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Raghani RM, Urie RR, Ma JA, Escalona G, Schrack IA, DiLillo KM, Kandagatla P, Decker JT, Morris AH, Arnold KB, Jeruss JS, Shea LD. Engineered Immunologic Niche Monitors Checkpoint Blockade Response and Probes Mechanisms of Resistance. IMMUNOMEDICINE 2024; 4:e1052. [PMID: 39246390 PMCID: PMC11376346 DOI: 10.1002/imed.1052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/07/2024] [Indexed: 09/10/2024]
Abstract
Antibodies to programmed cell death protein1 (anti-PD-1) have become a promising immunotherapy for triple negative breast cancer (TNBC), blocking PD-L1 signaling from pro-tumor cells through T cell PD-1 receptor binding. Nevertheless, only 10-20% of PD-L1+ metastatic TNBC patients who meet criteria benefit from ICB, and biomarkers to predict patient response have been elusive. We have previously developed an immunological niche, consisting of a microporous implant in the subcutaneous space, that supports tissue formation whose immune composition is consistent with that within vital organs. Herein, we investigated dynamic gene expression within this immunological niche to provide biomarkers of response to anti-PD-1. In a 4T1 model of metastatic TNBC, we observed sensitivity and resistance to anti-PD-1 based on primary tumor growth and survival. The niche was biopsied before, during, and after anti-PD-1 therapy, and analyzed for cell types and gene expression indicative of treatment refractivity. Myeloid cell-to-lymphocyte ratios were altered between ICB-sensitivity and resistance. Longitudinal analysis of gene expression implicated dynamic myeloid cell function that stratified sensitivity from resistance. A niche-derived gene signature predicted sensitivity or resistance prior to therapy. Analysis of the niche to monitor immunotherapy response presents a new opportunity to personalize care and investigate mechanisms underlying treatment resistance.
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Affiliation(s)
- Ravi M Raghani
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Russell R Urie
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey A Ma
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Guillermo Escalona
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Ian A Schrack
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Katarina M DiLillo
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | | | - Joseph T Decker
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
- Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan, Ann Arbor, Michigan
| | - Aaron H Morris
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Kelly B Arnold
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Jacqueline S Jeruss
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Lonnie D Shea
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan
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2
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Jaksik R, Szumała K, Dinh KN, Śmieja J. Multiomics-Based Feature Extraction and Selection for the Prediction of Lung Cancer Survival. Int J Mol Sci 2024; 25:3661. [PMID: 38612473 PMCID: PMC11011391 DOI: 10.3390/ijms25073661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Lung cancer is a global health challenge, hindered by delayed diagnosis and the disease's complex molecular landscape. Accurate patient survival prediction is critical, motivating the exploration of various -omics datasets using machine learning methods. Leveraging multi-omics data, this study seeks to enhance the accuracy of survival prediction by proposing new feature extraction techniques combined with unbiased feature selection. Two lung adenocarcinoma multi-omics datasets, originating from the TCGA and CPTAC-3 projects, were employed for this purpose, emphasizing gene expression, methylation, and mutations as the most relevant data sources that provide features for the survival prediction models. Additionally, gene set aggregation was shown to be the most effective feature extraction method for mutation and copy number variation data. Using the TCGA dataset, we identified 32 molecular features that allowed the construction of a 2-year survival prediction model with an AUC of 0.839. The selected features were additionally tested on an independent CPTAC-3 dataset, achieving an AUC of 0.815 in nested cross-validation, which confirmed the robustness of the identified features.
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Affiliation(s)
- Roman Jaksik
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
| | - Kamila Szumała
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland;
| | - Khanh Ngoc Dinh
- Irving Institute for Cancer Dynamics and Department of Statistics, Columbia University, New York, NY 10027, USA;
| | - Jarosław Śmieja
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
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3
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Pang WG, Ye M, Chen JR, Zhang L, Wang Z. Data mining-based identification of epigenetic signatures with discrimination potential of lung adenocarcinoma and squamous cell carcinoma. Mol Biol Rep 2024; 51:255. [PMID: 38302782 DOI: 10.1007/s11033-024-09216-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024]
Abstract
BACKGROUND Mounting evidence suggests that lung adenocarcinoma (LAC) and lung squamous cell carcinoma (LSC) have different biological behaviors and therapeutic regimens in clinical practice. However, limited improvements in molecular differential diagnosis of the two entities have been achieved in recent decades. We aimed to find novel markers that could define non-small cell lung cancer (NSCLC) subtypes. METHODS We first explored publically available databases to search for DNA methylation signatures that enable a precise discrimination of LAC and LSC. Next-generation sequencing (NGS) was then used to analyze the methylation status and sites of candidate genes in LAC/LSC tissue samples, and a quantitative methylation-sensitive PCR (qMS-PCR) assay was conducted to test the performance of the selected maker in tissue samples and bronchoalveolar lavage fluid (BALF) specimens. RESULTS We screened 19 top-ranked methylation loci that are differentially methylated between LAC and LSC. Among these hits, 6 methylation sites are enriched within the PREX1 gene promoter, thus becoming our focus. NGS analysis confirmed markedly higher PREX1 methylation levels in LAC than in LSC and revealed the right sites for detection of PREX1 methylation. Furthermore, PREX1 methylation analysis in lung cancer tissue samples defined 9 of 11 pathologically proven LACs, as well as 12 of 14 LSCs. In addition, ~ 80% LAC BALF samples showed methylated PREX1 compared to substantially lower test positivity (0-9%) of it in LSC and other lung conditions (P < 0.01). CONCLUSION Our pilot study identified a unique epigenetic signature that could effectively distinguish LAC from LSC in various lung samples. It may enhance our in-depth understanding of the biology of lung cancer and pave the way for better accurate diagnosis and treatment stratification in the future.
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Affiliation(s)
- Wen-Guang Pang
- Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Min Ye
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Jia-Rong Chen
- Department of Oncology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Liang Zhang
- Translational Medicine Center, Maternal and Child Health Research Institute, Guangdong Women and Children Hospital, 521 Xingnan Road, Guangzhou, 511400, China.
| | - Zheng Wang
- Department of Thoracic Surgery, The 2nd Clinical Medical College of Jinan University, 1017 Dongmen North Road, Luohu District, Shenzhen, 518020, China.
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Greco F, Piccolo CL, D’Andrea V, Scardapane A, Beomonte Zobel B, Mallio CA. Fat Matters: Exploring Cancer Risk through the Lens of Computed Tomography and Visceral Adiposity. J Clin Med 2024; 13:453. [PMID: 38256587 PMCID: PMC10817009 DOI: 10.3390/jcm13020453] [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: 12/16/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Obesity is an established risk factor for cancer. However, conventional measures like body mass index lack precision in assessing specific tissue quantities, particularly of the two primary abdominal fat compartments, visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT). Computed tomography (CT) stands as the gold standard for precisely quantifying diverse tissue types. VAT, distinguished by heightened hormonal and metabolic activity, plays a pivotal role in obesity-related tumor development. Excessive VAT is linked to aberrant secretion of adipokines, proinflammatory cytokines, and growth factors, fostering the carcinogenesis of obesity-related tumors. Accurate quantification of abdominal fat compartments is crucial for understanding VAT as an oncological risk factor. The purpose of the present research is to elucidate the role of CT, performed for staging purposes, in assessing VAT (quantity and distribution) as a critical factor in the oncogenesis of obesity-related tumors. In the field of precision medicine, this work takes on considerable importance, as quantifying VAT in oncological patients becomes fundamental in understanding the influence of VAT on cancer development-the potential "phenotypic expression" of excessive VAT accumulation. Previous studies analyzed in this research showed that VAT is a risk factor for clear cell renal cell carcinoma, non-clear cell renal cell carcinoma, prostate cancer, and hepatocarcinoma recurrence. Further studies will need to quantify VAT in other oncological diseases with specific mutations or gene expressions, in order to investigate the relationship of VAT with tumor genomics.
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Affiliation(s)
- Federico Greco
- Department of Radiology, Cittadella della Salute Azienda Sanitaria Locale di Lecce, Piazza Filippo Bottazzi 2, 73100 Lecce, Italy
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128 Roma, Italy; (C.L.P.); (B.B.Z.); (C.A.M.)
| | - Claudia Lucia Piccolo
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128 Roma, Italy; (C.L.P.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo 200, 00128 Roma, Italy
| | - Valerio D’Andrea
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128 Roma, Italy; (C.L.P.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo 200, 00128 Roma, Italy
| | - Arnaldo Scardapane
- Dipartimento Interdisciplinare di Medicina, Sezione di Diagnostica per Immagini, Università degli Studi di Bari “Aldo Moro”, Piazza Giulio Cesare 11, 70124 Bari, Italy;
| | - Bruno Beomonte Zobel
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128 Roma, Italy; (C.L.P.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo 200, 00128 Roma, Italy
| | - Carlo Augusto Mallio
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128 Roma, Italy; (C.L.P.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo 200, 00128 Roma, Italy
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5
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Wang Y, Liu S, Li J, Yin T, Liu Y, Wang Q, Liu X, Cheng L. Comprehensive serum N-glycan profiling identifies a biomarker panel for early diagnosis of non-small-cell lung cancer. Proteomics 2023; 23:e2300140. [PMID: 37474491 DOI: 10.1002/pmic.202300140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/01/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023]
Abstract
Aberrant serum N-glycan profiles have been observed in multiple cancers including non-small-cell lung cancer (NSCLC), yet the potential of N-glycans in the early diagnosis of NSCLC remains to be determined. In this study, serum N-glycan profiles of 275 NSCLC patients and 309 healthy controls were characterized by MALDI-TOF-MS. The levels of serum N-glycans and N-glycosylation patterns were compared between NSCLC and control groups. In addition, a panel of N-glycan biomarkers for NSCLC diagnosis was established and validated using machine learning algorithms. As a result, a total of 54 N-glycan structures were identified in human serum. Compared with healthy controls, 29 serum N-glycans were increased or decreased in NSCLC patients. N-glycan abundance in different histological types or clinical stages of NSCLC presented differentiated changes. Furthermore, an optimal biomarker panel of eight N-glycans was constructed based on logistic regression, with an AUC of 0.86 in the validation set. Notably, this model also showed a desirable capacity in distinguishing early-stage patients from healthy controls (AUC = 0.88). In conclusion, our work highlights the abnormal N-glycan profiles in NSCLC and provides supports potential application of N-glycan biomarker panel in clinical NSCLC detection.
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Affiliation(s)
- Yi Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Si Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tongxin Yin
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qiankun Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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6
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Ye CJ, Kong LJ, Wang YY, Dou C, Zheng J, Xu M, Xu Y, Li M, Zhao ZY, Lu JL, Chen YH, Ning G, Wang WQ, Bi YF, Wang TG. Mendelian randomization evidence for the causal effects of socio-economic inequality on human longevity among Europeans. Nat Hum Behav 2023; 7:1357-1370. [PMID: 37386110 DOI: 10.1038/s41562-023-01646-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/02/2023] [Indexed: 07/01/2023]
Abstract
Human longevity correlates with socio-economic status, and there is evidence that educational attainment increases human lifespan. However, to inform meaningful health policies, we need fine-grained causal evidence on which dimensions of socio-economic status affect longevity and the mediating roles of modifiable factors such as lifestyle and disease. Here we performed two-sample Mendelian randomization analyses applying genetic instruments of education, income and occupation (n = 248,847 to 1,131,881) to estimate their causal effects and consequences on parental lifespan and self-longevity (n = 28,967 to 1,012,240) from the largest available genome-wide association studies in populations of European ancestry. Each 4.20 years of additional educational attainment were causally associated with a 3.23-year-longer parental lifespan independently of income and occupation and were causally associated with 30-59% higher odds of self-longevity, suggesting that education was the primary determinant. By contrast, each one-standard-deviation-higher income and one-point-higher occupation was causally associated with 3.06-year-longer and 1.29-year-longer parental lifespans, respectively, but not independently of the other socio-economic indicators. We found no evidence for causal effects of income or occupation on self-longevity. Mediation analyses conducted in predominantly European-descent individuals through two-step Mendelian randomization suggested that among 59 candidates, cigarettes per day, body mass index, waist-to-hip ratio, hypertension, coronary heart disease, myocardial infarction, stroke, Alzheimer's disease, type 2 diabetes, heart failure and lung cancer individually played substantial mediating roles (proportion mediated, >10%) in the effect of education on specific longevity outcomes. These findings inform interventions for remediating longevity disparities attributable to socio-economic inequality.
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Affiliation(s)
- Chao-Jie Ye
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-Jie Kong
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi-Ying Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chun Dou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mian Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi-Yun Zhao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie-Li Lu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu-Hong Chen
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei-Qing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yu-Fang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Tian-Ge Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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7
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Zhou X, Ji L, Ma Y, Tian G, Lv K, Yang J. Intratumoral Microbiota-Host Interactions Shape the Variability of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma in Recurrence and Metastasis. Microbiol Spectr 2023; 11:e0373822. [PMID: 37074188 PMCID: PMC10269859 DOI: 10.1128/spectrum.03738-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/10/2023] [Indexed: 04/20/2023] Open
Abstract
Differences in tissue microbiota-host interaction between lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD) about recurrence and metastasis have not been well studied. In this study, we performed bioinformatics analyses to identify the genes and tissue microbes significantly associated with recurrence or metastasis. All lung cancer patients were divided into the recurrence or metastasis (RM) group and the nonrecurrence and nonmetastasis (non-RM) group according to whether or not they had recurred or metastasized within 3 years after the initial surgery. Results showed that there were significant differences between LUAD and LUSC in gene expression and microbial abundance associated with recurrence and metastasis. Compared with non-RM, the bacterial community of RM had a lower richness in LUSC. In LUSC, host genes significantly correlated with tissue microbe, whereas host-tissue microbe interaction in LUAD was rare. Then, we established a novel multimodal machine learning model based on genes and microbes to predict the recurrence and metastasis risk of a LUSC patient, which achieves an area under the curve (AUC) of 0.81. In addition, the predicted risk score was significantly associated with the patient's survival. IMPORTANCE Our study elucidates significant differences in RM-associated host-microbe interactions between LUAD and LUSC. Besides, the microbes in tumor tissue could be used to predict the RM risk of LUSC, and the predicted risk score is associated with patients' survival.
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Affiliation(s)
- Xiangfeng Zhou
- Department of Mathematics, Ocean University of China, Qingdao, China
- Geneis Beijing Co., Ltd., Beijing, China
| | - Lei Ji
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Yanyu Ma
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
- Department of Mathematics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang, China
| | - Geng Tian
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Kebo Lv
- Department of Mathematics, Ocean University of China, Qingdao, China
| | - Jialiang Yang
- Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
- Chifeng Municipal Hospital, Chifeng, Inner Mongolia, China
- Academician Workstation, Changsha Medical University, Changsha, China
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8
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Ton TVT, Hong HHL, Kovi RC, Shockley KR, Peddada SD, Gerrish KE, Janardhan KS, Flake G, Stout MD, Sills RC, Pandiri AR. Chronic Inhalation Exposure to Antimony Trioxide Exacerbates the MAPK Signaling in Alveolar Bronchiolar Carcinomas in B6C3F1/N Mice. Toxicol Pathol 2023; 51:39-55. [PMID: 37009983 PMCID: PMC11368139 DOI: 10.1177/01926233231157322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Antimony trioxide (AT) is used as a flame retardant in fabrics and plastics. Occupational exposure in miners and smelters is mainly through inhalation and dermal contact. Chronic inhalation exposure to AT particulates in B6C3F1/N mice and Wistar Han rats resulted in increased incidences and tumor multiplicities of alveolar/bronchiolar carcinomas (ABCs). In this study, we demonstrated Kras (43%) and Egfr (46%) hotspot mutations in mouse lung tumors (n = 80) and only Egfr (50%) mutations in rat lung tumors (n = 26). Interestingly, there were no differences in the incidences of these mutations in ABCs from rats and mice at exposure concentrations that did and did not exceed the pulmonary overload threshold. There was increased expression of p44/42 mitogen-activated protein kinase (MAPK) (Erk1/2) protein in ABCs harboring mutations in Kras and/or Egfr, confirming the activation of MAPK signaling. Transcriptomic analysis indicated significant alterations in MAPK signaling such as ephrin receptor signaling and signaling by Rho-family GTPases in AT-exposed ABCs. In addition, there was significant overlap between transcriptomic data from mouse ABCs due to AT exposure and human pulmonary adenocarcinoma data. Collectively, these data suggest chronic AT exposure exacerbates MAPK signaling in ABCs and, thus, may be translationally relevant to human lung cancers.
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Affiliation(s)
- Thai-Vu T. Ton
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology (DTT), National Institute Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709
| | - Hue-Hua L. Hong
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology (DTT), National Institute Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709
| | - Ramesh C. Kovi
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology (DTT), National Institute Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709
| | - Keith R. Shockley
- Biostatistics and Computational Biology Branch, NIEHS, Research Triangle Park, NC 27709
| | - Shyamal D. Peddada
- Biostatistics and Computational Biology Branch, NIEHS, Research Triangle Park, NC 27709
| | - Kevin E. Gerrish
- Molecular Genomics Core Laboratory, NIEHS, Research Triangle Park, NC 27709
| | - Kyathanahalli S. Janardhan
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology (DTT), National Institute Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709
| | - Gordon Flake
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology (DTT), National Institute Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709
| | - Mathew D. Stout
- Office of the Scientific Director, DTT, NIEHS, Research Triangle Park, NC 27709
| | - Robert C. Sills
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology (DTT), National Institute Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709
| | - Arun R. Pandiri
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology (DTT), National Institute Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709
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9
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Li G, Wu L, Yu J, Zhai S, Deng H, Wang Q. Identification and Validation of Three-Gene Signature in Lung Squamous Cell Carcinoma by Integrated Transcriptome and Methylation Analysis. JOURNAL OF ONCOLOGY 2022; 2022:9688040. [PMID: 36193204 PMCID: PMC9525794 DOI: 10.1155/2022/9688040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 11/21/2022]
Abstract
Since DNA methylation (DNAm) is associated with the carcinogenesis of various cancers, this study aimed to explore potential DNAm prognostic signatures of lung squamous cell carcinoma (LUSC). First, transcriptomic and methylation profiles of LUSC were obtained from The Cancer Genome Atlas database (TCGA). DNAm-related genes were screened by integrating DNAm and transcriptome profiles via MethylMix package. Subsequently, a prognostic signature was conducted with the least absolute shrinkage and selector operation (LASSO) Cox analysis. This signature combined with the clinicopathological parameters was then utilized to construct a prognostic nomogram via the rms package. A signature based on three DNAm-related genes claudin 1 (CLDN1), ATP-binding cassette subfamily C member 5 (ABCC5), and cystatin A (CSTA) that were hypomethylated and upregulated in LUSC was constructed. Univariate and multivariate Cox regression analysis suggested that this signature, combined with age and TNM.N stage, was significantly correlated with survival rate. Time-dependent receiver operating characteristics and calibration curves suggested the nomogram constructed with age and TNM.N stage variables could accurately evaluate the 3- and 5-year outcome of LUSC. Finally, the average mRNA and protein expression levels of CLDN1, ABCC5, and CSTA in LUSC were verified to be significantly higher than those in paracancerous tissues. Moreover, silencing CLDN1, ABCC5, and CSTA expressions could significantly reduce the carcinogenesis of the A549 cell line. The DNAm-driven prognostic signature consists of CLDN1, ABCC5, and CSTA incorporated with age and TNM. N stage could facilitate the prediction outcome of LUSC.
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Affiliation(s)
- Guanghua Li
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150000, China
| | - Libo Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Hainan Medical College, Haikou 570100, China
| | - Jiaxing Yu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150000, China
| | - Siyang Zhai
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150000, China
| | - Hailong Deng
- Department of Thoracic Surgery, Hailun People's Hospital, Hailun 152300, China
| | - Qiushi Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150000, China
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10
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Lu Y, Tang H, Huang P, Wang J, Deng P, Li Y, Zheng J, Weng L. Assessment of causal effects of visceral adipose tissue on risk of cancers: a Mendelian randomization study. Int J Epidemiol 2022; 51:1204-1218. [PMID: 35218345 PMCID: PMC9380424 DOI: 10.1093/ije/dyac025] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 02/05/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Despite the established association between obesity and cancer risk, it remains unclear whether visceral obesity is causally related to cancer risk and whether it is more pro-oncogenic than total body fat. METHODS We conducted two-sample Mendelian randomization (MR) analysis to assess the causal effects of visceral adipose tissue (VAT) on six common cancers. For exposure data, 221 genetic variants associated with the predicted volume of VAT in 325 153 Europeans from UK Biobank were used as instrumental variables. Genetic association data of six common cancers (breast, lung, colorectal, ovarian, pancreatic and prostate cancers) were obtained from large-scale consortia with an average of 19 576 cases and 43 272 controls. We performed univariable MR with five MR methods [inverse-variance weighted (IVW), MR-Egger regression, weighted median, MR-Pleiotropy Residual Sum and Outlier (MR-PRESSO) and Radial MR] and multivariable MR to estimate the effect of VAT independent of body mass index (BMI). Finally, we performed a series of sensitivity analyses as validation of primary MR results. RESULTS Two associations survived the false discovery rate correction for multiple testing (q-value < 0.05): in IVW, the odds ratios (95% CIs) per unit increase in genetically determined VAT were 1.65 (1.03 to 2.62) for pancreatic cancer and 1.47 (1.20 to 1.82) for lung squamous-cell carcinoma, respectively, which showed the same directions and overlapped confidence intervals with MR-Egger regression and weighted median results. There were no outlier variants identified by MR-PRESSO and no evidence supporting the presence of heterogeneity and pleiotropy in sensitivity analyses, although with wider confidence intervals that included the null, multivariable MR results for these two cancers showed the same directions and similar effect sizes as in IVW, which were independent of the effect from BMI. There was no evidence for a causal effect of VAT on the risk of other types of cancer. CONCLUSION Our findings suggest that lifelong exposure to elevated volumes of VAT might increase the risk of pancreatic cancer and lung squamous-cell carcinoma, highlighting the importance of revealing the underlying mechanisms for intervention targets.
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Affiliation(s)
- Yao Lu
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Schools of Life Course Sciences, King’s College London, London, UK
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Haibo Tang
- Department of Metabolic and Bariatric Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Peiyuan Huang
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Jie Wang
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Peizhi Deng
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yalan Li
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liang Weng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China
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11
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Li Y, Liu B, Yin X, Jiang Z, Fang C, Chen N, Zhang B, Dai L, Yin Y. Targeted demethylation of the SLC5A7 promotor inhibits colorectal cancer progression. Clin Epigenetics 2022; 14:92. [PMID: 35858918 PMCID: PMC9301853 DOI: 10.1186/s13148-022-01308-5] [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: 11/15/2021] [Accepted: 07/04/2022] [Indexed: 02/08/2023] Open
Abstract
Background SLC5A7 (solute carrier family 5 member 7), also known as choline transporter 1 (CHT1), is downregulated in colorectal cancer (CRC) and functions as a tumor suppressor. However, the mechanisms underlying the inactivation of SLC5A7 in CRC remain to be elucidated. Results In the present study, two broad-spectrum demethylation agents (azacitidine and decitabine) employed to treat CRC cells significantly upregulated SLC5A7 expression. Further results based on the CRC cohort and TCGA database indicated that SLC5A7 promoter methylation inversely correlated with SLC5A7 expression, and the status of SLC5A7 promotor methylation showed a promising prognostic value for patients with CRC. Next, the dCas9-multiGCN4/scFv-TET1CD-based precision demethylation system was constructed, which could significantly and specifically promote SLC5A7 expression in CRC cells through sgRNA targeting the SLC5A7 promoter. Both in vitro and in vivo experiments demonstrated that targeted demethylation of SLC5A7 by dCas9-multiGCN4/scFv-TET1CD-sgSLC5A7 inhibited tumor growth by stabilizing p53 and regulating downstream targets. Conclusions Collectively, DNA promoter methylation caused inactivation of SLC5A7 in CRC, and targeted demethylation of SLC5A7 might be a therapeutic target for CRC and other cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01308-5.
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Affiliation(s)
- Yang Li
- Department of Gastrointestinal Surgery, Guang'an People's Hospital, Guang'an, 638500, Sichuan, People's Republic of China.,Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Baike Liu
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xiaonan Yin
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Zhiyuan Jiang
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Chao Fang
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Na Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, Sichuan, People's Republic of China.,School of Pharmacy, Chengdu Medical College, Chengdu, 610500, People's Republic of China
| | - Bo Zhang
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
| | - Lei Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, Sichuan, People's Republic of China.
| | - Yuan Yin
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
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12
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Hoang PH, Landi MT. DNA Methylation in Lung Cancer: Mechanisms and Associations with Histological Subtypes, Molecular Alterations, and Major Epidemiological Factors. Cancers (Basel) 2022; 14:cancers14040961. [PMID: 35205708 PMCID: PMC8870477 DOI: 10.3390/cancers14040961] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is the major leading cause of cancer-related mortality worldwide. Multiple epigenetic factors-in particular, DNA methylation-have been associated with the development of lung cancer. In this review, we summarize the current knowledge on DNA methylation alterations in lung tumorigenesis, as well as their associations with different histological subtypes, common cancer driver gene mutations (e.g., KRAS, EGFR, and TP53), and major epidemiological risk factors (e.g., sex, smoking status, race/ethnicity). Understanding the mechanisms of DNA methylation regulation and their associations with various risk factors can provide further insights into carcinogenesis, and create future avenues for prevention and personalized treatments. In addition, we also highlight outstanding questions regarding DNA methylation in lung cancer to be elucidated in future studies.
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13
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He C, Huang D, Yang F, Huang D, Cao Y, Peng J, Luo X. High Expression of lncRNA HEIH is Helpful in the Diagnosis of Non-Small Cell Lung Cancer and Predicts Poor Prognosis. Cancer Manag Res 2022; 14:503-514. [PMID: 35173484 PMCID: PMC8841735 DOI: 10.2147/cmar.s320965] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background This study aims to investigate the expression and clinical value of long non-coding RNA (lncRNA) HEIH in peripheral blood of patients with non-small cell lung cancer (NSCLC). Methods Healthy subjects (N=70), patients with lung squamous cell carcinoma (LUSC, N=70) and patients with lung adenocarcinoma (LUAD, N=80) were included. LncRNA HEIH expression in peripheral blood of included subjects was detected using RT-qPCR. According to the median expression of lncRNA HEIH, LUSC and LUAD patients were allocated into lncRNA HEIH high/low expression groups. The correlation between lncRNA HEIH and clinical indicators of patients was analyzed; Logistic multifactor regression was used to analyze the independent risk factors influencing lncRNA HEIH level. Receiver-operating characteristic (ROC) curve was used to evaluate the diagnostic efficacy of lncRNA HEIH and carcinoembryonic antigen (CEA) in LUSC/LUAD patients. MedCalc-Comparison of ROC curves was used to compare the area under ROC curve. The cumulative survival rates of lncRNA HEIH high/low expression group were analyzed by Kaplan–Meier curve. COX multivariate analysis was used to assess the independent factors affecting prognosis of NSCLC. Results LncRNA HEIH in peripheral blood of LUSC/LUAD patients was higher than that in healthy controls, with no evident difference between LUSC and LUAD groups. In LUSC/LUAD patients, TNM stage, lymph node metastasis, distal metastasis, and CEA were independent risk factors affecting lncRNA HEIH; patients with high lncRNA HEIH expression had larger pack-years and tumor size, higher CEA level and tumor stage, and higher risk of lymph node metastasis and distal metastasis. LncRNA HEIH had higher diagnostic efficiency than CEA in NSCLC patients. High expression of lncRNA HEIH predicted poor prognosis in patients with NSCLC and was an independent risk factor for prognosis of NSCLC. Conclusion High expression of lncRNA HEIH is helpful in the diagnosis of NSCLC and predicts poor prognosis.
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Affiliation(s)
- Chaowen He
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
- Correspondence: Chaowen He, Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, No. 187 Guanlan Avenue, Longhua District, Shenzhen, 518110, Guangdong, People’s Republic of China, Tel +86-18123964996, Email
| | - Dongxuan Huang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
| | - Fan Yang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
| | - Dongsheng Huang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
| | - Yahui Cao
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
| | - Jianfeng Peng
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
| | - Xiaohua Luo
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
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14
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Huang H, Xie L, Feng X, Zheng Z, Ouyang J, Li Y, Yu J. An integrated analysis of DNA promoter methylation, microRNA regulation, and gene expression in gastric adenocarcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1414. [PMID: 34733966 PMCID: PMC8506766 DOI: 10.21037/atm-21-3211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/04/2021] [Indexed: 12/24/2022]
Abstract
Background Gastric adenocarcinoma (GAC), a common type of gastric cancer, poses a significant public health threat worldwide. This study aimed to determine the transcriptional regulatory mechanisms of GAC. Methods HTSeq-FPKM raw data were obtained from The Cancer Genome Atlas Stomach Adenocarcinoma data collection. Subsequently, the limma package in R was used to identify differentially expressed genes (DEGs). Differentially methylated genes (DMGs), DEGs, and differentially expressed microRNAs (miRNAs) in normal, and tumor tissues of the same patients were screened and compared using R software tools. A functional enrichment analysis was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) for various DEGs, DMGs, promoter methylation, and miRNAs. DEG-specific methylation and transcription factors were analyzed using ENCODE ChIP-seq. Results DEGs were centrally modified by the histone trimethylation of lysine 27 on histone H3 (H3K27me3). Upstream transcription factors of DEGs were enriched in different ChIP-seq clusters, such as Forkhead Box M1, E2F Transcription Factor 4, and suppressor of zest 12. Integrated regulatory networks of DEGs, promoter methylation, and miRNAs were constructed. Two miRNAs (hsa-mir-1 and hsa-mir-133a) and four DEGs (A disintegrin and metalloproteinase domain 12, transcription factor AP-2 alpha, solute carrier family 5 member 7, and cadherin 19) separately played important roles in the integrated regulatory network. Therefore, these DEGs, DMGs, promoter methylation, and miRNAs may play an important role in GAC pathogenesis. Conclusions In summary, the present study results provide insights into the oncogenesis and progression of GAC, thus accelerating the development of novel targeted GAC therapies.
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Affiliation(s)
- Hongyun Huang
- Department of General Surgery of Zhujiang Hospital, Southern Medical University, Guangzhou, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Lang Xie
- Department of General Surgery of Zhujiang Hospital, Southern Medical University, Guangzhou, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoxuan Feng
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zheng Zheng
- Department of General Surgery of Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Juntao Ouyang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yan Li
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jinlong Yu
- Department of General Surgery of Zhujiang Hospital, Southern Medical University, Guangzhou, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
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15
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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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16
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Liang Y, Lei Y, Du M, Liang M, Liu Z, Li X, Gao Y. The increased expression and aberrant methylation of SHC1 in non-small cell lung cancer: Integrative analysis of clinical and bioinformatics databases. J Cell Mol Med 2021; 25:7039-7051. [PMID: 34117717 PMCID: PMC8278126 DOI: 10.1111/jcmm.16717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
Despite the previous evidence showing that SHC adaptor protein 1 (SHC1) could encode three distinct isoforms (p46SHC, p52SHC and p66SHC) that function in different activities such as regulating life span and Ras activation, the precise underlying role of SHC1 in lung cancer also remains obscure. In this study, we firstly found that SHC1 expression was up‐regulated both in lung adenocarcinoma (LUAD) and in lung squamous cell carcinoma (LUSC) tissues. Furthermore, compared to patients with lower SHC1 expression, LUAD patients with higher expression of SHC1 had poorer overall survival (OS). Moreover, higher expression of SHC1 was also associated with worse OS in patients with stages 1 and 2 but not stage 3 lung cancer. Significantly, the analysis showed that SHC1 methylation level was associated with OS in lung cancer patients. It seemed that the methylation level at specific probes within SHC1 showed negative correlations with SHC1 expression both in LUAD and in LUSC tissues. The LUAD and LUSC patients with hypermethylated SHC1 at cg12473916 and cg19356022 probes had a longer OS. Therefore, it is reasonable to conclude that SHC1 has a potential clinical significance in LUAD and LUSC patients.
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Affiliation(s)
- Yicheng Liang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yangyang Lei
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Minjun Du
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mei Liang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zixu Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xingkai Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yushun Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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17
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Li G, Meng H, Bai Y, Wei W, Feng Y, Li M, Li H, He M, Zhang X, Wei S, Li Y, Guo H. DNA methylome analysis identifies BMI-related epigenetic changes associated with non-small cell lung cancer susceptibility. Cancer Med 2021; 10:3770-3781. [PMID: 33939316 PMCID: PMC8178488 DOI: 10.1002/cam4.3906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/16/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Background Body mass index (BMI) has been reported to be inversely associated with incident risk of non‐small cell lung cancer (NSCLC). However, the underlying mechanism is still unclear. This study aimed to investigate the role of DNA methylation in the relationship between BMI and NSCLC. Methods We carried out a genome‐wide DNA methylation study of BMI in peripheral blood among 2266 Chinese participants by using Illumina Methylation arrays. For the BMI‐related DNA methylation changes, their associations with NSCLC risk were further analyzed and their mediation effects on BMI‐NSCLC association were also evaluated. Results The methylation levels of four CpGs (cg12593793, cg17061862, cg11024682, and cg06500161, annotated to LMNA, ZNF143, SREBF1, and ABCG1, respectively) were found to be significantly associated with BMI. Methylation levels of cg12593793, cg11024682, and cg06500161 were observed to be inversely associated with NSCLC risk [OR (95%CI) =0.22 (0.16, 0.31), 0.39 (0.30, 0.50), and 0.66 (0.53, 0.82), respectively]. Additionally, cg11024682 in SREBF1 and cg06500161 in ABCG1 mediated 45.3% and 19.5% of the association between BMI and decreased NSCLC risk, respectively. Conclusions In this study, we identified four DNA methylation sites associated with BMI in the Chinese populations at the genome‐wide significant level. We also found that the BMI‐related methylations of SREBF1 and ABCG1 could mediate about a quintile‐to‐half of the effect of BMI on reduced NSCLC risk, which adds a potential mechanism underlying this association.
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Affiliation(s)
- Guyanan Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hua Meng
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yansen Bai
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Wei
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yue Feng
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mengying Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hang Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meian He
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Sheng Wei
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yangkai Li
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huan Guo
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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18
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Females and Males Show Differences in Early-Stage Transcriptomic Biomarkers of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. Diagnostics (Basel) 2021; 11:diagnostics11020347. [PMID: 33669819 PMCID: PMC7922551 DOI: 10.3390/diagnostics11020347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/25/2022] Open
Abstract
The incidence and mortality rates of lung cancers are different between females and males. Therefore, sex information should be an important part of how to train and optimize a diagnostic model. However, most of the existing studies do not fully utilize this information. This study carried out a comparative investigation between sex-specific models and sex-independent models. Three feature selection algorithms and five classifiers were utilized to evaluate the contribution of the sex information to the detection of early-stage lung cancers. Both lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) showed that the sex-specific models outperformed the sex-independent detection of early-stage lung cancers. The Venn plots suggested that females and males shared only a few transcriptomic biomarkers of early-stage lung cancers. Our experimental data suggested that sex information should be included in optimizing disease diagnosis models.
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19
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Lee N, Xia X, Meng H, Zhu W, Wang X, Zhang T, Zhang C, Zhang J, Luo P. Identification of a novel CpG methylation signature to predict prognosis in lung squamous cell carcinoma. Cancer Biomark 2021; 30:63-73. [PMID: 32924987 DOI: 10.3233/cbm-201564] [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] [Indexed: 12/13/2022]
Abstract
BACKGROUND DNA methylation plays a vital role in modulating genomic function and warrants evaluation as a biomarker for the diagnosis and treatment of lung squamous cell carcinoma (LUSC). OBJECTIVE In this study, we aimed to identify effective potential biomarkers for predicting prognosis and drug sensitivity in LUSC. METHODS A univariate Cox proportional hazards regression analysis, a random survival forests-variable hunting (RSFVH) algorithm, and a multivariate Cox regression analysis were adopted to analyze the methylation profile of patients with LUSC included in public databases: The Cancer Genome Atlas (TCGA), and the Gene Expression Omnibus (GEO). RESULTS A methylated region consisting of 3 sites (cg06675147, cg07064331, cg20429172) was selected. Patients were divided into a high-risk group and a low-risk group in the training dataset. High-risk patients had shorter overall survival (OS) (hazard ratio [HR]: 2.72, 95% confidence interval [CI]: 1.82-4.07, P< 0.001) compared with low-risk patients. The accuracy of the prognostic signature was validated in the test and validation cohorts (TCGA, n= 94; GSE56044, n= 23). Gene set variation analysis (GSVA) showed that activity in the cell cycle/mitotic, ERBB, and ERK/MAPK pathways was higher in the high-risk compared with the low-risk group, which may lead to differences in OS.Interestingly, we observed that patients in the high-risk group were more sensitive to gemcitabine and docetaxel than the low-risk group, which is consistent with results of the GSVA. CONCLUSION We report novel methylation sites that could be used as powerful tools for predicting risk factors for poorer survival in patients with LUSC.
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Affiliation(s)
- Nan Lee
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xuelian Xia
- Department of Anesthesiology, Luo He Central Hospital, Henan, China
| | - Hui Meng
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Weiliang Zhu
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiankai Wang
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Tianyuan Zhang
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chanyuan Zhang
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jian Zhang
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Peng Luo
- Department of Oncology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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20
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Yu M, Tian Y, Wu M, Gao J, Wang Y, Liu F, Sheng S, Huo S, Bai J. A comparison of mRNA and circRNA expression between squamous cell carcinoma and adenocarcinoma of the lungs. Genet Mol Biol 2020; 43:e20200054. [PMID: 33196759 PMCID: PMC7654371 DOI: 10.1590/1678-4685-gmb-2020-0054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/05/2020] [Indexed: 02/01/2023] Open
Abstract
Lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD) are the two major subtypes of non-small-cell lung cancer (NSCLC). This study aimed to compare mRNA and circRNA expression patterns between LUSC and LUAD. Cancer tissues from 8 LUSC patients and 12 LUAD patients were collected to obtain mRNA and circRNA expression profiles. The differentially expressed mRNAs (DEmRNAs) and circRNAs (DE-circRNAs) between LUSC and LUAD were screened. Afterwards, miRNA-DEcircRNA pairs and miRNA-DEmRNA pairs were predicted to construct a competing endogenous RNAs (ceRNAs) network, followed by functional enrichment analysis and survival analysis. In total, 635 DEmRNAs and 245 DEcircRNAs were obtained. The ceRNA analysis revealed that genes, such as EPHA2, EPHA7, NTRK2, CDK6, hsa_circ_027570, hsa_circ_006089, and hsa-circ_035997, had distinct expression patterns between LUSC and LUAD. Also, functional enrichment analysis indicated that DEmRNAs were mainly enriched in ERK1 and ERK2 cascade. Survival analyses suggested that STXBP1 and PMEPA1 were associated the prognosis of with both LUAD and LUSC, whereas EPHA2 and CDK6 might serve as prognostic factors for LUSC and LUAD, respectively. In conclusion, genes such as EPHA2, EPHA7, NTRK2, and CDK6 had different patterns in the two major histological subtypes of NSCLC. Notably, EPHA2 and CDK6 might be considered as potential therapeutic targets for LUSC and LUAD, respectively.
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Affiliation(s)
- Min Yu
- Shaanxi Provincial People's Hospital, Department of Oncology Medicine, Xi'an, Shaanxi, China
| | - Yingxuan Tian
- Shaanxi Provincial People's Hospital, Department of Elderly Respiratory Medicine, Xi'an, Shaanxi, China.,Shaanxi Provincial People's Hospital, Xi'an Medical College, Department of Elderly Medicine, Xi'an, Shaanxi, China
| | - Min Wu
- Shaanxi Provincial People's Hospital, Department of Elderly Respiratory Medicine, Xi'an, Shaanxi, China
| | - Jinglong Gao
- Shaanxi Provincial People's Hospital, Department of Elderly Medicine, Xi'an, Shaanxi, China
| | - Yuan Wang
- Shaanxi Provincial People's Hospital, Department of Preventive Health Section, Xi'an, Shaanxi, China
| | - Fuqiang Liu
- Shaanxi Provincial People's Hospital, Cardiovascular Department, Xi'an, Shaanxi, China
| | - Sen Sheng
- University of Arkansas for Medical Science, Neurology Department, Little Rock, AR, USA
| | - Shufen Huo
- Shaanxi Provincial People's Hospital, Department of Elderly Respiratory Medicine, Xi'an, Shaanxi, China
| | - Jun Bai
- Shaanxi Provincial People's Hospital, Department of Oncology Medicine, Xi'an, Shaanxi, China
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21
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A prognostic model for overall survival of patients with early-stage non-small cell lung cancer: a multicentre, retrospective study. LANCET DIGITAL HEALTH 2020; 2:e594-e606. [PMID: 33163952 PMCID: PMC7646741 DOI: 10.1016/s2589-7500(20)30225-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background Intratumoural heterogeneity has been previously shown to be related to clonal evolution and genetic instability and associated with tumour progression. Phenotypically, it is reflected in the diversity of appearance and morphology within cell populations. Computer-extracted features relating to tumour cellular diversity on routine tissue images might correlate with outcome. This study investigated the prognostic ability of computer-extracted features of tumour cellular diversity (CellDiv) from haematoxylin and eosin (H&E)-stained histology images of non-small cell lung carcinomas (NSCLCs). Methods In this multicentre, retrospective study, we included 1057 patients with early-stage NSCLC with corresponding diagnostic histology slides and overall survival information from four different centres. CellDiv features quantifying local cellular morphological diversity from H&E-stained histology images were extracted from the tumour epithelium region. A Cox proportional hazards model based on CellDiv was used to construct risk scores for lung adenocarcinoma (LUAD; 270 patients) and lung squamous cell carcinoma (LUSC; 216 patients) separately using data from two of the cohorts, and was validated in the two remaining independent cohorts (comprising 236 patients with LUAD and 335 patients with LUSC). We used multivariable Cox regression analysis to examine the predictive ability of CellDiv features for 5-year overall survival, controlling for the effects of clinical and pathological parameters. We did a gene set enrichment and Gene Ontology analysis on 405 patients to identify associations with differentially expressed biological pathways implicated in lung cancer pathogenesis. Findings For prognosis of patients with early-stage LUSC, the CellDiv LUSC model included 11 discriminative CellDiv features, whereas for patients with early-stage LUAD, the model included 23 features. In the independent validation cohorts, patients predicted to be at a higher risk by the univariable CellDiv model had significantly worse 5-year overall survival (hazard ratio 1·48 [95% CI 1·06–2·08]; p=0·022 for The Cancer Genome Atlas [TCGA] LUSC group, 2·24 [1·04–4·80]; p=0·039 for the University of Bern LUSC group, and 1·62 [1·15–2·30]; p=0·0058 for the TCGA LUAD group). The identified CellDiv features were also found to be strongly associated with apoptotic signalling and cell differentiation pathways. Interpretation CellDiv features were strongly prognostic of 5-year overall survival in patients with early-stage NSCLC and also associated with apoptotic signalling and cell differentiation pathways. The CellDiv-based risk stratification model could potentially help to determine which patients with early-stage NSCLC might receive added benefit from adjuvant therapy. Funding National Institue of Health and US Department of Defense.
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22
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Liu C, Jing W, An N, Li A, Yan W, Zhu H, Yu J. Prognostic significance of peripheral CD8+CD28+ and CD8+CD28- T cells in advanced non-small cell lung cancer patients treated with chemo(radio)therapy. J Transl Med 2019; 17:344. [PMID: 31623615 PMCID: PMC6796409 DOI: 10.1186/s12967-019-2097-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 10/11/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Noninvasive prognostic biomarkers are needed for advanced non-small cell lung cancer (NSCLC) patients with different histological types to identify cases with poor survival. Here, we investigated the prognostic values of peripheral CD8+CD28+ T cells and CD8+CD28- T cells in advanced NSCLC patients treated with chemo(radio)therapy and the impact of histological type on them. METHODS Of 232 registered advanced NSCLC patients, 101 treatment-naïve individuals were eligible and included in our study. Flow cytometry was used to evaluate CD8+CD28+ T cells, CD8+CD28- T cells, CD4+ CD25hi T cells, B cells, natural killer cells, γδT cells, and natural killer T cells in patients' peripheral blood. RESULTS The median follow-up time was 13.6 months. Fifty-nine (58.4%) patients died by the end of our study. Fifty-three of the 101 advanced NSCLC cases selected for our study were adenocarcinomas (ADs), and 48 were squamous cell carcinomas (SCCs). Multivariate analyses showed that increased levels of CD8+CD28+ T cells independently predicted favorable overall survival (OS) [hazard ratio (HR): 0.51, 95% confidence interval (CI) 0.30-0.89, P = 0.021] and progression-free survival (PFS) (HR: 0.66, 95% CI 0.37-0.93, P = 0.038) in ADs, but the prediction in SCCs was not statistically significant. In contrast, high levels of CD8+CD28- T cells independently predicted unfavorable OS (HR: 1.41, 95% CI 1.17-3.06, P = 0.035) and PFS (HR: 2.01, 95% CI 1.06-3.85, P = 0.029) in SCCs, but the prediction in ADs was not statistically significant. ADs had higher levels of CD4+CD25hi T cells and CD8+CD28- T cells and lower NK cells (all P < 0.05) than SCCs. CONCLUSIONS Our findings uncovered the prognostic values of peripheral CD8+CD28+ T cells and CD8+CD28- T cells in advanced NSCLC patients treated with chemo(radio)therapy, which could help to identify patients with poor outcomes and refine treatment strategies.
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Affiliation(s)
- Chao Liu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.,Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China.,Department of Radiation Oncology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing, 100071, China
| | - Wang Jing
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Ning An
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Aijie Li
- Weifang Medical University, Weifang, 261053, Shandong, China
| | - Weiwei Yan
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Hui Zhu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China.
| | - Jinming Yu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China. .,Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China.
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23
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Long non-coding RNA-HAGLR suppressed tumor growth of lung adenocarcinoma through epigenetically silencing E2F1. Exp Cell Res 2019; 382:111461. [PMID: 31194977 DOI: 10.1016/j.yexcr.2019.06.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/30/2019] [Accepted: 06/08/2019] [Indexed: 12/23/2022]
Abstract
Emerging evidence indicates that long noncoding RNAs (LncRNAs) are new players in gene regulation but their mechanisms of action are mainly undocumented. In this study, we investigated LncRNA alterations that contribute to lung cancer by analyzing published microarray data in Gene Expression Obminus (GEO) and The Cancer Genome Atlas RNA (TCGA) sequencing data. Here, we reported that HAGLR (also called HOXD-AS1) was frequently down-regulated in lung adenocarcinoma (LUAD) tissues, and decreased HAGLR expression was clinically associated with shorter survival of LUAD patients. Preclinical studies using multiple LUAD cells and in vivo mouse model indicated that HAGLR could attenuate LUAD cell growth in vitro and in vivo. Mechanistically, HAGLR could physically interact with DNMT1, and recruit DNMT1 on E2F1 promoter to increase local DNA methylation. Overall, our study demonstrated that HAGLR promoted LUAD progression by recruiting DNMT1 to modulate the promoter methylation and expression of E2F1, which expanded potential therapeutic strategies for LUAD treatment.
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24
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Mohindra P, Sawant A, Griffin RJ, Lamichhane N, Vlashi E, Xu‐Welliver M, Dominello M, Joiner MC, Burmeister J. Three discipline collaborative radiation therapy (3DCRT) special debate: I would treat all early-stage NSCLC patients with SBRT. J Appl Clin Med Phys 2019; 20:7-13. [PMID: 30793828 PMCID: PMC6414141 DOI: 10.1002/acm2.12545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 11/27/2022] Open
Affiliation(s)
- Pranshu Mohindra
- Department of Radiation OncologyUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Amit Sawant
- Department of Radiation OncologyUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Robert J. Griffin
- Department of Radiation OncologyUniversity of Arkansas for Medical SciencesLittle RockARUSA
| | - Narottam Lamichhane
- Department of Radiation OncologyUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Erina Vlashi
- Department of Radiation OncologyUniversity of California‐Los AngelesLos AngelesCAUSA
| | - Meng Xu‐Welliver
- Department of Radiation OncologyThe James Cancer CenterOhio State UniversityColumbusOHUSA
| | - Michael Dominello
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Michael C. Joiner
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Jay Burmeister
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
- Gershenson Radiation Oncology CenterBarbara Ann Karmanos Cancer InstituteDetroitMIUSA
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