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Porreca V, Barbagallo C, Corbella E, Peres M, Stella M, Mignogna G, Maras B, Ragusa M, Mancone C. Unveil Intrahepatic Cholangiocarcinoma Heterogeneity through the Lens of Omics and Multi-Omics Approaches. Cancers (Basel) 2024; 16:2889. [PMID: 39199659 DOI: 10.3390/cancers16162889] [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: 07/24/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 09/01/2024] Open
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is recognized worldwide as the second leading cause of morbidity and mortality among primary liver cancers, showing a continuously increasing incidence rate in recent years. iCCA aggressiveness is revealed through its rapid and silent intrahepatic expansion and spread through the lymphatic system leading to late diagnosis and poor prognoses. Multi-omics studies have aggregated information derived from single-omics data, providing a more comprehensive understanding of the phenomena being studied. These approaches are gradually becoming powerful tools for investigating the intricate pathobiology of iCCA, facilitating the correlation between molecular signature and phenotypic manifestation. Consequently, preliminary stratifications of iCCA patients have been proposed according to their "omics" features opening the possibility of identifying potential biomarkers for early diagnosis and developing new therapies based on personalized medicine (PM). The focus of this review is to provide new and advanced insight into the molecular pathobiology of the iCCA, starting from single- to the latest multi-omics approaches, paving the way for translating new basic research into therapeutic practices.
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Affiliation(s)
- Veronica Porreca
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Cristina Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Eleonora Corbella
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Marco Peres
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Michele Stella
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Giuseppina Mignogna
- Department of Biochemistry Science, Sapienza University of Rome, 00185 Rome, Italy
| | - Bruno Maras
- Department of Biochemistry Science, Sapienza University of Rome, 00185 Rome, Italy
| | - Marco Ragusa
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Carmine Mancone
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
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Alaimo L, Boggio S, Catalano G, Calderone G, Poletto E, De Bellis M, Campagnaro T, Pedrazzani C, Conci S, Ruzzenente A. Multi-Omics Classification of Intrahepatic Cholangiocarcinoma: A Systematic Review and Meta-Analysis. Cancers (Basel) 2024; 16:2596. [PMID: 39061233 PMCID: PMC11275091 DOI: 10.3390/cancers16142596] [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: 06/01/2024] [Revised: 07/04/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a heterogeneous disease characterized by a dismal prognosis. Various attempts have been made to classify ICC subtypes with varying prognoses, but a consensus has yet to be reached. This systematic review aims to gather relevant data on the multi-omics-based ICC classification. The PubMed, Embase, and Cochrane databases were searched for terms related to ICC and multi-omics analysis. Studies that identified multi-omics-derived ICC subtypes and investigated clinicopathological predictors of long-term outcomes were included. Nine studies, which included 910 patients, were considered eligible. Mean 3- and 5-year overall survival were 25.7% and 19.6%, respectively, for the multi-omics subtypes related to poor prognosis, while they were 70.2% and 63.3%, respectively, for the subtypes linked to a better prognosis. Several negative prognostic factors were identified, such as genes' expression profile promoting inflammation, mutations in the KRAS gene, advanced tumor stage, and elevated levels of oncological markers. The subtype with worse clinicopathological characteristics was associated with worse survival (Ref.: good prognosis subtype; pooled hazard ratio 2.06, 95%CI 1.67-2.53). Several attempts have been made to classify molecular ICC subtypes, but they have yielded heterogeneous results and need a clear clinical definition. More efforts are required to build a comprehensive classification system that includes both molecular and clinical characteristics before implementation in clinical practice to facilitate decision-making and select patients who may benefit the most from comprehensive molecular profiling in the disease's earlier stages.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Andrea Ruzzenente
- Department of Surgery, Dentistry, Gynecology, and Pediatrics, Division of General and Hepato-Biliary Surgery, University of Verona, University Hospital G.B. Rossi, 37134 Verona, Italy; (L.A.)
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3
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Liu YY, Li YY, Liu YS, Zhang ZL, Gao YJ. Establishment and validation of a nomogram containing cytokeratin fragment antigen 21-1 for the differential diagnosis of intrahepatic cholangiocarcinoma and hepatocellular carcinoma. Front Oncol 2024; 14:1404799. [PMID: 39007100 PMCID: PMC11239389 DOI: 10.3389/fonc.2024.1404799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/17/2024] [Indexed: 07/16/2024] Open
Abstract
Background Our study aimed to develop a nomogram incorporating cytokeratin fragment antigen 21-1 (CYFRA21-1) to assist in differentiating between patients with intrahepatic cholangiocarcinoma (ICC) and hepatocellular carcinoma (HCC). Methods A total of 487 patients who were diagnosed with ICC and HCC at Qilu Hospital of Shandong University were included in this study. The patients were divided into a training cohort and a validation cohort based on whether the data collection was retrospective or prospective. Univariate and multivariate analyses were employed to select variables for the nomogram. The discrimination and calibration of the nomogram were evaluated using the area under the receiver operating characteristic curve (AUC) and calibration plots. Decision curve analysis (DCA) was used to assess the nomogram's net benefits at various threshold probabilities. Results Six variables, including CYFRA21-1, were incorporated to establish the nomogram. Its satisfactory discriminative ability was indicated by the AUC (0.972 for the training cohort, 0.994 for the validation cohort), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) values. The Hosmer-Lemeshow test and the calibration plots demonstrated favorable consistency between the nomogram predictions and the actual observations. Moreover, DCA revealed the clinical utility and superior discriminative ability of the nomogram compared to the model without CYFRA21-1 and the model consisting of the logarithm of alpha-fetoprotein (Log AFP) and the logarithm of carbohydrate antigen 19-9 (Log CA19-9). Additionally, the AUC values suggested that the discriminative ability of Log CYFRA21-1 was greater than that of the other variables used as diagnostic biomarkers. Conclusions This study developed and validated a nomogram including CYFRA21-1, which can aid clinicians in the differential diagnosis of ICC and HCC patients.
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Affiliation(s)
- Yuan-Yuan Liu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Yue-Yue Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Yong-Shuai Liu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Zong-Li Zhang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Yan-Jing Gao
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
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Umezu T, Tanaka S, Kubo S, Enomoto M, Tamori A, Ochiya T, Taguchi Y, Kuroda M, Murakami Y. Characterization of circulating miRNAs in the treatment of primary liver tumors. Cancer Rep (Hoboken) 2024; 7:e1964. [PMID: 38146079 PMCID: PMC10849994 DOI: 10.1002/cnr2.1964] [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: 07/30/2023] [Revised: 11/13/2023] [Accepted: 12/06/2023] [Indexed: 12/27/2023] Open
Abstract
BACKGROUND AND AIM Circulating micro RNAs (miRNAs) indicate clinical pathologies such as inflammation and carcinogenesis. In this study, we aimed to investigate whether miRNA expression level patterns in could be used to diagnose hepatocellular carcinoma (HCC) and biliary tract cancer (BTC), and the relationship miRNA expression patterns and cancer etiology. METHODS Patients with HCC and BTC with indications for surgery were selected for the study. Total RNA was extracted from the extracellular vesicle (EV)-rich fraction of the serum and analyzed using Toray miRNA microarray. Samples were divided into two cohorts in order of collection, the first 85 HCC were analyzed using a microarray based on miRBase ver.2.0 (hereafter v20 cohort), and the second 177 HCC and 43 BTC were analyzed using a microarray based on miRBase ver.21 (hereafter v21 cohort). RESULTS Using miRNA expression patterns, we found that HCC and BTC could be identified with an area under curve (AUC) 0.754 (v21 cohort). Patients with anti-hepatitis C virus (HCV) treatment (SVR-HCC) and without antiviral treatment (HCV-HCC) could be distinguished by an AUC 0.811 (v20 cohort) and AUC 0.798 (v21 cohort), respectively. CONCLUSIONS In this study, we could diagnose primary hepatic malignant tumor using miRNA expression patterns. Moreover, the difference of miRNA expression in SVR-HCC and HCV-HCC can be important information for enclosing cases that are prone to carcinogenesis after being cured with antiviral agents, but also for uncovering the mechanism for some carcinogenic potential remains even after persistent virus infection has disappeared.
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Affiliation(s)
- Tomohiro Umezu
- Department of Molecular PathologyTokyo Medical UniversityTokyoJapan
| | - Shogo Tanaka
- Department of Hepato‐Biliary‐Pancreatic SurgeryOsaka Metropolitan University, Graduate School of MedicineOsakaJapan
| | - Shoji Kubo
- Department of Hepato‐Biliary‐Pancreatic SurgeryOsaka Metropolitan University, Graduate School of MedicineOsakaJapan
| | - Masaru Enomoto
- Department of Hepatology, Graduate School of MedicineOsaka Metropolitan University, Graduate School of MedicineOsakaJapan
| | - Akihiro Tamori
- Department of Hepatology, Graduate School of MedicineOsaka Metropolitan University, Graduate School of MedicineOsakaJapan
| | - Takahiro Ochiya
- Department of Molecular and Cellular Medicine, Institute of Medical ScienceTokyo Medical UniversityTokyoJapan
| | | | - Masahiko Kuroda
- Department of Molecular PathologyTokyo Medical UniversityTokyoJapan
| | - Yoshiki Murakami
- Department of Molecular PathologyTokyo Medical UniversityTokyoJapan
- Department of DentistryAsahi UniversityGifuJapan
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Lin J, Rao D, Zhang M, Gao Q. Metabolic reprogramming in the tumor microenvironment of liver cancer. J Hematol Oncol 2024; 17:6. [PMID: 38297372 PMCID: PMC10832230 DOI: 10.1186/s13045-024-01527-8] [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: 12/14/2023] [Accepted: 01/21/2024] [Indexed: 02/02/2024] Open
Abstract
The liver is essential for metabolic homeostasis. The onset of liver cancer is often accompanied by dysregulated liver function, leading to metabolic rearrangements. Overwhelming evidence has illustrated that dysregulated cellular metabolism can, in turn, promote anabolic growth and tumor propagation in a hostile microenvironment. In addition to supporting continuous tumor growth and survival, disrupted metabolic process also creates obstacles for the anticancer immune response and restrains durable clinical remission following immunotherapy. In this review, we elucidate the metabolic communication between liver cancer cells and their surrounding immune cells and discuss how metabolic reprogramming of liver cancer impacts the immune microenvironment and the efficacy of anticancer immunotherapy. We also describe the crucial role of the gut-liver axis in remodeling the metabolic crosstalk of immune surveillance and escape, highlighting novel therapeutic opportunities.
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Affiliation(s)
- Jian Lin
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dongning Rao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Mao Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Qiang Gao
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China.
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, 200032, China.
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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Yang F, Hilakivi-Clarke L, Shaha A, Wang Y, Wang X, Deng Y, Lai J, Kang N. Metabolic reprogramming and its clinical implication for liver cancer. Hepatology 2023; 78:1602-1624. [PMID: 36626639 PMCID: PMC10315435 DOI: 10.1097/hep.0000000000000005] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
Cancer cells often encounter hypoxic and hypo-nutrient conditions, which force them to make adaptive changes to meet their high demands for energy and various biomaterials for biomass synthesis. As a result, enhanced catabolism (breakdown of macromolecules for energy production) and anabolism (macromolecule synthesis from bio-precursors) are induced in cancer. This phenomenon is called "metabolic reprogramming," a cancer hallmark contributing to cancer development, metastasis, and drug resistance. HCC and cholangiocarcinoma (CCA) are 2 different liver cancers with high intertumoral heterogeneity in terms of etiologies, mutational landscapes, transcriptomes, and histological representations. In agreement, metabolism in HCC or CCA is remarkably heterogeneous, although changes in the glycolytic pathways and an increase in the generation of lactate (the Warburg effect) have been frequently detected in those tumors. For example, HCC tumors with activated β-catenin are addicted to fatty acid catabolism, whereas HCC tumors derived from fatty liver avoid using fatty acids. In this review, we describe common metabolic alterations in HCC and CCA as well as metabolic features unique for their subsets. We discuss metabolism of NAFLD as well, because NAFLD will likely become a leading etiology of liver cancer in the coming years due to the obesity epidemic in the Western world. Furthermore, we outline the clinical implication of liver cancer metabolism and highlight the computation and systems biology approaches, such as genome-wide metabolic models, as a valuable tool allowing us to identify therapeutic targets and develop personalized treatments for liver cancer patients.
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Affiliation(s)
- Flora Yang
- BA/MD Joint Admission Scholars Program, University of Minnesota, Minneapolis, Minnesota
| | - Leena Hilakivi-Clarke
- Food Science and Nutrition Section, The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Aurpita Shaha
- Tumor Microenvironment and Metastasis Section, the Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Yuanguo Wang
- Tumor Microenvironment and Metastasis Section, the Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Xianghu Wang
- Tumor Microenvironment and Metastasis Section, the Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Yibin Deng
- Department of Urology, Masonic Cancer Center, The University of Minnesota Medical School, Minneapolis, Minnesota
| | - Jinping Lai
- Department of Pathology and Laboratory Medicine, Kaiser Permanente Sacramento Medical Center, Sacramento, California
| | - Ningling Kang
- Tumor Microenvironment and Metastasis Section, the Hormel Institute, University of Minnesota, Austin, Minnesota
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7
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Ye C, Dong C, Lin Y, Shi H, Zhou W. Interplay between the Human Microbiome and Biliary Tract Cancer: Implications for Pathogenesis and Therapy. Microorganisms 2023; 11:2598. [PMID: 37894256 PMCID: PMC10608879 DOI: 10.3390/microorganisms11102598] [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: 08/29/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Biliary tract cancer, encompassing intrahepatic and extrahepatic cholangiocarcinoma as well as gallbladder carcinoma, stands as a prevalent malignancy characterized by escalating incidence rates and unfavorable prognoses. The onset of cholangiocarcinoma involves a multitude of risk factors and could potentially be influenced by microbial exposure. The human microbiome, encompassing the entirety of human microbial genetic information, assumes a pivotal role in regulating key aspects such as host digestion, absorption, immune responses, and metabolism. The widespread application of next-generation sequencing technology has notably propelled investigations into the intricate relationship between the microbiome and diseases. An accumulating body of evidence strongly suggests a profound interconnection between biliary tract cancer and the human microbiome. This article critically appraises the existing evidence pertaining to the microbiome milieu within patients afflicted by biliary tract cancer. Furthermore, it delves into potential mechanisms through which dysregulation of the human microbiome could contribute to the advancement of biliary tract cancer. Additionally, the article expounds on its role in the context of chemotherapy and immunotherapy for biliary tract cancer.
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Affiliation(s)
- Cheng Ye
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (C.Y.); (C.D.); (Y.L.); (H.S.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Chunlu Dong
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (C.Y.); (C.D.); (Y.L.); (H.S.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Yanyan Lin
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (C.Y.); (C.D.); (Y.L.); (H.S.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Huaqing Shi
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (C.Y.); (C.D.); (Y.L.); (H.S.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Wence Zhou
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (C.Y.); (C.D.); (Y.L.); (H.S.)
- Department of General Surgery, The Second Hospital of Lanzhou University, Lanzhou 730000, China
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8
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Xu D, Wei L, Zeng L, Mukiibi R, Xin H, Zhang F. An integrated mRNA-lncRNA signature for overall survival prediction in cholangiocarcinoma. Medicine (Baltimore) 2023; 102:e35348. [PMID: 37773863 PMCID: PMC10545162 DOI: 10.1097/md.0000000000035348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/01/2023] [Indexed: 10/01/2023] Open
Abstract
The combination of mRNA and lncRNA profiles for establishing an integrated mRNA-lncRNA prognostic signature has remained unexplored in cholangiocarcinoma (CCA) patients. We utilized a training dataset of 36 samples from The Cancer Genome Atlas dataset and a validation cohort (GSE107943) of 30 samples from Gene Expression Omnibus. Two mRNAs (CFHR3 and PIWIL4) and 2 lncRNAs (AC007285.1 and AC134682.1) were identified to construct the integrated signature through a univariate Cox regression (P-value = 1.35E-02) and a multivariable Cox analysis (P-value = 3.07E-02). Kaplan-Meier curve showed that patients with low risk scores had notably prolonged overall survival than those with high risk scores (P-value = 4.61E-03). Subsequently, the signature was validated in GSE107943 cohort with an area under the curve of 0.750 at 1-year and 0.729 at 3-year. The signature was not only independent from diverse clinical features (P-value = 3.07E-02), but also surpassed other clinical characteristics as prognostic biomarkers with area under the curve of 0.781 at 3-year. Moreover, the weighted gene co-expression network analysis and gene enrichment analyses found that the integrated signature were associated with metabolic-related biological process and lipid metabolism pathway, which has been implicated in the pathogenesis of CCA. Taken together, we developed an integrated mRNA-lncRNA signature that had an independent prognostic value in the risk stratification of patients with CCA.
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Affiliation(s)
- Derong Xu
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, The Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Lili Wei
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Liping Zeng
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, The Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Robert Mukiibi
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Hongbo Xin
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, The Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Feng Zhang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, The Institute of Translational Medicine, Nanchang University, Nanchang, China
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9
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Liu L, Shi Y, Zhang P, Zhang X. Integration analysis of miRNA-mRNA expression exploring their potential roles in intrahepatic cholangiocarcinoma. Sci Rep 2023; 13:8362. [PMID: 37225858 DOI: 10.1038/s41598-023-35288-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is the second common primary hepatic malignancy tumor. In this study, an integrative analysis of differentially expressed genes (DEGs) and miRNAs from the ICC onset and adjacent normal tissues were performed to explore the regulatory roles of miRNA-mRNA interaction. A total of 1018 DEGs and 39 miRNAs were likely involved in ICC pathogenesis, suggesting the changes in cell metabolism in ICC development. The built network indicated that 30 DEGs were regulated by 16 differentially expressed miRNA. The screened DEGs and miRNA together were probably considered the biomarkers of ICC, and their important roles in ICC pathogenesis remain to be elucidated. This study could provide a good basis to uncover the regulatory mechanism of miRNA and mRNAs in ICC pathogenesis.
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Affiliation(s)
- Liyan Liu
- Department of Blood Transfusion, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, People's Republic of China
| | - Yajun Shi
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Pengjie Zhang
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China.
| | - Xing Zhang
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, People's Republic of China.
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Silvestri M, Nghia Vu T, Nichetti F, Niger M, Di Cosimo S, De Braud F, Pruneri G, Pawitan Y, Calza S, Cappelletti V. Comprehensive transcriptomic analysis to identify biological and clinical differences in cholangiocarcinoma. Cancer Med 2023; 12:10156-10168. [PMID: 36938752 PMCID: PMC10166943 DOI: 10.1002/cam4.5719] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Cholangiocarcinoma (CC) is a rare and aggressive disease with limited therapeutic options and a poor prognosis. All available public records of cohorts reporting transcriptomic data on intrahepatic cholangiocarcinoma (ICC) and extrahepatic cholangiocarcinoma (ECC) were collected with the aim to provide a comprehensive gene expression-based classification with clinical relevance. METHODS A total of 543 patients with primary tumor tissues profiled by RNAseq and microarray platforms from seven public datasets were used as a discovery set to identify distinct biological subgroups. Group predictors developed on the discovery sets were applied to a single cohort of 131 patients profiled with RNAseq for validation and assessment of clinical relevance leveraging machine learning techniques. RESULTS By unsupervised clustering analysis of gene expression data we identified both in the ICC and ECC discovery datasets four subgroups characterized by a distinct type of immune infiltrate and signaling pathways. We next developed class predictors using short gene list signatures and identified in an independent dataset subgroups of ICC tumors at different prognosis. CONCLUSIONS The developed class-predictor allows identification of CC subgroups with specific biological features and clinical behavior at single-sample level. Such results represent the starting point for a complete molecular characterization of CC, including integration of genomics data to develop in clinical practice.
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Affiliation(s)
- Marco Silvestri
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy.,Unit of Biostatistics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Federico Nichetti
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy.,Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Monica Niger
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Serena Di Cosimo
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Filippo De Braud
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Giancarlo Pruneri
- Department Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Stefano Calza
- Unit of Biostatistics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Vera Cappelletti
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
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Sun H, Yang W, Zhou W, Zhou C, Liu S, Shi H, Tian W. Prognostic value of des-γ-carboxyprothrombin in patients with AFP-negative HCC treated with TACE. Oncol Lett 2022; 25:69. [PMID: 36644150 PMCID: PMC9827467 DOI: 10.3892/ol.2022.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/13/2022] [Indexed: 12/30/2022] Open
Abstract
In patients with AFP-negative hepatocellular carcinoma (HCC), des-γ-carboxyprothrombin (DCP) is an important prognostic indicator for the preoperative assessment of transarterial chemoembolization (TACE). However, the association between the serum DCP levels and the degree of progression and prognosis of patients with AFP-negative HCC treated with TACE has not been thoroughly investigated to date, and the molecular mechanism is also unclear. The present study retrospectively analyzed the clinical data of 107 patients with AFP-negative HCC treated with TACE and divided them into two groups based on the median serum DCP levels. The association between DCP and the clinical characteristics of the patients was analyzed, and the survival data were analyzed using Kaplan-Meier curves and Cox regression models. The results demonstrated that the median follow-up time was 755 days (range, 64-1,556 days), and patients in the low-DCP group (n=11; 20.8%) had a lower mortality rate than those in the high-DCP group (n=20; 37.0%). Cox multivariate regression analysis suggested that preoperative lymph node metastasis [hazard ratio (HR), 3.903; 95% CI, 1.778-8.519; P=0.001] and DCP group (HR, 2.465; 95% CI, 1.038-5.854; P=0.041) were independent risk factors. Furthermore, the Gene Expression Omnibus database was utilized to screen differentially expressed mRNAs. Enrichment analyses were then performed, and a protein-protein interaction (PPI) network was constructed to identify hub genes. A total of 169 differentially expressed genes were screened. Enrichment analyses revealed that cancer-related and ribosomal pathways were significantly enriched. Furthermore, 10 hub genes were identified in the PPI network by counting the number of gene interactions, the majority of which belonged to the ribosomal protein (RPS) family, and the top three significant genes were RPS23, RPS11 and RPS3A. In patients with AFP-negative HCC, higher serum DCP levels were associated with poor prognosis after TACE. This may be associated with genes such as those belonging to the RPS family, which may contribute to future personalized therapy for this disease.
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Affiliation(s)
- Hanyao Sun
- Department of Interventional Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Wei Yang
- Department of Interventional Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Weizhong Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Chungao Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Sheng Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Haibin Shi
- Department of Interventional Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China,Correspondence to: Dr Haibin Shi or Dr Wei Tian, Department of Interventional Radiology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu 210029, P.R. China, E-mail: , E-mail:
| | - Wei Tian
- Department of Interventional Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China,Correspondence to: Dr Haibin Shi or Dr Wei Tian, Department of Interventional Radiology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu 210029, P.R. China, E-mail: , E-mail:
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12
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Raggi C, Taddei ML, Rae C, Braconi C, Marra F. Metabolic reprogramming in cholangiocarcinoma. J Hepatol 2022; 77:849-864. [PMID: 35594992 DOI: 10.1016/j.jhep.2022.04.038] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 12/25/2022]
Abstract
Metabolic reprogramming is a hallmark of cancer and allows tumour cells to meet the increased energy demands required for rapid proliferation, invasion, and metastasis. Indeed, many tumour cells acquire distinctive metabolic and bioenergetic features that enable them to survive in resource-limited conditions, mainly by harnessing alternative nutrients. Several recent studies have explored the metabolic plasticity of cancer cells with the aim of identifying new druggable targets, while therapeutic strategies to limit the access to nutrients have been successfully applied to the treatment of some tumours. Cholangiocarcinoma (CCA), a highly heterogeneous tumour, is the second most common form of primary liver cancer. It is characterised by resistance to chemotherapy and poor prognosis, with 5-year survival rates of below 20%. Deregulation of metabolic pathways have been described during the onset and progression of CCA. Increased aerobic glycolysis and glutamine anaplerosis provide CCA cells with the ability to generate biosynthetic intermediates. Other metabolic alterations involving carbohydrates, amino acids and lipids have been shown to sustain cancer cell growth and dissemination. In this review, we discuss the complex metabolic rewiring that occurs during CCA development and leads to unique nutrient addiction. The possible role of therapeutic interventions based on metabolic changes is also thoroughly discussed.
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Affiliation(s)
- Chiara Raggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
| | - Maria Letizia Taddei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Colin Rae
- Institute of Cancer Sciences, The University of Glasgow, Glasgow, United Kingdom
| | - Chiara Braconi
- Institute of Cancer Sciences, The University of Glasgow, Glasgow, United Kingdom; Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Fabio Marra
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
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13
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Li J, Lu J, Lv S, Sun S, Liu C, Xu F, Sun H, Yang J, Wang X, Zhong X, Lu J. Linoleic acid pathway disturbance contributing to potential cancerization of intrahepatic bile duct stones into intrahepatic cholangiocarcinoma. BMC Gastroenterol 2022; 22:269. [PMID: 35637430 PMCID: PMC9153149 DOI: 10.1186/s12876-022-02354-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/20/2022] [Indexed: 11/26/2022] Open
Abstract
Background Intrahepatic cholangiocarcinoma (ICC) is the second most common primary hepatic malignancy with poor prognosis. Intrahepatic bile duct stone (IBDS) is one of the key causes to ICC occurrence and can increase morbidity rate of ICC about forty times. However, the specific carcinogenesis of IBDS is still far from clarified. Insight into the metabolic phenotype difference between IBDS and ICC can provide potential mechanisms and therapeutic targets, which is expected to inhibit the carcinogenesis of IBDS and improve the prognosis of ICC.
Methods A total of 34 participants including 25 ICC patients and 9 IBDS patients were recruited. Baseline information inclusive of liver function indicators, tumor biomarkers, surgery condition and constitution parameters etc. from patients were recorded. ICC and IBDS pathological tissues, as well as ICC para-carcinoma tissues, were collected for GC–MS based metabolomics experiments. Multivariate analysis was performed to find differentially expressed metabolites and differentially enriched metabolic pathways. Spearman correlation analysis was then used to construct correlation network between key metabolite and baseline information of patients. Results The IBDS tissue and para-carcinoma tissue have blurred metabolic phenotypic differences, but both of them essentially distinguished from carcinoma tissue of ICC. Metabolic differences between IBDS and ICC were enriched in linoleic acid metabolism pathway, and the level of 9,12-octadecadienoic acid in IBDS tissues was almost two times higher than in ICC pathological tissues. The correlation between 9,12-octadecadienoic acid level and baseline information of patients demonstrated that 9,12-octadecadienoic acid level in pathological tissue was negative correlation with gamma-glutamyl transpeptidase (GGT) and alkaline phosphatase (ALP) level in peripheral blood. These two indicators were all cancerization marker for hepatic carcinoma and disease characteristic of IBDS.
Conclusion Long-term monitoring of metabolites from linoleic acid metabolism pathway and protein indicators of liver function in IBDS patients has important guiding significance for the monitoring of IBDS carcinogenesis. Meanwhile, further insight into the causal relationship between linoleic acid pathway disturbance and changes in liver function can provide important therapeutic targets for both IBDS and ICC. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-022-02354-2.
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Affiliation(s)
- Jun Li
- The 1st Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jiongjiong Lu
- Department of Special Treatment, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Shaodong Lv
- The 5st Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Shujun Sun
- School of Biology and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Caifeng Liu
- The 1st Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Feng Xu
- The 1st Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Haiying Sun
- The 1st Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jiamei Yang
- Department of Special Treatment, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Xinjun Wang
- Institute of Intestinal Diseases, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China. .,Shanghai Institution of Gut Microbiota Research and Engineering Development, Tenth People's Hospital of Tongji University, Tongji University School of Medicine, Shanghai, China.
| | - Xingyang Zhong
- The 1st Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China.
| | - Junhua Lu
- The 5st Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China.
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14
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Chen Y, Hu L, Lin H, Yu H, You J. Serum metabolomic profiling for patients with adenocarcinoma of the esophagogastric junction. Metabolomics 2022; 18:26. [PMID: 35441991 DOI: 10.1007/s11306-022-01883-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/29/2022] [Indexed: 10/18/2022]
Abstract
INTRODUCTION The incidence of adenocarcinoma in the esophagogastric junction (AEG) has increased in the recent years. AEG is reported to have a worse prognosis compared with tumor confined to the stomach (non-AEG). Although the metabolic changes of non-AEG have been investigated in extensive studies, little effort focused on the metabolic profiling of AEG serum. OBJECTIVES Here we report an untargeted gas chromatography-mass spectrometry (GC-MS) method to explore the abnormal metabolism underlying AEG. METHODS GC-MS-based untargeted metabolomics approach combined with multivariate statistical analyses were used to study the metabolic profiling of serum samples from AEG patients (n = 70), non-AEG patients (n = 70) and health controls (n = 71). RESULTS A novel serum metabolic profiling of 18 metabolites from patients of AEG and non-AEG was indicated, in comparison with health controls. Moreover, AEG and non-AEG were also well-classified with 9 distinguishing metabolites including hypoxanthine, alanine, proline, pyroglutamate, glycine, lactate, succinic acid, glutamate and kynurenine, which produced a discriminatory model with an area under the Receiver Operating Characteristic (ROC) curve of 0.852, suggesting a distinct metabolic signature of AEG. Importantly, lactate and glutamate disclosed outcome-prediction values by multivariate cox-proportional hazard model and Kaplan-Meier method based on follow-up information for 2-5 years. CONCLUSION This is the first metabolomics study to identify serum metabolic signature of AEG. The distinguishing metabolites show a promising application on clinical diagnose and outcome prediction, and allow us to unveil several key metabolic variations coexisting in AEG, which may aid to understand the underlying metabolic mechanisms.
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Affiliation(s)
- Yinan Chen
- Department of Gastrointestinal Surgery, Cancer Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361000, China
| | - Lei Hu
- Department of General Surgery, The First Affliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Hexin Lin
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
| | - Huangdao Yu
- Department of Gastrointestinal Surgery, Cancer Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361000, China
| | - Jun You
- Department of Gastrointestinal Surgery, Cancer Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361000, China.
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15
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Eftekhari A, Maleki Dizaj S, Sharifi S, Salatin S, Khalilov R, Samiei M, Zununi Vahed S, Ahmadian E. Salivary biomarkers in cancer. Adv Clin Chem 2022; 110:171-192. [DOI: 10.1016/bs.acc.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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RTK25: A Comprehensive Molecular Profiling Strategy in Cholangiocarcinoma Using an Integrated Bioinformatics Approach. Pharmaceuticals (Basel) 2021; 14:ph14090898. [PMID: 34577598 PMCID: PMC8469883 DOI: 10.3390/ph14090898] [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: 07/29/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a heterogeneous group of malignancies that primarily originate from the bile duct. Tumor heterogeneity is a prime characteristic of CCA and considering the scarcity of approved targeted therapy drugs, this makes precision oncology impractical in CCA. Stratifying patients based on their molecular signature and biomarker-guided therapy may offer a conducive solution. Receptors tyrosine kinases (RTK) are potential targets for novel therapeutic strategies in CCA as RTK signaling is dysregulated in CCA. This study aims to identify targetable RTK profile in CCA using a bioinformatic approach. We discovered that CCA samples could be grouped into molecular subtypes based on the gene expression profile of selected RTKs (RTK25). Using the RTK25 gene list, we discovered five distinct molecular subtypes of CCA in this cohort. Tyrosine kinase inhibitors that target each RTK profile and their subsequent molecular signatures were also discovered. These results suggest that certain RTKs correlate with each other, indicating that tailored dual inhibition of RTKs may be more favorable than monotherapy. The results from this study can direct future investigative attention towards validating this concept in in vivo and in vitro systems. Ultimately, this will facilitate biomarker-guided clinical trials for the successful approval of novel therapeutic options in CCA.
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17
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Fujisawa K, Shimo M, Taguchi YH, Ikematsu S, Miyata R. PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients. Sci Rep 2021; 11:17351. [PMID: 34456333 PMCID: PMC8403676 DOI: 10.1038/s41598-021-95698-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/23/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is raging worldwide. This potentially fatal infectious disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the complete mechanism of COVID-19 is not well understood. Therefore, we analyzed gene expression profiles of COVID-19 patients to identify disease-related genes through an innovative machine learning method that enables a data-driven strategy for gene selection from a data set with a small number of samples and many candidates. Principal-component-analysis-based unsupervised feature extraction (PCAUFE) was applied to the RNA expression profiles of 16 COVID-19 patients and 18 healthy control subjects. The results identified 123 genes as critical for COVID-19 progression from 60,683 candidate probes, including immune-related genes. The 123 genes were enriched in binding sites for transcription factors NFKB1 and RELA, which are involved in various biological phenomena such as immune response and cell survival: the primary mediator of canonical nuclear factor-kappa B (NF-κB) activity is the heterodimer RelA-p50. The genes were also enriched in histone modification H3K36me3, and they largely overlapped the target genes of NFKB1 and RELA. We found that the overlapping genes were downregulated in COVID-19 patients. These results suggest that canonical NF-κB activity was suppressed by H3K36me3 in COVID-19 patient blood.
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Affiliation(s)
- Kota Fujisawa
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
| | - Mamoru Shimo
- Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Y-H Taguchi
- Department of Physics, Chuo University, Tokyo, 112-8551, Japan
| | - Shinya Ikematsu
- Department of Bioresources Engineering, National Institute of Technology, OkinawaCollege, Okinawa, 905-2192, Japan
| | - Ryota Miyata
- Faculty of Engineering, University of the Ryukyus, Okinawa, 903-0213, Japan.
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Raevskaya O, Appelman H, Razumilava N. A Contemporary Approach to Diagnosis and Treatment of Combined Hepatocellular-Cholangiocarcinoma. ACTA ACUST UNITED AC 2020; 19:478-485. [PMID: 33415066 DOI: 10.1007/s11901-020-00556-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Purpose of review To provide updates on terminology, epidemiology, diagnosis, and treatment of combined hepatocellular-cholangiocarcinoma (cHCC-CCA). Recent findings cHCC-CCAs are tumors that in the same nodule contain a variable degree of HCC and CCA components with a transition zone. cHCC-CCAs develop in cirrhotic and non-cirrhotic livers like and is associated with poor outcomes. Mutations in TP53, TERT promoter, and ARID1A are the most common genetic aberrations in cHCC-CCA. Fusion gene PTMS-AP1G1 is unique for cHCC-CCA. A biopsy is required for diagnosis. Surgical resection remains treatment of choice, while liver transplantation for early cHCC-CCA is associated with favorable outcomes. Gemcitabine-based therapy shows benefits for advanced cHCC-CCA. Summary cHCC-CCAs are a heterogeneous group of primary liver cancers with unique biological behavior. Multicenter studies are required for a molecular analysis to inform novel therapeutic approaches, and understand epidemiology and benefits of liver transplantation, liver-directed and targeted therapies for this rare aggressive cancer.
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Affiliation(s)
- Olga Raevskaya
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Henry Appelman
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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19
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Mishra NK, Niu M, Southekal S, Bajpai P, Elkholy A, Manne U, Guda C. Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles. Front Genet 2020; 11:522125. [PMID: 33193605 PMCID: PMC7606733 DOI: 10.3389/fgene.2020.522125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 08/21/2020] [Indexed: 12/30/2022] Open
Abstract
Background Cholangiocarcinoma (CCA) is a rare disease, but it is amongst the most lethal cancers with a median survival under 1 year. Variations in DNA methylation and gene expression have been extensively studied in other cancers for their role in pathogenesis and disease prognosis, but these studies are very limited in CCA. This study focusses on the identification of DNA methylation and gene expression prognostic biomarkers using multi-omics data of CCA tumors from The Cancer Genome Atlas (TCGA). Method We have conducted a genome-wide analysis of differential DNA methylation and gene/miRNA expression using data from 36 CCA tumor and 9 normal samples from TCGA. The impact of DNA methylation in promoters and long-range distal enhancers on the regulation and expression of CCA-associated genes was examined using linear regression. Next, we conducted network analyses on genes which are regulated by DNA methylation as well as by miRNA. Finally, we performed Kaplan–Meier and Cox proportional hazards regression analyses in order to identify the role of selected methylation sites and specific genes and miRNAs in patient survival. We also performed real-time quantitative PCR (qPCR) to confirm the change in gene expression in CCA patients’ tumor and adjacent normal samples. Results Altered DNA methylation was observed on 12,259 CpGs across all chromosomes, of which 78% were hypermethylated. We observed a strong negative relationship between promoter hypermethylation and corresponding gene expression in 92% of the CpGs. Differential expression analyses revealed altered expression patterns in 3,305 genes and 101 miRNAs. Finally, we identified 17 differentially methylated promoter CpGs, 72 differentially expressed genes, and two miRNAs that are likely associated with patient survival. Pathway analysis suggested that cell division, bile secretion, amino acid metabolism, PPAR signaling, hippo signaling were highly affected by gene expression and DNA methylation alterations. The qPCR analysis further confirmed that MDK, HNF1B, PACS1, and GLUD1 are differentially expressed in CCA. Conclusion Based on the survival analysis, we conclude that DEPDC1, FUT4, MDK, PACS1, PIWIL4 genes, miR-22, miR-551b microRNAs, and cg27362525 and cg26597242 CpGs can strongly support their use as prognostic markers of CCA.
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Affiliation(s)
- Nitish Kumar Mishra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Meng Niu
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Siddesh Southekal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Prachi Bajpai
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Amr Elkholy
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Upender Manne
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
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Omics-Based Platforms: Current Status and Potential Use for Cholangiocarcinoma. Biomolecules 2020; 10:biom10101377. [PMID: 32998289 PMCID: PMC7600697 DOI: 10.3390/biom10101377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/26/2020] [Accepted: 09/26/2020] [Indexed: 02/07/2023] Open
Abstract
Cholangiocarcinoma (CCA) has been identified as a highly malignant cancer that can be transformed from epithelial cells of the bile duct, including intrahepatic, perihilar and extrahepatic. High-resolution imaging tools (abdominal ultrasound, computed tomography and percutaneous transhepatic cholangial drainage) are recruited for diagnosis. However, the lack of early diagnostic biomarkers and treatment evaluation can lead to serious outcomes and poor prognosis (i.e., CA19-9, MUC5AC). In recent years, scientists have established a large number of omics profiles to reveal underlying mechanisms and networks (i.e., IL-6/STAT3, NOTCH). With these results, we achieved several genomic alteration events (i.e., TP53mut, KRASmut) and epigenetic modifications (i.e., DNA methylation, histone modification) in CCA cells and clinical patients. Moreover, we reviewed candidate gene (such as NF-kB, YAP1) that drive gene transcription factors and canonical pathways through transcriptomics profiles (including microarrays and next-generation sequencing). In addition, the proteomics database also indicates which molecules and their directly binding status could trigger dysfunction signatures in tumorigenesis (carbohydrate antigen 19-9, mucins). Most importantly, we collected metabolomics datasets and pivotal metabolites. These results reflect the pharmacotherapeutic options and evaluate pharmacokinetic/pharmacodynamics in vitro and in vivo. We reversed the panels and selected many potentially small compounds from the connectivity map and L1000CDS2 system. In this paper, we summarize the prognostic value of each candidate gene and correlate this information with clinical events in CCA. This review can serve as a reference for further research to clearly investigate the complex characteristics of CCA, which may lead to better prognosis, drug repurposing and treatment strategies.
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21
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Chen FY, Zhou C, Zhang XY, Zhou KQ, Peng YF, Yu L, Fan J, Zhou J, Hu J, Wang Z. Integrated Bioinformatics analysis and clinical validation reveals that high expression of mucin 1 in intrahepatic cholangiocarcinoma predicts recurrence after curative resection. Exp Ther Med 2020; 20:50. [PMID: 32952640 PMCID: PMC7480127 DOI: 10.3892/etm.2020.9178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/13/2019] [Indexed: 01/01/2023] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a cancer type with high malignancy and a current lack of biomarkers to predict recurrence. In the present study, to identify potential biomarkers, five ICC datasets from the Gene Expression Omnibus database were analyzed to construct initial datasets by using a robust rank aggregation approach. A total of 19 upregulated genes were identified in the initial datasets. The genes identified were then further analysed using data from The Cancer Genome Atlas. Only mucin 1 (MUC1) exhibited significance regarding differential expression and survival prediction. Finally, the expression levels of MUC1 were assessed using reverse transcription-quantitative PCR in 61 pairs of ICC tumor and matched non-cancerous samples. The expression of MUC1 was significantly elevated in ICC tissues compared with that in matched non-cancerous counterparts (P=0.001). Patients with high MUC1 expression levels had significantly shorter overall survival (OS, P=0.009) and recurrence-free survival (RFS, P=0.012). MUC1 was identified as an independent prognostic factor for OS [hazard ratio (HR)=2.364, 95%CI: 1.214-4.485; P=0.023] and RFS (HR=2.552 95%CI: 1.294-5.032; P=0.007) in the multivariate analysis. Using receiver operating characteristic analysis, a co-index including MUC1 had a high accuracy for predicting survival [MUC1 combined with serum levels of CEA and cancer antigen 19-9, and lymph node metastasis, area under curve (AUC)=0.746, 95%CI: 0.620-0.872] and recurrence (MUC1 combined with bile duct invasion and lymph node metastasis, AUC=0.729, 95%CI: 0.605-854). In conclusion, MUC1 is highly expressed in ICC tissue and is a potential prognostic biomarker and therapeutic target for ICC.
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Affiliation(s)
- Fei-Yu Chen
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai 200032, P.R. China
| | - Cheng Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai 200032, P.R. China
| | - Xiang-Yu Zhang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai 200032, P.R. China
| | - Kai-Qian Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai 200032, P.R. China
| | - Yuan-Fei Peng
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai 200032, P.R. China
| | - Lei Yu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai 200032, P.R. China
| | - Jia Fan
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai 200032, P.R. China.,State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200032, P.R. China.,Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Jian Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai 200032, P.R. China.,State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200032, P.R. China.,Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Jie Hu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai 200032, P.R. China
| | - Zheng Wang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai 200032, P.R. China
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Frieboes HB, Raghavan S, Godin B. Modeling of Nanotherapy Response as a Function of the Tumor Microenvironment: Focus on Liver Metastasis. Front Bioeng Biotechnol 2020; 8:1011. [PMID: 32974325 PMCID: PMC7466654 DOI: 10.3389/fbioe.2020.01011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
The tumor microenvironment (TME) presents a challenging barrier for effective nanotherapy-mediated drug delivery to solid tumors. In particular for tumors less vascularized than the surrounding normal tissue, as in liver metastases, the structure of the organ itself conjures with cancer-specific behavior to impair drug transport and uptake by cancer cells. Cells and elements in the TME of hypovascularized tumors play a key role in the process of delivery and retention of anti-cancer therapeutics by nanocarriers. This brief review describes the drug transport challenges and how they are being addressed with advanced in vitro 3D tissue models as well as with in silico mathematical modeling. This modeling complements network-oriented techniques, which seek to interpret intra-cellular relevant pathways and signal transduction within cells and with their surrounding microenvironment. With a concerted effort integrating experimental observations with computational analyses spanning from the molecular- to the tissue-scale, the goal of effective nanotherapy customized to patient tumor-specific conditions may be finally realized.
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Affiliation(s)
- Hermann B. Frieboes
- Department of Bioengineering, University of Louisville, Louisville, KY, United States
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, United States
- Center for Predictive Medicine, University of Louisville, Louisville, KY, United States
| | - Shreya Raghavan
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX, United States
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, United States
| | - Biana Godin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, United States
- Department of Obstetrics and Gynecology, Houston Methodist Hospital, Houston, TX, United States
- Developmental Therapeutics Program, Houston Methodist Cancer Center, Houston Methodist Hospital, Houston, TX, United States
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Chong J, Wishart DS, Xia J. Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis. ACTA ACUST UNITED AC 2020; 68:e86. [PMID: 31756036 DOI: 10.1002/cpbi.86] [Citation(s) in RCA: 1344] [Impact Index Per Article: 336.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MetaboAnalyst (https://www.metaboanalyst.ca) is an easy-to-use web-based tool suite for comprehensive metabolomic data analysis, interpretation, and integration with other omics data. Since its first release in 2009, MetaboAnalyst has evolved significantly to meet the ever-expanding bioinformatics demands from the rapidly growing metabolomics community. In addition to providing a variety of data processing and normalization procedures, MetaboAnalyst supports a wide array of functions for statistical, functional, as well as data visualization tasks. Some of the most widely used approaches include PCA (principal component analysis), PLS-DA (partial least squares discriminant analysis), clustering analysis and visualization, MSEA (metabolite set enrichment analysis), MetPA (metabolic pathway analysis), biomarker selection via ROC (receiver operating characteristic) curve analysis, as well as time series and power analysis. The current version of MetaboAnalyst (4.0) features a complete overhaul of the user interface and significantly expanded underlying knowledge bases (compound database, pathway libraries, and metabolite sets). Three new modules have been added to support pathway activity prediction directly from mass peaks, biomarker meta-analysis, and network-based multi-omics data integration. To enable more transparent and reproducible analysis of metabolomic data, we have released a companion R package (MetaboAnalystR) to complement the web-based application. This article provides an overview of the main functional modules and the general workflow of MetaboAnalyst 4.0, followed by 12 detailed protocols: © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Data uploading, processing, and normalization Basic Protocol 2: Identification of significant variables Basic Protocol 3: Multivariate exploratory data analysis Basic Protocol 4: Functional interpretation of metabolomic data Basic Protocol 5: Biomarker analysis based on receiver operating characteristic (ROC) curves Basic Protocol 6: Time-series and two-factor data analysis Basic Protocol 7: Sample size estimation and power analysis Basic Protocol 8: Joint pathway analysis Basic Protocol 9: MS peaks to pathway activities Basic Protocol 10: Biomarker meta-analysis Basic Protocol 11: Knowledge-based network exploration of multi-omics data Basic Protocol 12: MetaboAnalystR introduction.
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Affiliation(s)
- Jasmine Chong
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - David S Wishart
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada.,Department of Animal Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
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24
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Mocan T, Simão AL, Castro RE, Rodrigues CMP, Słomka A, Wang B, Strassburg C, Wöhler A, Willms AG, Kornek M. Liquid Biopsies in Hepatocellular Carcinoma: Are We Winning? J Clin Med 2020; 9:jcm9051541. [PMID: 32443747 PMCID: PMC7291267 DOI: 10.3390/jcm9051541] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/18/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) represents the sixth most common cancer worldwide and the third most common cause of cancer-related death. One of the major problems faced by researchers and clinicians in this area is the lack of reliable disease biomarkers, which would allow for an earlier diagnosis, follow-up or prediction of treatment response, among others. In this regard, the “HCC circulome”, defined as the pool of circulating molecules in the bloodstream derived from the primary tumor, represents an appealing target, the so called liquid biopsy. Such molecules encompass circulating tumor proteins, circulating tumor cells (CTCs), extracellular vesicles (EVs), tumor-educated platelets (TEPs), and circulating tumor nucleic acids, namely circulating tumor DNA (ctDNA) and circulating tumor RNA (ctRNA). In this article, we summarize recent findings highlighting the promising role of liquid biopsies as novel potential biomarkers in HCC, emphasizing on its clinical performance.
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Affiliation(s)
- Tudor Mocan
- Octavian Fodor Institute for Gastroenterology and Hepatology, Iuliu Haţieganu, University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania;
| | - André L. Simão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal; (A.L.S.); (R.E.C.); (C.M.P.R.)
| | - Rui E. Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal; (A.L.S.); (R.E.C.); (C.M.P.R.)
| | - Cecília M. P. Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal; (A.L.S.); (R.E.C.); (C.M.P.R.)
| | - Artur Słomka
- Department of Pathophysiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum, 85-094 Bydgoszcz, Poland;
| | - Bingduo Wang
- Department of Internal Medicine I, University Hospital of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany; (B.W.); (C.S.)
| | - Christian Strassburg
- Department of Internal Medicine I, University Hospital of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany; (B.W.); (C.S.)
| | - Aliona Wöhler
- Department of General, Visceral and Thoracic Surgery, German Armed Forces Central Hospital Koblenz, 56072 Koblenz, Germany; (A.W.); (A.G.W.)
| | - Arnulf G. Willms
- Department of General, Visceral and Thoracic Surgery, German Armed Forces Central Hospital Koblenz, 56072 Koblenz, Germany; (A.W.); (A.G.W.)
| | - Miroslaw Kornek
- Department of Internal Medicine I, University Hospital of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany; (B.W.); (C.S.)
- Correspondence:
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25
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Hsieh CH, Chu CY, Lin SE, Yang YCS, Chang HS, Yen Y. TESC Promotes TGF-α/EGFR-FOXM1-Mediated Tumor Progression in Cholangiocarcinoma. Cancers (Basel) 2020; 12:cancers12051105. [PMID: 32365487 PMCID: PMC7281536 DOI: 10.3390/cancers12051105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/25/2020] [Accepted: 04/26/2020] [Indexed: 02/07/2023] Open
Abstract
Cholangiocarcinoma is a relatively uncommon but highly lethal malignancy. Improving outcomes in patients depends on earlier diagnosis and appropriate treatment; however, no satisfactory diagnostic biomarkers or targeted therapies are currently available. To address this shortcoming, we analyzed the transcriptomic datasets of cholangiocarcinoma from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and found that TESC is highly expressed in cholangiocarcinoma. Elevated cellular levels of TESC are correlated with larger tumor size and predict a poor survival outcome for patients. Knockdown of TESC via RNA interference suppresses tumor growth. RNA-sequencing analysis showed that silencing of TESC decreases the level of FOXM1, leading to cell cycle arrest. Correlation analysis revealed that the cellular level of TESC is correlated with that of FOXM1 in cholangiocarcinoma patients. We further observed that upon TGF-α induction, TESC is upregulated through the EGFR-STAT3 pathway and mediates TGF-α-induced tumor cell proliferation. In vivo experiments revealed that knockdown of TESC significantly attenuates tumor cell growth. Therefore, our data provide novel insight into TESC-mediated oncogenesis and reveal that TESC is a potential biomarker or serves as a therapeutic target for cholangiocarcinoma.
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Affiliation(s)
- Cheng-Han Hsieh
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Cheng-Ying Chu
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
- CRISPR Gene Targeting Core Lab, Taipei Medical University, Taipei 110, Taiwan
| | - Sey-En Lin
- Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taipei 110, Taiwan
| | - Yu-Chen S.H. Yang
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei 110, Taiwan
| | - Hung-Shu Chang
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Yun Yen
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
- Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Taipei 110, Taiwan
- Cancer Center, Taipei Municipal Wanfang Hospital, Taipei 110, Taiwan
- Correspondence: ; Tel.: +886-2-2736-1661 (ext. 1588); Fax: +886-2-2378-7795
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26
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Amir Hashim NA, Ab-Rahim S, Wan Ngah WZ, Nathan S, Ab Mutalib NS, Sagap I, A Jamal AR, Mazlan M. Global metabolomics profiling of colorectal cancer in Malaysian patients. ACTA ACUST UNITED AC 2020; 11:33-43. [PMID: 33469506 PMCID: PMC7803921 DOI: 10.34172/bi.2021.05] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 12/24/2022]
Abstract
Introduction: The serum metabolomics approach has been used to identify metabolite biomarkers that can diagnose colorectal cancer (CRC) accurately and specifically. However, the biomarkers identified differ between studies suggesting that more studies need to be performed to understand the influence of genetic and environmental factors. Therefore, this study aimed to identify biomarkers and affected metabolic pathways in Malaysian CRC patients. Methods: Serum from 50 healthy controls and 50 CRC patients were collected at UKM Medical Centre. The samples were deproteinized with acetonitrile and untargeted metabolomics profile determined using liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOFMS, Agilent USA). The data were analysed using Mass Profiler Professional (Agilent, USA) software. The panel of biomarkers determined were then used to identify CRC from a new set of 20 matched samples. Results: Eleven differential metabolites were identified whose levels were significantly different between CRC patients compared to normal controls. Based on the analysis of the area under the curve, 7 of these metabolites showed high sensitivity and specificity as biomarkers. The use of the 11 metabolites on a new set of samples was able to differentiate CRC from normal samples with 80% accuracy. These metabolites were hypoxanthine, acetylcarnitine, xanthine, uric acid, tyrosine, methionine, lysoPC, lysoPE, citric acid, 5-oxoproline, and pipercolic acid. The data also showed that the most perturbed pathways in CRC were purine, catecholamine, and amino acid metabolisms. Conclusion: Serum metabolomics profiling can be used to identify distinguishing biomarkers for CRC as well as to further our knowledge of its pathophysiological mechanisms.
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Affiliation(s)
- Nurul Azmir Amir Hashim
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Kampus Sungai Buloh, 47000 Sungai Buloh, Selangor, Malaysia.,Institute of Medical and Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Kampus Sungai Buloh, 47000 Sungai Buloh, Selangor, Malaysia
| | - Sharaniza Ab-Rahim
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Kampus Sungai Buloh, 47000 Sungai Buloh, Selangor, Malaysia
| | - Wan Zurinah Wan Ngah
- Universiti Kebangsaaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, 56000 Batu 9 Cheras, Wilayah Persekututan Kuala Lumpur, Malaysia
| | - Sheila Nathan
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Nurul Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Ismail Sagap
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia
| | - A Rahman A Jamal
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Musalmah Mazlan
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Kampus Sungai Buloh, 47000 Sungai Buloh, Selangor, Malaysia
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27
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Multifaceted Aspects of Metabolic Plasticity in Human Cholangiocarcinoma: An Overview of Current Perspectives. Cells 2020; 9:cells9030596. [PMID: 32138158 PMCID: PMC7140515 DOI: 10.3390/cells9030596] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 12/14/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a deadly tumor without an effective therapy. Unique metabolic and bioenergetics features are important hallmarks of tumor cells. Metabolic plasticity allows cancer cells to survive in poor nutrient environments and maximize cell growth by sustaining survival, proliferation, and metastasis. In recent years, an increasing number of studies have shown that specific signaling networks contribute to malignant tumor onset by reprogramming metabolic traits. Several evidences demonstrate that numerous metabolic mediators represent key-players of CCA progression by regulating many signaling pathways. Besides the well-known Warburg effect, several other different pathways involving carbohydrates, proteins, lipids, and nucleic acids metabolism are altered in CCA. The goal of this review is to highlight the main metabolic processes involved in the cholangio-carcinogeneis that might be considered as potential novel druggable candidates for this disease.
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28
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Jia X, Lu S, Zeng Z, Liu Q, Dong Z, Chen Y, Zhu Z, Hong Z, Zhang T, Du G, Xiang J, Wu D, Bai W, Yang B, Li Y, Huang J, Li H, Safadi R, Lu Y. Characterization of Gut Microbiota, Bile Acid Metabolism, and Cytokines in Intrahepatic Cholangiocarcinoma. Hepatology 2020; 71:893-906. [PMID: 31298745 DOI: 10.1002/hep.30852] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 07/02/2019] [Indexed: 12/15/2022]
Abstract
Intrahepatic cholangiocarcinoma (ICC), a type of bile duct cancer, has a high mortality rate. Gut microbiota, bile acid (BA) metabolism, and cytokines have not been characterized in patients with ICC, and better noninvasive diagnostic approaches for ICC are essential to be established. Therefore, in this study we aimed to improve our understanding of changes in gut microbiota, BA metabolism, and cytokines in patients with ICC. We found that the α-diversities and β-diversities of ICC were highest and that the abundances of four genera (Lactobacillus, Actinomyces, Peptostreptococcaceae, and Alloscardovia) were increased in patients with ICC compared with those in patients with hepatocellular carcinoma or liver cirrhosis and in healthy individuals. The glycoursodeoxycholic acid and tauroursodeoxycholic acid (TUDCA) plasma-stool ratios were obviously increased in patients with ICC. Furthermore, the genera Lactobacillus and Alloscardovia that were positively correlated with TUDCA plasma-stool ratios were combined to discriminate ICC from the other three diseases. Vascular invasion (VI) frequently led to a poor prognosis in patients with ICC. Compared with patients with ICC without VI, patients with VI had a greater abundance of the family Ruminococcaceae, increased levels of plasma interleukin (IL)-4 and six conjugated BAs, and decreased levels of plasma IL-6 and chenodeoxycholic acid. A positive correlation between plasma taurocholic acid and IL-4 was observed in patients with ICC. Plasma TUDCA was negatively correlated with the abundance of the genus Pseudoramibacter and the survival time of patients with ICC, but had no effect on tumor size, as determined in two murine tumor models. Conclusion: In this study, we identified some biomarkers, including gut microbiota, BAs and inflammatory cytokines, for the diagnosis of ICC and prediction of VI in patients with ICC.
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Affiliation(s)
- Xiaodong Jia
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Shanshan Lu
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Zhen Zeng
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Qingyan Liu
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Zheng Dong
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yan Chen
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Zhenyu Zhu
- Hepatobiliary Surgery Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Zhixian Hong
- Department of Hepatobiliary Surgery, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Ting Zhang
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Guifang Du
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Jiao Xiang
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Dawei Wu
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Wenlin Bai
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Bin Yang
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yinyin Li
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Jiagan Huang
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Haiyang Li
- Department of Hepatobiliary Surgery, The Hospital Affiliated to Guizhou Medical University, Guiyang, Guizhou, China
| | - Rifaat Safadi
- Hadassah Medical Organization, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Yinying Lu
- Comprehensive Liver Cancer Center, The Fifth Medical Center of PLA General Hospital, Beijing, China.,Center for Synthetic and Systems Biology (CSSB), Tsinghua University, Beijing, China
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29
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Win Maung HM, Chan-On W, Kunkeaw N, Khaenam P. Common transcriptional programs and the role of chemokine (C-C motif) ligand 20 ( CCL20) in cell migration of cholangiocarcinoma. EXCLI JOURNAL 2020; 19:154-166. [PMID: 32194362 PMCID: PMC7068202 DOI: 10.17179/excli2019-1893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/14/2020] [Indexed: 12/15/2022]
Abstract
The incidence of cholangiocarcinoma (CCA) has risen in many countries, but there is still no appropriate screening and treatment available. The growing number of microarray data published todays can be a powerful resource for the discovery of biomarkers to tackle challenges in the management of CCA. This study analyzed multiple microarray datasets to identify the common transcriptional networks in CCA and select a possible biomarker for functional study in CCA cell lines. A systematic searching identified 4 microarray datasets from Gene Expression Omnibus (GEO) repository and PubMed articles. Differential expression analysis between tumor and normal tissues was performed in each dataset. In order to characterize the common expression pattern, differentially expressed genes (DEGs) from all datasets were combined and visualized by hierarchical clustering and heatmap. Gene enrichment analysis performed in each cluster revealed that over-expressed DEGs were enriched in cell cycle, cell migration and response to cytokines while under-expressed DEGs were enriched in metabolic processes such as oxidation-reduction, lipid, and drug. To explain tumor characteristics, genes enriched in cell migration and response to cytokines were further investigated. Among these genes, CCL20 was selected for functional study because its role has never been studied in CCA. Moreover, its signaling may be regulated by disrupting its only receptor, CCR6. Treatment with recombinant CCL20 induced higher cell migration and increased expression of N-cad. In contrast, knockdown of CCR6 by siRNA reduced cell migration ability and decreased N-cadherin level. Altogether, these results suggested the contribution of CCL20/CCR6 signaling in cell migration through epithelial-mesenchymal transition process. Thus, CCL20/CCR6 signaling might be a target for the management of CCA.
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Affiliation(s)
- Hay Mar Win Maung
- Center for Standardization and Product Validation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Waraporn Chan-On
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Nawapol Kunkeaw
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Prasong Khaenam
- Center for Standardization and Product Validation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, 73170, Thailand
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30
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Kaur H, Dhall A, Kumar R, Raghava GPS. Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale Transcriptomics Data. Front Genet 2020; 10:1306. [PMID: 31998366 PMCID: PMC6967266 DOI: 10.3389/fgene.2019.01306] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022] Open
Abstract
The high mortality rate of hepatocellular carcinoma (HCC) is primarily due to its late diagnosis. In the past, numerous attempts have been made to design genetic biomarkers for the identification of HCC; unfortunately, most of the studies are based on small datasets obtained from a specific platform or lack reasonable validation performance on the external datasets. In order to identify a universal expression-based diagnostic biomarker panel for HCC that can be applicable across multiple platforms, we have employed large-scale transcriptomic profiling datasets containing a total of 2,316 HCC and 1,665 non-tumorous tissue samples. These samples were obtained from 30 studies generated by mainly four types of profiling techniques (Affymetrix, Illumina, Agilent, and High-throughput sequencing), which are implemented in a wide range of platforms. Firstly, we scrutinized overlapping 26 genes that are differentially expressed in numerous datasets. Subsequently, we identified a panel of three genes (FCN3, CLEC1B, and PRC1) as HCC biomarker using different feature selection techniques. Three-genes-based HCC biomarker identified HCC samples in training/validation datasets with an accuracy between 93 and 98%, Area Under Receiver Operating Characteristic curve (AUROC) in a range of 0.97 to 1.0. A reasonable performance, i.e., AUROC 0.91–0.96 achieved on validation dataset containing peripheral blood mononuclear cells, concurred their non-invasive utility. Furthermore, the prognostic potential of these genes was evaluated on TCGA-LIHC and GSE14520 cohorts using univariate survival analysis. This analysis revealed that these genes are prognostic indicators for various types of the survivals of HCC patients (e.g., Overall Survival, Progression-Free Survival, Disease-Free Survival). These genes significantly stratified high-risk and low-risk HCC patients (p-value <0.05). In conclusion, we identified a universal platform-independent three-genes-based biomarker that can predict HCC patients with high precision and also possess significant prognostic potential. Eventually, we developed a web server HCCpred based on the above study to facilitate scientific community (http://webs.iiitd.edu.in/raghava/hccpred/).
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Affiliation(s)
- Harpreet Kaur
- Bioinformatics Center, CSIR-Institute of Microbial Technology, Chandigarh, India.,Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Rajesh Kumar
- Bioinformatics Center, CSIR-Institute of Microbial Technology, Chandigarh, India.,Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
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31
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Huang Q, Chen G, Huang Y, Li J, Ding Y, Zhang S, Chi X, Xie Q, Ning Q, Xu L, Zhang J. Genetic variant rs3750625 in the 3'UTR of ADRA2A affects the sleep quality of patients in the ICU by promoting miR‑34a binding to ADRA2A. Int J Mol Med 2020; 45:910-918. [PMID: 31922215 DOI: 10.3892/ijmm.2020.4456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 05/10/2019] [Indexed: 11/06/2022] Open
Abstract
Poor sleep is very common in patients in the ICU and hence, sleep quality is considered an important aspect of intensive care; however, the underlying mechanisms of poor sleep in patients in the ICU remain unknown. In this study, we aimed to explore the role of rs3750625, which is located in the 3'UTR of adrenoceptor alpha 2A (ADRA2A), in sleep quality. For this purpose, luciferase assay was conducted to investigate the association between miR‑34a and ADRA2A, and the effect of rs3750625 on the binding affinity between miR‑34a and ADRA2A was examined. RT‑qPCR and western blot analysis were carried out to examine the regulatory association between miR‑34a and ADRA2A. The differences in sleep time and efficiency were compared between groups carrying the AC and CC genotypes of rs3750625, respectively. According to the results from an online search, miR‑34a could directly bind to the 3'UTR of ADRA2A, and such binding was confirmed by the observation that miR‑34a inhibited the luciferase activity of major or minor ADRA2A 3'UTR in a dose‑dependent manner in HCN‑1A and U251 cells. In addition, the ADRA2A protein and mRNA levels in the HCN‑1A and U251 cells were evidently decreased following transfection with miR‑34a precursors. Notably, patients in the AC group exhibited a similar level of miR‑34a mRNA expression compared with patients in the CC group; however, the ADRA2A mRNA and protein levels in the CC group were significantly increased in comparison with those in the AC group. In addition, the sleep time and sleep efficiency in the CC group were much higher than those in the AC group. Furthermore, the mean arterial pressure (MAP) values in both the AC and CC groups remained stable from 22:00 to 08:00, and the respiratory rates in both groups were quite similar. However, the heart rate of patients in the CC group was much lower than that of patients in the AC group. On the whole, the findings of this study suggest that the genetic variant rs3750625 in the 3'UTR of ADRA2A affects the sleep quality of patients in the ICU by promoting the binding of miR‑34a to ADRA2A, and hence it may serve as a novel biomarker for the prediction of the sleep quality of patients in the ICU.
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Affiliation(s)
- Qingping Huang
- ICU, Dongguan Houjie Hospital, Dongguan, Guangdong 523945, P.R. China
| | - Ganhai Chen
- ICU, Dongguan Houjie Hospital, Dongguan, Guangdong 523945, P.R. China
| | - Yanfang Huang
- Nursing Department, Dongguan Houjie Hospital, Dongguan, Guangdong 523945, P.R. China
| | - Jinting Li
- ICU, Dongguan Houjie Hospital, Dongguan, Guangdong 523945, P.R. China
| | - Yanjing Ding
- ICU, Dongguan Houjie Hospital, Dongguan, Guangdong 523945, P.R. China
| | - Shuqing Zhang
- Nursing Department, Dongguan Houjie Hospital, Dongguan, Guangdong 523945, P.R. China
| | - Xiuwen Chi
- School of Nursing, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Qiong Xie
- Nursing Department, Dongguan Houjie Hospital, Dongguan, Guangdong 523945, P.R. China
| | - Qinrong Ning
- Department of General Surgery, Dongguan Houjie Hospital, Dongguan, Guangdong 523945, P.R. China
| | - Liuqin Xu
- Nursing Department, Dongguan Houjie Hospital, Dongguan, Guangdong 523945, P.R. China
| | - Jianrong Zhang
- Nursing Department, Dongguan Houjie Hospital, Dongguan, Guangdong 523945, P.R. China
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32
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Chong J, Xia J. Using MetaboAnalyst 4.0 for Metabolomics Data Analysis, Interpretation, and Integration with Other Omics Data. Methods Mol Biol 2020; 2104:337-360. [PMID: 31953825 DOI: 10.1007/978-1-0716-0239-3_17] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
MetaboAnalyst ( www.metaboanalyst.ca ) is an easy-to-use, comprehensive web-based tool, freely available for metabolomics data processing, statistical analysis, functional interpretation, as well as integration with other omics data. This chapter first provides an introductory overview to the current MetaboAnalyst (version 4.0) with regards to its underlying design concepts and user interface structure. Subsequent sections describe three common metabolomics data analysis workflows covering targeted metabolomics, untargeted metabolomics, and multi-omics data integration.
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Affiliation(s)
- Jasmine Chong
- Institute of Parasitology, McGill University, Montreal, QC, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, QC, Canada.
- Department of Animal Science, McGill University, Montreal, QC, Canada.
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
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He QL, Qin SY, Tao L, Ning HJ, Jiang HX. Prognostic value and prospective molecular mechanism of miR-100-5p in hepatocellular carcinoma: A comprehensive study based on 1,258 samples. Oncol Lett 2019; 18:6126-6142. [PMID: 31788087 PMCID: PMC6865135 DOI: 10.3892/ol.2019.10962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023] Open
Abstract
The prognostic value and molecular mechanism of microRNA-100-5p (miR-100-5p) in hepatocellular carcinoma (HCC) are still unclear. To explore the prognostic value and the mechanism of miR-100-5p in HCC, the present study analyzed the results of 18 previous studies and bioinformatic datasets. The clinical significance of miR-100-5p and its targets in HCC were investigated using The Cancer Genome Atlas and the Gene Expression Omnibus, as well as relevant literature. In total, 12 online tools were used to predict the target genes of miR-100-5p. Bioinformatics analysis and Spearman correlation analysis were performed, and genomic alterations of the hub genes were evaluated. A meta-analysis with 1,258 samples revealed that miR-100-5p was significantly downregulated in HCC [standard mean difference (SMD), -0.94; 95% confidence interval (CI), -1.14 to -0.74; I2, 35.2%]. Lower miR-100-5p expression was associated with poorer clinical characteristics and a poorer prognosis for patients with HCC. Additionally, bioinformatics analysis revealed that the 'regulation of transcription', 'chromatin remodeling complex', 'transcription regulator activity', 'pathways in cancer' and 'heparan sulfate biosynthesis' were the most enriched terms. Furthermore, expression of histone deacetylase (HDAC)2, HDAC3, SHC-transforming protein 1 (SHC1), Ras-related protein Rac1 (RAC1) and E3 ubiquitin-protein ligase CBL (CBL) was negatively correlated with miR-100-5p expression. Among these, upregulated HDAC2 [hazard ratio (HR), 1.910; 95% CI, 1.309-2.787; P=0.0007], HDAC3 (HR, 1.474; 95% CI, 1.012-2.146; P=0.0435), SHC1 (HR, 1.52; 95% CI, 1.043-2.215; P=0.0281) and RAC1 (HR, 1.817; 95% CI, 1.248-2.645; P=0.0022) were associated with shorter survival. Alterations in HDAC2, SHC1, RAC1 and IGF1R were linked with a poorer outcome for HCC, and alternative splicing of SHC and RAC1 were significantly decreased and increased in HCC, respectively. In summary, the downregulation of miR-100-5p may be involved in the progression and prognosis of HCC. The upregulation of HDAC2, HDAC3, SHC1 and RAC1 may indicate a poorer survival rate for patients with HCC. Thus, miR-100-5p and these 4 potential target genes may provide novel therapeutic targets and prognostic predictors for patients with HCC.
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Affiliation(s)
- Qing-Lin He
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Shan-Yu Qin
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Lin Tao
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hong-Jian Ning
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hai-Xing Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Satriano L, Lewinska M, Rodrigues PM, Banales JM, Andersen JB. Metabolic rearrangements in primary liver cancers: cause and consequences. Nat Rev Gastroenterol Hepatol 2019; 16:748-766. [PMID: 31666728 DOI: 10.1038/s41575-019-0217-8] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/19/2019] [Indexed: 02/07/2023]
Abstract
Primary liver cancer (PLC) is the fourth most frequent cause of cancer-related death. The high mortality rates arise from late diagnosis and the limited accuracy of diagnostic and prognostic biomarkers. The liver is a major regulator, orchestrating the clearance of toxins, balancing glucose, lipid and amino acid uptake, managing whole-body metabolism and maintaining metabolic homeostasis. Tumour onset and progression is frequently accompanied by rearrangements of metabolic pathways, leading to dysregulation of metabolism. The limitation of current therapies targeting PLCs, such as hepatocellular carcinoma and cholangiocarcinoma, points towards the importance of deciphering this metabolic complexity. In this Review, we discuss the role of metabolic liver disruptions and the implications of these processes in PLCs, emphasizing their clinical relevance and value in early diagnosis and prognosis and as putative therapeutic targets. We also describe system biology approaches able to reconstruct the metabolic complexity of liver diseases. We also discuss whether metabolic rearrangements are a cause or consequence of PLCs, emphasizing the opportunity to clinically exploit the rewired metabolism. In line with this idea, we discuss circulating metabolites as promising biomarkers for PLCs.
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Affiliation(s)
- Letizia Satriano
- Biotech Research and Innovation Centre (BRIC) Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Monika Lewinska
- Biotech Research and Innovation Centre (BRIC) Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pedro M Rodrigues
- Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Jesus M Banales
- Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC) Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Alsaleh M, Sithithaworn P, Khuntikeo N, Loilome W, Yongvanit P, Chamadol N, Hughes T, O'Connor T, Andrews RH, Holmes E, Taylor-Robinson SD. Characterisation of the Urinary Metabolic Profile of Liver Fluke-Associated Cholangiocarcinoma. J Clin Exp Hepatol 2019; 9:657-675. [PMID: 31889746 PMCID: PMC6926188 DOI: 10.1016/j.jceh.2019.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 06/26/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human infection with Opisthorchis viverrini, a carcinogenic liver fluke inhabiting the biliary tree, is endemic in Southeast Asia. Chronic infection is associated with a fatal complication, cholangiocarcinoma (CCA), a late-presenting and aggressive malignancy. Currently, annual mortality rates from CCA mirror trends in incidence, due in part to limited availability of efficient prognostic and early diagnostic biomarkers. With ability to detect thousands of urinary metabolites using metabonomics, the urine metabolome holds great potential in providing an insight into system-level alterations in carcinogenesis and in identifying metabolic markers altered in response to disturbed homoeostasis. METHODS Global molecular profiling using reversed-phase ultraperformance liquid chromatography mass spectrometry was utilised to acquire the urinary spectral profile of 137 Thai subjects (48 at high risk of infection, 41 with O. viverrini infection, 34 periportal fibrosis and 14 CCA) from Khon Kaen, Thailand. RESULTS Multivariate statistical analysis identified perturbation in several molecular classes related to purine metabolism and lipid metabolism in the CCA urine metabolome. These markers mainly reflect changes in energy metabolism to support proliferation (increased fatty acid oxidation and purine recycling), DNA methylation and hepatic injury. CONCLUSIONS Several metabolites of biological interest were discovered from this proof-of-principle dataset. Augmenting these findings is essential to accelerate the development of urinary metabolic markers in CCA.
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Key Words
- Opisthorchis viverrini
- acetaminophen, APAP
- bile duct cancer
- carnitine palmitoyltransferase 1, CPT1
- carnitine palmitoyltransferase 2, CPT2
- carnitine/acylcarnitine translocase, CACT
- cholangiocarcinoma screening and care program, CASCAP
- cholangiocarcinoma, CCA
- data-dependent acquisition, DDA
- electrospray ionisation, ESI
- hypoxanthine phosphoribosyltransferase 1, HPRT1
- hypoxanthine-guanine phosphoribosyltransferase, HPRT
- mass spectrometry
- metabonomics
- orthogonal projections to latent structures discriminant analysis, OPLS-DA
- periductal fibrosis, PDF
- periportal fibrosis, PPF
- primary biliary cholangitis, PBC
- primary sclerosing cholangitis, PSC
- principal component analysis, PCA
- reversed-phase ultra-performance liquid-chromatography mass spectrometry, RP-UPLC-MS
- ultra-performance liquid chromatography mass spectrometry, UPLC-MS
- variable importance in projection, VIP
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Affiliation(s)
- Munirah Alsaleh
- Division of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Paiboon Sithithaworn
- Cholangiocarcinoma Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Narong Khuntikeo
- Cholangiocarcinoma Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Watcharin Loilome
- Cholangiocarcinoma Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Puangrat Yongvanit
- Cholangiocarcinoma Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Nittaya Chamadol
- Cholangiocarcinoma Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Thomas Hughes
- Division of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Thomas O'Connor
- Division of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Ross H. Andrews
- Division of Surgery and Cancer, Imperial College London, London, United Kingdom
- Cholangiocarcinoma Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Elaine Holmes
- Division of Surgery and Cancer, Imperial College London, London, United Kingdom
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Wu HY, Xia S, Liu AG, Wei MD, Chen ZB, Li YX, He Y, Liao MJ, Hu QP, Pan SL. Upregulation of miR‑132‑3p in cholangiocarcinoma tissues: A study based on RT‑qPCR, The Cancer Genome Atlas miRNA sequencing, Gene Expression Omnibus microarray data and bioinformatics analyses. Mol Med Rep 2019; 20:5002-5020. [PMID: 31638221 PMCID: PMC6854587 DOI: 10.3892/mmr.2019.10730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/05/2019] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs/miRs) have been reported to be closely associated with numerous human diseases, including cholangiocarcinoma (CCA). However, the number of miRNAs known to be involved in CCA is limited, and the association between miR-132-3p and CCA remains unknown. In the present study, the clinical role of miR-132-3p and its potential signaling pathways were investigated by multiple approaches. Reverse transcription-quantitative PCR (RT-qPCR), CCA-associated Gene Expression Omnibus (GEO), ArrayExpress and Sequence Read Archive (SRA) miRNA-microarray or miRNA-sequencing data were screened, and meta-analyses were conducted, in order to calculate the receiver operating characteristic (ROC) curve and standardized mean difference (SMD). The predicted target genes of miR-132-3p were obtained from 12 online databases and were combined with the downregulated differentially expressed genes identified in the RNA-sequencing data of CCA. Gene Ontology annotation and pathway analysis were performed in WebGestalt. Protein-protein interaction analyses were conducted in STRING. The Cancer Genome Atlas (TCGA) mRNA expression profiles were used to validate the expression levels of hub genes at the mRNA level. The Human Protein Atlas was used to identify the protein expression levels of hub genes in CCA tissues and non-tumor biliary epithelium. The meta-analyses comprised 10 groups of RT-qPCR data, eight GEO microarray datasets and one TCGA miRNA-sequencing dataset. The SMD of miR-132-3p in CCA was 0.75 (95% CI: 0.25, 1.24), which indicated that miR-132-3p was overexpressed in CCA tissues. This finding was supported by a summary ROC value of 0.80 (95% CI: 0.76, 0.83). The pooled sensitivity and specificity were 0.81 (95% CI: 0.59, 0.93) and 0.71 (95% CI: 0.58, 0.81), respectively. The relative expression level of miR-132-3p in the early stage of CCA (stages I–II) was 6.8754±0.5279, which was markedly lower than that in the advanced stage (stages III–IVB), 7.3034±0.3267 (P=0.003). Consistently, the miR-132-3p level in low-grade CCA (grades G1-G2) was 6.7581±0.5297, whereas it was 7.1191±0.4651 in patients with high-grade CCA (grades G3-G4) (P=0.037). Furthermore, 555 potential target genes of miR-132-3p in CCA were mainly enriched in the ‘Focal Adhesion-PI3K-Akt-mTOR-signaling pathway’. In conclusion, upregulation of miR-132-3p may serve a pivotal role in the tumorigenesis and progression of CCA by targeting different pathways. Further in vitro and in vivo studies are required to support the current findings.
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Affiliation(s)
- Hua-Yu Wu
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Shuang Xia
- Department of Human Anatomy, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - An-Gui Liu
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Min-Da Wei
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Zhong-Biao Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yu-Xin Li
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yu He
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Min-Jun Liao
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Qi-Ping Hu
- Department of Cell Biology and Genetics, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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37
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Zahid KR, Yao S, Khan ARR, Raza U, Gou D. mTOR/HDAC1 Crosstalk Mediated Suppression of ADH1A and ALDH2 Links Alcohol Metabolism to Hepatocellular Carcinoma Onset and Progression in silico. Front Oncol 2019; 9:1000. [PMID: 31637215 PMCID: PMC6787164 DOI: 10.3389/fonc.2019.01000] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/17/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is ranked the third deadliest cancer worldwide whose molecular pathogenesis is not fully understood. Although deregulated metabolic pathways have been implicated in HCC onset and progression, the mechanisms triggering this metabolic imbalance are yet to be explored. Here, we identified a gene signature coding catabolic enzymes (Cat-GS) involved in key metabolic pathways like amino acid, lipid, carbohydrate, drug, and retinol metabolism as suppressed in HCC. A higher expression of deregulated Cat-GS is associated with good survival and less aggressive disease state in HCC patients. On the other hand, we identified mTOR signaling as a key determinant in HCC onset and progression, whose hyperactivation is found associated with poor survival and aggressive disease state in HCC patients. Next, out of Cat-GS, we established two key regulators of alcohol metabolism, alcohol dehydrogenase 1A (ADH1A) and aldehyde dehydrogenase 2 (ALDH2), as being transcriptionally suppressed by histone deacetylase 1 (HDAC1) at the downstream of mTORC1 signaling. Suppressed ADH1A and ALDH2 expression aligns well with HCC-specific molecular profile and can efficiently predict disease onset and progression, whereas higher ADH1A and ALDH2 expression is associated with good survival and less aggressive disease state in HCC patients. Overall, our in silico findings suggest that transcriptional suppression of alcohol metabolism regulators, ADH1A and ALDH2, at the downstream of mTOR signaling is, in part, responsible for triggering oncogenic transformation of hepatocytes resulting in disease onset and progression in HCC.
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Affiliation(s)
- Kashif Rafiq Zahid
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Provincial Key Laboratory of Regional Immunity and Diseases, Carson International Cancer Center, Shenzhen University, Shenzhen, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering Shenzhen University, Shenzhen, China
| | - Shun Yao
- Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Abdur Rehman Raza Khan
- Military College of Signals, National University of Science and Technology, Rawalpindi, Pakistan
| | - Umar Raza
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Provincial Key Laboratory of Regional Immunity and Diseases, Carson International Cancer Center, Shenzhen University, Shenzhen, China
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38
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Taguchi YH, Turki T. Tensor Decomposition-Based Unsupervised Feature Extraction Applied to Single-Cell Gene Expression Analysis. Front Genet 2019; 10:864. [PMID: 31608111 PMCID: PMC6761323 DOI: 10.3389/fgene.2019.00864] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/19/2019] [Indexed: 12/14/2022] Open
Abstract
Although single-cell RNA sequencing (scRNA-seq) technology is newly invented and a promising one, but because of lack of enough information that labels individual cells, it is hard to interpret the obtained gene expression of each cell. Because of insufficient information available, unsupervised clustering, for example, t-distributed stochastic neighbor embedding and uniform manifold approximation and projection, is usually employed to obtain low-dimensional embedding that can help to understand cell–cell relationship. One possible drawback of this strategy is that the outcome is highly dependent upon genes selected for the usage of clustering. In order to fulfill this requirement, there are many methods that performed unsupervised gene selection. In this study, a tensor decomposition (TD)-based unsupervised feature extraction (FE) was applied to the integration of two scRNA-seq expression profiles that measure human and mouse midbrain development. TD-based unsupervised FE could select not only coincident genes between human and mouse but also biologically reliable genes. Coincidence between two species as well as biological reliability of selected genes is increased compared with that using principal component analysis (PCA)-based FE applied to the same data set in the previous study. Since PCA-based unsupervised FE outperformed the other three popular unsupervised gene selection methods, highly variable genes, bimodal genes, and dpFeature, TD-based unsupervised FE can do so as well. In addition to this, 10 transcription factors (TFs) that might regulate selected genes and might contribute to midbrain development were identified. These 10 TFs, BHLHE40, EGR1, GABPA, IRF3, PPARG, REST, RFX5, STAT3, TCF7L2, and ZBTB33, were previously reported to be related to brain functions and diseases. TD-based unsupervised FE is a promising method to integrate two scRNA-seq profiles effectively.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, Tokyo, Japan
| | - Turki Turki
- Department of Computer Science, King Abdulaziz University, Jeddah, Saudi Arabia
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39
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Macias RIR, Kornek M, Rodrigues PM, Paiva NA, Castro RE, Urban S, Pereira SP, Cadamuro M, Rupp C, Loosen SH, Luedde T, Banales JM. Diagnostic and prognostic biomarkers in cholangiocarcinoma. Liver Int 2019; 39 Suppl 1:108-122. [PMID: 30843325 DOI: 10.1111/liv.14090] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
The high mortality rate of cholangiocarcinoma (CCA) is due, in part, to the lack of non-invasive approaches able to accurately detect this silent tumour at early stages, when therapeutic options can be potentially curative or may at least increase the overall survival of patients. The fact that the majority of CCA tumours are not linked to any known aetiological factor highly compromises the monitoring of patients at risk for tumour development and also their early diagnosis. Combination of clinical/biochemical features, imaging techniques and analysis of non-specific tumour biomarkers in serum are commonly used to help in the diagnosis of CCA, but tumour biopsy is usually required to confirm the diagnosis. Moreover, no prognostic biomarkers are currently used in the clinical setting, deserving more innovative research, and international validation and consensus. Important efforts have been made in the last few years to identify accurate non-invasive biomarkers, by using innovative techniques and high-throughput omics technologies. This review summarizes and discusses the advances in the investigation of novel diagnostic and prognostic biomarkers in CCA and envisions the future directions in this field of research.
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Affiliation(s)
- Rocio I R Macias
- Experimental Hepatology and Drug Targeting (HEVEFARM), University of Salamanca, IBSAL, Salamanca, Spain.,Centre for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Miroslaw Kornek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany.,Department of General, Visceral and Thoracic Surgery, German Armed Forces Central Hospital, Koblenz, Germany
| | - Pedro M Rodrigues
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Nuno A Paiva
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Rui E Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Sabine Urban
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Stephen P Pereira
- Institute for Liver & Digestive Health, Royal Free Hospital Campus, University College London, London, UK
| | | | - Christian Rupp
- Department of Internal Medicine IV, Medical University of Heidelberg, Heidelberg, Germany
| | - Sven H Loosen
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Tom Luedde
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany.,Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH, Aachen, Germany
| | - Jesus M Banales
- Centre for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain.,Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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40
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Sirica AE, Gores GJ, Groopman JD, Selaru FM, Strazzabosco M, Wang XW, Zhu AX. Intrahepatic Cholangiocarcinoma: Continuing Challenges and Translational Advances. Hepatology 2019; 69:1803-1815. [PMID: 30251463 PMCID: PMC6433548 DOI: 10.1002/hep.30289] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) has over the last 10-20 years become the focus of increasing concern, largely due to its rising incidence and high mortality rates worldwide. The significant increase in mortality rates from this primary hepatobiliary cancer, particularly over the past decade, has coincided with a rapidly growing interest among clinicians, investigators, and patient advocates to seek greater mechanistic insights and more effective biomarker-driven targeted approaches for managing and/or preventing this challenging liver cancer. In addition to discussing challenges posed by this aggressive cancer, this review will emphasize recent epidemiological, basic, and translational research findings for iCCA. In particular, we will highlight emerging demographic changes and evolving risk factors, the critical role of the tumor microenvironment, extracellular vesicle biomarkers and therapeutics, intertumoral and intratumoral heterogeneity, and current and emerging targeted therapies regarding iCCA. Specifically, recent evidence linking non-bile duct medical conditions, such as nonalcoholic fatty liver disease and nonspecific cirrhosis, to intrahepatic cholangiocarcinogenesis together with geographic and ethnic variation will be assessed. Recent developments concerning the roles played by transforming growth factor-β and platelet-derived growth factor D in driving the recruitment and expansion of cancer-associated myofibroblasts within cholangiocarcinoma (CCA) stroma as well as their therapeutic implications will also be discussed. In addition, the potential significance of extracellular vesicles as bile and serum biomarkers and therapeutic delivery systems for iCCA will be described. An integrated systems approach to classifying heterogeneous iCCA subtypes will be further highlighted, and recent clinical trials and emerging targeted therapies will be reviewed, along with recommendations for future translational research opportunities. Established international CCA networks are now facilitating collaborations aimed at advancing iCCA translational and clinical research.
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Affiliation(s)
- Alphonse E. Sirica
- Department of Pathology, Division of Cellular and Molecular Pathogenesis, Virginia Commonwealth University School of Medicine, Richmond, VA 23298;
| | - Gregory J. Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905;
| | - John D. Groopman
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205;
| | - Florin M. Selaru
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Johns Hopkins University, Baltimore, MD 21205;
| | - Mario Strazzabosco
- Liver Center, Section of Digestive Diseases, Department of Internal Medicine,Yale University School of Medicine, New Haven, CT 06520;
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Andrew X. Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114;
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41
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Taguchi YH. Drug candidate identification based on gene expression of treated cells using tensor decomposition-based unsupervised feature extraction for large-scale data. BMC Bioinformatics 2019; 19:388. [PMID: 30717646 PMCID: PMC7394334 DOI: 10.1186/s12859-018-2395-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/25/2018] [Indexed: 02/08/2023] Open
Abstract
Background Although in silico drug discovery is necessary for drug development, two major strategies, a structure-based and ligand-based approach, have not been completely successful. Currently, the third approach, inference of drug candidates from gene expression profiles obtained from the cells treated with the compounds under study requires the use of a training dataset. Here, the purpose was to develop a new approach that does not require any pre-existing knowledge about the drug–protein interactions, but these interactions can be inferred by means of an integrated approach using gene expression profiles obtained from the cells treated with the analysed compounds and the existing data describing gene–gene interactions. Results In the present study, using tensor decomposition-based unsupervised feature extraction, which represents an extension of the recently proposed principal-component analysis-based feature extraction, gene sets and compounds with a significant dose-dependent activity were screened without any training datasets. Next, after these results were combined with the data showing perturbations in single-gene expression profiles, genes targeted by the analysed compounds were inferred. The set of target genes thus identified was shown to significantly overlap with known target genes of the compounds under study. Conclusions The method is specifically designed for large-scale datasets (including hundreds of treatments with compounds), not for conventional small-scale datasets. The obtained results indicate that two compounds that have not been extensively studied, WZ-3105 and CGP-60474, represent promising drug candidates targeting multiple cancers, including melanoma, adenocarcinoma, liver carcinoma, and breast, colon, and prostate cancers, which were analysed in this in silico study. Electronic supplementary material The online version of this article (10.1186/s12859-018-2395-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan.
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42
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Transcriptome and metabolome analyses reveal global behaviour of a genetically engineered methanol-independent Pichia pastoris strain. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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43
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Ni JS, Zheng H, Huang ZP, Hong YG, Ou YL, Tao YP, Wang MC, Wang ZG, Yang Y, Zhou WP. MicroRNA-197-3p acts as a prognostic marker and inhibits cell invasion in hepatocellular carcinoma. Oncol Lett 2018; 17:2317-2327. [PMID: 30675297 PMCID: PMC6341871 DOI: 10.3892/ol.2018.9848] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 11/16/2018] [Indexed: 01/27/2023] Open
Abstract
MicroRNAs (miRNAs) serve an important regulatory role in carcinogenesis and cancer progression. Aberrant expression of miR-197-3p has been reported in various human malignancies. However, the role of miR-197-3p in the progression and prognosis of hepatocellular carcinoma (HCC) remains unknown. The present study demonstrated that miR-197-3p was downregulated in HCC tissues and that the low level of miR-197-3p expression in HCC tumours correlated with aggressive clinicopathological characteristics; thus, miR-197-3p may serve as a predictor for poor prognosis in patients with HCC. Additionally, miR-197-3p markedly inhibited the metastasis of HCC cells in vitro and in vivo. Bioinformatics analysis further identified zinc finger protein interacted with K protein 1 (ZIK1) as a novel target of miR-197-3p in HCC cells. These findings suggest that miR-197-3p may regulate the survival of HCC cells, partially through the downregulation of ZIK1. Therefore, the miR-197-3p/ZIK1 axis may serve as a novel therapeutic target in patients with HCC.
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Affiliation(s)
- Jun-Sheng Ni
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Hao Zheng
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Zhi-Ping Huang
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China.,Department of Hepatobiliary Surgery, General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, P.R. China
| | - Yong-Gang Hong
- Department of Colorectal Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Yang-Liu Ou
- Department of Colorectal Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Yuan-Ping Tao
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Meng-Chao Wang
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Zhen-Guang Wang
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Yuan Yang
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Wei-Ping Zhou
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
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44
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Zhou G, Xia J. Using OmicsNet for Network Integration and 3D Visualization. ACTA ACUST UNITED AC 2018; 65:e69. [DOI: 10.1002/cpbi.69] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Guangyan Zhou
- Institute of Parasitology, McGill University, Sainte Anne de Bellevue; Quebec Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Sainte Anne de Bellevue; Quebec Canada
- Department of Animal Sciences, McGill University, Sainte Anne de Bellevue; Quebec Canada
- Department of Microbiology and Immunology, McGill University; Montreal Quebec Canada
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Pan WY, Zeng JH, Wen DY, Wang JY, Wang PP, Chen G, Feng ZB. Oncogenic value of microRNA-15b-5p in hepatocellular carcinoma and a bioinformatics investigation. Oncol Lett 2018; 17:1695-1713. [PMID: 30675229 PMCID: PMC6341845 DOI: 10.3892/ol.2018.9748] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 10/12/2018] [Indexed: 02/07/2023] Open
Abstract
miR-15b-5p has frequently been reported to function as a biomarker in some malignancies; however, the function of miR-15b-5p in hepatocellular carcinoma (HCC) and its molecular mechanism are still not well understood. The present study was designed to confirm the clinical value of miR-15b-5p and further explore its underlying molecular mechanism. A comprehensive investigation of the clinical value of miR-15b-5p in HCC was investigated by data mining The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets as well as literature. In addition, intersected target genes of miR-15b-5p were predicted using the miRWalk database and differentially expressed genes of HCC from TCGA. Furthermore, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were carried out. Then, a protein-protein interaction network (PPI) was constructed to reveal the interactions between some hub target genes of miR-15b-5p. The miR-15b-5p expression level in HCC was predominantly overexpressed compared with non-HCC tissues samples (SMD=0.618, 95% CI: 0.207, 1.029; P<0.0001) based on 991 HCC and 456 adjacent non-HCC tissue samples. The pooled summary receiver operator characteristic (SROC) of miR-15b-5p was 0.81 (Q*=0.74), and the pooled sensitivity and specificity of miR-15b-5p in HCC were 72% (95% CI: 69–75%) and 68% (95% CI: 65–72%), respectively. Bioinformatically, 225 overlapping genes were selected as prospective target genes of miR-15b-5p in HCC, and profoundly enriched GO terms and KEGG pathway investigation in silico demonstrated that the target genes were associated with prostate cancer, proximal tubule bicarbonate reclamation, heart trabecula formation, extracellular space, and interleukin-1 receptor activity. Five genes (ACACB, RIPK4, MAP2K1, TLR4 and IGF1) were defined as hub genes from the PPI network. The high expression of miR-15b-5p could play an essential part in hepatocarcinogenesis through diverse regulation approaches.
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Affiliation(s)
- Wen-Ya Pan
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jiang-Hui Zeng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Dong-Yue Wen
- Department of Ultrasonography, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jie-Yu Wang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Peng-Peng Wang
- Department of Nursing, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Zhen-Bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Zhong XZ, Deng Y, Chen G, Yang H. Investigation of the clinical significance and molecular mechanism of miR-21-5p in hepatocellular carcinoma: A systematic review based on 24 studies and bioinformatics investigation. Oncol Lett 2018; 17:230-246. [PMID: 30655760 PMCID: PMC6313181 DOI: 10.3892/ol.2018.9627] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 06/26/2018] [Indexed: 12/31/2022] Open
Abstract
To investigate the prospective roles and the clinicopathological application of microRNA-21-5p (miR-21-5p) in hepatocellular carcinoma (HCC), the present review is based on 24 studies and bioinformatics investigation. Firstly, HCC-associated miR-21-5p data were aggregated from literature databases and two public genomic data repositories, including the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Potential target genes of miR-21-5p in HCC were identified using TCGA and GEO, Natural Language Processing and 14 online software packages. The oncogenic roles of these target genes was probed for understanding using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis. Hub genes were further investigated by protein-protein interaction network (PPI) analysis. Comprehensive meta-analysis, including 10 microarrays from GEO datasets, 13 literature studies and TCGA-based RNA sequencing data, indicated a reliable diagnostic capacity of miR-21-5p [area under the curve (AUC), 0.887; sensitivity, 0.78% and specificity, 0.79%]. The healthy control group (AUC, 0.926; sensitivity, 0.87% and specificity, 0.82%) demonstrated high diagnostic capacity of miR-21-5p compared with the chronic hepatitis B infection group (AUC, 0.904; sensitivity, 0.75% and specificity, 0.84%). A total of 10 significant enrichment pathways were indicated by KEGG analysis, with cytokine-cytokine receptor interaction exhibiting the highest score. A total of 5 genes, hepatocyte growth factor, forkhead box O1 (FOXO1), thrombospondin 1, estrogen receptor 1 (ESR1) and C-X-C motif chemokine ligand 12 were selected from 39 overlapping genes, according to the PPI network. Target genes were assembled in GO terms associated with ‘response to chemical stimulus’, ‘cell surface’ and ‘growth factor binding’. In particular, low expression of FOXO1 and ESR1 was associated with miR-21-5p expression. In conclusion, upregulated expression of miR-21-5p may be a functional regulator of the metabolism or apoptosis in HCC and a novel tumor marker for the early diagnosis of HCC.
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Affiliation(s)
- Xiao-Zhu Zhong
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yun Deng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hong Yang
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Wen DY, Huang JC, Wang JY, Pan WY, Zeng JH, Pang YY, Yang H. Potential clinical value and putative biological function of miR-122-5p in hepatocellular carcinoma: A comprehensive study using microarray and RNA sequencing data. Oncol Lett 2018; 16:6918-6929. [PMID: 30546424 PMCID: PMC6256359 DOI: 10.3892/ol.2018.9523] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023] Open
Abstract
In order to determine the diagnostic efficacy of microRNA (miR)-122-5p and to identify the potential molecular signaling pathways underlying the function of miR-122-5p in hepatocellular carcinoma (HCC), the expression profiles of data collected from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and literature databases were analyzed, along with any associations between clinicopathological characteristics and the diagnostic value of miR-122-5p in HCC. The intersection of 12 online prediction databases and differentially expressed genes from TCGA and GEO were utilized in order to select the prospective target genes of miR-122-5p in HCC. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction network (PPI) analyses were subsequently performed based on the selected target genes. The average expression level of miR-122-5p was decreased in HCC patients compared with controls from TCGA database (P<0.001), and the downregulation of miR-122-5p was significantly associated with HCC tissues (P<0.001), tumor vascular invasion (P<0.001), metastasis (P=0.001), sex (P=0.006), virus infection status (P=0.001) and tissue (compared with serum; P<0.001) in cases from the GEO database. The pooled sensitivity and specificity for miR-122-5p to diagnose HCC were 0.60 [95% confidence interval (CI), 0.48–0.71] and 0.81 (95% CI, 0.70–0.89), respectively. The area under the curve (AUC) value was 0.76 (95% CI, 0.72–0.80), while in Meta-DiSc 1.4, the AUC was 0.76 (Q*=0.70). The pooled sensitivity and specificity were 0.60 (95% CI, 0.57–0.62) and 0.79 (95% CI, 0.76–0.81), respectively. A total of 198 overlapping genes were selected as the potential target genes of miR-122-5p, and 7 genes were defined as the hub genes from the PPI network. Cell division cycle 6 (CDC6), minichromosome maintenance complex component 4 (MCM4) and MCM8, which serve pivotal functions in the occurrence and development of HCC, were the most significant hub genes. The regulation of cell proliferation for cellular adhesion and the biosynthesis of amino acids was highlighted in the GO and KEGG pathway analyses. The downregulation of miR-122-5p in HCC demonstrated diagnostic value, worthy of further attention. Therefore, miR-122-5p may function as a tumor suppressor by modulating genome replication.
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Affiliation(s)
- Dong-Yue Wen
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jia-Cheng Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jie-Yu Wang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Wen-Ya Pan
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jiang-Hui Zeng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yu-Yan Pang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hong Yang
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Novel tumor suppressor SPRYD4 inhibits tumor progression in hepatocellular carcinoma by inducing apoptotic cell death. Cell Oncol (Dordr) 2018; 42:55-66. [PMID: 30238408 DOI: 10.1007/s13402-018-0407-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-associated deaths worldwide. Although recent studies have proposed different biomarkers for HCC progression and therapy resistance, a better understanding of the molecular mechanisms underlying HCC progression and recurrence, as well as the identification of molecular markers with a higher diagnostic accuracy, are necessary for the development of more effective clinical management strategies. Here, we aimed to identify novel players in HCC progression. METHODS SPRYD4 mRNA and protein expression analyses were carried out on a normal liver-derived cell line (HL-7702) and four HCC-derived cell lines (HepG2, SMMC7721, Huh-7, BEL-7402) using qRT-PCR and Western blotting, respectively. Cell proliferation Cell Counting Kit-8 (CCK-8) assays, protein expression analyses for apoptosis markers using Western blotting, and Caspase-Glo 3/7 apoptosis assays were carried out on the four HCC-derived cell lines. Expression comparison, functional annotation, gene set enrichment, correlation and survival analyses were carried out on patient data retrieved from the NCBI Gene module, the NCBI GEO database and the TCGA database. RESULTS Through a meta-analysis we found that the expression of SPRYD4 was downregulated in primary HCC tissues compared to non-tumor tissues. We also found that the expression of SPRYD4 was downregulated in HCC-derived cells compared to normal liver-derived cells. Subsequently, we found that the expression of SPRYD4 was inversely correlated with a gene signature associated with HCC cell proliferation. Exogenous SPRYD4 expression was found to inhibit HCC cell proliferation by inducing apoptotic cell death. We also found that SPRYD4 expression was associated with a good prognosis and that its expression became downregulated when HCCs progressed towards more aggressive stages and higher grades. Finally, we found that SPRYD4 expression may serve as a biomarker for a good overall and relapse-free survival in HCC patients. CONCLUSIONS Our data indicate that a decreased SPRYD4 expression may serve as an independent predictor for a poor prognosis in patients with HCC and that increased SPRYD4 expression may reduce HCC growth and progression through the induction of apoptotic cell death, thereby providing a potential therapeutic target.
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Principal Component Analysis-Based Unsupervised Feature Extraction Applied to Single-Cell Gene Expression Analysis. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/978-3-319-95933-7_90] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Taguchi YH. Tensor Decomposition-Based Unsupervised Feature Extraction Can Identify the Universal Nature of Sequence-Nonspecific Off-Target Regulation of mRNA Mediated by MicroRNA Transfection. Cells 2018; 7:cells7060054. [PMID: 29867052 PMCID: PMC6025034 DOI: 10.3390/cells7060054] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 12/14/2022] Open
Abstract
MicroRNA (miRNA) transfection is known to degrade target mRNAs and to decrease mRNA expression. In contrast to the notion that most of the gene expression alterations caused by miRNA transfection involve downregulation, they often involve both up- and downregulation; this phenomenon is thought to be, at least partially, mediated by sequence-nonspecific off-target effects. In this study, I used tensor decomposition-based unsupervised feature extraction to identify genes whose expression is likely to be altered by miRNA transfection. These gene sets turned out to largely overlap with one another regardless of the type of miRNA or cell lines used in the experiments. These gene sets also overlap with the gene set associated with altered expression induced by a Dicer knockout. This result suggests that the off-target effect is at least as important as the canonical function of miRNAs that suppress translation. The off-target effect is also suggested to consist of competition for the protein machinery between transfected miRNAs and miRNAs in the cell. Because the identified genes are enriched in various biological terms, these genes are likely to play critical roles in diverse biological processes.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, Tokyo 112-8551, Japan.
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