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Du C, Cai J, Tang J, Chen Y, Díaz-Peña R, Tomita Y, Jassem J, Zhao J, Zheng D, Tu Z. Cell-free DNA methylation profile potential in the diagnosis of lung squamous cell carcinoma. J Thorac Dis 2024; 16:553-563. [PMID: 38410586 PMCID: PMC10894382 DOI: 10.21037/jtd-23-1827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 02/28/2024]
Abstract
Background Aberrant methylation plays an essential role in early cancer development. In this study, we investigated methylation patterns in lung squamous cell carcinoma (LUSC) and matched non-tumor tissue and plasma samples to evaluate the potential of these patterns in the diagnosis of LUSC. Methods The study group included 49 patients with stage I-III LUSC. We collected resected tumor tissue, paired peritumoral tissue, distant normal tissue, and corresponding plasma samples. A bespoke lung cancer bisulfite sequencing panel was used to profile the methylation level. Another 48 healthy volunteers provided control plasma samples. Results Peritumoral and distant normal tissues presented similar methylation signatures, distinct from those in tumor tissue samples. A comparison of methylation profiles led to the identification of 871 tumor-specific differentially methylated blocks, including 847 hypermethylated and 24 hypomethylated blocks (adjusted P value <0.05). All top-ranked blocks were tumor-related. Tissue samples were analyzed for field cancerization to identify progressively aggravating aberrant methylations during tumor initiation and development. The analysis revealed that 221 blocks presented a stepwise increase in methylation levels, while seven blocks presented a stepwise decrease in methylation pattern as the sampling drew nearer to the tumor. The malignant contaminated ratio (MCR) confirmed the presence of distinct methylation patterns between tumor and peritumoral tissue samples. We then constructed a diagnostic panel using a combined diagnostic score of cell-free DNA (cfDNA) that showed high sensitivity and specificity. The healthy controls had a significantly lower combined diagnostic score (cd-score) than LUSC patients. Additionally, based on the methylation profiles, LUSC could be classified into two subgroups, C1 and C2. The methylation profile of the C2 group was not distinct from the healthy controls, which had a significantly lower cd-score than did the C1 group. Conclusions LUSC-specific methylation patterns could potentially discriminate between peritumoral tissue, distant normal tumor tissue, and tumor tissues. This preliminary study also supported the potential utility of cfDNA methylation analysis in diagnosing LUSC.
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Affiliation(s)
- Chengli Du
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jin Cai
- Special Clinical Lab, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Jie Tang
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunhao Chen
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Roberto Díaz-Peña
- Fundación Pública Galega de Medicina Xenómica, SERGAS, Grupo de Medicina Xenómica-USC, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Faculty of Health Sciences, Universidad Autónoma de Chile, Talca, Chile
| | - Yusuke Tomita
- Department of Respiratory Medicine, Kumamoto University Hospital, Kumamoto, Japan
| | - Jacek Jassem
- Department of Oncology and Radiotherapy, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Jiangang Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Difang Zheng
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengliang Tu
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Cao L, Zhong J, Liu Z, Jiang J, Zhu C, Liu F, Wang B. Increased LOXL2 expression is related to poor prognosis in lung squamous cell carcinoma. J Thorac Dis 2024; 16:581-592. [PMID: 38410543 PMCID: PMC10894394 DOI: 10.21037/jtd-23-1848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024]
Abstract
Background The lysyl oxidate-like (LOXL) family was reported to be involved in the process of cancer development. However, the prognostic value of LOXL in lung cancer is unknown. We aimed to study the expression pattern and prognostic value of LOXL family members in lung squamous cell carcinoma (LUSC). Methods The Wilcoxon test and logistic regression analysis were used to study the expression level of LOXLs and its correlation with clinical characteristics. The Kaplan-Meier method and Cox regression analysis were performed to estimate the correlation of LOXsL expression with the survival of LUSC patients. Receiver operator characteristic (ROC) curves were plotted, and areas under the curves (AUCs) were calculated to estimate the diagnostic and prognostic power of LOXL. Cell Counting Kit-8 (CCK-8) assays, wound healing assays and Transwell assays were used to estimate the impact of LOXL2 on LUSC cells. Results LOXL1 and LOXL2 expression was upregulated in LUSC tissues (P<0.001). LOXL1 and LOXL2 showed high diagnostic power in LUSC patients, with AUCs of 0.784 and 0.751, respectively. Patients with high LOXL2 expression levels showed poor overall survival (OS) (P=0.019) and progression-free survival (PFS) (P=0.015). High LOXL2 expression was an independent prognostic factor for poor survival (P=0.026). Inhibition of LOXL2 suppressed proliferation, migration and invasion in LUSC cell lines. Conclusions Increased LOXL2 was related to poor survival in LUSC. LOXL2 may be a potential prognostic biomarker and therapeutic target in LUSC.
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Affiliation(s)
- Lei Cao
- Department of Thoracic Surgery, Nanjing Chest Hospital, Affiliated Nanjing Brain Hospital Nanjing Medical University, Nanjing, China
| | - Jian Zhong
- Department of Thoracic Surgery, Nanjing Chest Hospital, Affiliated Nanjing Brain Hospital Nanjing Medical University, Nanjing, China
| | - Zicheng Liu
- Department of Thoracic Surgery, Nanjing Chest Hospital, Affiliated Nanjing Brain Hospital Nanjing Medical University, Nanjing, China
| | - Jie Jiang
- Department of Thoracic Surgery, Nanjing Chest Hospital, Affiliated Nanjing Brain Hospital Nanjing Medical University, Nanjing, China
| | - Chenyao Zhu
- Shenzhen Yuce Biotechnology Co., Ltd., Shenzhen, China
| | - Feng Liu
- Department of Thoracic Surgery, Nanjing Chest Hospital, Affiliated Nanjing Brain Hospital Nanjing Medical University, Nanjing, China
| | - Bo Wang
- Department of Thoracic Surgery, Nanjing Chest Hospital, Affiliated Nanjing Brain Hospital Nanjing Medical University, Nanjing, China
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Hui G, Xie Y, Niu L, Liu J. A novel gene signature related to focal adhesions for distinguishing and predicting the prognosis of lung squamous cell carcinoma. Front Med (Lausanne) 2024; 10:1284490. [PMID: 38259849 PMCID: PMC10800788 DOI: 10.3389/fmed.2023.1284490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
Background Lung squamous cell carcinoma (LUSC) is a devastating and difficult-to-treat type of lung cancer, and the prognosis of LUSC is the worst. The functional roles of focal adhesion-related genes were explored in LUSC based on data from The Cancer Genome Atlas (TCGA). Methods RNA sequencing data and clinical characteristics of LUSC patients in TCGA-LUSC were obtained from the TCGA database. Through systematic analysis, we screened the prognostic genes and determined the focal adhesion-related pathways closely associated with LUSC. Results We identified 444 prognostic genes and focal adhesion-related pathways intimately associated with LUSC. According to the focal adhesion-related genes, TCGA-LUSC patients were well divided into two groups: the low-risk group (G1) and the high-risk group (G2). A differential expression analysis identified 44 differentially expressed genes (DEGs) upregulated in the low-risk G1 group and 379 DEGs upregulated in the high-risk G2 group. The upregulated DEGs in the G1 group were primarily related to tyrosine metabolism, steroid hormone biosynthesis, retinol metabolism, platinum drug resistance, pentose and glucuronate interconversions, and metabolism of xenobiotics by cytochrome P450, while the downregulated DEGs in the G1 group were primarily related to ECM-receptor interaction, focal adhesion, proteoglycans in cancer, small cell lung cancer, cytokine-cytokine receptor interaction, and TGF-beta signaling pathway. The immune activity of the G1 group was lower than that of the G2 group, and the half-maximal inhibitory concentration (IC50) of five chemotherapy drugs (i.e., gemcitabine, methotrexate, vinorelbine, paclitaxel, and cisplatin) was significantly different between the G1 and G2 groups. Furthermore, a 10-gene prognostic model was constructed to predict the prognosis for LUSC patients: ITGA3, VAV2, FLNC, FLT4, HGF, MYL2, ITGB1, PDGFRA, CCND2, and PPP1CB. Conclusion The status of focal adhesion-related genes has a close relationship with tumor classification and immunity in LUSC patients. A novel focal adhesion-related signature had good prognostic and predictive performance for LUSC. Our findings may provide new insight into the diagnosis and treatment of LUSC.
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Affiliation(s)
- Gang Hui
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yuancai Xie
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Li Niu
- Shenzhen Cheerland Biotechnology Co., Ltd., Southern University of Science and Technology, Shenzhen, China
- CheerLand Clinical Laboratory Co., Ltd., Peking University Medical Industrial Park, Beijing, China
| | - Jixian Liu
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen, China
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Song GQ, Wu HM, Ji KJ, He TL, Duan YM, Zhang JW, Hu GQ. The necroptosis signature and molecular mechanism of lung squamous cell carcinoma. Aging (Albany NY) 2023; 15:12907-12926. [PMID: 37976123 DOI: 10.18632/aging.205210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/15/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Given the poor prognosis of lung squamous cell carcinoma (LUSC), the aim of this study was to screen for new prognostic biomarkers. METHODS The TGCA_LUSC dataset was used as the training set, and GSE73403 was used as the validation set. The genes involved in necroptosis-related pathways were acquired from the KEGG database, and the differential genes between the LUSC and normal samples were identified using the GSEA. A necroptosis signature was constructed by survival analysis, and its correlation with patient prognosis and clinical features was evaluated. The molecular characteristics and drug response associated with the necroptosis signature were also identified. The drug candidates were then validated at the cellular level. RESULTS The TCGA_LUSC dataset included 51 normal samples and 502 LUSC samples. The GSE73403 dataset included 69 samples. 159 genes involved in necroptosis pathways were acquired from the KEGG database, of which most showed significant differences between two groups in terms of genomic, transcriptional and methylation alterations. In particular, CHMP4C, IL1B, JAK1, PYGB and TNFRSF10B were significantly associated with the survival (p < 0.05) and were used to construct the necroptosis signature, which showed significant correlation with patient prognosis and clinical features in univariate and multivariate analyses (p < 0.05). Furthermore, CHMP4C, IL1B, JAK1 and PYGB were identified as potential targets of trametinib, selumetinib, SCH772984, PD 325901 and dasatinib. Finally, knockdown of these genes in LUSC cells increased chemosensitivity to those drugs. CONCLUSION We identified a necroptosis signature in LUSC that can predict prognosis and identify patients who can benefit from targeted therapies.
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Affiliation(s)
- Guo-Qiang Song
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Hua-Man Wu
- Department of Pulmonary and Critical Care Medicine, Zigong First People’s Hospital, Zigong, China
| | - Ke-Jie Ji
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Tian-Li He
- Department of Radiotherapy, Changxing People’s Hospital, Huzhou, China
| | - Yi-Meng Duan
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Jia-Wen Zhang
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
| | - Guo-Qiang Hu
- Department of Pulmonary, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
- Department of Cancer Center, Changxing County Hospital of Traditional Chinese Medicine, Huzhou, China
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Sasa GBK, Xuan C, Chen M, Jiang Z, Ding X. Clinicopathological implications of lncRNAs, immunotherapy and DNA methylation in lung squamous cell carcinoma: a narrative review. Transl Cancer Res 2022; 10:5406-5429. [PMID: 35116387 PMCID: PMC8799054 DOI: 10.21037/tcr-21-1607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/16/2021] [Indexed: 11/06/2022]
Abstract
Objective To explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in lung squamous cell carcinoma (LUSC), emphasizing their exact roles in carcinogenesis and modes of action. Background LUSC is the second most prevalent form, accounting for around 30% of non-small cell lung cancer (NSCLC). To date, molecular-targeted treatments have significantly improved overall survival in lung adenocarcinoma patients but have had little effect on LUSC therapy. As a result, there is an urgent need to discover new treatments for LUSC that are based on existing genomic methods. Methods In this review, we summarized and analyzed recent research on the biological activities and processes of lncRNA, immunotherapy, and DNA methylation in the formation of LUSC. The relevant studies were retrieved using a thorough search of Pubmed, Web of Science, Science Direct, Google Scholar, and the university's online library, among other sources. Conclusions LncRNAs are the primary components of the mammalian transcriptome and are emerging as master regulators of a number of cellular processes, including the cell cycle, differentiation, apoptosis, and growth, and are implicated in the pathogenesis of a variety of cancers, including LUSC. Understanding their role in LUSC in detail may help develop innovative treatment methods and tactics for LUSC. Meanwhile, immunotherapy has transformed the LUSC treatment and is now considered the new standard of care. To get a better knowledge of LUSC biology, it is critical to develop superior modeling systems. Preclinical models, particularly those that resemble human illness by preserving the tumor immune environment, are essential for studying cancer progression and evaluating novel treatment targets. DNA methylation, similarly, is a component of epigenetic alterations that regulate cellular function and contribute to cancer development. By methylating the promoter regions of tumor suppressor genes, abnormal DNA methylation silences their expression. DNA methylation indicators are critical in the early detection of lung cancer, predicting therapy efficacy, and tracking treatment resistance. As such, this review seeks to explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in LUSC, emphasizing their exact roles in carcinogenesis and modes of action.
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Affiliation(s)
- Gabriel B K Sasa
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Cheng Xuan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Meiyue Chen
- The fourth affiliated hospital, Zhejiang University of Medicine, Hangzhou, China
| | - Zhenggang Jiang
- Department of Science Research and Information Management, Zhejiang Provincial Centers for Disease Control and Prevention, Hangzhou, China
| | - Xianfeng Ding
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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6
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Acker F, Stratmann J, Aspacher L, Nguyen NTT, Wagner S, Serve H, Wild PJ, Sebastian M. KRAS Mutations in Squamous Cell Carcinomas of the Lung. Front Oncol 2022; 11:788084. [PMID: 34976827 PMCID: PMC8714661 DOI: 10.3389/fonc.2021.788084] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
KRAS is one of the most commonly mutated oncogenes in cancer, enabling tumor proliferation and maintenance. After various approaches to target KRAS have failed over the past decades, the first specific inhibitor of the p.G12C mutation of KRAS was recently approved by the FDA after showing promising results in adenocarcinomas of the lung and other solid tumors. Lung cancer, the most common cancer worldwide, is a promising use case for these new therapies, as adenocarcinomas in particular frequently harbor KRAS mutations. However, in squamous cell carcinoma (SCC) of the lung, KRAS mutations are rare and their impact on clinical outcome is poorly understood. In this review, we discuss the current knowledge on the prevalence and prognostic and predictive significance of KRAS mutations in the context of SCC.
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Affiliation(s)
- Fabian Acker
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Jan Stratmann
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Lukas Aspacher
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | | | - Sebastian Wagner
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Hubert Serve
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Peter J Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany.,Wildlab, University Hospital MVZ GmbH, Frankfurt, Germany.,Frankfurt Institute for Advanced Studies (FIAS), Frankfurt, Germany
| | - Martin Sebastian
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
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Zhang K, Han Z, Zhao H, Liu S, Zeng F. An integrated model of FTO and METTL3 expression that predicts prognosis in lung squamous cell carcinoma patients. Ann Transl Med 2021; 9:1523. [PMID: 34790729 PMCID: PMC8576700 DOI: 10.21037/atm-21-4470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/02/2021] [Indexed: 12/13/2022]
Abstract
Background Lung squamous cell carcinoma (LUSC) approximately accounts for a third of lung cancers. However, the role of N6-methyladenosine (m6A) in LUSC remains largely unknown according to previous studies. Methods In this study, we investigated the mutations, copy number variants (CNVs), expression of 20 m6A RNA methylation regulators, and clinical data from The Cancer Genome Atlas-LUSC (TCGA-LUSC). These data were used for the training cohort of screening potential biomarkers. The prognostic model of m6A RNA methylation regulators was constructed. A receiver operating characteristic (ROC) analysis was undertaken to determine the area under the curves (AUCs) (for 3- and 5-year survival) for the model. Additionally, the accuracy of the two-gene model was confirmed with external data verifications. Combined two-gene model and clinincal information were performed to construct a nomogram to predict patient’s prognostic risk assessment. Results Fat mass- and obesity-associated protein (FTO) and methyltransferase-like 3 (METTL3) were identified as potential prognostic biomarkers to evaluate benign and malignant tumors and prognosticate. The following prognostic model of m6A RNA methylation regulators was constructed: risk score = 0.162 × FTO − 0.069 × METTL3. Patients in low-risk group [median overall survival (mOS), 43.4 months] had longer survival than those with high-risk (mOS, 67.3 months) with P=0.0023. The smoking grade and risk score could be independent prognostic factors (P=0.00098 and P=0.0014, respectively). Ultimately, a nomogram was developed to assist clinicians to predict clinical outcomes. Conclusions FTO and METTL3 are potential prognostic biomarkers of LUSC. The two-gene model’s use of prognostic risk scores may provide guidance in the selection of therapeutic strategies.
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Affiliation(s)
- Kun Zhang
- Department of Thoracic Surgery, Sichuan Provincial People's Hospital, Chengdu, China
| | - Zhaojie Han
- Department of Thoracic Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Hongmei Zhao
- Chosen Med Technology (Beijing) Co., Ltd., Beijing, China
| | - Siyao Liu
- Chosen Med Technology (Beijing) Co., Ltd., Beijing, China
| | - Fuchun Zeng
- Department of Thoracic Surgery, Sichuan Provincial People's Hospital, Chengdu, China
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Wang P, Wang F, He H, Chen Y, Lin H, Chen P, Chen X, Liu S. TP53 and CDKN2A mutations in patients with early-stage lung squamous cell carcinoma: an analysis of the correlations and prognostic outcomes. Ann Transl Med 2021; 9:1330. [PMID: 34532467 PMCID: PMC8422115 DOI: 10.21037/atm-21-3709] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/16/2021] [Indexed: 12/04/2022]
Abstract
Background Lung squamous cell carcinoma (LUSC) is characterized by frequent mutations of tumor protein p53 (TP53) and cyclin dependent kinase inhibitor 2A (CDKN2A). However, to date, the impact of TP53/CDKN2A status on the clinical outcome of patients with early-stage LUSC is unclear. Methods Tissue samples from 16 early-stage, surgically resected LUSCs were analyzed by next-generation sequencing (NGS). Information regarding TP53 and CDKN2A alterations and patient survival time was downloaded from The Cancer Genome Atlas (TCGA) database. The associations between TP53 and CDKN2A status and tumor characteristics, outcomes including overall survival (OS) and disease-free survival (DFS), and mutation counts were investigated. Results TP53 and CDKN2A exhibited a high frequency of somatic mutations in early-stage LUSC in our center. Data for 1,176 samples were collected from TCGA. CDKN2A mutation status was associated with TP53 mutation status (P=0.040). TP53 mutation was a favorable prognostic factor for early-stage LUSC. The OS times of patients with wild-type and mutated TP53 were 28.94 and 60.48 months, respectively (P=0.002). In contrast, CDKN2A mutations were significantly associated with a shorter survival time in early-stage LUSC. The OS times for wild-type and mutated CDKN2A patients were 62.81 and 37.55 months, respectively (P=0.026). Patients with TP53 mutations had higher total mutation counts compared to patients with wild-type TP53. Furthermore, OS was significantly shorter in patients with a low mutation count compared to patients with a median or high mutation count. Conclusions Early-stage LUSC patients with TP53 mutations had a longer OS, while those with CDKN2A mutations had a shorter OS. Furthermore, patients with TP53 mutation/CDKN2A wild-type status had a longer OS. CDKN2A mutation is a vital indicator for prognostic assessment according to TP53 status. The prolonged survival of patients with TP53 mutations may be due to their high mutation counts. Larger datasets are required to validate these observations.
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Affiliation(s)
- Peiyuan Wang
- Department of Thoracic Oncology Surgery, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China.,Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, China.,Fujian Provincial Key Laboratory of Tumor Biotherapy, Fuzhou, China
| | - Feng Wang
- Department of Thoracic Oncology Surgery, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Hao He
- Department of Thoracic Oncology Surgery, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Yujie Chen
- Department of Thoracic Oncology Surgery, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Hui Lin
- Department of Thoracic Oncology Surgery, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Peng Chen
- Department of Thoracic Oncology Surgery, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Xiaofeng Chen
- Department of Thoracic Oncology Surgery, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Shuoyan Liu
- Department of Thoracic Oncology Surgery, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
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9
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Zhang S, Liu S, Liu X, Liu J, Wu W. Identification of JAK2 and FOXM1 expression as novel candidate biomarkers for predicting the benefit of immunotherapy in lung squamous cell carcinoma. Ann Transl Med 2021; 9:1081. [PMID: 34422993 PMCID: PMC8339858 DOI: 10.21037/atm-21-2186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/21/2021] [Indexed: 12/13/2022]
Abstract
Background Lung squamous cell carcinoma (LUSC) accounts for about 30% of all non-small cell lung cancers (NSCLC). However, only a small percentage of LUSC patients gain benefit from immune checkpoint inhibitors (ICIs). Methods This study analyzed LUSC patients from The Cancer Genome Atlas (TCGA), which were divided into 2 groups: PD-L1 high-expression/TMB-high (TPH) and PD-L1 low-expression/TMB-low (TPL) group based on programmed death-ligand 1 (PD-L1) expression and tumor mutational burden (TMB) status. The differences in tumor-infiltrating immune cells were estimated between the 2 groups. The overlap of differentially expressed genes and proteins (DEGs and DEPs) between 2 groups were used as candidate biomarkers. Kaplan-Meier curves were used to evaluate the association between risk score and overall survival (OS). Results More abundant immune infiltration fractions were found in TPH group. Janus kinase 2 (JAK2) and forkhead box protein M1 (FOXM1) were identified as DEGs between the TPH and TPL groups. Subsequently, we developed a risk score that combined the expression of JAK2 and FOXM1 in an effort to accurately determine the survival risk of LUSC patients. Patients with high-risk [hazard ratio (HR), median OS, 43.1 months 1.924; 95% confidence interval (CI): 1.256 to 2.945; P=0.002) had shorter survival than those with low-risk (median OS, 70.0 months). External data verification found that JAK2 and FOXM1 were significantly expressed at a higher level in the responders receiving immunotherapy (P=0.038 and P=0.009, respectively). Conclusions The expressions of JAK2 and FOXM1 can be used as novel candidate biomarkers for predicting the benefit of immunotherapy in LUSC.
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Affiliation(s)
- Shixin Zhang
- Department of Thoracic Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Shuai Liu
- Department of Thoracic Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xi Liu
- Department of Thoracic Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jie Liu
- Department of Thoracic Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Wei Wu
- Department of Thoracic Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
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10
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Guo L, Yi J, Liu M, Li J. The prognostic landscape of tumor-infiltrating immune cells in lung squamous cell carcinoma. Ann Transl Med 2021; 9:799. [PMID: 34268412 PMCID: PMC8246229 DOI: 10.21037/atm-21-1852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/06/2021] [Indexed: 11/06/2022]
Abstract
Background Exploring novel biomarkers and developing effective therapeutic strategies can improve the prognosis of lung squamous cell carcinoma (LUSC) in the future. The prognostic value of tumor-infiltrating immune cells (TICs) in solid tumors has been extensively studied. However, the landscape of TICs involved in the prognosis of non-small cell lung cancer (NSCLC), especially in LUSC, remains unclear and should be systematically investigated. Methods This retrospective study analyzed the immune-related transcriptional profiles of 490 LUSC patients from The Cancer Genome Atlas (TCGA) cohort. Using the CIBERSORT method, TICs were evaluated and examined for their association with overall survival (OS) in LUSC. Results Out of the 27 TICs, 14 were correlated with prognosis in LUSC. A novel prognostic model characterized by fewer memory B cells and more central memory CD8 T cells, regulatory T cells (Tregs), and plasmacytoid dendritic cell (pDC) infiltration predicted poor OS in LUSC with high accuracy. The 1-, 3-, and 5-year areas under the curve (AUC) were 0.95, 0.98, and 0.96, respectively, in the training cohort. This finding was further validated in the validation cohort, where the 1-, 3-, and 5-year AUCs were 0.95, 0.98, and 0.95, respectively. Conclusions These findings may provide more effective prognostic biomarkers and potential therapeutic targets for the immunotherapy of LUSC.
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Affiliation(s)
- Liang Guo
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiaoyu Yi
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Ming Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Juanjuan Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, China
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11
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Shen D, Wang J, Wu J, Chen S, Li J, Liu J, Chen Q, Jiang Y. Neoadjuvant pembrolizumab with chemotherapy for the treatment of stage IIB-IIIB resectable lung squamous cell carcinoma. J Thorac Dis 2021; 13:1760-1768. [PMID: 33841966 PMCID: PMC8024839 DOI: 10.21037/jtd-21-103] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background Researches on programmed cell death (PD-1) as neoadjuvant immunotherapy for resectable non-small cell lung cancer is underway, which brings hope for individuals with the disease. However, a study dedicated to lung squamous cell carcinoma (LUSC) specifically has yet to be conducted. Now, data from our pilot prospective research neoadjuvant study provide new insights in the field of neoadjuvant regimen for LUSC. Methods Between June 2019 and July 2020, 37 adults with untreated, surgically resectable stage IIB–IIIB LUSC were enrolled into this prospective study. Patients received 2 cycles of pembrolizumab (2 mg/kg) with chemotherapy (albumin-bound paclitaxel 100 mg/m2 on days 1 and 8 + carboplatin AUC 5) via intravenous administration every 3 weeks, and underwent surgical treatment 3–4 weeks after the second cycle. The primary endpoint of the study was the tumor pathologic complete response (pCR) rate. The toxicity profile, tumor major pathological remission, complete resection rate, response rate, and operative and postoperative complications were also evaluated. Results The postoperative pathological specimens of 17 (45.9%) patients suggested pCR. Neoadjuvant pembrolizumab with chemotherapy had an acceptable side-effect profile, and no patients withdrew from the study preoperatively due to disease progression or toxicity. A major pathological response occurred in 24 (64.9%) resected tumors. All tumors were completely resected (R0, 100%). According to the Response Evaluation Criteria in Solid Tumors (RESIST), a response was evaluated before surgery in 32 (86.5%) patients by computed tomography. Twenty-five (67.6%) patients underwent thoracoscopic surgery. No deaths or postoperative major complications requiring reoperation occurred. Recurrence or metastasis was found in 2 patients during follow-up of 2–14 months. Conclusions The early outcomes of pembrolizumab with chemotherapy in the neoadjuvant setting as a novel treatment for resectable stage IIB–IIIB LUSC showed a high pCR rate that has not been seen previously, as well as a high R0 resection rate and a low toxicity profile. The long-term efficacy of this novel treatment and the validity of the present findings should be confirmed with longer follow-up and prospective comparative trials.
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Affiliation(s)
- Dijian Shen
- Department of Thoracic Surgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Science, Hangzhou, China
| | - Jiangfeng Wang
- Department of Thoracic Surgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Science, Hangzhou, China
| | - Jie Wu
- Department of Thoracic Surgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Science, Hangzhou, China
| | - Sheng Chen
- Department of Thoracic Surgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Science, Hangzhou, China
| | - Jianqiang Li
- Department of Thoracic Surgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Science, Hangzhou, China
| | - Jinshi Liu
- Department of Thoracic Surgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Science, Hangzhou, China
| | - Qixun Chen
- Department of Thoracic Surgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Science, Hangzhou, China
| | - Youhua Jiang
- Department of Thoracic Surgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Science, Hangzhou, China
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12
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Zengin T, Önal-Süzek T. Comprehensive Profiling of Genomic and Transcriptomic Differences between Risk Groups of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. J Pers Med 2021; 11:154. [PMID: 33672117 PMCID: PMC7926392 DOI: 10.3390/jpm11020154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Lung cancer is the second most frequently diagnosed cancer type and responsible for the highest number of cancer deaths worldwide. Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) are subtypes of non-small-cell lung cancer which has the highest frequency of lung cancer cases. We aimed to analyze genomic and transcriptomic variations including simple nucleotide variations (SNVs), copy number variations (CNVs) and differential expressed genes (DEGs) in order to find key genes and pathways for diagnostic and prognostic prediction for lung adenocarcinoma and lung squamous cell carcinoma. We performed a univariate Cox model and then lasso-regularized Cox model with leave-one-out cross-validation using The Cancer Genome Atlas (TCGA) gene expression data in tumor samples. We generated 35- and 33-gene signatures for prognostic risk prediction based on the overall survival time of the patients with LUAD and LUSC, respectively. When we clustered patients into high- and low-risk groups, the survival analysis showed highly significant results with high prediction power for both training and test datasets. Then, we characterized the differences including significant SNVs, CNVs, DEGs, active subnetworks, and the pathways. We described the results for the risk groups and cancer subtypes separately to identify specific genomic alterations between both high-risk groups and cancer subtypes. Both LUAD and LUSC high-risk groups have more downregulated immune pathways and upregulated metabolic pathways. On the other hand, low-risk groups have both up- and downregulated genes on cancer-related pathways. Both LUAD and LUSC have important gene alterations such as CDKN2A and CDKN2B deletions with different frequencies. SOX2 amplification occurs in LUSC and PSMD4 amplification in LUAD. EGFR and KRAS mutations are mutually exclusive in LUAD samples. EGFR, MGA, SMARCA4, ATM, RBM10, and KDM5C genes are mutated only in LUAD but not in LUSC. CDKN2A, PTEN, and HRAS genes are mutated only in LUSC samples. The low-risk groups of both LUAD and LUSC tend to have a higher number of SNVs, CNVs, and DEGs. The signature genes and altered genes have the potential to be used as diagnostic and prognostic biomarkers for personalized oncology.
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Affiliation(s)
- Talip Zengin
- Department of Molecular Biology and Genetics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey;
- Department of Bioinformatics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
| | - Tuğba Önal-Süzek
- Department of Bioinformatics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
- Department of Computer Engineering, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
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13
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Zhuang Y, Li S, Liu C, Li G. Identification of an Individualized Immune-Related Prognostic Risk Score in Lung Squamous Cell Cancer. Front Oncol 2021; 11:546455. [PMID: 33747902 PMCID: PMC7966508 DOI: 10.3389/fonc.2021.546455] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 02/09/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Lung squamous cell carcinoma (LUSC) is one of the most common histological subtypes of non-small cell lung cancer (NSCLC), and its morbidity and mortality are steadily increasing. The purpose of this study was to study the relationship between the immune-related gene (IRGs) profile and the outcome of LUSC in patients by analyzing datasets from The Cancer Genome Atlas (TCGA). Methods: We obtained publicly available LUSC RNA expression data and clinical survival data from The Cancer Genome Atlas (TCGA), and filtered IRGs based on The ImmPort database. Then, we identified risk immune-related genes (r-IRGs) for model construction using Cox regression analysis and defined the risk score in this model as the immune gene risk index (IRI). Multivariate analysis was used to verify the independent prognostic value of IRI and its association with other clinicopathological features. Pearson correlation analysis was used to explore the molecular mechanism affecting the expression of IRGs and the correlation between IRI and immune cell infiltration. Results: We screened 15 r-IRGs for constructing the risk model. The median value of IRI stratified the patients and there were significant survival differences between the two groups (p = 4.271E-06). IRI was confirmed to be an independent prognostic factor (p < 0.001) and had a close correlation with the patients' age (p < 0.05). Interestingly, the infiltration of neutrophils or dendritic cells was strongly upregulated in the high-IRI groups (p < 0.05). Furthermore, by investigating differential transcription factors (TFs) and functional enrichment analysis, we explored potential mechanisms that may affect IRGs expression in tumor cells. Conclusion: In short, this study used 15 IRGs to build an effective risk prediction model, and demonstrated the significance of IRGs-based personalized immune scores in LUSC prognosis.
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14
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Xu Y, Li H, Huang Z, Chen K, Yu X, Sheng J, Zhang HH, Fan Y. Predictive values of genomic variation, tumor mutational burden, and PD-L1 expression in advanced lung squamous cell carcinoma treated with immunotherapy. Transl Lung Cancer Res 2020; 9:2367-2379. [PMID: 33489799 PMCID: PMC7815375 DOI: 10.21037/tlcr-20-1130] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Immune checkpoint inhibitors (ICIs) prolong overall survival (OS) in patients with advanced lung squamous cell carcinoma (LUSC). However, predictive and prognostic factors related to ICIs in LUSC remain elusive. This study aimed to identify predictors that are related to better clinical benefit and outcomes in LUSC patients treated with immunotherapy. Methods Capture-based targeted sequencing was performed in 64 patients with advanced LUSC who underwent immunotherapy. Tumor mutational burden (TMB) was defined as the sum of nonsynonymous single nucleotide and indel variants. Programmed cell death ligand-1 (PD-L1) expression was evaluated by immunohistochemical analysis. Clinicopathological characteristics including age, sex, performance status, smoking history, body mass index (BMI), blood fat, brain metastases, liver metastases, previous thoracic radiotherapy, and treatment lines were analyzed. Results The most commonly mutated genes included TP53, CDKN2A, KEAP1, CREBBP, KRAS, BIM, AMER1, and APC. Copy number variations most frequently occurred in AR, SOX2, PIK3CA, EGFR, RICTOR, FGFR1, and ZNF703. The median and mean TMB was 9.35 and 10.62 mutations per megabase, respectively. Positive PD-L1 expression was detected in 29.7% patients. Patients with a history of heavy smoking (≥ 40 pack-years) were more likely to have positive PD-L1 expression (35% vs. 16.7%, P=0.04) and higher TMB (11.1 vs. 9.8 mut/Mb, P=0.04). Gene alterations had no impact on PD-L1 expression or TMB level. The median progression-free survival (PFS) was 6.7 months and median OS was 13.7 months. Higher TMB was independently associated with longer PFS (P=0.01) and OS (P=0.02), and this correlation was more pronounced in patients treated with ICIs as a single agent (P=0.0001). Higher TMB was also associated with better disease control rate (DCR) (P=0.02). Compared with wild-type, patients with KRAS mutation and EGFR amplification had higher objective response rates (ORR, P=0.01). Conclusions The predictive value of TMB is more significant in LUSC patients receiving ICI as a single agent than as a combination therapy. The combination of Eastern Cooperative Oncology Group performance status (ECOG-PS), smoking status, TMB, PD-L1, and genomic variation might be helpful for personalized immunotherapy decisions in clinical practice for advanced LUSC.
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Affiliation(s)
- Yanjun Xu
- Department of Medical Thoracic Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Hangzhou, China
| | - Hui Li
- Department of Medical Thoracic Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Hangzhou, China
| | - Zhiyu Huang
- Department of Medical Thoracic Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Hangzhou, China
| | - Kaiyan Chen
- Department of Medical Thoracic Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Hangzhou, China
| | - Xiaoqing Yu
- Department of Medical Thoracic Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Hangzhou, China
| | - Jiamin Sheng
- Department of Medical Thoracic Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Hangzhou, China
| | | | - Yun Fan
- Wenzhou Medical University, Wenzhou, China
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15
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Liu Y, Feng Y, Hou T, Lizaso A, Xu F, Xing P, Wang H, Kang Q, Zhang L, Shi Y, Hu X. Investigation on the potential of circulating tumor DNA methylation patterns as prognostic biomarkers for lung squamous cell carcinoma. Transl Lung Cancer Res 2020; 9:2356-2366. [PMID: 33489798 PMCID: PMC7815356 DOI: 10.21037/tlcr-20-1070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Aberrant epigenetic modifications play a key role in lung tumorigenesis. In our study, we aimed to explore the clinical implications of baseline circulating tumor DNA (ctDNA) somatic and methylation profiles in patients with lung squamous cell carcinoma (LUSC). Methods A total of 26 patients with LUSC of various stages were included in this study. Somatic mutations and methylation levels were profiled from the plasma-derived ctDNA obtained at the time of diagnosis using unique molecular identifier (UMI)-based targeted sequencing and bisulfite sequencing, respectively. The correlation between baseline ctDNA mutation and methylation profile, and overall survival (OS), were analyzed. Results Somatic mutations were detected in 80.8% (20/26) of the patients. Patients harboring somatic mutations with maximum allelic fraction (maxAF) of >5% had significantly shorter OS compared to those with maxAF ≤5% (7.1 vs. 54.6 months; P=0.020). ctDNA methylation level was found to be strongly correlated with maxAF (Pearson correlation =0.934; P<0.001). Consistent with maxAF, higher methylation levels were also associated with poorer OS (hazard ratio =2.377; 95% CI: 1.283–4.405; P=0.006). Moreover, a total of 1,956 ctDNA methylation blocks were differentially methylated in patients with maxAF >0 (P<0.05). Least absolute shrinkage and selection operator (LASSO) regression analysis revealed a significant correlation between methylation signatures from 5 methylation blocks and OS (hazard ratio =183.20, 95% CI: 2.74–12,243.32; P=0.015). These 5 methylation blocks could serve as an alternative to maxAF and can be explored as prognostic biomarkers. Conclusions Our study identified several ctDNA methylation blocks that can potentially predict the prognosis of LUSC at the time of diagnosis.
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Affiliation(s)
- Yutao Liu
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu Feng
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ting Hou
- Burning Rock Biotech, Guangzhou, China
| | | | - Feng Xu
- Burning Rock Biotech, Guangzhou, China
| | - Puyuan Xing
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hongyu Wang
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | | | - Lu Zhang
- Burning Rock Biotech, Guangzhou, China
| | - Yuankai Shi
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xingsheng Hu
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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16
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Cai X, Chen Z, Deng M, Li Z, Wu Q, Wei J, Dai C, Wang G, Luo C. Unique genomic features and prognostic value of COSMIC mutational signature 4 in lung adenocarcinoma and lung squamous cell carcinoma. Ann Transl Med 2020; 8:1176. [PMID: 33241025 PMCID: PMC7576056 DOI: 10.21037/atm-20-5952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Analysis of mutational signatures is becoming routine in cancer genomics, with implications for pathogenesis, classification, and prognosis. Among the signatures cataloged at COSMIC, mutational signature 4 has been linked to smoking. However, the distribution of signature 4 in Chinese lung cancer patients has not been evaluated, and its clinical value has not been evaluated. Here we survey mutational signatures in Chinese lung cancer patients and explore the relationship between signature 4 and other genomic features in the patients. Methods We extracted mutational signatures from whole-exome sequencing data of Chinese non-small cell lung cancer patients. The data included 401 lung adenocarcinoma (LUAD) and 92 squamous cell carcinoma (LUSC). We then performed statistical analysis to search for genomic and clinical features that can be linked to mutation signatures. Results We found signature 4 is the most frequent mutational signature in LUSC and the second most frequent in LUAD. Fifty-six LUAD and thirty-five LUSC patients were named with high signature 4 similarities (cosine similarity >0.7). These patients have shorter survival and higher tumor mutational burden comparing to those with low signature 4 similarities. Dozens of genes with single nucleotide variation, index mutations, and copy number variations were differentially enriched in the patients with high signature 4 similarities. Among these genes, CSMD3, LRP1B, TP53, SYNE1, SLIT2, FGF4, and FGF19 are common in both LUADs and LUSCs with high signature 4 similarities, showing that these genes are tightly associated with signature 4. Conclusions The present study is the first to report a comparison in Chinese NSCLC patients with or without COSMIC mutational signature 4. These results will help find the Signature 4 related mutational process in NSCLC.
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Affiliation(s)
- Xiuyu Cai
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhenghe Chen
- Department of Neurosurgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Guangzhou, China.,Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Meiling Deng
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - Zhiyong Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qianchao Wu
- GenomiCare Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Jinwang Wei
- GenomiCare Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Chun Dai
- GenomiCare Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Guan Wang
- GenomiCare Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Chun Luo
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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17
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Ren P, Xing L, Hong X, Chang L, Zhang H. LncRNA PITPNA-AS1 boosts the proliferation and migration of lung squamous cell carcinoma cells by recruiting TAF15 to stabilize HMGB3 mRNA. Cancer Med 2020; 9:7706-7716. [PMID: 32871048 PMCID: PMC7571819 DOI: 10.1002/cam4.3268] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/25/2020] [Accepted: 06/02/2020] [Indexed: 12/21/2022] Open
Abstract
Plenty of reports have probed the involvement of abnormally expressed lncRNAs in multiple cancers, including lung squamous cell carcinoma (LUSC). Through online database GEPIA, lncRNA PITPNA antisense RNA 1 (PITPNA-AS1) was highly expressed in LUSC samples, and these tendency was further affirmed in LUSC cells. The aim of current study was to investigate the related mechanism of PITPNA-AS1 in LUSC. Functional experiments verified that depletion of PITPNA-AS1 hampered the proliferative and migratory abilities, but accelerated apoptosis of LUSC cells. Additionally, we observed the increased expression of HMGB3 and its positive correlation with PITPNA-AS1 in LUSC samples. Interestingly, PITPNA-AS1 mainly located in the cytosol of LUSC cells, and also affected mRNA stability of HMGB3. Furthermore, the repressed mRNA stability of HMGB3 by PITPNA-AS1 via TAF15 was exposed through mechanism experiments. The mediatory function of PITPNA-AS1 on HMGB3 was validated via rescue assays. All in all, PITPNA-AS1 promoted the proliferation and migration of LUSC cells via stabilizing HMGB3 by TAF15. In conclusion, our study displayed a novel mechanism underlying PITPNA-AS1 in LUSC cells.
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Affiliation(s)
- Ping Ren
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, P.R. China
| | - Lei Xing
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, P.R. China
| | - Xiaodong Hong
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, P.R. China
| | - Liang Chang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, P.R. China
| | - Hong Zhang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, P.R. China
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18
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Peng Y, Yuan C, Tao X, Zhao Y, Yao X, Zhuge L, Huang J, Zheng Q, Zhang Y, Hong H, Chen H, Sun Y. Integrated analysis of optical mapping and whole-genome sequencing reveals intratumoral genetic heterogeneity in metastatic lung squamous cell carcinoma. Transl Lung Cancer Res 2020; 9:670-681. [PMID: 32676329 PMCID: PMC7354123 DOI: 10.21037/tlcr-19-401] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Intratumoral heterogeneity is a crucial factor to the outcome of patients and resistance to therapies, in which structural variants play an indispensable but undiscovered role. Methods We performed an integrated analysis of optical mapping and whole-genome sequencing on a primary tumor (PT) and matched metastases including lymph node metastasis (LNM) and tumor thrombus in the pulmonary vein (TPV). Single nucleotide variants, indels and structural variants were analyzed to reveal intratumoral genetic heterogeneity among tumor cells in different sites. Results Our results demonstrated there were less nonsynonymous somatic variants shared with PT in LNM than in TPV, while there were more structural variants shared with PT in LNM than in TPV. More private variants and its affected genes associated with tumorigenesis and progression were identified in TPV than in LNM. It should be noticed that optical mapping detected an average of 77.1% (74.5-78.5%) large structural variants (>5,000 bp) not detected by whole-genome sequencing and identified several structural variants private to metastases. Conclusions Our study does demonstrate structural variants, especially large structural variants play a crucial role in intratumoral genetic heterogeneity and optical mapping could make up for the deficiency of whole-genome sequencing to identify structural variants.
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Affiliation(s)
- Yizhou Peng
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chongze Yuan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiaoting Tao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yue Zhao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xingxin Yao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lingdun Zhuge
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | | | - Qiang Zheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yue Zhang
- Berry Genomics Corporation, Beijing 100015, China
| | - Hui Hong
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yihua Sun
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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19
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Yang S, Sui J, Liu T, Wu W, Xu S, Yin L, Pu Y, Zhang X, Zhang Y, Shen B, Liang G. Expression of miR-486-5p and its significance in lung squamous cell carcinoma. J Cell Biochem 2019; 120:13912-13923. [PMID: 30963622 DOI: 10.1002/jcb.28665] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/21/2019] [Accepted: 02/28/2019] [Indexed: 12/14/2022]
Abstract
Lung squamous cell carcinoma (LUSC) is one of the main histological types of lung cancer with high mortality. The role of microRNA-486-5p in LUSC remains unclear. In the current study, the aim was to explore miR-486-5p expression and its role in LUSC. The miR-486-5p expression was significantly low-expressed in patients with LUSC from The Cancer Genome Atlas database, which was further confirmed in the Gene Expression Omnibus database, patients' tissues, different cell lines by quantitative real-time polymerase chain reaction, and the high-throughput gene sequencing data of lung tissues of mice after a long-term B(a)P exposure. The meta-analysis was performed to evaluate the expression and diagnosis power of miR-486-5p (standard mean difference = -2.25; 95% confidence interval: -3.47 to -1.03; P = 0.0003; area under curve = 0.9082). Functional enrichment analysis revealed the potential function of miR-486-5p in LUSC using gene set enrichment analysis and clusterProfiler package in R software. At last, the hub genes (PTEN, TEK, PIK3R1, PPM1B, SMAD2, and SPTA1) of miR-486-5p were verified. In conclusion, miR-486-5p may be a LUSC antioncogene, playing an important role to serve as a biomarker in LUSC.
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Affiliation(s)
- Sheng Yang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, P.R. China
| | - Jing Sui
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, P.R. China
| | - Tong Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, P.R. China
| | - Wenjuan Wu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, P.R. China
| | - Siyi Xu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, P.R. China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, P.R. China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, P.R. China
| | - Xiaomei Zhang
- Department of Oncology, Jiangsu Cancer Hospital, Nanjing, Jiangsu, P.R. China
| | - Yan Zhang
- Department of Oncology, Jiangsu Cancer Hospital, Nanjing, Jiangsu, P.R. China
| | - Bo Shen
- Department of Oncology, Jiangsu Cancer Hospital, Nanjing, Jiangsu, P.R. China
| | - Geyu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, P.R. China
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Meng F, Zhang L, Ren Y, Ma Q. The genomic alterations of lung adenocarcinoma and lung squamous cell carcinoma can explain the differences of their overall survival rates. J Cell Physiol 2018; 234:10918-10925. [PMID: 30549039 DOI: 10.1002/jcp.27917] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022]
Abstract
In the US, lung carcinoma accounted for over 150,000 deaths in 2018 and the advances in increasing survival rates are still limited. In this study, we investigated the cohorts with lung adenocarcinoma (LUAD) or lung squamous cell carcinoma (LUSC) from The Cancer Genome Atlas to figure out the risk factors and genomic alterations that affected their prognosis. The histoclinical factors that differed between LUAD and LUSC were identified and the risk factors affecting the overall survival were figured out for both LUAD and LUSC. Next, the patterns of nucleotides substitutions and the mutational signatures were extracted to illustrate whether different mutational processes performed for them. Finally, the genes that had different frequencies of mutation were identified. LUAD and LUSC presented differences in histoclinical factors including age at the time of diagnosis, sex, smoking history, pathological T classification, and overall survival. This was caused by the distinct genomic alterations including the transition-to-transversion ratios, mutational signatures, and the frequently mutated genes. We proposed that the mutational signature associated with aging could be used to predict the prognosis of patients with LUAD. On the other hand, the AID/APOBEC family was associated with the prognosis of LUSC. Finally, SNTG1 and LRRK2 might be important in LUAD and LUSC, respectively.
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Affiliation(s)
- Fanlu Meng
- Oncology Department, Tianjin Medical University General Hospital, Tianjin, China
| | - Linlin Zhang
- Oncology Department, Tianjin Medical University General Hospital, Tianjin, China
| | - Yaoyao Ren
- Oncology Department, Tianjin Medical University General Hospital, Tianjin, China
| | - Qing Ma
- Oncology Department, Tianjin Medical University General Hospital, Tianjin, China
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