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Takemoto Y, Ito D, Komori S, Kishimoto Y, Yamada S, Hashizume A, Katsuno M, Nakatochi M. Comparing preprocessing strategies for 3D-Gene microarray data of extracellular vesicle-derived miRNAs. BMC Bioinformatics 2024; 25:221. [PMID: 38902629 PMCID: PMC11188187 DOI: 10.1186/s12859-024-05840-4] [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: 01/29/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Extracellular vesicle-derived (EV)-miRNAs have potential to serve as biomarkers for the diagnosis of various diseases. miRNA microarrays are widely used to quantify circulating EV-miRNA levels, and the preprocessing of miRNA microarray data is critical for analytical accuracy and reliability. Thus, although microarray data have been used in various studies, the effects of preprocessing have not been studied for Toray's 3D-Gene chip, a widely used measurement method. We aimed to evaluate batch effect, missing value imputation accuracy, and the influence of preprocessing on measured values in 18 different preprocessing pipelines for EV-miRNA microarray data from two cohorts with amyotrophic lateral sclerosis using 3D-Gene technology. RESULTS Eighteen different pipelines with different types and orders of missing value completion and normalization were used to preprocess the 3D-Gene microarray EV-miRNA data. Notable results were suppressed in the batch effects in all pipelines using the batch effect correction method ComBat. Furthermore, pipelines utilizing missForest for missing value imputation showed high agreement with measured values. In contrast, imputation using constant values for missing data exhibited low agreement. CONCLUSIONS This study highlights the importance of selecting the appropriate preprocessing strategy for EV-miRNA microarray data when using 3D-Gene technology. These findings emphasize the importance of validating preprocessing approaches, particularly in the context of batch effect correction and missing value imputation, for reliably analyzing data in biomarker discovery and disease research.
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Affiliation(s)
- Yuto Takemoto
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-Ku, Nagoya, 461-8673, Japan
| | - Daisuke Ito
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Shota Komori
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Yoshiyuki Kishimoto
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Shinichiro Yamada
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Atsushi Hashizume
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
- Department of Clinical Research Education, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
- Department of Clinical Research Education, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-Ku, Nagoya, 461-8673, Japan.
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Li Y, Sui S, Goel A. Extracellular vesicles associated microRNAs: Their biology and clinical significance as biomarkers in gastrointestinal cancers. Semin Cancer Biol 2024; 99:5-23. [PMID: 38341121 DOI: 10.1016/j.semcancer.2024.02.001] [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: 10/13/2023] [Revised: 01/26/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Gastrointestinal (GI) cancers, including colorectal, gastric, esophageal, pancreatic, and liver, are associated with high mortality and morbidity rates worldwide. One of the underlying reasons for the poor survival outcomes in patients with these malignancies is late disease detection, typically when the tumor has already advanced and potentially spread to distant organs. Increasing evidence indicates that earlier detection of these cancers is associated with improved survival outcomes and, in some cases, allows curative treatments. Consequently, there is a growing interest in the development of molecular biomarkers that offer promise for screening, diagnosis, treatment selection, response assessment, and predicting the prognosis of these cancers. Extracellular vesicles (EVs) are membranous vesicles released from cells containing a repertoire of biological molecules, including nucleic acids, proteins, lipids, and carbohydrates. MicroRNAs (miRNAs) are the most extensively studied non-coding RNAs, and the deregulation of miRNA levels is a feature of cancer cells. EVs miRNAs can serve as messengers for facilitating interactions between tumor cells and the cellular milieu, including immune cells, endothelial cells, and other tumor cells. Furthermore, recent years have witnessed considerable technological advances that have permitted in-depth sequence profiling of these small non-coding RNAs within EVs for their development as promising cancer biomarkers -particularly non-invasive, liquid biopsy markers in various cancers, including GI cancers. Herein, we summarize and discuss the roles of EV-associated miRNAs as they play a seminal role in GI cancer progression, as well as their promising translational and clinical potential as cancer biomarkers as we usher into the area of precision oncology.
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Affiliation(s)
- Yuan Li
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA, USA; Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Silei Sui
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA, USA; Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA, USA.
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Muazzam Ali Shah S, Ou YY. Disto-TRP: An approach for identifying transient receptor potential (TRP) channels using structural information generated by AlphaFold. Gene 2023; 871:147435. [PMID: 37075925 DOI: 10.1016/j.gene.2023.147435] [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: 08/11/2022] [Revised: 03/13/2023] [Accepted: 04/13/2023] [Indexed: 04/21/2023]
Abstract
The ability to predict 3D protein structures computationally has significantly advanced biological research. The AlphaFold protein structure database, developed by DeepMind, has provided a wealth of predicted protein structures and has the potential to bring about revolutionary changes in the field of life sciences. However, directly determining the function of proteins from their structures remains a challenging task. The Distogram from AlphaFold is used in this study as a novel feature set to identify transient receptor potential (TRP) channels. Distograms feature vectors and pre-trained language model (BERT) features were combined to improve prediction performance for transient receptor potential (TRP) channels. The method proposed in this study demonstrated promising performance on many evaluation metrics. For five-fold cross-validation, the method achieved a Sensitivity (SN) of 87.00%, Specificity (SP) of 93.61%, Accuracy (ACC) of 93.39%, and a Matthews correlation coefficient (MCC) of 0.52. Additionally, on an independent dataset, the method obtained 100.00% SN, 95.54% SP, 95.73% ACC, and an MCC of 0.69. The results demonstrate the potential for using structural information to predict protein function. In the future, it is hoped that such structural information will be incorporated into artificial intelligence networks to explore more useful and valuable functional information in the biological field.
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Affiliation(s)
- Syed Muazzam Ali Shah
- Department of Computer Science & Engineering, Yuan Ze University, Chungli 32003, Taiwan; National University of Computer and Emerging Sciences, Karachi 75050, Pakistan
| | - Yu-Yen Ou
- Department of Computer Science & Engineering, Yuan Ze University, Chungli 32003, Taiwan; Graduate Program in Biomedical Informatics, Yuan Ze University, Chungli 32003, Taiwan.
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Hepatitis Viruses Control Host Immune Responses by Modifying the Exosomal Biogenesis Pathway and Cargo. Int J Mol Sci 2022; 23:ijms231810862. [PMID: 36142773 PMCID: PMC9505460 DOI: 10.3390/ijms231810862] [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: 08/11/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The development of smart immune evasion mechanisms is crucial for the establishment of acute and chronic viral hepatitis. Hepatitis is a major health problem worldwide arising from different causes, such as pathogens, metabolic disorders, and xenotoxins, with the five hepatitis viruses A, B, C, D, and E (HAV, HBV, HCV, HDV, and HEV) representing the majority of the cases. Most of the hepatitis viruses are considered enveloped. Recently, it was reported that the non-enveloped HAV and HEV are, in reality, quasi-enveloped viruses exploiting exosomal-like biogenesis mechanisms for budding. Regardless, all hepatitis viruses use exosomes to egress, regulate, and eventually escape from the host immune system, revealing another key function of exosomes apart from their recognised role in intercellular communication. This review will discuss how the hepatitis viruses exploit exosome biogenesis and transport capacity to establish successful infection and spread. Then, we will outline the contribution of exosomes in viral persistence and liver disease progression.
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Liu C, Yang H, Feng Y, Liu C, Rui F, Cao Y, Hu X, Xu J, Fan J, Zhu Q, Li J. A K-nearest Neighbor Model to Predict Early Recurrence of Hepatocellular Carcinoma After Resection. J Clin Transl Hepatol 2022; 10:600-607. [PMID: 36062279 PMCID: PMC9396318 DOI: 10.14218/jcth.2021.00348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/25/2021] [Accepted: 10/10/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND AND AIMS Patients with hepatocellular carcinoma (HCC) surgically resected are at risk of recurrence; however, the risk factors of recurrence remain poorly understood. This study intended to establish a novel machine learning model based on clinical data for predicting early recurrence of HCC after resection. METHODS A total of 220 HCC patients who underwent resection were enrolled. Classification machine learning models were developed to predict HCC recurrence. The standard deviation, recall, and precision of the model were used to assess the model's accuracy and identify efficiency of the model. RESULTS Recurrent HCC developed in 89 (40.45%) patients at a median time of 14 months from primary resection. In principal component analysis, tumor size, tumor grade differentiation, portal vein tumor thrombus, alpha-fetoprotein, protein induced by vitamin K absence or antagonist-II (PIVKA-II), aspartate aminotransferase, platelet count, white blood cell count, and HBsAg were positive prognostic factors of HCC recurrence and were included in the preoperative model. After comparing different machine learning methods, including logistic regression, decision tree, naïve Bayes, deep neural networks, and k-nearest neighbor (K-NN), we choose the K-NN model as the optimal prediction model. The accuracy, recall, precision of the K-NN model were 70.6%, 51.9%, 70.1%, respectively. The standard deviation was 0.020. CONCLUSIONS The K-NN classification algorithm model performed better than the other classification models. Estimation of the recurrence rate of early HCC can help to allocate treatment, eventually achieving safe oncological outcomes.
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Affiliation(s)
- Chuanli Liu
- Department of Infectious Disease, Shandong Provincial Hospital Affiliated to Shandong Frist Medical University, Ji'nan, Shandong, China
| | - Hongli Yang
- Department of Infectious Disease, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Yuemin Feng
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong Frist Medical University, Ji'nan, Shandong, China
| | - Cuihong Liu
- Department of Ultrasound Diagnosis and Treatment, Shandong Provincial Hospital Affiliated to Shandong Frist Medical University, Ji'nan, Shandong, China
| | - Fajuan Rui
- Department of Infectious Disease, Shandong Provincial Hospital Affiliated to Shandong Frist Medical University, Ji'nan, Shandong, China
| | - Yuankui Cao
- School of Computer Science, China University of Geosciences, Wuhan, Hubei, China
| | - Xinyu Hu
- Department of Infectious Disease, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Jiawen Xu
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong Frist Medical University, Ji'nan, Shandong, China
| | - Junqing Fan
- School of Computer Science, China University of Geosciences, Wuhan, Hubei, China
| | - Qiang Zhu
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong Frist Medical University, Ji'nan, Shandong, China
| | - Jie Li
- Department of Infectious Disease, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
- Institute of Viruses and Infectious Diseases, Nanjing University, Nanjing, Jiangsu, China
- Correspondence to: Jie Li, Department of Infectious Diseases, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210000, China; ORCID: https://orcid.org/0000-0003-0973-8645. Tel: +86-15863787910,
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Liu J, Xiao P, Jiang W, Wang Y, Huang Y. Diagnostic value of exosomes in patients with liver cancer: a systematic review. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2022; 24:2285-2294. [PMID: 35947296 DOI: 10.1007/s12094-022-02906-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/23/2022] [Indexed: 10/15/2022]
Abstract
BACKGROUND Liver cancer is a disease with high morbidity and mortality. More and more studies have shown that exosomes can be used as biomarkers for the diagnosis of liver cancer, but their diagnostic accuracy is still unclear. Therefore, this meta-analysis summarizes various studies on the diagnostic value of exosomes for liver cancer. METHODS A comprehensive search was carried out based on the set search terms in PubMed, Web of Science and Wiley until April 1, 2022. All statistical analyses were performed by STATA 17 statistical software and Review Manager 5.4. Quality Assessment for Studies of Diagnostic Accuracy 2 tool was applied to evaluate the quality of included articles. Random effects model was used to calculate various diagnostic indicators. RESULTS A total of 47 studies were included in this meta-analysis. The number of participants was 3196. The combined sensitivity, specificity and the area under the curve with 95% confidence intervals (95% CI) were, respectively 0.80 (0.75-0.84), 0.83 (0.79-0.87), 0.89 (0.85-0.91). CONCLUSIONS This meta-analysis shows that exosomes have good diagnostic accuracy for liver cancer and can be used as an effective biomarker for the diagnosis of liver cancer.
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Affiliation(s)
- Jusong Liu
- Department of Transfusion, The Affiliated Hospital of Southwest Medical University, 25 Taiping Road, Luzhou, 646000, Sichuan, People's Republic of China
| | - Pan Xiao
- Department of Transfusion, The Affiliated Hospital of Southwest Medical University, 25 Taiping Road, Luzhou, 646000, Sichuan, People's Republic of China
| | - Wenxue Jiang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Yuhan Wang
- Department of Transfusion, Yaan People's Hospital, Yaan, 625000, China
| | - Yuanshuai Huang
- Department of Transfusion, The Affiliated Hospital of Southwest Medical University, 25 Taiping Road, Luzhou, 646000, Sichuan, People's Republic of China.
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Yang S, Wang J, Wang S, Zhou A, Zhao G, Li P. Roles of small extracellular vesicles in the development, diagnosis and possible treatment strategies for hepatocellular carcinoma (Review). Int J Oncol 2022; 61:91. [PMID: 35674180 PMCID: PMC9262158 DOI: 10.3892/ijo.2022.5381] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common malignancy of hepatocytes accounting for 75-85% of primary hepatic carcinoma cases. Small extracellular vesicles (sEVs), previously known as exosomes with a diameter of 30-200 nm, can transport a variety of biological molecules between cells, and have been proposed to function in physiological and pathological processes. Recent studies have indicated that the cargos of sEVs are implicated in intercellular crosstalk among HCC cells, paratumor cells and the tumor microenvironment. sEV-encapsulated substances (including DNA, RNA, proteins and lipids) regulate signal transduction pathways in recipient cells and contribute to cancer initiation and progression in HCC. In addition, the differential expression of sEV cargos between patients facilitates the potential utility of sEVs in the diagnosis and prognosis of patients with HCC. Furthermore, the intrinsic properties of low immunogenicity and high stability render sEVs ideal vehicles for targeted drug delivery in the treatment of HCC. The present review article summarizes the carcinogenic and anti-neoplastic capacities of sEVs and discusses the potential and prospective diagnostic and therapeutic applications of sEVs in HCC.
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Affiliation(s)
- Shuyue Yang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Jiaxin Wang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Shidong Wang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Anni Zhou
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Guiping Zhao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Peng Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
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Tsuchiya A, Natsui K, Ishii Y, Koseki Y, Takeda N, Tomiyoshi K, Yamazaki F, Yoshida Y, Terai S. Small extracellular vesicles and liver diseases: From diagnosis to therapy. World J Hepatol 2022; 14:1307-1318. [PMID: 36158910 PMCID: PMC9376785 DOI: 10.4254/wjh.v14.i7.1307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/20/2022] [Accepted: 07/06/2022] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs), especially small EVs (sEVs) derived from liver cells, have been the focus of much attention in the normal physiology and pathogenesis of various diseases affecting the liver. sEVs are approximately 100 nm in size, enclosed within lipid bilayers, and are very stable. The lipids, proteins, and nucleic acids, including miRNAs, contained within these vesicles are known to play important roles in intercellular communication. This mini-review summarizes the application of sEVs. First, liver diseases and the related diagnostic markers are described, and the current active status of miRNA research in diagnosis of hepatocellular carcinoma (HCC) is reported. Second, the biodistribution and pharmacokinetics of sEVs are described, and the liver is highlighted as the organ with the highest accumulation of sEVs. Third, the relationship between sEVs and the pathogenesis of liver disorders is described with emphesis on the current active status of miRNA research in HCC recurrence and survival. Finally, the possibility of future therapy using sEVs from mesenchymal stem (stromal) cells for cirrhosis and other diseases is described.
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Affiliation(s)
- Atsunori Tsuchiya
- Division of Gastroenterology and Hepatology, Niigata University Medical and Dental Hospital, Niigata 951-8510, Japan
| | - Kazuki Natsui
- Department of Gastroenterology and Hepatology, Niigata University, Niigata 951-8510, Japan
| | - Yui Ishii
- Department of Gastroenterology and Hepatology, Niigata University, Niigata 951-8510, Japan
| | - Yohei Koseki
- Department of Gastroenterology and Hepatology, Niigata University, Niigata 951-8510, Japan
| | - Nobutaka Takeda
- Department of Gastroenterology and Hepatology, Niigata University, Niigata 951-8510, Japan
| | - Kei Tomiyoshi
- Department of Gastroenterology and Hepatology, Niigata University, Niigata 951-8510, Japan
| | - Fusako Yamazaki
- Department of Gastroenterology and Hepatology, Niigata University, Niigata 951-8510, Japan
| | - Yuki Yoshida
- Department of Gastroenterology and Hepatology, Niigata University, Niigata 951-8510, Japan
| | - Shuji Terai
- Department of Gastroenterology and Hepatology, Niigata University, Niigata 951-8510, Japan
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Biomarkers for the Detection and Management of Hepatocellular Carcinoma in Patients Treated with Direct-Acting Antivirals. Cancers (Basel) 2022; 14:cancers14112700. [PMID: 35681679 PMCID: PMC9179595 DOI: 10.3390/cancers14112700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Chronic Hepatitis C virus (HCV) represents the main etiological factor for hepatocellular carcinoma (HCC) in developed countries. The introduction of direct-acting antivirals (DAAs) improved the eradication of the hepatitis C virus (HCV) but not the reduction in the incidence of HCV-associated HCC. Some patients still develop HCC, even after reaching a sustained virological response (SVR). This review is a summary of pre-clinical studies that investigated predictive biomarkers for HCC occurrence and recurrence in HCV-infected patients treated with DAAs. The presented biomarkers are found dysregulated in serum or tissue at specific time points (before, during, after DAA treatment or post SVR) and correlated with HCC-predisposing conditions. Thus, this review aims to improve the management of patients developing HCV-induced HCC. Abstract Hepatocellular carcinoma (HCC) is the sixth-most common type of cancer worldwide and chronic Hepatitis C virus (HCV) represents the main etiological factor in developed countries. HCV promotes hepatocarcinogenesis through persistent liver inflammation and dysregulation of cell signaling pathways. The introduction of direct-acting antivirals (DAAs) resulted in a significant improvement in the eradication of the virus, with an expected reduction of HCC incidence. However, the risk of HCC development can persist after DAA treatment. Recent studies have investigated the potential use of molecular biomarkers that predict HCC occurrence or recurrence helping the stratification of patients under surveillance. This review aimed to summarize all pre-clinical exploration of predictive biomarkers to identify DAA-treated patients at risk for HCC development. Dysregulated microRNAs, lncRNAs, histone modifications, cytokines, proteins, and sphingolipids represent various classes of HCC risk predictors identified in two different biological sources (tissue and serum). The non-invasive serum markers can provide a more accessible means to perform clinical monitoring and predict the risk of HCC. In addition, conditions like cirrhosis, predisposing to HCC, strongly correlate with most of the molecular predictors identified, supporting the value of these molecules as possible biomarkers of HCC in DAA-treated patients.
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Mawatari S, Kumagai K, Oda K, Tabu K, Ijuin S, Fujisaki K, Tashima S, Inada Y, Uto H, Saisyoji A, Hiramine Y, Hashiguchi M, Tamai T, Hori T, Taniyama O, Toyodome A, Sakae H, Kure T, Sakurai K, Moriuchi A, Kanmura S, Ido A. Features of patients who developed hepatocellular carcinoma after direct-acting antiviral treatment for hepatitis C Virus. PLoS One 2022; 17:e0262267. [PMID: 35020772 PMCID: PMC8754290 DOI: 10.1371/journal.pone.0262267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 12/21/2021] [Indexed: 02/07/2023] Open
Abstract
Background The features of hepatitis C virus patients with a sustained virologic response (SVR) who developed hepatocellular carcinoma (HCC) after direct-acting antiviral (DAA) therapy are unclear. Methods The study population included 1494 DAA-SVR patients without a history of HCC. The cumulative carcinogenesis rate after the end of treatment (EOT) and factors related to HCC were analyzed. Results Sixty (4.0%) patients developed HCC during a median observation period of 47.6 months. At four years, the cumulative carcinogenesis rate was 4.7%. A Cox proportional hazards analysis showed that age ≥73 years (hazard ratio [HR]: 2.148), male sex (HR: 3.060), hyaluronic acid (HA) ≥75 ng/mL (HR: 3.996), alpha-fetoprotein at EOT (EOT-AFP) ≥5.3 ng/mL (HR: 4.773), and albumin at EOT (EOT-Alb) <3.9 g/dL (HR: 2.305) were associated with HCC development. Especially, EOT-AFP ≥5.3 ng/mL was associated with HCC development after 3 years from EOT (HR: 6.237). Among patients who developed HCC, AFP did not increase in patients with EOT-AFP <5.3 ng/mL at the onset of HCC. Of these 5 factors, EOT-AFP ≥5.3 ng/mL was scored as 2 points; the others were scored as 1 point. The 4-year cumulative carcinogenesis rate for patients with total scores of 0–2, 3–4, and 5–6 points were 0.6%, 11.9%, and 27.1%, respectively (p<0.001). Conclusions EOT-AFP ≥5.3 ng/mL is useful for predicting HCC development after an SVR. However, AFP does not increase in patients with EOT-AFP <5.3 ng/mL at the onset of HCC. The combination of EOT-AFP, age, sex, HA, and EOT-Alb is important for predicting carcinogenesis.
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Affiliation(s)
- Seiichi Mawatari
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- * E-mail:
| | - Kotaro Kumagai
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kohei Oda
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuaki Tabu
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Sho Ijuin
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kunio Fujisaki
- Department of Hepatology, Kirishima Medical Center, Hayato-cho, Kirishima, Kagoshima, Japan
| | - Shuzo Tashima
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department of Hepatology, Kirishima Medical Center, Hayato-cho, Kirishima, Kagoshima, Japan
| | - Yukiko Inada
- Center for Digestive and Liver Diseases, Miyazaki Medical Center Hospital, Miyazaki, Japan
| | - Hirofumi Uto
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Center for Digestive and Liver Diseases, Miyazaki Medical Center Hospital, Miyazaki, Japan
| | - Akiko Saisyoji
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department of Internal Medicine, Kagoshima Kouseiren Hospital, Kagoshima, Japan
| | - Yasunari Hiramine
- Department of Internal Medicine, Kagoshima Kouseiren Hospital, Kagoshima, Japan
| | - Masafumi Hashiguchi
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department of Gastroenterology and Hepatology, Kagoshima City Hospital, Kagoshima, Japan
| | - Tsutomu Tamai
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department of Gastroenterology and Hepatology, Kagoshima City Hospital, Kagoshima, Japan
| | - Takeshi Hori
- Department of Gastroenterology and Hepatology, Kagoshima City Hospital, Kagoshima, Japan
| | - Ohki Taniyama
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Ai Toyodome
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Haruka Sakae
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Takeshi Kure
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department of Gastroenterology, Kagoshima Medical Association Hospital, Kagoshima, Japan
| | - Kazuhiro Sakurai
- Department of Gastroenterology, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan
| | - Akihiro Moriuchi
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department of Gastroenterology, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan
| | - Shuji Kanmura
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Akio Ido
- Department of Human and Environmental Sciences, Digestive and Lifestyle Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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11
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Mariam A, Miller-Atkins G, Moro A, Rodarte AI, Siddiqi S, Acevedo-Moreno LA, Brown JM, Allende DS, Aucejo F, Rotroff DM. Salivary miRNAs as non-invasive biomarkers of hepatocellular carcinoma: a pilot study. PeerJ 2022; 10:e12715. [PMID: 35036096 PMCID: PMC8742548 DOI: 10.7717/peerj.12715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/09/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Improved detection of hepatocellular carcinoma (HCC) is needed, as current detection methods, such as alpha fetoprotein (AFP) and ultrasound, suffer from poor sensitivity. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate many cellular functions and impact cancer development and progression. Notably, miRNAs are detectable in saliva and have shown potential as non-invasive biomarkers for a number of cancers including breast, oral, and lung cancers. Here, we present, to our knowledge, the first report of salivary miRNAs in HCC and compare these findings to patients with cirrhosis, a high-risk cohort for HCC. METHODS We performed small RNA sequencing in 20 patients with HCC and 19 with cirrhosis. Eleven patients with HCC had chronic liver disease, and analyses were performed with these samples combined and stratified by the presence of chronic liver disease. P values were adjusted for multiple comparisons using a false discovery rate (FDR) approach and miRNA with FDR P < 0.05 were considered statistically significant. Differential expression of salivary miRNAs was compared to a previously published report of miRNAs in liver tissue of patients with HCC vs cirrhosis. Support vector machines and leave-one-out cross-validation were performed to determine if salivary miRNAs have predictive potential for detecting HCC. RESULTS A total of 4,565 precursor and mature miRNAs were detected in saliva and 365 were significantly different between those with HCC compared to cirrhosis (FDR P < 0.05). Interestingly, 283 of these miRNAs were significantly downregulated in patients with HCC. Machine-learning identified a combination of 10 miRNAs and covariates that accurately classified patients with HCC (AUC = 0.87). In addition, we identified three miRNAs that were differentially expressed in HCC saliva samples and in a previously published study of miRNAs in HCC tissue compared to cirrhotic liver tissue. CONCLUSIONS This study demonstrates, for the first time, that miRNAs relevant to HCC are detectable in saliva, that salivary miRNA signatures show potential to be highly sensitive and specific non-invasive biomarkers of HCC, and that additional studies utilizing larger cohorts are needed.
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Affiliation(s)
- Arshiya Mariam
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, United States
| | - Galen Miller-Atkins
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, United States
| | - Amika Moro
- Department of General Surgery, Cleveland Clinic, Cleveland, Ohio, United States
| | | | - Shirin Siddiqi
- Department of General Surgery, Cleveland Clinic, Cleveland, Ohio, United States
| | | | - J. Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, United States
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, Ohio, United States
| | - Daniela S. Allende
- Department of Pathology, Cleveland Clinic, Cleveland, Ohio, United States
| | - Federico Aucejo
- Department of General Surgery, Cleveland Clinic, Cleveland, Ohio, United States
| | - Daniel M. Rotroff
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, United States
- Endocrinology and Metabolism Institute, Cleveland Clinic, Cleveland, Ohio, United States
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12
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Ali Shah SM, Ou YY. TRP-BERT: Discrimination of transient receptor potential (TRP) channels using contextual representations from deep bidirectional transformer based on BERT. Comput Biol Med 2021; 137:104821. [PMID: 34508974 DOI: 10.1016/j.compbiomed.2021.104821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022]
Abstract
Transient receptor potential (TRP) channels are non-selective cation channels that act as ion channels and are primarily found on the plasma membrane of numerous animal cells. These channels are involved in the physiology and pathophysiology of a wide variety of biological processes, including inhibition and progression of cancer, pain initiation, inflammation, regulation of pressure, thermoregulation, secretion of salivary fluid, and homeostasis of Ca2+ and Mg2+. Increasing evidences indicate that mutations in the gene encoding TRP channels play an essential role in a broad array of diseases. Therefore, these channels are becoming popular as potential drug targets for several diseases. The diversified role of these channels demands a prediction model to classify TRP channels from other channel proteins (non-TRP channels). Therefore, we presented an approach based on the Support Vector Machine (SVM) classifier and contextualized word embeddings from Bidirectional Encoder Representations from Transformers (BERT) to represent protein sequences. BERT is a deeply bidirectional language model and a neural network approach to Natural Language Processing (NLP) that achieves outstanding performance on various NLP tasks. We apply BERT to generate contextualized representations for every single amino acid in a protein sequence. Interestingly, these representations are context-sensitive and vary for the same amino acid appearing in different positions in the sequence. Our proposed method showed 80.00% sensitivity, 96.03% specificity, 95.47% accuracy, and a 0.56 Matthews correlation coefficient (MCC) for an independent test set. We suggest that our proposed method could effectively classify TRP channels from non-TRP channels and assist biologists in identifying new potential TRP channels.
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Affiliation(s)
- Syed Muazzam Ali Shah
- Department of Computer Science & Engineering, Yuan Ze University, Chungli, 32003, Taiwan
| | - Yu-Yen Ou
- Department of Computer Science & Engineering, Yuan Ze University, Chungli, 32003, Taiwan.
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13
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Supadmanaba IGP, Mantini G, Randazzo O, Capula M, Muller IB, Cascioferro S, Diana P, Peters GJ, Giovannetti E. Interrelationship between miRNA and splicing factors in pancreatic ductal adenocarcinoma. Epigenetics 2021; 17:381-404. [PMID: 34057028 PMCID: PMC8993068 DOI: 10.1080/15592294.2021.1916697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers because of diagnosis at late stage and inherent/acquired chemoresistance. Recent advances in genomic profiling and biology of this disease have not yet been translated to a relevant improvement in terms of disease management and patient’s survival. However, new possibilities for treatment may emerge from studies on key epigenetic factors. Deregulation of microRNA (miRNA) dependent gene expression and mRNA splicing are epigenetic processes that modulate the protein repertoire at the transcriptional level. These processes affect all aspects of PDAC pathogenesis and have great potential to unravel new therapeutic targets and/or biomarkers. Remarkably, several studies showed that they actually interact with each other in influencing PDAC progression. Some splicing factors directly interact with specific miRNAs and either facilitate or inhibit their expression, such as Rbfox2, which cleaves the well-known oncogenic miRNA miR-21. Conversely, miR-15a-5p and miR-25-3p significantly downregulate the splicing factor hnRNPA1 which acts also as a tumour suppressor gene and is involved in processing of miR-18a, which in turn, is a negative regulator of KRAS expression. Therefore, this review describes the interaction between splicing and miRNA, as well as bioinformatic tools to explore the effect of splicing modulation towards miRNA profiles, in order to exploit this interplay for the development of innovative treatments. Targeting aberrant splicing and deregulated miRNA, alone or in combination, may hopefully provide novel therapeutic approaches to fight the complex biology and the common treatment recalcitrance of PDAC.
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Affiliation(s)
- I Gede Putu Supadmanaba
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.,Biochemistry Department, Faculty of Medicine, Universitas Udayana, Denpasar, Bali, Indonesia
| | - Giulia Mantini
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.,Cancer Pharmacology Lab, AIRC Start up Unit, Fondazione Pisana per La Scienza, Pisa, Italy
| | - Ornella Randazzo
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.,Dipartimento Di Scienze E Tecnologie Biologiche Chimiche E Farmaceutiche (STEBICEF), Università Degli Studi Di Palermo, Palermo, Italy
| | - Mjriam Capula
- Cancer Pharmacology Lab, AIRC Start up Unit, Fondazione Pisana per La Scienza, Pisa, Italy.,Institute of Life Sciences, Sant'Anna School of Advanced Studies, Pisa, Italy
| | - Ittai B Muller
- Department of Clinical Chemistry, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands
| | - Stella Cascioferro
- Dipartimento Di Scienze E Tecnologie Biologiche Chimiche E Farmaceutiche (STEBICEF), Università Degli Studi Di Palermo, Palermo, Italy
| | - Patrizia Diana
- Dipartimento Di Scienze E Tecnologie Biologiche Chimiche E Farmaceutiche (STEBICEF), Università Degli Studi Di Palermo, Palermo, Italy
| | - Godefridus J Peters
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.,Department of Biochemistry, Medical University of Gdansk, Poland
| | - Elisa Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.,Cancer Pharmacology Lab, AIRC Start up Unit, Fondazione Pisana per La Scienza, Pisa, Italy
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14
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Tertiary Prevention of HCC in Chronic Hepatitis B or C Infected Patients. Cancers (Basel) 2021; 13:cancers13071729. [PMID: 33917345 PMCID: PMC8038691 DOI: 10.3390/cancers13071729] [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: 03/16/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Hepatocellular carcinoma (HCC) recurrence is the major obstacle concerning patients’ survival. Tertiary prevention by antiviral therapies could reduce HCC recurrence rate in both chronic hepatitis B virus (HBV) or hepatitis C virus (HCV) infected patients. In chronic hepatitis B (CHB) patients, nucleos(t)ide analogues (Nuc) provide a more effective HCC tertiary prevention effect than an interferon (IFN)-based regimen. In chronic hepatitis C (CHC) patients, the tertiary prevention effect by direct acting antiviral agents (DAAs) was reported non-inferior to that by IFN-based therapy. Chronic hepatitis C patients left untreated had the worst survival benefit as well as shorted recurrence-free interval than those treated by either type of antiviral regimen. Although the risk of HCC recurrence could only be decreased but not diminished by antiviral therapies due to host and microenvironmental factors beyond virus infection, antiviral therapy helps to preserve and improve liver function which makes multi-modality anticancer treatment feasible to improve survival. Abstract Hepatocellular carcinoma (HCC) ranks as a leading cause of common cancer and cancer-related death. The major etiology of HCC is due to chronic hepatitis virus including HBV and HCV infections. Scheduled HCC surveillance in high risk populations improves the early detection rate and the feasibility of curative treatment. However, high HCC recurrence rate still accounts for the poor prognosis of HCC patients. In this article, we critically review the pathogenesis of viral hepatitis-related hepatocellular carcinoma and the evidence of tertiary prevention efficacy by current available antiviral treatment, and discuss the knowledge gap in viral hepatitis-related HCC tertiary prevention.
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15
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Yan H, Li Y, Cheng S, Zeng Y. Advances in Analytical Technologies for Extracellular Vesicles. Anal Chem 2021; 93:4739-4774. [PMID: 33635060 DOI: 10.1021/acs.analchem.1c00693] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- He Yan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yutao Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Shibo Cheng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States.,University of Florida Health Cancer Center, Gainesville, Florida 32610, United States
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16
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Chen Y, Wu T, Zhu Z, Huang H, Zhang L, Goel A, Yang M, Wang X. An integrated workflow for biomarker development using microRNAs in extracellular vesicles for cancer precision medicine. Semin Cancer Biol 2021; 74:134-155. [PMID: 33766650 DOI: 10.1016/j.semcancer.2021.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023]
Abstract
EV-miRNAs are microRNA (miRNA) molecules encapsulated in extracellular vesicles (EVs), which play crucial roles in tumor pathogenesis, progression, and metastasis. Recent studies about EV-miRNAs have gained novel insights into cancer biology and have demonstrated a great potential to develop novel liquid biopsy assays for various applications. Notably, compared to conventional liquid biomarkers, EV-miRNAs are more advantageous in representing host-cell molecular architecture and exhibiting higher stability and specificity. Despite various available techniques for EV-miRNA separation, concentration, profiling, and data analysis, a standardized approach for EV-miRNA biomarker development is yet lacking. In this review, we performed a substantial literature review and distilled an integrated workflow encompassing important steps for EV-miRNA biomarker development, including sample collection and EV isolation, EV-miRNA extraction and quantification, high-throughput data preprocessing, biomarker prioritization and model construction, functional analysis, as well as validation. With the rapid growth of "big data", we highlight the importance of efficient mining of high-throughput data for the discovery of EV-miRNA biomarkers and integrating multiple independent datasets for in silico and experimental validations to increase the robustness and reproducibility. Furthermore, as an efficient strategy in systems biology, network inference provides insights into the regulatory mechanisms and can be used to select functionally important EV-miRNAs to refine the biomarker candidates. Despite the encouraging development in the field, a number of challenges still hinder the clinical translation. We finally summarize several common challenges in various biomarker studies and discuss potential opportunities emerging in the related fields.
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Affiliation(s)
- Yu Chen
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Tan Wu
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Zhongxu Zhu
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Hao Huang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong; Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong Province, China
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Mengsu Yang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong; Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong Province, China
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong; Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong Province, China.
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17
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Prediction of early recurrence of hepatocellular carcinoma after resection using digital pathology images assessed by machine learning. Mod Pathol 2021; 34:417-425. [PMID: 32948835 PMCID: PMC7817520 DOI: 10.1038/s41379-020-00671-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 01/03/2023]
Abstract
Hepatocellular carcinoma (HCC) is a representative primary liver cancer caused by long-term and repetitive liver injury. Surgical resection is generally selected as the radical cure treatment. Because the early recurrence of HCC after resection is associated with low overall survival, the prediction of recurrence after resection is clinically important. However, the pathological characteristics of the early recurrence of HCC have not yet been elucidated. We attempted to predict the early recurrence of HCC after resection based on digital pathologic images of hematoxylin and eosin-stained specimens and machine learning applying a support vector machine (SVM). The 158 HCC patients meeting the Milan criteria who underwent surgical resection were included in this study. The patients were categorized into three groups: Group I, patients with HCC recurrence within 1 year after resection (16 for training and 23 for test); Group II, patients with HCC recurrence between 1 and 2 years after resection (22 and 28); and Group III, patients with no HCC recurrence within 4 years after resection (31 and 38). The SVM-based prediction method separated the three groups with 89.9% (80/89) accuracy. Prediction of Groups I was consistent for all cases, while Group II was predicted to be Group III in one case, and Group III was predicted to be Group II in 8 cases. The use of digital pathology and machine learning could be used for highly accurate prediction of HCC recurrence after surgical resection, especially that for early recurrence. Currently, in most cases after HCC resection, regular blood tests and diagnostic imaging are used for follow-up observation; however, the use of digital pathology coupled with machine learning offers potential as a method for objective postoprative follow-up observation.
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18
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Thietart S, Rautou PE. Extracellular vesicles as biomarkers in liver diseases: A clinician's point of view. J Hepatol 2020; 73:1507-1525. [PMID: 32682050 DOI: 10.1016/j.jhep.2020.07.014] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 02/09/2023]
Abstract
Extracellular vesicles are membrane-bound vesicles containing proteins, lipids, RNAs and microRNAs. They can originate from both healthy and stressed cells, and provide a snapshot of the cell of origin in physiological and pathological circumstances. Various processes that may give rise to the release of extracellular vesicles occur in liver diseases, including hepatocyte apoptosis, hepatic stellate cell activation, liver innate immune system activation, systemic inflammation, and organelle dysfunction (mitochondrial dysfunction and endoplasmic reticulum stress). Numerous studies have therefore investigated the potential role of extracellular vesicles as biomarkers in liver diseases. This review provides an overview of the methods that can be used to measure extracellular vesicle concentrations in clinical settings, ranging from plasma preparation to extracellular vesicle measurement techniques, as well as looking at the challenges of using extracellular vesicles as biomarkers. We also provide a comprehensive review of studies that test extracellular vesicles as diagnostic, severity and prognostic biomarkers in various liver diseases, including non-alcoholic and alcoholic steatohepatitis, viral hepatitis B and C infections, cirrhosis, primary liver cancers, primary sclerosing cholangitis and acute liver failure. In particular, extracellular vesicles could be useful tools to evaluate activity and fibrosis in non-alcoholic fatty liver disease, predict risk of hepatitis B virus reactivation, predict complications and mortality in cirrhosis, detect early hepatocellular carcinoma, detect malignant transformation in primary sclerosing cholangitis and predict outcomes in acute liver failure. While most studies draw on data derived from pilot studies, which still require clinical validation, some extracellular vesicle subpopulations have already been evaluated in solid prospective studies.
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Affiliation(s)
- Sara Thietart
- Université de Paris, Centre de recherche sur l'inflammation, Inserm, F-75018 Paris, France
| | - Pierre-Emmanuel Rautou
- Université de Paris, Centre de recherche sur l'inflammation, Inserm, F-75018 Paris, France; Service d'Hépatologie, DHU Unity, Pôle des Maladies de l'Appareil Digestif, Hôpital Beaujon, AP-HP, Clichy, France; Centre de Référence des Maladies Vasculaires du Foie, French Network for Rare Liver Diseases (FILFOIE), European Reference Network (ERN) 'Rare-Liver'.
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19
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Słomka A, Mocan T, Wang B, Nenu I, Urban SK, Gonzalez-Carmona MA, Schmidt-Wolf IGH, Lukacs-Kornek V, Strassburg CP, Spârchez Z, Kornek M. EVs as Potential New Therapeutic Tool/Target in Gastrointestinal Cancer and HCC. Cancers (Basel) 2020; 12:E3019. [PMID: 33080904 PMCID: PMC7603109 DOI: 10.3390/cancers12103019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/04/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
For more than a decade, extracellular vesicles (EVs) have been in focus of science. Once thought to be an efficient way to eliminate undesirable cell content, EVs are now well-accepted as being an important alternative to cytokines and chemokines in cell-to-cell communication route. With their cargos, mainly consisting of functional proteins, lipids and nucleic acids, they can activate signalling cascades and thus change the phenotype of recipient cells at local and systemic levels. Their substantial role as modulators of various physiological and pathological processes is acknowledged. Importantly, more and more evidence arises that EVs play a pivotal role in many stages of carcinogenesis. Via EV-mediated communication, tumour cells can manipulate cells from host immune system or from the tumour microenvironment, and, ultimately, they promote tumour progression and modulate host immunity towards tumour's favour. Additionally, the role of EVs in modulating resistance to pharmacological and radiological therapy of many cancer types has become evident lately. Our understanding of EV biology and their role in cancer promotion and drug resistance has evolved considerably in recent years. In this review, we specifically discuss the current knowledge on the association between EVs and gastrointestinal (GI) and liver cancers, including their potential for diagnosis and treatment.
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Affiliation(s)
- Artur Słomka
- Department of Pathophysiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum in Bydgoszcz, 85-067 Bydgoszcz, Poland;
| | - Tudor Mocan
- Octavian Fodor Institute for Gastroenterology and Hepatology, Iuliu Haţieganu, University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania; (T.M.); (I.N.); (Z.S.)
| | - Bingduo Wang
- Department of Internal Medicine I, University Hospital of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany; (B.W.); (S.K.U.); (M.G.-C.); (C.P.S.)
| | - Iuliana Nenu
- Octavian Fodor Institute for Gastroenterology and Hepatology, Iuliu Haţieganu, University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania; (T.M.); (I.N.); (Z.S.)
| | - Sabine K. Urban
- Department of Internal Medicine I, University Hospital of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany; (B.W.); (S.K.U.); (M.G.-C.); (C.P.S.)
| | - Maria A. Gonzalez-Carmona
- Department of Internal Medicine I, University Hospital of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany; (B.W.); (S.K.U.); (M.G.-C.); (C.P.S.)
| | - Ingo G. H. Schmidt-Wolf
- Department of Integrated Oncology, Center for Integrated Oncology (CIO), University Hospital of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany;
| | - Veronika Lukacs-Kornek
- Institute of Experimental Immunology, University Hospital of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany;
| | - Christian P. Strassburg
- Department of Internal Medicine I, University Hospital of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany; (B.W.); (S.K.U.); (M.G.-C.); (C.P.S.)
| | - Zeno Spârchez
- Octavian Fodor Institute for Gastroenterology and Hepatology, Iuliu Haţieganu, University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania; (T.M.); (I.N.); (Z.S.)
| | - Miroslaw Kornek
- Department of Internal Medicine I, University Hospital of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany; (B.W.); (S.K.U.); (M.G.-C.); (C.P.S.)
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