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Wei S, Zhang Y, Kang BE, Park W, Guo H, Nam S, Kang JS, Jeong JH, Jo Y, Ryu D, Jiang Y, Ha KT. CDKN2 expression is a potential biomarker for T cell exhaustion in hepatocellular carcinoma. BMB Rep 2024; 57:287-292. [PMID: 38523373 PMCID: PMC11214889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/27/2023] [Accepted: 12/08/2023] [Indexed: 03/26/2024] Open
Abstract
Hepatocellular Carcinoma (HCC), the predominant primary hepatic malignancy, is the prime contributor to mortality. Despite the availability of multiple surgical interventions, patient outcomes remain suboptimal. Immunotherapies have emerged as effective strategies for HCC treatment with multiple clinical advantages. However, their curative efficacy is not always satisfactory, limited by the dysfunctional T cell status. Thus, there is a pressing need to discover novel potential biomarkers indicative of T cell exhaustion (Tex) for personalized immunotherapies. One promising target is Cyclin-dependent kinase inhibitor 2 (CDKN2) gene, a key cell cycle regulator with aberrant expression in HCC. However, its specific involvement remains unclear. Herein, we assessed the potential of CDKN2 expression as a promising biomarker for HCC progression, particularly for exhausted T cells. Our transcriptome analysis of CDKN2 in HCC revealed its significant role involving in HCC development. Remarkably, single-cell transcriptomic analysis revealed a notable correlation between CDKN2 expression, particularly CDKN2A, and Tex markers, which was further validated by a human cohort study using human HCC tissue microarray, highlighting CDKN2 expression as a potential biomarker for Tex within the intricate landscape of HCC progression. These findings provide novel perspectives that hold promise for addressing the unmet therapeutic need within HCC treatment. [BMB Reports 2024; 57(6): 287-292].
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Affiliation(s)
- Shibo Wei
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, China
| | - Yan Zhang
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, China
| | - Baeki E. Kang
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon 16419, China
| | - Wonyoung Park
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan 50612, Korea, Changchun 130041, China
| | - He Guo
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun 130041, China, Changchun 130041, China
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, China
| | - Jong-Sun Kang
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, China
| | - Jee-Heon Jeong
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, China
| | - Yunju Jo
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea, Changchun 130041, China
| | - Dongryeol Ryu
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea, Changchun 130041, China
| | - Yikun Jiang
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun 130041, China
| | - Ki-Tae Ha
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan 50612, Korea, Changchun 130041, China
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2
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Wang F, Cao H, Xia Q, Liu Z, Wang M, Gao F, Xu D, Deng B, Diao Y, Kapranov P. Lessons from discovery of true ADAR RNA editing sites in a human cell line. BMC Biol 2023; 21:160. [PMID: 37468903 PMCID: PMC10357658 DOI: 10.1186/s12915-023-01651-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Conversion or editing of adenosine (A) into inosine (I) catalyzed by specialized cellular enzymes represents one of the most common post-transcriptional RNA modifications with emerging connection to disease. A-to-I conversions can happen at specific sites and lead to increase in proteome diversity and changes in RNA stability, splicing, and regulation. Such sites can be detected as adenine-to-guanine sequence changes by next-generation RNA sequencing which resulted in millions reported sites from multiple genome-wide surveys. Nonetheless, the lack of extensive independent validation in such endeavors, which is critical considering the relatively high error rate of next-generation sequencing, leads to lingering questions about the validity of the current compendiums of the editing sites and conclusions based on them. RESULTS Strikingly, we found that the current analytical methods suffer from very high false positive rates and that a significant fraction of sites in the public databases cannot be validated. In this work, we present potential solutions to these problems and provide a comprehensive and extensively validated list of A-to-I editing sites in a human cancer cell line. Our findings demonstrate that most of true A-to-I editing sites in a human cancer cell line are located in the non-coding transcripts, the so-called RNA 'dark matter'. On the other hand, many ADAR editing events occurring in exons of human protein-coding mRNAs, including those that can recode the transcriptome, represent false positives and need to be interpreted with caution. Nonetheless, yet undiscovered authentic ADAR sites that increase the diversity of human proteome exist and warrant further identification. CONCLUSIONS Accurate identification of human ADAR sites remains a challenging problem, particularly for the sites in exons of protein-coding mRNAs. As a result, genome-wide surveys of ADAR editome must still be accompanied by extensive Sanger validation efforts. However, given the vast number of unknown human ADAR sites, there is a need for further developments of the analytical techniques, potentially those that are based on deep learning solutions, in order to provide a quick and reliable identification of the editome in any sample.
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Affiliation(s)
- Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
| | - Qiu Xia
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ziheng Liu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ming Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fan Gao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Bolin Deng
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Yong Diao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
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Lin SH, Chen SCC. RNA Editing in Glioma as a Sexually Dimorphic Prognostic Factor That Affects mRNA Abundance in Fatty Acid Metabolism and Inflammation Pathways. Cells 2022; 11:cells11071231. [PMID: 35406793 PMCID: PMC8997934 DOI: 10.3390/cells11071231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/16/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023] Open
Abstract
RNA editing alters the nucleotide sequence and has been associated with cancer progression. However, little is known about its prognostic and regulatory roles in glioma, one of the most common types of primary brain tumors. We characterized and analyzed RNA editomes of glioblastoma and isocitrate dehydrogenase mutated (IDH-MUT) gliomas from The Cancer Genome Atlas and the Chinese Glioma Genome Atlas (CGGA). We showed that editing change during glioma progression was another layer of molecular alterations and that editing profiles predicted the prognosis of glioblastoma and IDH-MUT gliomas in a sex-dependent manner. Hyper-editing was associated with poor survival in females but better survival in males. Moreover, noncoding editing events impacted mRNA abundance of the host genes. Genes associated with inflammatory response (e.g., EIF2AK2, a key mediator of innate immunity) and fatty acid oxidation (e.g., acyl-CoA oxidase 1, the rate-limiting enzyme in fatty acid β-oxidation) were editing-regulated and associated with glioma progression. The above findings were further validated in CGGA samples. Establishment of the prognostic and regulatory roles of RNA editing in glioma holds promise for developing editing-based therapeutic strategies against glioma progression. Furthermore, sexual dimorphism at the epitranscriptional level highlights the importance of developing sex-specific treatments for glioma.
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Tang Y, Yang CM, Su S, Wang WJ, Fan LP, Shu J. Machine learning-based Radiomics analysis for differentiation degree and lymphatic node metastasis of extrahepatic cholangiocarcinoma. BMC Cancer 2021; 21:1268. [PMID: 34819043 PMCID: PMC8611922 DOI: 10.1186/s12885-021-08947-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/01/2021] [Indexed: 12/15/2022] Open
Abstract
Background Radiomics may provide more objective and accurate predictions for extrahepatic cholangiocarcinoma (ECC). In this study, we developed radiomics models based on magnetic resonance imaging (MRI) and machine learning to preoperatively predict differentiation degree (DD) and lymph node metastasis (LNM) of ECC. Methods A group of 100 patients diagnosed with ECC was included. The ECC status of all patients was confirmed by pathology. A total of 1200 radiomics features were extracted from axial T1 weighted imaging (T1WI), T2-weighted imaging (T2WI), diffusion weighted imaging (DWI), and apparent diffusion coefficient (ADC) images. A systematical framework considering combinations of five feature selection methods and ten machine learning classification algorithms (classifiers) was developed and investigated. The predictive capabilities for DD and LNM were evaluated in terms of area under precision recall curve (AUPRC), area under the receiver operating characteristic (ROC) curve (AUC), negative predictive value (NPV), accuracy (ACC), sensitivity, and specificity. The prediction performance among models was statistically compared using DeLong test. Results For DD prediction, the feature selection method joint mutual information (JMI) and Bagging Classifier achieved the best performance (AUPRC = 0.65, AUC = 0.90 (95% CI 0.75–1.00), ACC = 0.85 (95% CI 0.69–1.00), sensitivity = 0.75 (95% CI 0.30–0.95), and specificity = 0.88 (95% CI 0.64–0.97)), and the radiomics signature was composed of 5 selected features. For LNM prediction, the feature selection method minimum redundancy maximum relevance and classifier eXtreme Gradient Boosting achieved the best performance (AUPRC = 0.95, AUC = 0.98 (95% CI 0.94–1.00), ACC = 0.90 (95% CI 0.77–1.00), sensitivity = 0.75 (95% CI 0.30–0.95), and specificity = 0.94 (95% CI 0.72–0.99)), and the radiomics signature was composed of 30 selected features. However, these two chosen models were not significantly different to other models of higher AUC values in DeLong test, though they were significantly different to most of all models. Conclusion MRI radiomics analysis based on machine learning demonstrated good predictive accuracies for DD and LNM of ECC. This shed new light on the noninvasive diagnosis of ECC.
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Affiliation(s)
- Yong Tang
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, Sichuan, China
| | - Chun Mei Yang
- Department of Radiology, The Affiliated Hospital of Southwest Medical University, and Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, 646000, Sichuan, China
| | - Song Su
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, 646000, Sichuan, China
| | - Wei Jia Wang
- School of Information and Software Engineering, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, Sichuan, China
| | - Li Ping Fan
- Department of Ultrasound, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, 646000, Sichuan, China.
| | - Jian Shu
- Department of Radiology, The Affiliated Hospital of Southwest Medical University, and Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, 646000, Sichuan, China.
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Tanabe S, Perkins EJ, Ono R, Sasaki H. Artificial intelligence in gastrointestinal diseases. Artif Intell Gastroenterol 2021; 2:69-76. [DOI: 10.35712/aig.v2.i3.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/09/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Artificial intelligence (AI) applications are growing in medicine. It is important to understand the current state of the AI applications prior to utilizing in disease research and treatment. In this review, AI application in the diagnosis and treatment of gastrointestinal diseases are studied and summarized. In most cases, AI studies had large amounts of data, including images, to learn to distinguish disease characteristics according to a human’s perspectives. The detailed pros and cons of utilizing AI approaches should be investigated in advance to ensure the safe application of AI in medicine. Evidence suggests that the collaborative usage of AI in both diagnosis and treatment of diseases will increase the precision and effectiveness of medicine. Recent progress in genome technology such as genome editing provides a specific example where AI has revealed the diagnostic and therapeutic possibilities of RNA detection and targeting.
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Affiliation(s)
- Shihori Tanabe
- Division of Risk Assessment, Center for Biological Safety and Research, National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Edward J Perkins
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS 3180, United States
| | - Ryuichi Ono
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research, National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Hiroki Sasaki
- Department of Clinical Genomics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo 104-0045, Japan
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Zhang B, Li Q, Wu B, Zhang S, Li L, Jin K, Li S, Li K, Wang Z, Lu Y, Xia L, Sun C. Long non-coding RNA TP73-AS1 is a potential immune related prognostic biomarker for glioma. Aging (Albany NY) 2021; 13:5638-5649. [PMID: 33589576 PMCID: PMC7950234 DOI: 10.18632/aging.202490] [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: 06/15/2020] [Accepted: 11/25/2020] [Indexed: 12/26/2022]
Abstract
Glioma is one of the most common primary brain tumors, and is divided into low-grade and high-grade gliomas. Long non-coding RNAs have been increasingly implicated in the pathogenesis and prognosis of glioma. Here, we demonstrated that the long non-coding RNA TP73-AS1 is differentially expressed among gliomas with different clinicopathological features in The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), and GEO glioma datasets; high expression of TP73-AS1 was associated with poor clinical features, including age, stage, IDH mutation status, 1p/19q co-deletion status and overall survival. Measuring TP73-AS1 expression using real-time PCR showed the same result for 76 glioma tissue samples from our hospital. The infiltration levels of various immune cells in the tumor microenvironment were found to be significantly higher in patients with high expression of TP73-AS1. Taken together, our results suggest that TP73-AS1 has potential as a prognostic glioma biomarker. Moreover, the knowledge that TP73-AS1 affects the glioma immune microenvironment may provide new information for the immunological research and treatment of glioma.
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Affiliation(s)
- Bo Zhang
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Integrative Chinese and Western Medicine, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China
| | - Qinglin Li
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Scientific Research Department, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China
| | - Bin Wu
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China
| | - Shuyuan Zhang
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China
| | - Liwen Li
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China
| | - Kai Jin
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China
| | - Sheng Li
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Medical Imaging, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China
| | - Kai Li
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Medical Imaging, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China
| | - Zeng Wang
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Scientific Research Department, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China
| | - Yi Lu
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Integrative Chinese and Western Medicine, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China
| | - Liang Xia
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China.,Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang Province, Hangzhou 310022, People's Republic of China
| | - Caixing Sun
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China.,Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang Province, Hangzhou 310022, People's Republic of China
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