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Huang J, Mao L, Lei Q, Guo AY. Bioinformatics tools and resources for cancer and application. Chin Med J (Engl) 2024:00029330-990000000-01162. [PMID: 39075637 DOI: 10.1097/cm9.0000000000003254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Indexed: 07/31/2024] Open
Abstract
ABSTRACT Tumor bioinformatics plays an important role in cancer research and precision medicine. The primary focus of traditional cancer research has been molecular and clinical studies of a number of fundamental pathways and genes. In recent years, driven by breakthroughs in high-throughput technologies, large-scale cancer omics data have accumulated rapidly. How to effectively utilize and share these data is particularly important. To address this crucial task, many computational tools and databases have been developed over the past few years. To help researchers quickly learn and understand the functions of these tools, in this review, we summarize publicly available bioinformatics tools and resources for pan-cancer multi-omics analysis, regulatory analysis of tumorigenesis, tumor treatment and prognosis, immune infiltration analysis, immune repertoire analysis, cancer driver gene and driver mutation analysis, and cancer single-cell analysis, which may further help researchers find more suitable tools for their research.
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Affiliation(s)
- Jin Huang
- Department of Thoracic Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lingzi Mao
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qian Lei
- Department of Thoracic Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - An-Yuan Guo
- Department of Thoracic Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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Zhao X, Chen G, Wu Y, Li X, Zhang Z, Xie L, Song X, Song X. TEP SNORD12B, SNORA63, and SNORD14E as novel biomarkers for hepatitis B virus-related hepatocellular carcinoma (HBV-related HCC). Cancer Cell Int 2024; 24:3. [PMID: 38167096 PMCID: PMC10763353 DOI: 10.1186/s12935-023-03179-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
PURPOSE The alterations of RNA profile in tumor-educated platelets (TEPs) have been described as a novel biosource for cancer diagnostics. This study aimed to explore the potential snoRNAs in TEP as biomarkers for diagnostics of hepatitis B virus-related hepatocellular carcinoma (HBV-related HCC). METHODS Platelets were isolated using low-speed centrifugation and subjected to a quantitative polymerase chain reaction (qPCR) for snoRNAs detection. RESULTS Down-regulated SNORD12B and SNORD14E as well as up-regulated SNORA63 were identified in TEP from HBV-related HCC, which could act as diagnostic biomarkers for HBV-related HCC as well as the early disease. Besides, TEP SNORD12B, SNORD14E, and SNORA63 facilitate the diagnostic performance of AFP and achieve favorable diagnostics efficiency for HBV-related HCC when combined with platelet parameters. CONCLUSIONS Aberrant expression of SNORD12B, SNORA63, and SNORD14E in TEPs could serve as the novel and non-invasive biomarkers for HBV-related HCC diagnosis.
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Affiliation(s)
- Xuan Zhao
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, PR China
| | - Guanxuan Chen
- Department of Intensive Care Unit, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, PR China
| | - Yawen Wu
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, PR China
| | - Xiao Li
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, PR China
| | - Zhe Zhang
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, PR China
| | - Li Xie
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, PR China
| | - Xianrang Song
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, PR China
| | - Xingguo Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, PR China.
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Wen X, Yang G, Dong Y, Luo L, Cao B, Mengesha BA, Zu R, Liao Y, Liu C, Li S, Deng Y, Zhang K, Ma X, Huang J, Wang D, Zhao K, Leng P, Luo H. Selection and Validation of Reference Genes for Pan-Cancer in Platelets Based on RNA-Sequence Data. Front Genet 2022; 13:913886. [PMID: 35770000 PMCID: PMC9234127 DOI: 10.3389/fgene.2022.913886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Many studies in recent years have demonstrated that some messenger RNA (mRNA) in platelets can be used as biomarkers for the diagnosis of pan-cancer. The quantitative real-time polymerase chain reaction (RT-qPCR) molecular technique is most commonly used to determine mRNA expression changes in platelets. Accurate and reliable relative RT-qPCR is highly dependent on reliable reference genes. However, there is no study to validate the reference gene in platelets for pan-cancer. Given that the expression of some commonly used reference genes is altered in certain conditions, selecting and verifying the most suitable reference gene for pan-cancer in platelets is necessary to diagnose early stage cancer. This study performed bioinformatics and functional analysis from the RNA-seq of platelets data set (GSE68086). We generated 95 candidate reference genes after the primary bioinformatics step. Seven reference genes (YWHAZ, GNAS, GAPDH, OAZ1, PTMA, B2M, and ACTB) were screened out among the 95 candidate reference genes from the data set of the platelets’ transcriptome of pan-cancer and 73 commonly known reference genes. These candidate reference genes were verified by another platelets expression data set (GSE89843). Then, we used RT-qPCR to confirm the expression levels of these seven genes in pan-cancer patients and healthy individuals. These RT-qPCR results were analyzed using the internal stability analysis software programs (the comparative Delta CT method, geNorm, NormFinder, and BestKeeper) to rank the candidate genes in the order of decreasing stability. By contrast, the GAPDH gene was stably and constitutively expressed at high levels in all the tested samples. Therefore, GAPDH was recommended as the most suitable reference gene for platelet transcript analysis. In conclusion, our result may play an essential part in establishing a molecular diagnostic platform based on the platelets to diagnose pan-cancer.
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Affiliation(s)
- Xiaoxia Wen
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guishu Yang
- Department of Clinical Laboratory, Guangyuan Central Hospital, Guangyuan, China
| | | | - Liping Luo
- Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Bangrong Cao
- Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Birga Anteneh Mengesha
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruiling Zu
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yulin Liao
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Chang Liu
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shi Li
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yao Deng
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Kaijiong Zhang
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xin Ma
- GenomCan Inc., Chengdu, China
| | - Jian Huang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Keyan Zhao
- GenomCan Inc., Chengdu, China
- *Correspondence: Keyan Zhao, ; Ping Leng, ; Huaichao Luo,
| | - Ping Leng
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Keyan Zhao, ; Ping Leng, ; Huaichao Luo,
| | - Huaichao Luo
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Keyan Zhao, ; Ping Leng, ; Huaichao Luo,
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