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Ma Y, Fei X, Jiang C, Chen H, Wang Z, Bao Y. Lung adenocarcinoma manifested as ground-glass nodules in teenagers: characteristics, surgical outcomes and management strategies. Eur J Cardiothorac Surg 2024; 66:ezae291. [PMID: 39073900 DOI: 10.1093/ejcts/ezae291] [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: 02/06/2024] [Revised: 07/09/2024] [Accepted: 07/27/2024] [Indexed: 07/31/2024] Open
Abstract
OBJECTIVES Ground-glass nodules-featured lung cancer have been identified in some teenagers in recent years. This study aims to investigate the characteristics and surgical outcomes of these patients and explore proper management strategy. METHODS Patients aged ≤20 with incidentally diagnosed lung cancer were retrospectively reviewed from February 2016 to March 2023. Based on lymph node evaluation status, these patients were divided into non-lymph node evaluation and lymph node evaluation groups. The clinical and pathological characteristics were analysed. RESULTS A total of 139 teenage patients were included, with an obviously increased cases observed from 2019, corresponding to the COVID-19 pandemic. The median age of the 139 patients was 18 years (range 12-20). Eighty-five patients had pure ground-glass nodules, while others had mixed ground-glass nodules. The mean diameter of nodules was 8.87 ± 2.20 mm. Most of the patients underwent wedge resection (64%) or segmentectomy (31.7%). Fifty-two patients underwent lymph node sampling or dissection. None of these patients had lymph node metastasis. The majority of lesions were adenocarcinoma in situ (63 cases) and minimally invasive adenocarcinoma (72 cases), while four lesions were invasive adenocarcinoma. The median follow-up time was 2.46 years, and none of these patients experienced recurrence or death during follow-up. The lymph node evaluation group had longer hospital stays (P < 0.001), longer surgery time (P < 0.001), and greater blood loss (P = 0.047) than the non-lymph node evaluation group. CONCLUSIONS The COVID-19 pandemic significantly increased the number of teenage patients incidentally diagnosed with lung cancer, presenting as ground-glass nodules on CT scans. These patients have favourable surgical outcomes. We propose a management strategy for teenage patients, and suggest that sub-lobar resection without lymph node dissection may be an acceptable surgical procedure for these patients.
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Affiliation(s)
- Yi Ma
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiang Fei
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chao Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Haiming Chen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China
| | - Ziming Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Bao
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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Zheng X, Shen J, Jiang H, Tian M, Wang Q, Guo K, Chen R, Xia Q, Yan Q, Du L, Duan S. Exploring the multifaceted role of GCN1: Implications in cellular responses and disease pathogenesis. Biomed Pharmacother 2024; 175:116681. [PMID: 38705128 DOI: 10.1016/j.biopha.2024.116681] [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: 02/04/2024] [Revised: 04/21/2024] [Accepted: 04/29/2024] [Indexed: 05/07/2024] Open
Abstract
GCN1 is a highly conserved protein present widely across eukaryotes. As an upstream activator of protein kinase GCN2, GCN1 plays a pivotal role in integrated stress responses, such as amino acid starvation and oxidative stress. Through interaction with GCN2, GCN1 facilitates the activation of GCN2, thus initiating downstream signaling cascades in response to cellular stressors. In these contexts, the activation of GCN2 necessitates the presence and action of GCN1. Notably, GCN1 also operates as a ribosome collision sensor, contributing significantly to the translation quality control pathway. These discoveries offer valuable insights into cellular responses to internal stresses, vital for maintaining cellular homeostasis. Additionally, GCN1 exhibits the ability to regulate the cell cycle and suppress inflammation, among other processes, independently of GCN2. Our review outlines the structural characteristics and biological functions of GCN1, shedding light on its significant involvement in the onset and progression of various cancer and non-cancer diseases. Our work underscores the role of GCN1 in the context of drug therapeutic effects, hinting at its potential as a promising drug target. Furthermore, our work delves deep into the functional mechanisms of GCN1, promising innovative avenues for the diagnosis and treatment of diseases in the future. The exploration of GCN1's multifaceted roles not only enhances our understanding of its mechanisms but also paves the way for novel therapeutic interventions. The ongoing quest to unveil additional functions of GCN1 holds the promise of further enriching our comprehension of its mode of action.
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Affiliation(s)
- Xinying Zheng
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Hongting Jiang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Mei Tian
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China; Geriatric Medicine Center, Department of Endocrinology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Qurui Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Kailin Guo
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Ruixiu Chen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Qing Xia
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Qibin Yan
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Lihua Du
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China.
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Yang Z, Zhou B, Guo W, Peng Y, Tian H, Xu J, Wang S, Chen X, Hu B, Liu C, Wang Z, Li C, Gao S, He J. Genomic characteristics and immune landscape of super multiple primary lung cancer. EBioMedicine 2024; 101:105019. [PMID: 38364701 PMCID: PMC10878856 DOI: 10.1016/j.ebiom.2024.105019] [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: 10/30/2023] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND In recent years, a growing number of patients with multiple primary lung cancer (MPLC) are being diagnosed, and a subset of these patients is found to have a large number of lesions at the time of diagnosis, which are referred to as 'super MPLC'. METHODS Here, we perform whole exome sequencing (WES) and immunohistochemistry (IHC) analysis of PD-L1 and CD8 on 212 tumor samples from 42 patients with super MPLC. FINDINGS We report the genomic alteration landscape of super MPLC. EGFR, RBM10 and TP53 mutation and TERT amplification are important molecular events in the evolution of super MPLC. We propose the conception of early intrapulmonary metastasis, which exhibits different clinical features from conventional metastasis. The IHC analyses of PD-L1 and CD8 reveal a less inflamed microenvironment of super MPLC than that of traditional non-small cell lung cancer (NSCLC). We identify the potentially susceptible germline mutations for super MPLC. INTERPRETATION Our study depicts the genomic characteristics and immune landscape, providing insights into the pathogenesis and possible therapeutic guidance of super MPLC. FUNDING A full list of funding bodies that supported this study can be found in the Acknowledgements section.
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Affiliation(s)
- Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Bolun Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Wei Guo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Yue Peng
- Department of Thoracic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - He Tian
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Jiachen Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China; Guangdong Provincial People's Hospital/Guangdong Provincial Academy of Medical Sciences, Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer, Guangdong, 519041, China
| | - Shuaibo Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Xiaowei Chen
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Bin Hu
- Department of Thoracic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Chengming Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Zhijie Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China.
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China.
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Florez N, Kiel L, Riano I, Patel S, DeCarli K, Dhawan N, Franco I, Odai-Afotey A, Meza K, Swami N, Patel J, Sequist LV. Lung Cancer in Women: The Past, Present, and Future. Clin Lung Cancer 2024; 25:1-8. [PMID: 37940410 DOI: 10.1016/j.cllc.2023.10.007] [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: 06/12/2023] [Revised: 09/29/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023]
Abstract
Lung cancer is the leading cause of cancer death for women in multiple countries including the United States. Women are exposed to unique risk factors that remain largely understudied such as indoor pollution, second-hand tobacco exposure, biological differences, gender differences in tolerability and response to therapy in lung cancer, and societal gender roles, that create distinct survivorship needs. Women continue to lack representation in lung cancer clinical trials and are typically treated with data generated from majority male patient study populations, which may be inappropriate to extrapolate and generalize to females. Current lung cancer treatment and screening guidelines do not incorporate sex-specific differences and physicians also often do not account for gender differences when choosing treatments or discussing survivorship needs. To best provide targeted treatment approaches, greater representation of women in lung cancer clinical trials and further research is necessary. Clinicians should understand the unique factors and consequences associated with lung cancer in women; thus, a holistic approach that acknowledges environmental and societal factors is necessary.
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Affiliation(s)
- Narjust Florez
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.
| | | | - Ivy Riano
- Section of Hematology and Medical Oncology, Dartmouth Cancer Center, Geisel School of Medicine Dartmouth, Lebanon, NH
| | - Shruti Patel
- Department of Medicine, Division of Medical Oncology, Stanford University, Stanford, CA
| | - Kathryn DeCarli
- Division of Hematology/Oncology, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Natasha Dhawan
- Section of Hematology and Medical Oncology, Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Ivy Franco
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | - Kelly Meza
- Dana-Farber Cancer Institute, Boston, MA
| | - Nishwant Swami
- University of Massachusetts Medical School, Worcester, MA; Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA
| | | | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
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Sorscher S, LoPiccolo J, Heald B, Chen E, Bristow SL, Michalski ST, Nielsen SM, Lacoste A, Keyder E, Lee H, Nussbaum RL, Martins R, Esplin ED. Rate of Pathogenic Germline Variants in Patients With Lung Cancer. JCO Precis Oncol 2023; 7:e2300190. [PMID: 37992258 PMCID: PMC10681406 DOI: 10.1200/po.23.00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 11/24/2023] Open
Abstract
PURPOSE Germline genetic testing (GGT) is now recommended for all patients diagnosed with ovarian or pancreatic cancer and for a large proportion of patients based solely on a diagnosis of colorectal or breast cancer. However, GGT is not yet recommended for all patients diagnosed with lung cancer (LC), primarily because of a lack of evidence that supports a significant frequency of identifying pathogenic germline variants (PGVs) in these patients. This study characterizes GGT results in a cohort of patients with LC. METHODS We reviewed deidentified data for 7,788 patients with GGT (2015-2022). PGV frequencies were compared to a control cohort of unaffected individuals. GGT results were stratified by genomic ancestry, history of cancer, and PGV clinical actionability per current guidelines. RESULTS Of all patients with LC, 14.9% (1,161/7,788) had PGVs. The rate was similar when restricted to patients with no cancer family history (FH) or personal history (PH) of other cancers (14.3%). PGVs were significantly enriched in BRCA2, ATM, CHEK2, BRCA1, and mismatch repair genes compared with controls. Patients of European (EUR) genomic ancestry had the highest PGV rate (18%) and variants of uncertain significance were significantly higher in patients of non-EUR genomic ancestry. Of the PGVs identified, 61.3% were in DNA damage repair (DDR) genes and 95% were clinically actionable. CONCLUSION This retrospective study shows a LC diagnosis identifies patients with a significant likelihood of having a cancer-predisposing PGV across genomic ancestries. Enrichment of PGVs in DDR genes suggests that these PGVs may contribute to LC cancer predisposition. The frequency of PGVs among patients with LC did not differ significantly according to FH or PH of other cancers.
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Affiliation(s)
| | - Jaclyn LoPiccolo
- Hematology/Oncology Division, Dana-Farber Cancer Center, Boston, MA
| | | | | | | | | | | | | | | | - Hayan Lee
- Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA
| | | | - Renato Martins
- Hematology, Oncology and Palliative Care Division, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA
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Xu Y, Yang Y, Wang Y, Su J, Chan T, Zhou J, Gong Y, Wang K, Gu Y, Zhang C, Wu G, Bi L, Qin X, Han J. Molecular fingerprints of nuclear genome and mitochondrial genome for early diagnosis of lung adenocarcinoma. J Transl Med 2023; 21:250. [PMID: 37038181 PMCID: PMC10084603 DOI: 10.1186/s12967-023-04099-2] [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: 01/08/2023] [Accepted: 03/30/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the most prevalent subtype of lung cancer with high morbidity and mortality rates. Due to the heterogeneity of LUAD, its characteristics remain poorly understood. Exploring the clinical and molecular characteristics of LUAD is challenging but vital for early diagnosis. METHODS This observational and validation study enrolled 80 patients and 13 healthy controls. Nuclear and mtDNA-captured sequencings were performed. RESULTS This study identified a spectrum of nuclear and mitochondrial genome mutations in early-stage lung adenocarcinoma and explored their association with diagnosis. The correlation coefficient for somatic mutations in cfDNA and patient-matched tumor tissues was high in nuclear and mitochondrial genomes. The mutation number of highly mutated genes was evaluated, and the Least Absolute Shrinkage and Selection Operator (LASSO) established a diagnostic model. Receiver operating characteristic (ROC) curve analysis explored the diagnostic ability of the two panels. All models were verified in the testing cohort, and the mtDNA panel demonstrated excellent performance. This study identified somatic mutations in the nuclear and mitochondrial genomes, and detecting mutations in cfDNA displayed good diagnostic performance for early-stage LUAD. Moreover, detecting somatic mutations in the mitochondria may be a better tool for diagnosing early-stage LUAD. CONCLUSIONS This study identified specific and sensitive diagnostic biomarkers for early-stage LUAD by focusing on nuclear and mitochondrial genome mutations. This also further developed an early-stage LUAD-specific mutation gene panel for clinical utility. This study established a foundation for further investigation of LUAD molecular pathogenesis.
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Affiliation(s)
- Yichun Xu
- National Engineering Research Center for Biochip at Shanghai and Shanghai Biochip Limited Corporation, No.151, Libing Road, Shanghai, 201203, China.
- Department of Pathology, Shanghai Tongji Hospital, Tongji Hospital Affiliated to Tongji University, Shanghai, China.
| | - Yong Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, No.241, Huaihai West Road, Shanghai, China
| | - Yichao Wang
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Road, Shanghai, China
| | - Jun Su
- National Engineering Research Center for Biochip at Shanghai and Shanghai Biochip Limited Corporation, No.151, Libing Road, Shanghai, 201203, China
- Department of Pathology, Shanghai Tongji Hospital, Tongji Hospital Affiliated to Tongji University, Shanghai, China
| | - Tianlong Chan
- National Engineering Research Center for Biochip at Shanghai and Shanghai Biochip Limited Corporation, No.151, Libing Road, Shanghai, 201203, China
| | - Jiajing Zhou
- National Engineering Research Center for Biochip at Shanghai and Shanghai Biochip Limited Corporation, No.151, Libing Road, Shanghai, 201203, China
| | - Yi Gong
- National Engineering Research Center for Biochip at Shanghai and Shanghai Biochip Limited Corporation, No.151, Libing Road, Shanghai, 201203, China
- Department of Pathology, Shanghai Tongji Hospital, Tongji Hospital Affiliated to Tongji University, Shanghai, China
| | - Ke Wang
- Acupuncture Anesthesia Clinical Research Institute, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yifeng Gu
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Road, Shanghai, China
| | - Congmeng Zhang
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Road, Shanghai, China
| | - Guanjin Wu
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Road, Shanghai, China
| | - Ling Bi
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Road, Shanghai, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiong Qin
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, No.241, Huaihai West Road, Shanghai, China.
| | - Junsong Han
- National Engineering Research Center for Biochip at Shanghai and Shanghai Biochip Limited Corporation, No.151, Libing Road, Shanghai, 201203, China.
- Department of Pathology, Shanghai Tongji Hospital, Tongji Hospital Affiliated to Tongji University, Shanghai, China.
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Yang R, Liu Z, Cao H, Shi Y. LINC01089, suppressed by YY1, inhibits lung cancer progression by targeting miR-301b-3p/HPDG axis. Cell Biol Toxicol 2022; 38:1063-1077. [PMID: 34561789 DOI: 10.1007/s10565-021-09643-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 08/09/2021] [Indexed: 01/25/2023]
Abstract
PURPOSE LINC01089 is a newly identified lncRNA and rarely reported in human cancers. Our study aimed to investigate its role in lung cancer. METHODS YY1, LINC01089, and miR-301b-3p levels in lung cancer tissues and cells were assessed using qRT-PCR. Bioinformatics analysis and luciferase reporter, ChIP, and RIP assays were carried out for determining the relationships among YY1, LINC01089, miR-301b-3p, and HPGD. Gain- and loss-of-function assays were carried out to confirm the impacts of LINC01089 and HPDG in lung cancer cells. CCK-8 assay was used to assess cell proliferation rate, and Transwell assay was applied to measure cell invasion and migration. An in vivo tumor model was applied for validating the role of LINC01089. RESULTS LINC01089 was decreased in lung cancer tissues and cells, and low LINC01089 level predicted a poor clinical outcome. YY1 directly bound to LINC01089 promoter region and inhibited its transcription. LINC01089 knockdown thwarted the proliferation, invasion, and migration capacity of H1299 and A549 cells and aggravated tumor growth. Specifically, LINC01089 functioned as a competing endogenous RNA of miR-301b-3p to modulate HPGD and thereby affected lung cancer progression. CONCLUSION Our data revealed that LINC01089, directly suppressed by YY1, inhibited lung cancer progression by targeting the miR-301b-3p/HPGD axis. Graphical abstract 1. LINC01089 expression was downregulated in lung cancer tisuues and cell lines, and low LINC01089 levels predicted a poor clinical outcome. 2. LINC01089 knockdown enhanced proliferation, invasion, and migration of H1299 and A549 cells in vitro and promoted lung cancer cell tumorigenesis and metastasis in vivo. 3. LINC01089, directly suppressed by YY1, functioned as a competing endogenous RNA against miR-301b-3p to increase HPGD expression.
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Affiliation(s)
- Rusong Yang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanjing Medical University, No.121 Jiangjiayuan Road, Gulou District, Nanjing, Jiangsu, 210011, People's Republic of China.
| | - Zhengcheng Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanjing Medical University, No.121 Jiangjiayuan Road, Gulou District, Nanjing, Jiangsu, 210011, People's Republic of China
| | - Hui Cao
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanjing Medical University, No.121 Jiangjiayuan Road, Gulou District, Nanjing, Jiangsu, 210011, People's Republic of China
| | - Ye Shi
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanjing Medical University, No.121 Jiangjiayuan Road, Gulou District, Nanjing, Jiangsu, 210011, People's Republic of China
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Sorscher S. Germline Testing of Patients With Non-small Cell Lung Cancers Demonstrating Incidentally Uncovered BRCA2 Apparent Pathogenic Germline Variants. Clin Lung Cancer 2022; 23:e405-e407. [PMID: 35977876 DOI: 10.1016/j.cllc.2022.07.011] [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: 11/20/2021] [Accepted: 12/17/2021] [Indexed: 01/27/2023]
Abstract
Tumor next generation sequencing (NGS) is used to interrogate nearly every non-small cell lung cancer (NSCLC) for the purpose of identifying actionable genetic alterations. Occasionally, tumor NGS also uncovers "incidental" apparent pathogenic germline variants (PGVs), with BRCA2 being among the most common of those. If germline testing confirms a BRCA2 PGV in a patient with NSCLC, therapies targeting that BRCA2 PGV might be considered, if the patient has exhausted standard NSCLC therapeutic options. Surveillance and preventive therapies for BRCA2-related cancers would be recommended or considered for that patient, as well as for family members found to carry that same BRCA2 PGV. Here, I offer my perspective related to the evidence supporting and against germline testing in patients with NSCLCs that show incidental BRCA2 apparent PGVs. I use an example to underscore how important it is to explain to patients, before tumor NGS, the possibility of uncovering an incidental PGV. I also review the myriad uncertainties related to identifying a BRCA2 PGV, when the sole indication for germline testing was the uncovering of the incidental BRCA2 apparent PGV.
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Ruiz R, Galvez-Nino M, Roque K, Montes J, Nuñez M, Raez L, Sánchez-Gambetta S, Jaúregui S, Viale S, Smith ES, Pinto JA, Mas L. Genomic landscape of the lung cancer in the young. Front Oncol 2022; 12:910117. [PMID: 36263208 PMCID: PMC9575317 DOI: 10.3389/fonc.2022.910117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/02/2022] [Indexed: 12/04/2022] Open
Abstract
Background Lung cancer in the young is a rare entity of great interest due to the high frequency of targetable mutations. In this study, we explored the genomic landscape of non-small cell lung cancer (NSCLC) in young patients and compared it with genetic alterations in older patients. Methods Comparative study of the genomic profile of NSCLC young (≤40 years old) vs older patients (>40 years old) from Instituto Nacional de Enfermedades Neoplásicas (INEN) in Lima, Peru. Archival paraffin-embedded tumor samples were profiled with FoundationOne CDx assay to identify short variants alterations (insertions and deletions), copy number variations (CNV), tumor mutational burden and microsatellite instability in 324 driver genes and rearrangements in 28 commonly rearranged genes. A targetable alteration was defined as any alteration in a driver oncogene for which an FDA approved therapy existed at the time of study enrollment. Results Overall, 62 tumors were profiled, 32 from young and 30 from older patients. All clinicopathological features (smoking status, clinical stage, and histology) were similar between groups, except for gender (65.6% of females in the younger group vs 40% in the older group, P=0.043). At least one actionable mutation was present in 84.4% and 83.3% in younger and older patients, respectively. Alteration rates in the main genes were: BRAF, 3.1%(n=1) vs 0%; EGFR, 46.9% (n=15) vs 43.3% (n=13); ERBB2, 12.5% (n=4) vs 16.7% (n=5); KRAS, 15.6% (n=5) vs 16.7% (n=5); ALK, 6.3% (n=2) vs 3.3% (n=1); RET, 0.0% vs 3.3% (n=1); ROS1, 3.1% (n=1) vs 3.3% (n=1); NTRK1, 0.0% vs 3.3% (n=1) and MET, 3.1% (n=1) vs 13.3% (n=4). Mean TMB was 4.04 Mut/Mb (SD ± 3.98) for young vs 8.06 Mut/Mb (SD ± 9.84) for older patients (P=0.016). There were not significant differences in CNV, frequency of gene rearrangements, or microsatellites instability. Conclusion NSCLC in the young in our cohort was characterized by a high frequency of actionable genetic aberrations and a low TMB, which was also true for our older patients. The enrichment of actionable mutations in young patients described in other reports might be attributed to differences in the etiology and clinicopathological characteristics between younger and older patients and therefore not be applicable to all populations.
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Affiliation(s)
- Rossana Ruiz
- Departamento de Oncología Médica, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Marco Galvez-Nino
- Departamento de Oncología Médica, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Katia Roque
- Departamento de Oncología Médica, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Jaime Montes
- Departamento de Oncología Médica, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Maria Nuñez
- Departamento de Oncología Médica, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Luis Raez
- Departamento de Patología, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Sergio Sánchez-Gambetta
- Memorial Cancer Institute/ Memorial Health Care System, Florida International University (FIU), Miami, FL, United States
| | - Sandra Jaúregui
- Memorial Cancer Institute/ Memorial Health Care System, Florida International University (FIU), Miami, FL, United States
| | - Sandra Viale
- Memorial Cancer Institute/ Memorial Health Care System, Florida International University (FIU), Miami, FL, United States
| | - Edward S. Smith
- Memorial Cancer Institute/ Memorial Health Care System, Florida International University (FIU), Miami, FL, United States
| | - Joseph A. Pinto
- Roche Farma, Lima, Peru
- Centro de Investigación Básica y Traslacional, Auna Ideas, Lima, Peru
- *Correspondence: Joseph A. Pinto,
| | - Luis Mas
- Departamento de Oncología Médica, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
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10
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Sipilä LJ, Seppä K, Aavikko M, Ravantti J, Heikkinen S, Aaltonen LA, Pitkäniemi J. Sex-specific familial aggregation of cancers in Finland. Sci Rep 2022; 12:15126. [PMID: 36068325 PMCID: PMC9448814 DOI: 10.1038/s41598-022-19039-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
Despite the fact that the effect of sex on the occurrence of cancers has been studied extensively, it remains unclear whether sex modifies familial aggregation of cancers. We explored sex-specific familial aggregation of cancers in a large population-based historical cohort study. We combined cancer and population registry data, inferring familial relationships from birth municipality-surname-sex (MNS) combinations. Our data consisted of 391,529 incident primary cancers in 377,210 individuals with 319,872 different MNS combinations. Cumulative sex-specific numbers of cancers were compared to expected cumulative incidence. Familial cancer risks were similar between the sexes in our population-wide analysis. Families with concordant cancer in both sexes exhibited similar sex-specific cancer risks. However, some families had exceptionally high sex-specific cumulative cancer incidence. We identified six families with exceptionally strong aggregation in males: three families with thyroid cancer (ratio between observed and expected incidence 184.6; 95% credible interval (95% CI) 33.1–1012.7, 173.4 (95% CI 65.4–374.3), and 161.4 (95% CI 29.6–785.7), one with stomach (ratio 14.4 (95% CI 6.9–37.2)), colon (ratio 15.5 (95% CI 5.7–56.3)) cancers and one with chronic lymphocytic leukaemia (ratio 33.5 (95% CI 17.2–207.6)). Our results imply that familial aggregation of cancers shows no sex-specific preference. However, the atypical sex-specific aggregation of stomach cancer, colon cancer, thyroid cancer and chronic lymphocytic leukaemia in certain families is difficult to fully explain with present knowledge of possible causes, and could yield useful knowledge if explored further.
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Affiliation(s)
- Lauri J Sipilä
- Department of Medical and Clinical Genetics, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, PO Box 63, 00014, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, PO Box 63, 00014, Helsinki, Finland.,Finnish Cancer Registry, Unioninkatu 22, 00130, Helsinki, Finland
| | - Karri Seppä
- Finnish Cancer Registry, Unioninkatu 22, 00130, Helsinki, Finland
| | - Mervi Aavikko
- Department of Medical and Clinical Genetics, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, PO Box 63, 00014, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, PO Box 63, 00014, Helsinki, Finland.,Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Janne Ravantti
- Department of Medical and Clinical Genetics, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, PO Box 63, 00014, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, PO Box 63, 00014, Helsinki, Finland.,Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Sanna Heikkinen
- Finnish Cancer Registry, Unioninkatu 22, 00130, Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, PO Box 63, 00014, Helsinki, Finland.,Applied Tumor Genomics Research Program, Research Programs Unit, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, PO Box 63, 00014, Helsinki, Finland
| | - Janne Pitkäniemi
- Finnish Cancer Registry, Unioninkatu 22, 00130, Helsinki, Finland. .,Health Sciences Unit, Faculty of Social Sciences (Health Sciences), Tampere University, Tampere, Finland. .,Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Institute for Statistical and Epidemiological Cancer Research, Finnish Cancer Registry, Unioninkatu 22, 00130, Helsinki, Finland.
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11
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Qi J, Deng Z, Sun G, Qian S, Liu L, Xu B. One-step algorithm for fast-track localization and multi-category classification of histological subtypes in lung cancer. Eur J Radiol 2022; 154:110443. [PMID: 35901600 DOI: 10.1016/j.ejrad.2022.110443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/18/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUNDS Accumulated evidence has proven that computer-derived features from computed tomography (CT) through radiomics and deep learning technologies can identify extensive characteristics of pulmonary malignancies, such as nodules detection and malignant lesion discrimination. However, there are few studies on whether CT images can reflect histological subtypes of lung cancer through computer-derived features. METHODS Contrast-enhanced CT images prior treatment from 417 patients diagnosed with small cell lung cancer (SCLC), lung adenocarcinoma (ADC), or lung squamous cell carcinoma (SCC) were collected. ITK-SNAP software was used by trained radiologists for the manual delineation of tumor volume. Patients of each category (SCLC, ADC, SCC) were then randomly split into training datasets and test datasets in an approximately ratio of 8:2. After image pre-processing and augmentation, 25,042 CT images from the training datasets were used to train our self-developed deep learning model for fast-tracking tumor lesions and classifying corresponding histological subtypes simultaneously. The performance of the network was evaluated by accuracy, F1-score and weighted F1-average using 1,921 testing images based on parameters generated during training. RESULTS The prediction accuracy of SCLC, ADC, and SCC were 0.83, 0.75 and 0.67, respectively. The weighted F1-average was 0.75. ADC obtained the best F1-score of 0.78, which was outperformed SCLC (0.77) and SCC (0.66). The corresponding AUC values of SCLC, ADC, and SCC were 0.87, 0.84, and 0.76, respectively. Only 0.24 s were required to simultaneously achieve functions of tumor localization and histological classification on a thoracic CT image slice. The heat map visualization illustrated the extracted tumor features to classify subtypes of lung cancer by the proposed model. CONCLUSIONS The newly developed multi-task algorithm provides a CNN-based DL approach in lung cancer for automatically fast-tracking tumor lesions and classifying corresponding histological subtypes in one-step.
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Affiliation(s)
- Jing Qi
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Zhengqiao Deng
- School of Big Data and Software Engineering, Chongqing University, Chongqing 401331, China
| | - Guogui Sun
- North China University of Science and Technology Affiliated Peoples Hospital, School of Public Health, North China University of Science and Technology, Tangshan 063001, China
| | - Shuang Qian
- School of Big Data and Software Engineering, Chongqing University, Chongqing 401331, China
| | - Li Liu
- School of Big Data and Software Engineering, Chongqing University, Chongqing 401331, China.
| | - Bo Xu
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China; Center for Intelligent Oncology, Chongqing University Cancer Hospital, Chongqing University School of Medicine, Chongqing Key Laboratory of Intelligent Oncology for Breast Cancer, Chongqing 400030, China.
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12
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Ding D, Zhang Y, Zhang X, Shi K, Shang W, Ying J, Wang L, Chen Z, Hong H. MiR-30a-3p Suppresses the Growth and Development of Lung Adenocarcinoma Cells Through Modulating GOLM1/JAK-STAT Signaling. Mol Biotechnol 2022; 64:1143-1151. [PMID: 35438415 DOI: 10.1007/s12033-022-00497-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
A considerable amount of people succumbs to lung adenocarcinoma (LUAD) due to its high incidence and mortality. This study attempted to reveal the impacts of GOLM1 on LUAD. This work analyzed GOLM1 expression in LUAD and normal tissue and studied its prognostic value utilizing data from The Cancer Genome Atlas. RNA and protein levels were, respectively, determined utilizing qRT-PCR and western blot. Cell-aggressive behaviors were assessed employing Cell Counting Kit-8, scratch healing, and Transwell assays. The targetting relationship between GOLM1 and miR-30a-3p was assayed by dual-luciferase method. GOLM1 up-regulation in LUAD was found in TCGA and it was also a negative factor for survival in patients. GOLM1 overexpression promoted cell progression in LUAD. Down-regulated miR-30a-3p in LUAD was an upstream regulatory miRNA of GOLM1 in terms of molecular mechanism. Further, rescue assays illustrated that miR-30a-3p overexpression attenuated the GOLM1 facilitating impacts on LUAD progression. Finally, we proved that miR-30a-3p/GOLM1 regulated progression of LUAD cells via JAK-STAT pathway. Collectively, the inhibitory impacts of miR-30a-3p on LUAD growth may be mediated by GOLM1/JAK-STAT, which may contribute to the diagnosis of LUAD therapy and the development of therapeutic tools.
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Affiliation(s)
- Dongxiao Ding
- Department of Thoracic Surgery, The People's Hospital of Beilun District (Beilun Branch of the First Affiliated Hospital of Medical College of Zhejiang University), No.1288, East Lushan Road, Xinqi Sub-District, Beilun District, Zhejiang Province, Ningbo City, 315800, China
| | - Yunqiang Zhang
- Department of Thoracic Surgery, The People's Hospital of Beilun District (Beilun Branch of the First Affiliated Hospital of Medical College of Zhejiang University), No.1288, East Lushan Road, Xinqi Sub-District, Beilun District, Zhejiang Province, Ningbo City, 315800, China
| | - Xuede Zhang
- Department of Thoracic Surgery, The People's Hospital of Beilun District (Beilun Branch of the First Affiliated Hospital of Medical College of Zhejiang University), No.1288, East Lushan Road, Xinqi Sub-District, Beilun District, Zhejiang Province, Ningbo City, 315800, China
| | - Ke Shi
- Department of Thoracic Surgery, The People's Hospital of Beilun District (Beilun Branch of the First Affiliated Hospital of Medical College of Zhejiang University), No.1288, East Lushan Road, Xinqi Sub-District, Beilun District, Zhejiang Province, Ningbo City, 315800, China
| | - Wenjun Shang
- Department of Thoracic Surgery, The People's Hospital of Beilun District (Beilun Branch of the First Affiliated Hospital of Medical College of Zhejiang University), No.1288, East Lushan Road, Xinqi Sub-District, Beilun District, Zhejiang Province, Ningbo City, 315800, China
| | - Junjie Ying
- Department of Thoracic Surgery, The People's Hospital of Beilun District (Beilun Branch of the First Affiliated Hospital of Medical College of Zhejiang University), No.1288, East Lushan Road, Xinqi Sub-District, Beilun District, Zhejiang Province, Ningbo City, 315800, China
| | - Li Wang
- Department of Thoracic Surgery, The People's Hospital of Beilun District (Beilun Branch of the First Affiliated Hospital of Medical College of Zhejiang University), No.1288, East Lushan Road, Xinqi Sub-District, Beilun District, Zhejiang Province, Ningbo City, 315800, China
| | - Zhongjie Chen
- Department of Thoracic Surgery, The People's Hospital of Beilun District (Beilun Branch of the First Affiliated Hospital of Medical College of Zhejiang University), No.1288, East Lushan Road, Xinqi Sub-District, Beilun District, Zhejiang Province, Ningbo City, 315800, China
| | - Haihua Hong
- Department of Thoracic Surgery, The People's Hospital of Beilun District (Beilun Branch of the First Affiliated Hospital of Medical College of Zhejiang University), No.1288, East Lushan Road, Xinqi Sub-District, Beilun District, Zhejiang Province, Ningbo City, 315800, China.
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13
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Fanale D, Pivetti A, Cancelliere D, Spera A, Bono M, Fiorino A, Pedone E, Barraco N, Brando C, Perez A, Guarneri MF, Russo TDB, Vieni S, Guarneri G, Russo A, Bazan V. BRCA1/2 variants of unknown significance in hereditary breast and ovarian cancer (HBOC) syndrome: looking for the hidden meaning. Crit Rev Oncol Hematol 2022; 172:103626. [PMID: 35150867 DOI: 10.1016/j.critrevonc.2022.103626] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Hereditary breast and ovarian cancer syndrome is caused by germline mutations in BRCA1/2 genes. These genes are very large and their mutations are heterogeneous and scattered throughout the coding sequence. In addition to the above-mentioned mutations, variants of uncertain/unknown significance (VUSs) have been identified in BRCA genes, which make more difficult the clinical management of the patient and risk assessment. In the last decades, several laboratories have developed different databases that contain more than 2000 variants for the two genes and integrated strategies which include multifactorial prediction models based on direct and indirect genetic evidence, to classify the VUS and attribute them a clinical significance associated with a deleterious, high-low or neutral risk. This review provides a comprehensive overview of literature studies concerning the VUSs, in order to assess their impact on the population and provide new insight for the appropriate patient management in clinical practice.
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Affiliation(s)
- Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Pivetti
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Daniela Cancelliere
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Spera
- Department of Radiotherapy, San Giovanni di Dio Hospital, ASP of Agrigento, Agrigento, Italy
| | - Marco Bono
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Erika Pedone
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Nadia Barraco
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessandro Perez
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | | | - Tancredi Didier Bazan Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Salvatore Vieni
- Division of General and Oncological Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Italy
| | - Girolamo Guarneri
- Gynecology Section, Mother - Child Department, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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14
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Germline testing of patients with non-small cell lung cancers demonstrating incidentally uncovered BRCA2 apparent pathogenic germline variants. Clin Lung Cancer 2021. [DOI: 10.1016/j.cllc.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Devarakonda S, Li Y, Martins Rodrigues F, Sankararaman S, Kadara H, Goparaju C, Lanc I, Pepin K, Waqar SN, Morgensztern D, Ward J, Masood A, Fulton R, Fulton L, Gillette MA, Satpathy S, Carr SA, Wistuba I, Pass H, Wilson RK, Ding L, Govindan R. Genomic Profiling of Lung Adenocarcinoma in Never-Smokers. J Clin Oncol 2021; 39:3747-3758. [PMID: 34591593 PMCID: PMC8601276 DOI: 10.1200/jco.21.01691] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/20/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Approximately 10%-40% of patients with lung cancer report no history of tobacco smoking (never-smokers). We analyzed whole-exome and RNA-sequencing data of 160 tumor and normal lung adenocarcinoma (LUAD) samples from never-smokers to identify clinically actionable alterations and gain insight into the environmental and hereditary risk factors for LUAD among never-smokers. METHODS We performed whole-exome and RNA-sequencing of 88 and 69 never-smoker LUADs. We analyzed these data in conjunction with data from 76 never-smoker and 299 smoker LUAD samples sequenced by The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium. RESULTS We observed a high prevalence of clinically actionable driver alterations in never-smoker LUADs compared with smoker LUADs (78%-92% v 49.5%; P < .0001). Although a subset of never-smoker samples demonstrated germline alterations in DNA repair genes, the frequency of samples showing germline variants in cancer predisposing genes was comparable between smokers and never-smokers (6.4% v 6.9%; P = .82). A subset of never-smoker samples (5.9%) showed mutation signatures that were suggestive of passive exposure to cigarette smoke. Finally, analysis of RNA-sequencing data showed distinct immune transcriptional subtypes of never-smoker LUADs that varied in their expression of clinically relevant immune checkpoint molecules and immune cell composition. CONCLUSION In this comprehensive genomic and transcriptome analysis of never-smoker LUADs, we observed a potential role for germline variants in DNA repair genes and passive exposure to cigarette smoke in the pathogenesis of a subset of never-smoker LUADs. Our findings also show that clinically actionable driver alterations are highly prevalent in never-smoker LUADs, highlighting the need for obtaining biopsies with adequate cellularity for clinical genomic testing in these patients.
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Affiliation(s)
- Siddhartha Devarakonda
- Division of Oncology, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, St Louis, MO
| | - Yize Li
- Division of Oncology, Washington University School of Medicine, St Louis, MO
- McDonnell Genome Institute, St Louis, MO
- Division of Biological and Biomedical Sciences, Washington University in St Louis, St Louis, MO
| | - Fernanda Martins Rodrigues
- Division of Oncology, Washington University School of Medicine, St Louis, MO
- McDonnell Genome Institute, St Louis, MO
- Division of Biological and Biomedical Sciences, Washington University in St Louis, St Louis, MO
| | | | | | | | | | - Kymberlie Pepin
- Division of Oncology, Washington University School of Medicine, St Louis, MO
| | - Saiama N. Waqar
- Division of Oncology, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, St Louis, MO
| | - Daniel Morgensztern
- Division of Oncology, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, St Louis, MO
| | - Jeffrey Ward
- Division of Oncology, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, St Louis, MO
| | | | | | | | - Michael A. Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Steven A. Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | | | - Harvey Pass
- New York University Langone Medical Center, New York, NY
| | | | - Li Ding
- Division of Oncology, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, St Louis, MO
- McDonnell Genome Institute, St Louis, MO
- Department of Genetics, Washington University in St Louis, St Louis, MO
- Department of Medicine, Washington University in St Louis, St Louis, MO
| | - Ramaswamy Govindan
- Division of Oncology, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, St Louis, MO
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16
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Mao W, Chen R, Lu R, Wang S, Song H, You D, Liu F, He Y, Zheng M. Germline mutation analyses of malignant ground glass opacity nodules in non-smoking lung adenocarcinoma patients. PeerJ 2021; 9:e12048. [PMID: 34540367 PMCID: PMC8415279 DOI: 10.7717/peerj.12048] [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: 01/29/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background Germline mutations play an important role in the pathogenesis of lung cancer. Nonetheless, research on malignant ground glass opacity (GGO) nodules is limited. Methods A total of 13 participants with malignant GGO nodules were recruited in this study. Peripheral blood was used for exome sequencing, and germline mutations were analyzed using InterVar. The whole exome sequencing dataset was analyzed using a filtering strategy. KOBAS 3.0 was used to analyze KEGG pathway to further identify possible deleterious mutations. Results There were seven potentially deleterious germline mutations. NM_001184790:exon8: c.C1070T in PARD3, NM_001170721:exon4:c.C392T in BCAR1 and NM_001127221:exon46: c.G6587A in CACNA1A were present in three cases each; rs756875895 frameshift in MAX, NM_005732: exon13:c.2165_2166insT in RAD50 and NM_001142316:exon2:c.G203C in LMO2, were present in two cases each; one variant was present in NOTCH3. Conclusions Our results expand the germline mutation spectrum in malignant GGO nodules. Importantly, these findings will potentially help screen the high-risk population, guide their health management, and contribute to their clinical treatment and determination of prognosis.
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Affiliation(s)
- Wenjun Mao
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Ruo Chen
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Rongguo Lu
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Shengfei Wang
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Huizhu Song
- Department of Pharmacy, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Dan You
- Department of Pharmacy, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Feng Liu
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Yijun He
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Mingfeng Zheng
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
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17
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Rammal S, Kourie HR, Jalkh N, Mehawej C, Chouery E, Moujaess E, Dabar G. Molecular pathogenesis of hereditary lung cancer: a literature review. Pharmacogenomics 2021; 22:791-803. [PMID: 34410147 DOI: 10.2217/pgs-2020-0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Among all cancer types, pulmonary cancer has the highest mortality rate. Tobacco consumption remains the major risk factor for the development of lung cancer. However, many studies revealed a correlation between inherited genetic variants and predisposition to lung cancer, especially in nonsmokers. To date, genetic testing for the detection of germline mutations is not yet recommended in patients with lung cancer and testing is focused on somatic alterations given their implication in the treatment choice. Understanding the impact of genetic predisposition on the occurrence of lung cancer is essential to enable the introduction of accurate guidelines and recommendations that might reduce mortality. In this review paper, we describe familial lung cancer, and expose germline mutations that are linked to this type of cancer. We also report pathogenic genetic variants linked to syndromes associated with lung cancer.
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Affiliation(s)
- Souraya Rammal
- Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Hampig Raphael Kourie
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Nadine Jalkh
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Cybel Mehawej
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Eliane Chouery
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Elissar Moujaess
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Georges Dabar
- Pulmonary & Critical Care Division, Hotel Dieu de France, Saint Joseph University of Beirut, Beirut, Lebanon
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18
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Xu L, Su Z, Xie B. Diagnostic value of conventional tumor markers in young patients with pulmonary nodules. J Clin Lab Anal 2021; 35:e23912. [PMID: 34296781 PMCID: PMC8418517 DOI: 10.1002/jcla.23912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 01/25/2023] Open
Abstract
Background Lung cancer is one of the most common malignancies, and there is a trend of increasing incidence in young patients. The preoperative diagnosis of pulmonary nodules is mainly based on the combination of imaging and tumor markers. There is no relevant report on the diagnostic value of tumor markers in young pulmonary nodules. Our study was designed to explore the value of five tumor markers in young patients with pulmonary nodules. Methods We reviewed the medical records of 390 young patients (age ≤45 years) with pulmonary nodules treated at two separate centers from January 1, 2015, to January 1, 2021. Malignant pulmonary nodules were confirmed in 318 patients, and the other 72 patients were diagnosed with benign pulmonary nodules. The gold standard for diagnosis of pulmonary nodules was surgical biopsy. The conventional serum biomarkers included cytokeratin 19 (CYFRA21‐1), pro‐gastrin‐releasing‐peptide (ProGRP), carcinoembryonic antigen (CEA), neuron‐specific enolase (NSE), and squamous cell carcinoma‐associated antigen (SCCA). The diagnostic values of five tumor markers were analyzed by receiver operating characteristic (ROC) curves. Results There were no significant differences in the expression of five tumor markers between the groups (p > 0.05). Single tumor marker (CYFRA21‐1, ProGRP, CEA, NSE, and SCCA) showed a limited value in the diagnosis of malignant pulmonary nodules, with the AUC of 0.506, 0.503 0.532, 0.548, and 0.562, respectively. The AUC of the combined examination was only 0.502~0.596, which did not improve the diagnostic value. Conclusions Five conventional tumor markers had a limited diagnostic value in young patients with pulmonary nodules.
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Affiliation(s)
- Lihuan Xu
- Department of Pulmonary and Critical Care Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
| | - Zhiming Su
- Fujian Medical University Union Hospital, Fuzhou, China
| | - Baosong Xie
- Department of Pulmonary and Critical Care Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
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Moin AT, Sarkar B, Ullah MA, Araf Y, Ahmed N, Rudra B. In silico assessment of EpCAM transcriptional expression and determination of the prognostic biomarker for human lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Biochem Biophys Rep 2021; 27:101074. [PMID: 34345719 PMCID: PMC8319582 DOI: 10.1016/j.bbrep.2021.101074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 12/24/2022] Open
Abstract
Epithelial cell adhesion molecule (EpCAM) is a transmembrane glycoprotein which is involved in cell signaling, proliferation, maturation, and movement, all of which are crucial for the proper development of cells and tissues. Cleavage of the EpCAM protein leads to the up-regulation of c-myc, e-fabp, and cyclins A and E which promote tumorigenesis. EpCAM can act as potential diagnostic and prognostic biomarker for different types of cancers as it is also found to be expressed in epithelia and epithelial-derived neoplasms. Hence, we aimed to analyze the EpCAM gene expression and any associated feedback in the patients of two major types of lung cancer (LC) i.e., lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), based on the publicly available online databases. In this study, server-based gene expression analysis represents the up-regulation of EpCAM in both LUAD and LUSC subtypes as compared to the corresponding normal tissues. Besides, the histological sections revealed the over-expression of EpCAM protein in cancerous tissues by depicting strong staining signals. Furthermore, mutation analysis suggested missense as the predominant type of mutation both in LUAD and LUSC in the EpCAM gene. A significant correlation (P-value < 0.05) between the higher EpCAM expression and lower patient survival was also found in this study. Finally, the co-expressed genes were identified with their ontological features and signaling pathways associated in LC development. The overall study suggests EpCAM to be a significant biomarker for human LC prognosis.
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Affiliation(s)
- Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Bishajit Sarkar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Asad Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Nafisa Ahmed
- Biotechnology Program, Department of Mathematics and Natural Sciences, School of Data and Sciences, BRAC University, Dhaka, Bangladesh
| | - Bashudev Rudra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
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20
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Diossy M, Sztupinszki Z, Borcsok J, Krzystanek M, Tisza V, Spisak S, Rusz O, Timar J, Csabai I, Fillinger J, Moldvay J, Pedersen AG, Szuts D, Szallasi Z. A subset of lung cancer cases shows robust signs of homologous recombination deficiency associated genomic mutational signatures. NPJ Precis Oncol 2021; 5:55. [PMID: 34145376 PMCID: PMC8213828 DOI: 10.1038/s41698-021-00199-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/28/2021] [Indexed: 01/14/2023] Open
Abstract
PARP inhibitors are approved for the treatment of solid tumor types that frequently harbor alterations in the key homologous recombination (HR) genes, BRCA1/2. Other tumor types, such as lung cancer, may also be HR deficient, but the frequency of such cases is less well characterized. Specific DNA aberration profiles (mutational signatures) are induced by homologous recombination deficiency (HRD) and their presence can be used to assess the presence or absence of HR deficiency in a given tumor biopsy even in the absence of an observed alteration of an HR gene. We derived various HRD-associated mutational signatures from whole-genome and whole-exome sequencing data in the lung adenocarcinoma and lung squamous carcinoma cases from TCGA, and in a patient of ours with stage IVA lung cancer with exceptionally good response to platinum-based therapy, and in lung cancer cell lines. We found that a subset of the investigated cases, both with and without biallelic loss of BRCA1 or BRCA2, showed robust signs of HR deficiency. The extreme platinum responder case also showed a robust HRD-associated genomic mutational profile. HRD-associated mutational signatures were also associated with PARP inhibitor sensitivity in lung cancer cell lines. Consequently, lung cancer cases with HRD, as identified by diagnostic mutational signatures, may benefit from PARP inhibitor therapy.
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Affiliation(s)
- Miklos Diossy
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, Kgs. Lyngby, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Judit Borcsok
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Orsolya Rusz
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Jozsef Timar
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Janos Fillinger
- Department of Pathology, National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Judit Moldvay
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
- Department of Tumor Biology, National Korányi Institute of Pulmonology-Semmelweis University, Budapest, Hungary
| | - Anders Gorm Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, Kgs. Lyngby, Denmark
| | - David Szuts
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary.
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21
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Vashistha V, Garg A, Iyer H, Jain D, Madan K, Hadda V, Guleria R, Mohan A. A comprehensive comparison between young and older-age non-small cell lung cancer patients at a public referral centre in Delhi, India. Ecancermedicalscience 2021; 15:1223. [PMID: 34158827 PMCID: PMC8183650 DOI: 10.3332/ecancer.2021.1223] [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: 11/20/2020] [Indexed: 12/02/2022] Open
Abstract
Purpose Given the increasing number of non-small cell lung cancer (NSCLC) patients in India, a comparative analysis between patients under 40 years and those of older age at a major public referral centre would provide insight into the phenotypic patterns of this group. Methods NSCLC patients who were accessioned within the lung cancer clinic database of the Pulmonary Medicine Department at the all India institute of medical sciences – Delhi between 2008 and 2019 were reviewed. Patients 40 years or younger and 60 years or older were selected and categorised as young and older patients, respectively. Baseline clinical characteristics, histologic profiles, treatments administered and survival outcomes were compared between both groups. Results Following the database review, 154 young and 1,058 older patients were selected for inclusion. Clinically, young patients were more often female (26.0% versus 14.5%, p < 0.001), retained a more independent performance status (64.1% versus 45.5%; p < 0.001) and never smoked (63.7 % versus 18.8%, p < 0.001). Regarding disease profiles, young patients were more frequently diagnosed with adenocarcinoma (p < 0.001) and 12 young patients had adenoid cystic carcinoma. Rates of stage IV disease at presentation were higher among young patients (78.0% versus 63.0%, p < 0.001). Regarding treatment, no differences in systemic therapies administered or survival were identified. Conclusion In India, young NSCLC patients are frequently non-smokers and diagnosed with advanced disease. Despite better performance status, young patients do not share better outcomes. Efforts should be directed towards optimising intensive treatment for young patients.
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Affiliation(s)
- Vishal Vashistha
- Raymond G. Murphy New Mexico Veterans Affairs Healthcare System, Section of Haematology and Oncology, 1501 San Pedro Dr SE, Albuquerque, NM 87108, USA.,Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi 110608, India.,Fulbright-Nehru Fellowship Programme, United States-India Educational Foundation, Fulbright House, 12 Hailey Rd, New Delhi 110002, India
| | - Avneet Garg
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi 110608, India.,Adesh Institute of Medical Sciences and Research, Department of Pulmonary Medicine, Barnala Bypass, Bathinda 151109, India
| | - Hariharan Iyer
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi 110608, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, Sri Aurobindo Marg, Ansari Nagar, Ansari Nagar East, New Delhi 110029, India
| | - Karan Madan
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi 110608, India
| | - Vijay Hadda
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi 110608, India
| | - Randeep Guleria
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi 110608, India
| | - Anant Mohan
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi 110608, India
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22
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Xue D, Lin H, Lin L, Wei Q, Yang S, Chen X. TTN/ TP53 mutation might act as the predictor for chemotherapy response in lung adenocarcinoma and lung squamous carcinoma patients. Transl Cancer Res 2021; 10:1284-1294. [PMID: 35116455 PMCID: PMC8798240 DOI: 10.21037/tcr-20-2568] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/18/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Chemotherapy is the preferred treatment in many types of cancer including lung cancer. However, most of patients resist chemotherapy resulting in disease progressive and recurrence. Titin (TTN) mutation is proved as a beneficial role in lung squamous carcinoma (LUSC), but the predictive role on chemotherapy resistance of lung cancer is still limited and discussable. METHODS Clinical information and related somatic mutation profiles were obtained from The Cancer Genome Atlas (TCGA) database and analyzed by R-Studio using R-package. Overall survival (OS) curve and the association between gene mutation and clinical features were determined by GraphPad 6.0 software. RESULTS Available data including 563 lung adenocarcinoma (LUAD) and 505 LUSC subjects were included in this study. Among all patients, 205 out of 563 LUAD and 326 out of 505 LUSC patients displayed TTN gene mutation. When comparing the clinical features in TTN-mutated patients to patients without TTN mutation who received chemotherapy, the tumors were always located in the upper lung in LUAD patients with TTN mutation and most of TTN-mutated subjects were at low pathological stage, which was not observed in LUSC patients. However, patients with TTN-mutation, particularly missense mutation, had a higher chemosensitivity and longer OS period than that patients without TTN mutation in both LUAD and LUSC. Of note, LUAD and LUSC patients possessed favorable OS and better chemotherapy response benefiting from TTN/tumor protein 53 (TP53) double mutation compared to TTN and TP53 mutation alone, respectively. Additionally, TTN/TP53 double mutation-initiated high rate of chemotherapy response were largely concentrated within LUAD and LUSC patients whose anatomic neoplasm subdivision were located in the upper lung. CONCLUSIONS Collectively, TTN/TP53 co-mutation is possibly served as an effective predictor for OS and chemotherapy response in lung cancer.
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Affiliation(s)
- Dan Xue
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Hongguang Lin
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Lan Lin
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Qiongying Wei
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Sheng Yang
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Xiangqi Chen
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, China
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23
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Kong W, Chen Y, Zhao Z, Zhang L, Lin X, Luo X, Wang S, Song Z, Lin X, Lai G, Yu Z. EXT1 methylation promotes proliferation and migration and predicts the clinical outcome of non-small cell lung carcinoma via WNT signalling pathway. J Cell Mol Med 2021; 25:2609-2620. [PMID: 33565239 PMCID: PMC7933929 DOI: 10.1111/jcmm.16277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 01/15/2023] Open
Abstract
DNA methylation is important for lung cancer prognosis. In this work, it is aimed to seek novel biomarkers with DNA methylation‐expression‐pathway pattern and explore its underlying mechanism. Prognostic DNA methylation sites and mRNAs were screened in NSCLC data set from TCGA, and further validated using the samples retrospectively collected, and EXT1 was identified as a potential target. Gene body methylation of three CpG sites (cg03276982, cg11592677, cg16286281) on EXT1 was significantly associated with clinical outcome, and the EXT1 gene expression also predicted prognosis. The expression level of EXT1 was also correlated with its DNA methylation level. This observation was further validated in a new data set consist of 170 samples. Knocking down of EXT1 resulted in decreased proliferation and migration. EXT1 targets were analysed using GSEA. It is found that the WNT signalling is the potential downstream target of EXT1. Further analyses revealed that the EXT1 targets the beta‐catenin and effect migration rate of NSCLC cell lines. The WNT signalling inhibitor, XAV‐939, effectively disrupted the migration promotion effect induced by EXT1. In summary, EXT1 methylation regulates the gene expression, effects the proliferation and migration via WNT pathway and predicted a poor prognosis for NSCLC.
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Affiliation(s)
- Wencui Kong
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Ying Chen
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Zhongquan Zhao
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Lei Zhang
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Xiandong Lin
- Laboratory of Radiation Oncology and Radiobiology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Xingguang Luo
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, West Haven, CT, USA
| | - Shuiliang Wang
- Department of Urology, 900th Hospital of the Joint Logistics Team Support Force, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Transplant Biology, Affiliated Dongfang Hospital, Xiamen University School of Medicine, Fuzhou, China
| | - Zhengbo Song
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou, China.,Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, China.,Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Xiangwu Lin
- Medical Oncology, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Guoxiang Lai
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Zongyang Yu
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fujian Medical University,Affiliated Dongfang Hospital, Xiamen University School of Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
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24
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Fan Y, He L, Wang Y, Fu S, Han Y, Fan J, Wen Q. CLIP4 Shows Putative Tumor Suppressor Characteristics in Breast Cancer: An Integrated Analysis. Front Mol Biosci 2021; 7:616190. [PMID: 33575272 PMCID: PMC7870488 DOI: 10.3389/fmolb.2020.616190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
Background: CAP-Gly domain containing linker protein family member 4 (CLIP4) plays an important role in cancers. However, its expression, prognostic value, and biological effect in breast cancer remain unclear. Methods: Data on patients diagnosed with breast cancer were retrieved from the TCGA-BRCA and other public omics databases. The expression profile of CLIP4 was analyzed using Oncomine, bc-GenExMiner, and TCGA. The prognostic value of CLIP4 was determined by Kaplan-Meier Plotter and Human Protein Atlas. Identification of genes co-expressed with CLIP4 and potential mechanism analyses were performed using UALCAN, STRING, Metascape, and GSEA. The epigenetic characteristics of CLIP4 were determined by DiseaseMeth and MEXPRESS. Results: CLIP4 was downregulated and its expression was negatively correlated with estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor type 2 (HER2) status, Nottingham prognostic index (NPI), and Scarff-Bloom-Richardson (SBR) grade in breast cancer, whereas it was positively linked to basal-like and triple negative breast cancer status. Ectopic expression of CLIP4 was related with poor prognosis. In the analysis of genes co-expressed with CLIP4, GSEA showed that the Hedgehog (Hh), JAK-STAT, ERBB, Wnt signaling pathway, cell adhesion molecules, and pathways in cancer were dissimilarly enriched in the CLIP4 expression high phenotype. Analysis of the genetics and epigenetics of CLIP4 indicated that its expression was negatively correlated with DNA methylation. Conclusion: Methylated CLIP4 may be a novel prognostic and therapeutic biomarker for breast cancer.
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Affiliation(s)
- Yu Fan
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Lijia He
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Yu Wang
- Health Management Department, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shaozhi Fu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Yunwei Han
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Juan Fan
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Academician (Expert) Workstation of Sichuan Province, Luzhou, China
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25
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Yu L, Qiao R, Xu J, Han B, Zhong R. FAM207BP, a pseudogene-derived lncRNA, facilitates proliferation, migration and invasion of lung adenocarcinoma cells and acts as an immune-related prognostic factor. Life Sci 2021; 268:119022. [PMID: 33434533 DOI: 10.1016/j.lfs.2021.119022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022]
Abstract
AIMS This study aimed to characterize the functions of pseudogene-derived long non-coding RNA (lncRNA) FAM207BP in lung adenocarcinoma (LUAD). MATERIALS AND METHODS Through the Cancer Genome Atlas (TCGA)-Genotype Tissue Expression (GTEx) database, FAM207BP expression was detected in LUAD and normal tissues. Overall survival (OS) and disease-free survival (DFS) analysis was presented using log-rank test or univariate Cox regression analysis. The relationships between FAM207BP expression and clinical features were analyzed. FAM207BP expression was validated in LUAD tissues and cells using RT-qPCR. Cell viability of LUAD cells was evaluated after silencing or overexpressing FAM207BP. Furthermore, migrated and invasive abilities were examined by Transwell and scratch assays. The correlation between FAM207BP expression and the immune infiltration levels was analyzed. Gene Set Enrichment Analysis (GSEA) was performed for high- and low-expression of FAM207BP using C2 collection in the Molecular Signatures Database (MSigDB) database. KEY FINDINGS FAM207BP expression was distinctly higher in LUAD than normal tissues. Patients with its high expression indicated worse OS and DFS time. FAM207BP expression was significantly related to gender. RT-qPCR results confirmed that FAM207BP was significantly highly expressed in LUAD tissues and cells. Knockdown of FAM207BP distinctly suppressed cellular viability, migration and invasion for LUAD cells. Also, its expression was negatively related to B cell infiltration levels. GSEA results indicated that high FAM207BP expression was involved in regulation of gene expression. Its low expression was related to immune response. SIGNIFICANCE Pseudogene-derived lncRNA FAM207BP could induce proliferation and migration of LUAD cells, which could act as an immune-related prognostic factor.
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Affiliation(s)
- Lian Yu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Jianlin Xu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China.
| | - Runbo Zhong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China.
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Liu C, Li X, Shao H, Li D. Identification and Validation of Two Lung Adenocarcinoma-Development Characteristic Gene Sets for Diagnosing Lung Adenocarcinoma and Predicting Prognosis. Front Genet 2020; 11:565206. [PMID: 33408736 PMCID: PMC7779611 DOI: 10.3389/fgene.2020.565206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/26/2020] [Indexed: 12/25/2022] Open
Abstract
Background: Lung adenocarcinoma (LUAD) is one of the main types of lung cancer. Because of its low early diagnosis rate, poor late prognosis, and high mortality, it is of great significance to find biomarkers for diagnosis and prognosis. Methods: Five hundred and twelve LUADs from The Cancer Genome Atlas were used for differential expression analysis and short time-series expression miner (STEM) analysis to identify the LUAD-development characteristic genes. Survival analysis was used to identify the LUAD-unfavorable genes and LUAD-favorable genes. Gene set variation analysis (GSVA) was used to score individual samples against the two gene sets. Receiver operating characteristic (ROC) curve analysis and univariate and multivariate Cox regression analysis were used to explore the diagnostic and prognostic ability of the two GSVA score systems. Two independent data sets from Gene Expression Omnibus (GEO) were used for verifying the results. Functional enrichment analysis was used to explore the potential biological functions of LUAD-unfavorable genes. Results: With the development of LUAD, 185 differentially expressed genes (DEGs) were gradually upregulated, of which 84 genes were associated with LUAD survival and named as LUAD-unfavorable gene set. While 237 DEGs were gradually downregulated, of which 39 genes were associated with LUAD survival and named as LUAD-favorable gene set. ROC curve analysis and univariate/multivariate Cox proportional hazards analyses indicated both of LUAD-unfavorable GSVA score and LUAD-favorable GSVA score were a biomarker of LUAD. Moreover, both of these two GSVA score systems were an independent factor for LUAD prognosis. The LUAD-unfavorable genes were significantly involved in p53 signaling pathway, Oocyte meiosis, and Cell cycle. Conclusion: We identified and validated two LUAD-development characteristic gene sets that not only have diagnostic value but also prognostic value. It may provide new insight for further research on LUAD.
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Affiliation(s)
- Cheng Liu
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiang Li
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hua Shao
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dan Li
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
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27
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Li J, Wang B, Li X, Zhu Y. Estimation of Hub Genes and Infiltrating Immune Cells in Non-Smoking Females with Lung Adenocarcinoma by Integrated Bioinformatic Analysis. Med Sci Monit 2020; 26:e922680. [PMID: 32669531 PMCID: PMC7384333 DOI: 10.12659/msm.922680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In recent years, the morbidity and mortality rates of lung adenocarcinoma in non-smoking females have been increasing dramatically. Although much research has been done with some progress, the molecular mechanism remains unclear. In this study we aimed to estimate hub genes and infiltrating immune cells in non-smoking females with lung adenocarcinoma. MATERIAL AND METHODS Firstly, we obtained differentially expressed genes (DEGs) by GEO2R analysis based on 3 independent mRNA microarray datasets of GSE10072, GSE31547, and GSE32863. The DAVID database was utilized for functional enrichment analysis of DEGs. Moreover, we identified hub genes with prognostic value by STRING, Cytoscape, and Kaplan Meier plotter. Subsequently, these genes were further analyzed by Gene Expression Profiling Interactive Analysis, Oncomine, Tumor Immune Estimation Resource, and Human Protein Atlas. Finally, the immune infiltration analysis was performed by CIBERSORT and The Cancer Genome Atlas with R packages. RESULTS We found 315 DEGs enriching in the extracellular matrix organization, cell adhesion, integrin binding, angiogenesis, and hypoxic response. And among these DEGs, we identified 10 hub genes (SPP1, ENG, ATF3, TOP2A, COL1A1, PAICS, CAV1, CAT, TGFBR2, and ANGPT1) of significant prognostic value. Simultaneously, we illustrated the distribution and differential expressions of 22 immune cell subtypes. and dendritic cells resting and macrophages M1 were identified with prognostic significance. CONCLUSIONS The results indicated that 10 hub genes and 2 immune cell subtypes might be promising biomarkers for lung adenocarcinoma in non-smoking females. This finding needs to be further evaluated.
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Affiliation(s)
- Jie Li
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland)
| | - Ben Wang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland)
| | - Xin Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland)
| | - Yuxi Zhu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland)
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Duan Y, Li WX, Wang Y, Zhao Y, Shen J, Deng CJ, Li Q, Chen R, Liu X, Zhang YL. Integrated Analysis of lncRNAs and mRNAs Identifies a Potential Driver lncRNA FENDRR in Lung Cancer in Xuanwei, China. Nutr Cancer 2020; 73:983-995. [PMID: 32590916 DOI: 10.1080/01635581.2020.1779323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
This study was to screen out potential driver long non-coding RNAs (lncRNAs) in lung cancer in Xuanwei (LCXW) differently expressed mRNAs and lncRNAs were detected by gene expression microarrays in 23 paired lung adenocarcinoma and adjacent tissues. Combined bioinformatics analysis was performed to identify potential driver lncRNAs and their potential regulatory relationships. Transcriptome and clinical data in TCGA-LUAD were used as comparison and validation dataset. The comparison of LCXW and TCGA-LUAD revealed significant differences in expression of some genes, signaling pathways affected by differentially expressed genes, and the 5-year survival rate of patients. We identified 14 consistently deregulated mRNAs and 5 lncRNAs as candidate genes, which affected multiple cancer-related pathways and influenced patients' overall survival. By combined bioinformatics analysis, we further identified a potential driver lncRNA fetal-lethal non-coding developmental regulatory RNA (FENDRR) and proposed its possible regulation mechanism. The low expression of FENDRR was positively correlated with Krüppel-like factor4 (KLF4), KLF4 down-regulation may loss the activation function of cyclin-dependent kinase inhibitor 1A (CDKN1A) and cyclin-dependent kinase inhibitor 1C (CDKN1C) and the inhibition function of CyclinB1 (CCNB1), eventually cause excessive cell cycle activation and lead to lung cancer. This study revealed a potential FENDRR-KLF4-cell cycle regulation axis. These results lay an important foundation for further research on the pathogenesis of LCXW and identification of potential novel biomarkers or therapeutic targets.
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Affiliation(s)
- Yong Duan
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.,Yunnan Institute of Laboratory Diagnosis, Kunming, China.,Innovation Team of Yunnan Provincial Clinical Laboratory and Diagnosis, Kunming, China
| | - Wen-Xing Li
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yan Wang
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.,Yunnan Institute of Laboratory Diagnosis, Kunming, China.,Innovation Team of Yunnan Provincial Clinical Laboratory and Diagnosis, Kunming, China
| | - Ying Zhao
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.,Yunnan Institute of Laboratory Diagnosis, Kunming, China.,Innovation Team of Yunnan Provincial Clinical Laboratory and Diagnosis, Kunming, China
| | - Jie Shen
- Second Department of Internal Medicine, Kunming Third People's Hospital, Kunming, China
| | - Cheng-Jun Deng
- Department of Gastroenterology, Kunming Children's Hospital, Kunming, China
| | - Qing Li
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.,Yunnan Institute of Laboratory Diagnosis, Kunming, China.,Innovation Team of Yunnan Provincial Clinical Laboratory and Diagnosis, Kunming, China
| | - Ran Chen
- Department of Clinical Laboratory, Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiao Liu
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.,Yunnan Institute of Laboratory Diagnosis, Kunming, China.,Innovation Team of Yunnan Provincial Clinical Laboratory and Diagnosis, Kunming, China
| | - Yan-Liang Zhang
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.,Yunnan Institute of Laboratory Diagnosis, Kunming, China.,Innovation Team of Yunnan Provincial Clinical Laboratory and Diagnosis, Kunming, China
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Liu M, Liu X, Suo P, Gong Y, Qu B, Peng X, Xiao W, Li Y, Chen Y, Zeng Z, Lu Y, Huang T, Zhao Y, Liu M, Li L, Chen Y, Zhou Y, Liu G, Yao J, Chen S, Song L. The contribution of hereditary cancer-related germline mutations to lung cancer susceptibility. Transl Lung Cancer Res 2020; 9:646-658. [PMID: 32676327 PMCID: PMC7354149 DOI: 10.21037/tlcr-19-403] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Germline variations may contribute to lung cancer susceptibility besides environmental factors. The influence of germline mutations on lung cancer susceptibility and their correlation with somatic mutations has not been systematically investigated. Methods In this study, germline mutations from 1,026 non-small cell lung cancer (NSCLC) patients were analyzed with a 58-gene next-generation sequencing (NGS) panel containing known hereditary cancer-related genes, and were categorized based on American College of Medical Genetics and Genomics (ACMG) guidelines in pathogenicity, and the corresponding somatic mutations were analyzed using a 605-gene NGS panel containing known cancer-related genes. Results Plausible genetic susceptibility was found in 4.7% of lung cancer patients, in which 14 patients with pathogenic mutations (P group) and 34 patients with likely-pathogenic mutations (LP group) were identified. The ratio of the first degree relatives with lung cancer history of the P groups was significantly higher than the Non-P group (P=0.009). The ratio of lung cancer patients with history of other cancers was higher in P (P=0.0007) or LP (P=0.017) group than the Non-P group. Pathogenic mutations fell most commonly in BRCA2, followed by CHEK2 and ATM. Likely-pathogenic mutations fell most commonly in NTRK1 and EXT2, followed by BRIP1 and PALB2. These genes are involved in DNA repair, cell cycle regulation and tumor suppression. By comparing the germline mutation frequency from this study with that from the whole population or East Asian population (gnomAD database), we found that the overall odds ratio (OR) for P or LP group was 17.93 and 15.86, respectively, when compared with the whole population, and was 2.88 and 3.80, respectively, when compared with the East Asian population, suggesting the germline mutations of the P and LP groups were risk factors for lung cancer. Somatic mutation analysis revealed no significant difference in tumor mutation burden (TMB) among the groups, although a trend of lower TMB in the pathogenic group was found. The SNV/INDEL mutation frequency of TP53 in the P group was significantly lower than the other two groups, and the copy number variation (CNV) mutation frequency of PIK3CA and MET was significantly higher than the Non-P group. Pathway enrichment analysis found no significant difference in aberrant pathways among the three groups. Conclusions A proportion of 4.7% of patients carrying germline variants may be potentially linked to increased susceptibility to lung cancer. Patients with pathogenic germline mutations exhibited stronger family history and higher lung cancer risk.
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Affiliation(s)
- Mengyuan Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Xinyi Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Peisu Suo
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yuan Gong
- The Second Medical Center of the Chinese PLA General Hospital, Beijing 100853, China
| | - Baolin Qu
- The Second Medical Center of the Chinese PLA General Hospital, Beijing 100853, China
| | - Xiumei Peng
- The Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100037, China
| | - Wenhua Xiao
- The Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100037, China
| | - Yuemin Li
- The Eighth Medical Center of the Chinese PLA General Hospital, Beijing 100091, China
| | - Yan Chen
- The Fifth Medical Center of the Chinese PLA General Hospital, Beijing 100039, China
| | - Zhen Zeng
- The Fifth Medical Center of the Chinese PLA General Hospital, Beijing 100039, China
| | - Yinying Lu
- The Fifth Medical Center of the Chinese PLA General Hospital, Beijing 100039, China
| | - Tanxiao Huang
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yingshen Zhao
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Ming Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Lifeng Li
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yaru Chen
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yanqing Zhou
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Guifeng Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Jianfei Yao
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Shifu Chen
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Lele Song
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China.,The Eighth Medical Center of the Chinese PLA General Hospital, Beijing 100091, China
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30
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Bermisheva MA, Gilyazova IR, Zinnatullina GF, Khusnutdinova EK. Analysis of Rare Variant c.2395C>T (p.Arg799Trp) in Gene ERCC4 in Breast Cancer Patients from Bashkortostan. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420050026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Rotunno M, Barajas R, Clyne M, Hoover E, Simonds NI, Lam TK, Mechanic LE, Goldstein AM, Gillanders EM. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:1519-1534. [PMID: 32467344 DOI: 10.1158/1055-9965.epi-19-1551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/17/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing (NGS) technologies in cancer research has accelerated the discovery of somatic mutations; however, progress in the identification of germline variation associated with cancer risk is less clear. We conducted a systematic literature review of cancer genetic susceptibility studies that used NGS technologies at an exome/genome-wide scale to obtain a fuller understanding of the research landscape to date and to inform future studies. The variability across studies on methodologies and reporting was considerable. Most studies sequenced few high-risk (mainly European) families, used a candidate analysis approach, and identified potential cancer-related germline variants or genes in a small fraction of the sequenced cancer cases. This review highlights the importance of establishing consensus on standards for the application and reporting of variants filtering strategies. It also describes the progress in the identification of cancer-related germline variation to date. These findings point to the untapped potential in conducting studies with appropriately sized and racially diverse families and populations, combining results across studies and expanding beyond a candidate analysis approach to advance the discovery of genetic variation that accounts for the unexplained cancer heritability.
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Affiliation(s)
- Melissa Rotunno
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland.
| | - Rolando Barajas
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Mindy Clyne
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elise Hoover
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | | | - Tram Kim Lam
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Leah E Mechanic
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Alisa M Goldstein
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elizabeth M Gillanders
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
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Cui X, Han D, Heuvelmans MA, Du Y, Zhao Y, Zhang L, Groen HJ, de Bock GH, Dorrius MD, Oudkerk M, Vliegenthart R, Ye Z. Clinical characteristics and work-up of small to intermediate-sized pulmonary nodules in a Chinese dedicated cancer hospital. Cancer Biol Med 2020; 17:199-207. [PMID: 32296586 PMCID: PMC7142837 DOI: 10.20892/j.issn.2095-3941.2019.0028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/30/2019] [Indexed: 12/23/2022] Open
Abstract
Objectives: To evaluate the characteristics and work-up of small to intermediate-sized pulmonary nodules in a Chinese dedicated cancer hospital. Methods: Patients with pulmonary nodules 4-25 mm in diameter detected via computed tomography (CT) in 2013 were consecutively included. The analysis was restricted to patients with a histological nodule diagnosis or a 2-year follow-up period without nodule growth confirming benign disease. Patient information was collected from hospital records. Results: Among the 314 nodules examined in 299 patients, 212 (67.5%) nodules in 206 (68.9%) patients were malignant. Compared to benign nodules, malignant nodules were larger (18.0 mm vs. 12.5 mm, P < 0.001), more often partly solid (16.0% vs. 4.7%, P < 0.001) and more often spiculated (72.2% vs. 41.2%, P < 0.001), with higher density in contrast-enhanced CT (67.0 HU vs. 57.5 HU, P = 0.015). Final diagnosis was based on surgery in 232 out of 314 (73.9%) nodules, 166 of which were identified as malignant [30 (18.1%) stage III or IV] and 66 as benign. In 36 nodules (11.5%), diagnosis was confirmed by biopsy and the remainder verified based on stability of nodule size at follow-up imaging (n = 46, 14.6%). Among 65 nodules subjected to gene (EGFR) mutation analyses, 28 (43.1%) cases (EGFR19 n = 13; EGFR21 n = 15) were identified as EGFR mutant and 37 (56.9%) as EGFR wild-type. Prior to surgery, the majority of patients [n = 194 (83.6%)] received a contrast-enhanced CT scan for staging of both malignant [n = 140 (84.3%)] and benign [n = 54 (81.8%)] nodules. Usage of positron emission tomography (PET)-CT was relatively uncommon [n = 38 (16.4%)]. Conclusions: CT-derived nodule assessment assists in diagnosis of small to intermediate- sized malignant pulmonary nodules. Currently, contrast-enhanced CT is commonly used as the sole diagnostic confirmation technique for pre-surgical staging, often resulting in surgery for late-stage disease and unnecessary surgery in cases of benign nodules.
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Affiliation(s)
- Xiaonan Cui
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
- Department of Radiology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
| | - Daiwei Han
- Department of Radiology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
| | - Marjolein A. Heuvelmans
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
- Medisch Spectrum Twente, Department of Pulmonology, Enschede 7512 KZ, The Netherlands
| | - Yihui Du
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
| | - Yingru Zhao
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
| | - Lei Zhang
- Department of Thoracic Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
| | - Harry J.M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
| | - Geertruida H. de Bock
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
| | - Monique D. Dorrius
- Department of Radiology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
| | - Matthijs Oudkerk
- University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
| | - Rozemarijn Vliegenthart
- Department of Radiology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
| | - Zhaoxiang Ye
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
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Wang H, Zhang Z, Xu K, Wei S, Li L, Wang L. Exploration of estrogen receptor-associated hub genes and potential molecular mechanisms in non-smoking females with lung adenocarcinoma using integrated bioinformatics analysis. Oncol Lett 2019; 18:4605-4612. [PMID: 31611968 PMCID: PMC6781748 DOI: 10.3892/ol.2019.10845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 07/26/2019] [Indexed: 12/15/2022] Open
Abstract
The present study aimed to explore important estrogen receptor-associated genes and to determine the potential pathogenic and prognostic factors for lung adenocarcinoma in non-smoking females. The gene expression profiles of the two datasets (GSE32863 and GSE75037) were downloaded from the Gene Expression Omnibus (GEO) database. Data for non-smoking female patients with lung adenocarcinoma from The Cancer Genome Atlas (TCGA) database were also downloaded. The Linear Models for Microarray Data package in R was used to explore the differentially expressed genes (DEGs) between samples from non-smoking female patients with lung adenocarcinoma and samples of adjacent non-cancerous lung tissue. The Database for Annotation, Visualization and Integrated Discovery was used for functional enrichment of the DEGs. The Search Tool for the Retrieval of Interacting Genes/Proteins and Cytoscape software were used to obtain a protein-protein interaction (PPI) network and to identify the hub genes. In addition, the network between the estrogen receptor and the DEGs was constructed. A Kaplan-Meier survival plot was used to analyze the overall survival (OS). In total, 248 DEGs were identified in the GEO database, and 2,362 DEGs were identified in TCGA database. The intersection of the two datasets (DEGs in GEO and TCGA) revealed 170 DEGs, and these were selected for further investigation. Gene Ontology was used to group the 170 DEGs into biological process, molecular function and cellular component categories. Kyoto Encyclopedia of Genes and Genomes pathway analysis was subsequently performed. A total of 27 hub genes, including caveolin 1 (CAV1), matrix metallopeptidase 9 (MMP9), secreted phosphoprotein 1 (SPP1) and collagen type I α 1 chain (COL1A1), were closely associated with the estrogen receptor. CAV1 and SPP1 were associated with the OS. However, MMP9 and COL1A1 did not have any significant effect on OS. In summary, the identification of CAV1, MMP9, SPP1 and COL1A1 may provide novel insights into the molecular mechanism of lung adenocarcinoma in non-smoking female patients, and the results obtained in the current study may guide future clinical studies.
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Affiliation(s)
- Hao Wang
- Department of Respiratory Oncology, Anhui Provincial Cancer Hospital (The First Affiliated Hospital of USTC West District), Hefei, Anhui 230031, P.R. China
| | - Zhihong Zhang
- Department of Respiratory Oncology, Anhui Provincial Cancer Hospital (The First Affiliated Hospital of USTC West District), Hefei, Anhui 230031, P.R. China
| | - Ke Xu
- Department of Respiratory Oncology, Anhui Provincial Cancer Hospital (The First Affiliated Hospital of USTC West District), Hefei, Anhui 230031, P.R. China
| | - Song Wei
- Department of Respiratory Oncology, Anhui Provincial Cancer Hospital (The First Affiliated Hospital of USTC West District), Hefei, Anhui 230031, P.R. China
| | - Lailing Li
- Department of Respiratory Oncology, Anhui Provincial Cancer Hospital (The First Affiliated Hospital of USTC West District), Hefei, Anhui 230031, P.R. China
| | - Lijun Wang
- Department of Respiratory Disease, Tongling People's Hospital, Tongling, Anhui 244000, P.R. China
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Kaur P, Purewal SS, Sandhu KS, Kaur M. DNA damage protection: an excellent application of bioactive compounds. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0237-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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