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Li M, Deng X, Zhou D, Liu X, Dai J, Liu Q. A Novel Methylation-based Model for Prognostic Prediction in Lung Adenocarcinoma. Curr Genomics 2024; 25:26-40. [PMID: 38544827 PMCID: PMC10964088 DOI: 10.2174/0113892029277397231228062412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 08/25/2024] Open
Abstract
Objectives Specific methylation sites have shown promise in the early diagnosis of lung adenocarcinoma (LUAD). However, their utility in predicting LUAD prognosis remains unclear. This study aimed to construct a reliable methylation-based predictor for accurately predicting the prognosis of LUAD patients. Methods DNA methylation data and survival data from LUAD patients were obtained from the TCGA and a GEO series. A DNA methylation-based signature was developed using univariate least absolute shrinkage and selection operators and multivariate Cox regression models. Results Eight CpG sites were identified and validated as optimal prognostic signatures for the overall survival of LUAD patients. Receiver operating characteristic analysis demonstrated the high predictive ability of the eight-site methylation signature combined with clinical factors for overall survival. Conclusion This research successfully identified a novel eight-site methylation signature for predicting the overall survival of LUAD patients through bioinformatic integrated analysis of gene methylation markers used in the early diagnosis of lung cancer.
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Affiliation(s)
- Manyuan Li
- Department of Thoracic Surgery, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037, China
| | - Xufeng Deng
- Department of Thoracic Surgery, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037, China
| | - Dong Zhou
- Department of Thoracic Surgery, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037, China
| | - Xiaoqing Liu
- Department of Thoracic Surgery, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037, China
| | - Jigang Dai
- Department of Thoracic Surgery, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037, China
| | - Quanxing Liu
- Department of Thoracic Surgery, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037, China
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Mokhtari K, Peymani M, Rashidi M, Hushmandi K, Ghaedi K, Taheriazam A, Hashemi M. Colon cancer transcriptome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:49-82. [PMID: 37059270 DOI: 10.1016/j.pbiomolbio.2023.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Over the last four decades, methodological innovations have continuously changed transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples using RNA sequencing (RNA-seq). These transcriptomes serve as a connection between cellular behaviors and their underlying molecular mechanisms, such as mutations. This relationship, in the context of cancer, provides a chance to unravel tumor complexity and heterogeneity and uncover novel biomarkers or treatment options. Since colon cancer is one of the most frequent malignancies, its prognosis and diagnosis seem to be critical. The transcriptome technology is developing for an earlier and more accurate diagnosis of cancer which can provide better protectivity and prognostic utility to medical teams and patients. A transcriptome is a whole set of expressed coding and non-coding RNAs in an individual or cell population. The cancer transcriptome includes RNA-based changes. The combined genome and transcriptome of a patient may provide a comprehensive picture of their cancer, and this information is beginning to affect treatment decision-making in real-time. A full assessment of the transcriptome of colon (colorectal) cancer has been assessed in this review paper based on risk factors such as age, obesity, gender, alcohol use, race, and also different stages of cancer, as well as non-coding RNAs like circRNAs, miRNAs, lncRNAs, and siRNAs. Similarly, they have been examined independently in the transcriptome study of colon cancer.
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Affiliation(s)
- Khatere Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Valencia K, Sainz C, Bértolo C, de Biurrun G, Agorreta J, Azpilikueta A, Larrayoz MJ, Bosco G, Zandueta C, Redrado M, Redín E, Exposito F, Serrano D, Echepare M, Ajona D, Melero I, Pio R, Thomas R, Calvo A, Montuenga LM. Two alternative cell line models for the study of multiorganic metastasis and immunotherapy in Lung Squamous Cell Carcinoma. Dis Model Mech 2021; 15:273637. [PMID: 34870316 PMCID: PMC8822220 DOI: 10.1242/dmm.049137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/29/2021] [Indexed: 11/20/2022] Open
Abstract
There is a paucity of adequate mouse models and cell lines available to study lung squamous cell carcinoma (LUSC). We have generated and characterized two models of phenotypically different transplantable LUSC cell lines (UN-SCC679 and UN-SCC680) derived from an N-nitroso-tris-chloroethylurea (NTCU) chemically-induced mouse model in A/J mice. Furthermore, we genetically characterized and compared both LUSC cell lines by performing whole exome and RNA sequencing. These experiments revealed similar genetic and transcriptomic patterns that may correspond to the classical LUSC human subtype. In addition, we compared the immune landscape generated by both tumor cells lines in vivo and assessed their response to immune checkpoint inhibition. The differences between the two cell lines are a good model for the remarkable heterogeneity of human squamous cell carcinoma. Study of the metastatic potential of these models revealed that both cell lines represent the human LUSC organotropism to the brain, bones, liver and adrenal glands. In summary, we have generated a very valuable cell line tools for LUSC research that recapitulates the complexity of the human disease.
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Affiliation(s)
- Karmele Valencia
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain.,Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Cristina Sainz
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Cristina Bértolo
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Gabriel de Biurrun
- Department of Environmental Biology School of Sciences, University of Navarra, Pamplona, Spain
| | - Jackeline Agorreta
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Health Sciences, Biochemistry Area, Public University of Navarra, Pamplona, Spain
| | - Arantza Azpilikueta
- Program of Immunology and Immunotherapy, CIMA-University of Navarra, Pamplona, Spain
| | - Marta J Larrayoz
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Graziella Bosco
- Department of Translational Genomics, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Carolina Zandueta
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Miriam Redrado
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Esther Redín
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Francisco Exposito
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Diego Serrano
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Mirari Echepare
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Daniel Ajona
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain.,Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Ignacio Melero
- Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain.,Program of Immunology and Immunotherapy, CIMA-University of Navarra, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ruben Pio
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain.,Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Roman Thomas
- Department of Translational Genomics, Medical Faculty, University of Cologne, 50931 Cologne, Germany.,Department of Pathology, University Hospital Cologne, 50937 Cologne, Germany.,German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Alfonso Calvo
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
| | - Luis M Montuenga
- Program in Solid Tumors, CIMA-University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Consorcio de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain
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