis" related genes; 305 IME marker genes hypermethylated in HME and IME, but not in LME, with enrichment "embryonic organ morphogenesis"-related genes; 257 Common marker genes hypermethylated commonly in all cancer cases, with enrichment of "regionalization"-related genes. We extracted surrogate markers for each epigenotype and designed pyrosequencing primers for five HME markers (TCERG1L, CXCL12, FAM181B, HOXA11, GAD2), three IME markers (TBX18, ZNF154, NWD2) and three Common markers (SCT, GJD2, BARHL2). DNA methylation profiling using Infinium data was validated by pyrosequencing, and HME cases defined by pyrosequencing results also showed the worse recurrence-free survival. In conclusion, lung adenocarcinomas are stratified into subtypes with distinct DNA methylation levels, and the high-methylation subtype correlated with MPP-predominant cases and those with MPP components and showed a poor prognosis.
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Affiliation(s)
- Yuki Ito
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Genki Usui
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motoaki Seki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuki Sata
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Junichi Morimoto
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Hata
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takahiro Nakajima
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Taisuke Kaiho
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Terunaga Inage
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazuhisa Tanaka
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuichi Sakairi
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hidemi Suzuki
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Yoshino
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Shi T, Hu Z, Tian L, Yang Y. Pan-cancer landscape of CENPO and its underlying mechanism in LUAD. Respir Res 2023; 24:113. [PMID: 37061713 PMCID: PMC10105544 DOI: 10.1186/s12931-023-02408-3] [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: 11/11/2022] [Accepted: 03/24/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Centromere protein O (CENPO) is a newly discovered constitutive centromeric protein, associated with cell death. However, little is known about how CENPO expression is associated with human cancers or immune infiltration. Here, we assessed the function of CENPO in pan-cancer and further verified the results in lung adenocarcinoma (LUAD) through in vitro and in vivo experiments. METHODS Sangerbox and TCGA databases were used to evaluate the CENPO expression level in different human cancer types. A subsequent evaluation of the potential role of CENPO as a diagnostic and prognostic biomarker in pancancer was conducted. The CENPO mutations were analyzed using the cBioPortal database and its function was analyzed using the LinkedOmics and CancerSEA databases. The TIMER2 and TISIDB websites were used to find out how CENPO affects immune infiltration. The expression level of CENPO in LUAD was revealed by TCGA database and immunohistochemical (IHC) staining. Targetscan, miRWalk, miRDB, miRabel, LncBase databases, and Cytoscape tool were used to identify microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) that regulate expression and construct ceRNA network. Subsequently, loss-of-function assays were performed to identify the functions of CENPO on the malignant behavior and tumor growth of LUAD in vitro and in vivo experiments. RESULTS In most cancers, CENPO was upregulated and mutated, which predicted a poorer prognosis. Furthermore, infiltration of CENPO and myeloid-derived suppressor cells (MDSC) showed a significant positive correlation, while T-cell NK infiltration showed a significant negative correlation in most cancers. CENPO was expressed at high levels in LUAD and was correlated with p-TNM stage. Furthermore, CENPO knockdown suppressed the malignant phenotypes of LUAD cells, manifested by slower proliferation, cycle in G2, increased apoptosis, decreased migration, and attenuated tumorigenesis. Furthermore, CENPO knockdown decreased CDK1/6, PIK3CA, and inhibited mTOR phosphorylation, suggesting that the mTOR signaling pathway may be involved in CENPO-mediated regulation of LUAD development. CONCLUSIONS In pan-cancer, especially LUAD, CENPO may be a potential biomarker and oncogene. Furthermore, CENPO has been implicated in immune cell infiltration in pan-cancer and represents a potential immunotherapeutic target for tumor therapy.
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Affiliation(s)
- Tongdong Shi
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital of Chongqing Medical University, No.288 Tianwen Avenue, Nan'an District, Chongqing, 401336, People's Republic of China
| | - Zaoxiu Hu
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University, No.519 Kunzhou Road, Xishan District, Kunming, 650118, Yunnan, People's Republic of China
| | - Li Tian
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases and Institute for Viral Hepatitis, Chongqing Medical University the Second Affiliated Hospital, 74 Linjiang Road, Chongqing, 400010, People's Republic of China
| | - Yanlong Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, No.295 Xichang Road, Wuhua District, Kunming, 650032, Yunnan, People's Republic of China.
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Owusu-Ansah M, Guptan N, Alindogan D, Morizono M, Caldovic L. NAGS, CPS1, and SLC25A13 (Citrin) at the Crossroads of Arginine and Pyrimidines Metabolism in Tumor Cells. Int J Mol Sci 2023; 24:ijms24076754. [PMID: 37047726 PMCID: PMC10094985 DOI: 10.3390/ijms24076754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023] Open
Abstract
Urea cycle enzymes and transporters collectively convert ammonia into urea in the liver. Aberrant overexpression of carbamylphosphate synthetase 1 (CPS1) and SLC25A13 (citrin) genes has been associated with faster proliferation of tumor cells due to metabolic reprogramming that increases the activity of the CAD complex and pyrimidine biosynthesis. N-acetylglutamate (NAG), produced by NAG synthase (NAGS), is an essential activator of CPS1. Although NAGS is expressed in lung cancer derived cell lines, expression of the NAGS gene and its product was not evaluated in tumors with aberrant expression of CPS1 and citrin. We used data mining approaches to identify tumor types that exhibit aberrant overexpression of NAGS, CPS1, and citrin genes, and evaluated factors that may contribute to increased expression of the three genes and their products in tumors. Median expression of NAGS, CPS1, and citrin mRNA was higher in glioblastoma multiforme (GBM), glioma, and stomach adenocarcinoma (STAD) samples compared to the matched normal tissue. Median expression of CPS1 and citrin mRNA was higher in the lung adenocarcinoma (LUAD) sample while expression of NAGS mRNA did not differ. High NAGS expression was associated with an unfavorable outcome in patients with glioblastoma and GBM. Low NAGS expression was associated with an unfavorable outcome in patients with LUAD. Patterns of DNase hypersensitive sites and histone modifications in the upstream regulatory regions of NAGS, CPS1, and citrin genes were similar in liver tissue, lung tissue, and A549 lung adenocarcinoma cells despite different expression levels of the three genes in the liver and lung. Citrin gene copy numbers correlated with its mRNA expression in glioblastoma, GBM, LUAD, and STAD samples. There was little overlap between NAGS, CPS1, and citrin sequence variants found in patients with respective deficiencies, tumor samples, and individuals without known rare genetic diseases. The correlation between NAGS, CPS1, and citrin mRNA expression in the individual glioblastoma, GBM, LUAD, and STAD samples was very weak. These results suggest that the increased cytoplasmic supply of either carbamylphosphate, produced by CPS1, or aspartate may be sufficient to promote tumorigenesis, as well as the need for an alternative explanation of CPS1 activity in the absence of NAGS expression and NAG.
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Affiliation(s)
- Melissa Owusu-Ansah
- Columbian College of Arts and Sciences, George Washington University, Washington, DC 20052, USA
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20052, USA
| | - Nikita Guptan
- Columbian College of Arts and Sciences, George Washington University, Washington, DC 20052, USA
| | - Dylon Alindogan
- Columbian College of Arts and Sciences, George Washington University, Washington, DC 20052, USA
| | - Michio Morizono
- School of Mathematics, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ljubica Caldovic
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20052, USA
- Center for Genetic Medicine Research, Children’s National Research Institute, Children’s National Hospital, Washington, DC 20010, USA
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45
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Karasaki T, Moore DA, Veeriah S, Naceur-Lombardelli C, Toncheva A, Magno N, Ward S, Bakir MA, Watkins TBK, Grigoriadis K, Huebner A, Hill MS, Frankell AM, Abbosh C, Puttick C, Zhai H, Gimeno-Valiente F, Saghafinia S, Kanu N, Dietzen M, Pich O, Lim EL, Martínez-Ruiz C, Black JRM, Biswas D, Campbell BB, Lee C, Colliver E, Enfield KSS, Hessey S, Hiley CT, Zaccaria S, Litchfield K, Birkbak NJ, Cadieux EL, Demeulemeester J, Van Loo P, Adusumilli PS, Tan KS, Cheema W, Sanchez-Vega F, Jones DR, Rekhtman N, Travis WD, Hackshaw A, Marafioti T, Salgado R, Le Quesne J, Nicholson AG, McGranahan N, Swanton C, Jamal-Hanjani M. Evolutionary characterization of lung adenocarcinoma morphology in TRACERx. Nat Med 2023; 29:833-845. [PMID: 37045996 PMCID: PMC7614478 DOI: 10.1038/s41591-023-02230-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 01/24/2023] [Indexed: 04/14/2023]
Abstract
Lung adenocarcinomas (LUADs) display a broad histological spectrum from low-grade lepidic tumors through to mid-grade acinar and papillary and high-grade solid, cribriform and micropapillary tumors. How morphology reflects tumor evolution and disease progression is poorly understood. Whole-exome sequencing data generated from 805 primary tumor regions and 121 paired metastatic samples across 248 LUADs from the TRACERx 421 cohort, together with RNA-sequencing data from 463 primary tumor regions, were integrated with detailed whole-tumor and regional histopathological analysis. Tumors with predominantly high-grade patterns showed increased chromosomal complexity, with higher burden of loss of heterozygosity and subclonal somatic copy number alterations. Individual regions in predominantly high-grade pattern tumors exhibited higher proliferation and lower clonal diversity, potentially reflecting large recent subclonal expansions. Co-occurrence of truncal loss of chromosomes 3p and 3q was enriched in predominantly low-/mid-grade tumors, while purely undifferentiated solid-pattern tumors had a higher frequency of truncal arm or focal 3q gains and SMARCA4 gene alterations compared with mixed-pattern tumors with a solid component, suggesting distinct evolutionary trajectories. Clonal evolution analysis revealed that tumors tend to evolve toward higher-grade patterns. The presence of micropapillary pattern and 'tumor spread through air spaces' were associated with intrathoracic recurrence, in contrast to the presence of solid/cribriform patterns, necrosis and preoperative circulating tumor DNA detection, which were associated with extra-thoracic recurrence. These data provide insights into the relationship between LUAD morphology, the underlying evolutionary genomic landscape, and clinical and anatomical relapse risk.
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Affiliation(s)
- Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Antonia Toncheva
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Neil Magno
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kristiana Grigoriadis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare Puttick
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Haoran Zhai
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Francisco Gimeno-Valiente
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sadegh Saghafinia
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Dhruva Biswas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Brittany B Campbell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Claudia Lee
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Katey S S Enfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sonya Hessey
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Elizabeth Larose Cadieux
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Medical Genomics, University College London Cancer Institute, London, UK
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Integrative Cancer Genomics Laboratory, Department of Oncology, KU Leuven, Leuven, Belgium
- VIB - KU Leuven Center for Cancer Biology, Leuven, Belgium
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Prasad S Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Waseem Cheema
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco Sanchez-Vega
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David R Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - John Le Quesne
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Pathology Department, Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Andrew G Nicholson
- Department of Histopathology, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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Yalimaimaiti S, Liang X, Zhao H, Dou H, Liu W, Yang Y, Ning L. Establishment of a prognostic signature for lung adenocarcinoma using cuproptosis-related lncRNAs. BMC Bioinformatics 2023; 24:81. [PMID: 36879187 PMCID: PMC9990240 DOI: 10.1186/s12859-023-05192-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
OBJECTIVE To establish a prognostic signature for lung adenocarcinoma (LUAD) based on cuproptosis-related long non-coding RNAs (lncRNAs), and to study the immune-related functions of LUAD. METHODS First, transcriptome data and clinical data related to LUAD were downloaded from the Cancer Genome Atlas (TCGA), and cuproptosis-related genes were analyzed to identify cuproptosis-related lncRNAs. Univariate COX analysis, least absolute shrinkage and selection operator (LASSO) analysis, and multivariate COX analysis were performed to analyze the cuproptosis-related lncRNAs, and a prognostic signature was established. Second, univariate COX analysis and multivariate COX analysis were performed for independent prognostic analyses. Receiver operating characteristic (ROC) curves, C index, survival curve, nomogram, and principal component analysis (PCA) were performed to evaluate the results of the independent prognostic analyses. Finally, gene enrichment analyses and immune-related function analyses were also carried out. RESULTS (1) A total of 1,297 cuproptosis-related lncRNAs were screened. (2) A LUAD prognostic signature containing 13 cuproptosis-related lncRNAs was constructed (NIFK-AS1, AC026355.2, SEPSECS-AS1, AL360270.1, AC010999.2, ABCA9-AS1, AC032011.1, AL162632.3, LINC02518, LINC0059, AL031600.2, AP000346.1, AC012409.4). (3) The area under the multi-indicator ROC curves at 1, 3, and 5 years were AUC1 = 0.742, AUC2 = 0.708, and AUC3 = 0.762, respectively. The risk score of the prognostic signature could be used as an independent prognostic factor that was independent of other clinical indicators. (4) The results of gene enrichment analyses showed that 13 biomarkers were primarily related to amoebiasis, the wnt signaling pathway, hematopoietic cell lineage. The ssGSEA volcano map showed significant differences between high- and low-risk groups in immune-related functions, such as human leukocyte antigen (HLA), Type_II_IFN_Reponse, MHC_class_I, and Parainflammation (P < 0.001). CONCLUSIONS Thirteen cuproptosis-related lncRNAs may be clinical molecular biomarkers for the prognosis of LUAD.
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Affiliation(s)
- Saiyidan Yalimaimaiti
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Xiaoqiao Liang
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Haili Zhao
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Hong Dou
- Xinjiang Uygur Autonomous Region Occupational Disease Hospital, Urumqi, 830011, Xinjiang, China
| | - Wei Liu
- Xinjiang Uygur Autonomous Region Occupational Disease Hospital, Urumqi, 830011, Xinjiang, China
| | - Ying Yang
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Li Ning
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China.
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Li P, Li H, Wan Z, Lu Y. Effect of sample size on prognostic genes analysis in non-small cell lung cancer. Mol Genet Genomics 2023; 298:549-554. [PMID: 36853413 DOI: 10.1007/s00438-023-01999-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/15/2023] [Indexed: 03/01/2023]
Abstract
The identification of prognostic genes can help in the clinical management of non-small cell lung cancer (NSCLC). However, there is little overlap in the prognostic genes identified in different NSCLC studies. One reason for this may be the inadequate sample size. Here, the effect of sample size on prognostic genes analysis was investigated based on 515 stage II/III NSCLC cases from two cohorts detected by whole-exome sequencing. Prognostic genes analysis was repeatedly performed 100 times for each sample size level using random resampling methods. In stage II lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) cases from the TCGA Pan-Lung Cancer cohort, the number of statistically significant prognostic genes first increased with sample size in a power law, then fluctuated steadily, and finally decreased slightly. The power law growth curves were also observed in stage III LUAD and LUSC cases from the TCGA Pan-Lung Cancer cohort and stage III Chinese LUAD cases from the OncoSG cohort. The correlation R2 of the fitted power law growth curves were all greater than 0.99. In addition, at the sample size level where the number of prognostic genes peaked, the mean proportion of true prognostic genes in patients with stage II LUAD and LUSC was 28.32% and 23.12%, which could partly explain the little overlap in prognostic genes between reports. In conclusion, the number of prognostic genes takes a power law growth with the sample size in NSCLC, independent of histopathological subtype, race, and stage. These results also show how sample size affects the reliability of prognostic genes and will aid trial design for genomic mutation-based prognostic studies in NSCLC.
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Affiliation(s)
- Pingdong Li
- Department of Otolaryngology, Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Haiyang Li
- Department of Otolaryngology, People's Hospital of Beijing Daxing District, Beijing, China
| | - Zhiyi Wan
- School of Biomedicine, Beijing City University, Beijing, China
| | - Yanan Lu
- School of Biomedicine, Beijing City University, Beijing, China.
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Li F, Wang S, Wang Y, Lv Z, Jin D, Yi H, Fu L, Zhai S, Xiao T, Mao Y. Multi-omics analysis unravels the underlying mechanisms of poor prognosis and differential therapeutic responses of solid predominant lung adenocarcinoma. Front Immunol 2023; 14:1101649. [PMID: 36845145 PMCID: PMC9946976 DOI: 10.3389/fimmu.2023.1101649] [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: 11/18/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
Background Solid predominant adenocarcinoma (SPA) has been reported to be a subtype with poor prognosis and unsatisfactory response to chemotherapy and targeted therapy in lung adenocarcinoma (LUAD). However, the underlying mechanisms remain largely unknown and the suitability of immunotherapy for SPA has not been investigated. Methods We conducted a multi-omics analysis of 1078 untreated LUAD patients with clinicopathologic, genomic, transcriptomic, and proteomic data from both public and internal cohorts to determine the underlying mechanisms of poor prognosis and differential therapeutic responses of SPA and to investigate the potential of immunotherapy for SPA. The suitability of immunotherapy for SPA was further confirmed in a cohort of LUAD patients who received neoadjuvant immunotherapy in our center. Results Along with its aggressive clinicopathologic behaviors, SPA had significantly higher tumor mutation burden (TMB) and number of pathways altered, lower TTF-1 and Napsin-A expression, higher proliferation score and a more immunoresistant microenvironment than non-solid predominant adenocarcinoma (Non-SPA), accounting for its worse prognosis. Additionally, SPA had significantly lower frequency of therapeutically targetable driver mutations and higher frequency of EGFR/TP53 co-mutation which was related to resistance to EGFR tyrosine kinase inhibitors, indicating a lower potential for targeted therapy. Meanwhile, SPA was enriched for molecular features associated with poor response to chemotherapy (higher chemoresistence signature score, lower chemotherapy response signature score, hypoxic microenvironment, and higher frequency of TP53 mutation). Instead, muti-omics profiling revealed that SPA had stronger immunogenicity and was enriched for positive biomarkers for immunotherapy (higher TMB and T cell receptor diversity; higher PD-L1 expression and more immune cell infiltration; higher frequency of gene mutations predicting efficacious immunotherapy, and elevated expression of immunotherapy-related gene signatures). Furthermore, in the cohort of LUAD patients who received neoadjuvant immunotherapy, SPA had higher pathological regression rates than Non-SPA and patients with major pathological response were enriched in SPA, confirming that SPA was more prone to respond to immunotherapy. Conclusions Compared with Non-SPA, SPA was enriched for molecular features associated with poor prognosis, unsatisfactory response to chemotherapy and targeted therapy, and good response to immunotherapy, indicating more suitability for immunotherapy while less suitability for chemotherapy and targeted therapy.
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Affiliation(s)
- Feng Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuaibo Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaru Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhuoheng Lv
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Donghui Jin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hang Yi
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Fu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Suokai Zhai
- Department of Cardiothoracic Surgery, Zibo First Hospital, Weifang Medical University, Zibo, Shandong, China
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,*Correspondence: Ting Xiao, ; Yousheng Mao,
| | - Yousheng Mao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,*Correspondence: Ting Xiao, ; Yousheng Mao,
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TANG R, BI L, XIANG B, YE L, CHEN Y, LI G, ZHAO G, HUANG Y. [Advances in the Study of Invasive Non-mucinous Adenocarcinoma
with Different Pathological Subtypes]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2023; 26:22-30. [PMID: 36792077 PMCID: PMC9987059 DOI: 10.3779/j.issn.1009-3419.2022.102.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Indexed: 02/17/2023]
Abstract
Lung cancer is the leading cause of cancer death in the world today, and adenocarcinoma is the most common histopathological type of lung cancer. In May 2021, World Health Organization (WHO) released the 5th edition of the WHO classification of thoracic tumors, which classifies invasive non-mucinous adenocarcinoma (INMA) into lepidic adenocarcinoma, acinar adenocarcinoma, papillary adenocarcinoma, solid adenocarcinoma, and micropapillary adenocarcinoma based on its histological characteristics. These five pathological subtypes differ in clinical features, treatment and prognosis. A complete understanding of the characteristics of these subtypes is essential for the clinical diagnosis, treatment options, and prognosis predictions of patients with lung adenocarcinoma, including recurrence and progression. This article will review the grading system, morphology, imaging prediction, lymph node metastasis, surgery, chemotherapy, targeted therapy and immunotherapy of different pathological subtypes of INMA.
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Moorthi S, Paguirigan A, Ko M, Pettinger M, Hoge ACH, Nag A, Patel NA, Wu F, Sather C, Fitzgibbon MP, Thorner AR, Anderson GL, Ha G, Berger AH. Somatic mutation but not aneuploidy differentiates lung cancer in never-smokers and smokers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522947. [PMID: 36712079 PMCID: PMC9881937 DOI: 10.1101/2023.01.05.522947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Lung cancer in never-smokers disproportionately affects older women. To understand the mutational landscape of this cohort, we performed detailed genome characterization of 73 lung adenocarcinomas from participants of the Women’s Health Initiative (WHI). We find enrichment of EGFR mutations in never-/light-smokers and KRAS mutations in heavy smokers as expected, but we also show that the specific variants of these genes differ by smoking status, with important therapeutic implications. Mutational signature analysis revealed signatures of clock, APOBEC, and DNA repair deficiency in never-/light-smokers; however, the mutational load of these signatures did not differ significantly from those found in smokers. Last, tumors from both smokers and never-/light-smokers shared copy number subtypes, with no significant differences in aneuploidy. Thus, the genomic landscape of lung cancer in never-/light-smokers and smokers is predominantly differentiated by somatic mutations and not copy number alterations.
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