1
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Matboli M, Diab GI, Saad M, Khaled A, Roushdy M, Ali M, ELsawi HA, Aboughaleb IH. Machine-Learning-Based Identification of Key Feature RNA-Signature Linked to Diagnosis of Hepatocellular Carcinoma. J Clin Exp Hepatol 2024; 14:101456. [PMID: 39055616 PMCID: PMC11268357 DOI: 10.1016/j.jceh.2024.101456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/09/2024] [Indexed: 07/27/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the third prime cause of malignancy-related mortality worldwide. Early and accurate identification of HCC is crucial for good prognosis, efficacy of therapy, and survival rates of the patients. We aimed to develop a machine-learning model incorporating differentially expressed RNA signatures with laboratory parameters to construct an RNA signature-based diagnostic model for HCC. Methods We have used five classifiers (KNN, RF, SVM, LGBM, and DNNs) to predict the liver disease (HCC). The classifiers were trained on 187 samples and then tested on 80 samples. The model included 22 features (age, sex, smoking, cirrhosis, non-cirrhosis, albumin, ALT, AST bilirubin (total and direct), INR, AFP, HBV Ag, HCV Abs, RQmiR-1298, RQmiR-1262, RQmiR-106b-3p, RQmRNARAB11A, and RQSTAT1, RQmRNAATG12, RQLnc-WRAP53, RQLncRNA- RP11-513I15.6). Results LGBM achieved the highest accuracy of 98.75% in predicting HCC among all models surpassing Random Forest (96.25%), DNN (91.25%), SVC (88.75%), and KNN (87.50%). Conclusion Our machine-learning model incorporating the expression data of RAB11A/STAT1/ATG12/miR-1262/miR-1298/miR-106b-3p/lncRNA-RP11-513I15.6/lncRNA-WRAP53 signature and clinical data represents a potential novel diagnostic model for HCC.
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Affiliation(s)
- Marwa Matboli
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine Ain Shams University, Cairo 11566, Egypt
| | - Gouda I. Diab
- Biomedical Engineering Department, Egyptian Armed Forces, Cairo, Egypt
| | - Maha Saad
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Modern University for Technology and Information, Cairo, Egypt
| | - Abdelrahman Khaled
- Bioinformatics Group, Center of Informatics Sciences (CIS), School of Information Technology and Computer Sciences, Nile University, Giza, Egypt
| | - Marian Roushdy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine Ain Shams University, Cairo 11566, Egypt
| | - Marwa Ali
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine Ain Shams University, Cairo 11566, Egypt
| | - Hind A. ELsawi
- Department of Internal Medicine, Badr University in Cairo, Badr City, Egypt
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2
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Shetti D, Mallela VR, Ye W, Sharif M, Ambrozkiewicz F, Trailin A, Liška V, Hemminki K. Emerging role of circulating cell-free RNA as a non-invasive biomarker for hepatocellular carcinoma. Crit Rev Oncol Hematol 2024; 200:104391. [PMID: 38795877 DOI: 10.1016/j.critrevonc.2024.104391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/30/2024] [Accepted: 05/19/2024] [Indexed: 05/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a severe neoplastic disease associated with high morbidity and mortality rates. HCC is often detected at advanced stages leading to ineffective curative treatments. Recently, liquid biopsy has emerged as a non-invasive method to identify highly specific HCC biomarkers in bodily fluids such as blood, serum, urine, and saliva. Circulating cell-free nucleic acids (cfNAs), particularly cell-free DNA (cfDNA) and cell-free RNA (cfRNA), have become promising candidates for biomarkers in liquid biopsy applications. While cfDNA presented significant challenges, researchers have turned their attention to cfRNA, which can be efficiently identified through various methods and is considered a potential biomarker for cancer diagnosis and prognosis. This review primarily focuses on studies related to detecting various cfRNA in body fluids as biomarkers. The aim is to provide a summary of available information to assist researchers in their investigations and the development of new diagnostic and prognostic tools.
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Affiliation(s)
- Dattatrya Shetti
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic.
| | - Venkata Ramana Mallela
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Wenjing Ye
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Mahyar Sharif
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University,Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Filip Ambrozkiewicz
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Andriy Trailin
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Václav Liška
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic; Department of Surgery, University Hospital in Pilsen and Faculty of Medicine in Pilsen, Charles University, Alej Svobody 80, Pilsen 323 00, Czech Republic
| | - Kari Hemminki
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic; Department of Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
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3
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Leng X, Zhang M, Xu Y, Wang J, Ding N, Yu Y, Sun S, Dai W, Xue X, Li N, Yang Y, Shi Z. Non-coding RNAs as therapeutic targets in cancer and its clinical application. J Pharm Anal 2024; 14:100947. [PMID: 39149142 PMCID: PMC11325817 DOI: 10.1016/j.jpha.2024.02.001] [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: 10/27/2023] [Revised: 01/12/2024] [Accepted: 02/01/2024] [Indexed: 08/17/2024] Open
Abstract
Cancer genomics has led to the discovery of numerous oncogenes and tumor suppressor genes that play critical roles in cancer development and progression. Oncogenes promote cell growth and proliferation, whereas tumor suppressor genes inhibit cell growth and division. The dysregulation of these genes can lead to the development of cancer. Recent studies have focused on non-coding RNAs (ncRNAs), including circular RNA (circRNA), long non-coding RNA (lncRNA), and microRNA (miRNA), as therapeutic targets for cancer. In this article, we discuss the oncogenes and tumor suppressor genes of ncRNAs associated with different types of cancer and their potential as therapeutic targets. Here, we highlight the mechanisms of action of these genes and their clinical applications in cancer treatment. Understanding the molecular mechanisms underlying cancer development and identifying specific therapeutic targets are essential steps towards the development of effective cancer treatments.
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Affiliation(s)
- Xuejiao Leng
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Mengyuan Zhang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yujing Xu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jingjing Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yancheng Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shanliang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Weichen Dai
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Nianguang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ye Yang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhihao Shi
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, 211198, China
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4
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Anuntakarun S, Khamjerm J, Tangkijvanich P, Chuaypen N. Classification of Long Non-Coding RNAs s Between Early and Late Stage of Liver Cancers From Non-coding RNA Profiles Using Machine-Learning Approach. Bioinform Biol Insights 2024; 18:11779322241258586. [PMID: 38846329 PMCID: PMC11155358 DOI: 10.1177/11779322241258586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 05/10/2024] [Indexed: 06/09/2024] Open
Abstract
Long non-coding RNAs (lncRNAs), which are RNA sequences greater than 200 nucleotides in length, play a crucial role in regulating gene expression and biological processes associated with cancer development and progression. Liver cancer is a major cause of cancer-related mortality worldwide, notably in Thailand. Although machine learning has been extensively used in analyzing RNA-sequencing data for advanced knowledge, the identification of potential lncRNA biomarkers for cancer, particularly focusing on lncRNAs as molecular biomarkers in liver cancer, remains comparatively limited. In this study, our objective was to identify candidate lncRNAs in liver cancer. We employed an expression data set of lncRNAs from patients with liver cancer, which comprised 40 699 lncRNAs sourced from The CancerLivER database. Various feature selection methods and machine-learning approaches were used to identify these candidate lncRNAs. The results showed that the random forest algorithm could predict lncRNAs using features extracted from the database, which achieved an area under the curve (AUC) of 0.840 for classifying lncRNAs between early (stage 1) and late stages (stages 2, 3, and 4) of liver cancer. Five of 23 significant lncRNAs (WAC-AS1, MAPKAPK5-AS1, ARRDC1-AS1, AC133528.2, and RP11-1094M14.11) were differentially expressed between early and late stage of liver cancer. Based on the Gene Expression Profiling Interactive Analysis (GEPIA) database, higher expression of WAC-AS1, MAPKAPK5-AS1, and ARRDC1-AS1 was associated with shorter overall survival. In conclusion, the classification model could predict the early and late stages of liver cancer using the signature expression of lncRNA genes. The identified lncRNAs might be used as early diagnostic and prognostic biomarkers for patients with liver cancer.
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Affiliation(s)
- Songtham Anuntakarun
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jakkrit Khamjerm
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Biomedical Engineering Program, Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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5
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Wang X, Wang X. The regulation of hypoxia-related lncRNAs in hepatocellular carcinoma. Discov Oncol 2024; 15:144. [PMID: 38713276 PMCID: PMC11076439 DOI: 10.1007/s12672-024-01002-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is still a public health disease with its high prevalence and morbidity. Short of early diagnosis biomarkers and effective therapy, the treatment of HCC patients hasn't achieved ideal effect. Hypoxia is a hallmark of HCC, which is mainly induced by imbalance of tumor cell proliferation and insufficient supply of oxygen. Recently, amounting evidence suggested lncRNAs, especially hypoxia-related lncRNAs play a pivotal role in regulating HCC. Hypoxia-related lncRNAs are involved in altering glucose metabolism, maintaining of cancer stem cell-like properties (CSCs), cell apotosis, proliferation and immune escape, which all contribute to the poor prognosis of HCC patients. The novel identified hypoxia-related lncRNAs could be the potential target or biomarkers of HCC, which are beneficial to the clinical treatment. Herein, we summarized currently reported hypoxia-related lncRNAs and their related mechanisms, providing potential application and future perspective of hypoxia-related lncRNAs as a potential therapeutic target.
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Affiliation(s)
- Xuejing Wang
- Department of Integrated Traditional Chinese and Western Medicine, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xiaojun Wang
- Department of Integrated Traditional Chinese and Western Medicine, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
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6
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Saranya I, Dharshini VS, Akshaya RL, Subhashini PS, Selvamurugan N. Regulatory and therapeutic implications of competing endogenous RNA network in breast cancer progression and metastasis: A review. Int J Biol Macromol 2024; 266:131075. [PMID: 38531528 DOI: 10.1016/j.ijbiomac.2024.131075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 03/28/2024]
Abstract
Breast cancer (BC) is a global health concern, and development of diagnostic tools and targeted treatments for BC remains challenging. Therapeutic approaches for BC often involve a combination of surgery, radiation therapy, chemotherapy, targeted therapy, and hormone therapy. In recent years, there has been a growing interest in the role of noncoding RNAs (ncRNAs), including long ncRNAs (lncRNAs) and microRNAs (miRNAs), in BC and their therapeutic implications. Various biological processes such as cell proliferation, migration, and apoptosis rely on the activities of these ncRNAs, and their dysregulation has been implicated in BC progression. The regulatory function of the competitive endogenous RNA (ceRNA) network, which comprises lncRNAs, miRNAs, and mRNAs, has been the subject of extensive pathophysiological research. Most lncRNAs serve as molecular sponges for miRNAs and sequester their activities, thereby regulating the expression of target mRNAs and contributing to the promotion or inhibition of BC progression. This review summarizes recent findings on the role of ceRNA networks in BC progression, metastasis, and therapeutic resistance, and highlights the association of ceRNA networks with transcription factors and signaling pathways. Understanding the ceRNA network can lead to the discovery of biomarkers and targeted treatment methods to prevent the spread and metastasis of BC.
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Affiliation(s)
- I Saranya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - V Sowfika Dharshini
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - R L Akshaya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - P Sakthi Subhashini
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - N Selvamurugan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India.
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7
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Lumkul L, Jantaree P, Jaisamak K, Wongkummool W, Lapisatepun W, Orrapin S, Udomruk S, Lo Piccolo L, Chaiyawat P. Combinatorial Gene Expression Profiling of Serum HULC, HOTAIR, and UCA1 lncRNAs to Differentiate Hepatocellular Carcinoma from Liver Diseases: A Systematic Review and Meta-Analysis. Int J Mol Sci 2024; 25:1258. [PMID: 38279264 PMCID: PMC10816616 DOI: 10.3390/ijms25021258] [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: 12/27/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) presents a significant global health challenge due to limited early detection methods, primarily relying on conventional approaches like imaging and alpha-fetoprotein (AFP). Although non-coding RNAs (ncRNAs) show promise as potential biomarkers in HCC, their true utility remains uncertain. We conducted a comprehensive review of 76 articles, analyzing 88 circulating lncRNAs in 6426 HCC patients. However, the lack of a standardized workflow protocol has hampered holistic comparisons across the literature. Consequently, we herein confined our meta-analysis to only a subset of these lncRNAs. The combined analysis of serum highly upregulated in liver cancer (HULC) gene expression with homeobox transcript antisense intergenic RNA (HOTAIR) and urothelial carcinoma-associated 1 (UCA1) demonstrated markedly enhanced sensitivity and specificity in diagnostic capability compared to traditional biomarkers or other ncRNAs. These findings could have substantial implications for the early diagnosis and tailored treatment of HCC.
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MESH Headings
- Humans
- Carcinoma, Hepatocellular/diagnosis
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Liver Neoplasms/diagnosis
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- RNA, Long Noncoding/metabolism
- Genes, Homeobox
- RNA, Antisense
- Carcinoma, Transitional Cell/genetics
- Gene Expression Regulation, Neoplastic
- Urinary Bladder Neoplasms/genetics
- RNA, Untranslated
- Biomarkers
- Gene Expression Profiling
- Biomarkers, Tumor/genetics
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Affiliation(s)
- Lalita Lumkul
- Center of Multidisciplinary Technology for Advanced Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (L.L.); (P.J.); (K.J.); (W.W.); (S.O.); (S.U.)
- Center for Clinical Epidemiology and Clinical Statistics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Phatcharida Jantaree
- Center of Multidisciplinary Technology for Advanced Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (L.L.); (P.J.); (K.J.); (W.W.); (S.O.); (S.U.)
| | - Kritsada Jaisamak
- Center of Multidisciplinary Technology for Advanced Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (L.L.); (P.J.); (K.J.); (W.W.); (S.O.); (S.U.)
| | - Wasinee Wongkummool
- Center of Multidisciplinary Technology for Advanced Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (L.L.); (P.J.); (K.J.); (W.W.); (S.O.); (S.U.)
| | - Worakitti Lapisatepun
- Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Santhasiri Orrapin
- Center of Multidisciplinary Technology for Advanced Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (L.L.); (P.J.); (K.J.); (W.W.); (S.O.); (S.U.)
| | - Sasimol Udomruk
- Center of Multidisciplinary Technology for Advanced Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (L.L.); (P.J.); (K.J.); (W.W.); (S.O.); (S.U.)
| | - Luca Lo Piccolo
- Center of Multidisciplinary Technology for Advanced Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (L.L.); (P.J.); (K.J.); (W.W.); (S.O.); (S.U.)
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (L.L.); (P.J.); (K.J.); (W.W.); (S.O.); (S.U.)
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8
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Jia X, Wang Y, Yang Y, Fu Y, Liu Y. Constructed Risk Prognosis Model Associated with Disulfidptosis lncRNAs in HCC. Int J Mol Sci 2023; 24:17626. [PMID: 38139458 PMCID: PMC10744246 DOI: 10.3390/ijms242417626] [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: 10/20/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Disulfidptosis is a novel cell death mode in which the accumulation of disulfide bonds in tumor cells leads to cell disintegration and death. Long-stranded noncoding RNAs (LncRNAs) are aberrantly expressed in hepatocellular carcinoma (HCC) and have been reported to carry significant potential as a biomarker for HCC prognosis. However, lncRNA studies with disulfidptosis in hepatocellular carcinoma have rarely been reported. Therefore, this study aimed to construct a risk prognostic model based on the disulfidptosis-related lncRNA and investigate the mechanisms associated with disulfidptosis in hepatocellular carcinoma. The clinical and transcriptional information of 424 HCC patients was downloaded from The Cancer Genome Atlas (TCGA) and divided into test and validation sets. Furthermore, 1668 lncRNAs associated with disulfidptosis were identified using Pearson correlation. Six lncRNA constructs were finally identified for the risk prognostic model using one-way Cox proportional hazards (COX), multifactorial COX, and lasso regression. Kaplan-Meier (KM) analysis, principal component analysis, receiver operating characteristic curve (ROC), C-index, and column-line plot results confirmed that the constructed model was an independent prognostic factor. Based on the disulfidptosis risk score, risk groups were identified as potential predictors of immune cell infiltration, drug sensitivity, and immunotherapy responsiveness. Finally, we confirmed that phospholipase B domain containing 1 antisense RNA 1 (PLBD1-AS1) and muskelin 1 antisense RNA (MKLN1-AS) were highly expressed in hepatocellular carcinoma and might be potential biomarkers in HCC by KM analysis and quantitative real-time PCR (RT-qPCR). This study demonstrated that lncRNA related to disulfidptosis could serve as a biomarker to predict prognosis and treatment targets for HCC.
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Affiliation(s)
| | | | | | | | - Yijin Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China; (X.J.); (Y.W.); (Y.Y.); (Y.F.)
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9
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Shehab-Eldeen S, Essa A, Arafat ES, Sleem AS, Alhosary AA, Darwish E, Essa A, Al-Omair OA, Al-Khoufi EA, Al Abdulqader AK, Nada A. Serum LINC00152 and UCA1 in HCV-Induced Hepatocellular Carcinoma: Clinical Significance and Prognostic Value. Biologics 2023; 17:137-149. [PMID: 37854341 PMCID: PMC10581015 DOI: 10.2147/btt.s433872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/07/2023] [Indexed: 10/20/2023]
Abstract
Background Despite significant advancements in the molecular characterization of hepatocellular carcinoma (HCC), no oncogene addiction has been discovered. Long noncoding RNAs (lncRNAs) have a lot of promise as cancer biomarkers. LINC00152 and UCA1 have shown potential as diagnostic, prognostic, and therapeutic targets for human cancers. Aim To investigate the diagnostic and prognostic potential of serum LINC00152 and UCA1 in hepatocellular carcinoma (HCC). Methods The expression levels of LINC00152 and UCA1 in blood samples from 120 patients (60 with HCC, 60 with liver cirrhosis) and 40 healthy subjects were assessed using real-time qRT-PCR. Results Serum LINC00152 and UCA1 expression were considerably higher in HCC patients compared to patients with liver cirrhosis and the healthy controls (p<0.001 and p<0.001 respectively). And their expressions in the liver cirrhosis group were significantly higher than in healthy controls. Both lncRNAs performed well in the ROC analysis, distinguishing HCC patients from patients with liver cirrhosis. Higher levels of LINC00152 expression were linked to lesions in both lobes of the liver (p=0.02), while higher levels of UCA1 expression were linked to vascular invasion and the late stage (p=0.01, p=0.03 respectively). The multivariate analysis showed that a high level of LINC00152 in the blood was an independent indicator of a bad outcome for HCC patients (HR=2.23, 95% CI= 1.30-5.29, p=0.03). Conclusion Serum LINC00152 and UCA1 expression were upregulated in patients with HCC, suggesting their use as non-invasive biomarkers for HCC. Furthermore, LINC00152 has the potential to serve as a prognostic indicator.
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Affiliation(s)
- Somaia Shehab-Eldeen
- Internal Medicine Department, College of Medicine, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
- Tropical Medicine Department, Faculty of Medicine, Menoufia University, Shebin Elkom, Egypt
| | - Abdallah Essa
- Internal Medicine Department, College of Medicine, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
- Tropical Medicine Department, Faculty of Medicine, Menoufia University, Shebin Elkom, Egypt
| | - Eman Salah Arafat
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Shebin Elkom, Egypt
| | - Asmaa Shaaban Sleem
- Medical Microbiology and Immunology Department, Faculty of Medicine, Menoufia University, Shebin Elkom, Egypt
| | | | - Ehab Darwish
- Tropical Medicine Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
- Gastroenterology and Infectious Diseases Unit, College of Medicine, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | - Ali Essa
- Medical Student, Faculty of Medicine, Menoufia University, Shebin Elkom, Egypt
| | - Omar Ahmed Al-Omair
- Internal Medicine Department, College of Medicine, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | - Emad Ali Al-Khoufi
- Internal Medicine Department, College of Medicine, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | | | - Ali Nada
- Hepatology and Gastroenterology Department, National Liver Institute, Menoufia University, Shebin Elkom, Egypt
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10
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Jin Z, Meng YJ, Xu YS, Wang MM, Chen D, Jiang X, Xiong ZF. Prognostic and clinicopathological values of LINC00665 in cancers: a systematic review and China population-based meta-analysis. Clin Exp Med 2023; 23:1475-1487. [PMID: 36219365 DOI: 10.1007/s10238-022-00912-2] [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: 04/10/2022] [Accepted: 10/01/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Recent studies have uncovered that the aberrant expression of LINC00665 contributes to the malignant pathological process of various cancers and is closely related to the unfavorable prognosis of patients with cancer. However, a systematic analysis of the prognostic and clinicopathologic values of LINC00665 in cancers has not been conducted. OBJECTIVE We aim to clarify the association of LINC00665 expression with patient survival and clinicopathologic phenotypes in cancers. METHODS An electronic search of PubMed, Embase and Web of Science was performed to select eligible literature. Pooled hazard ratio (HR) and odds ratio (OR) were calculated to assess the clinical importance of LINC00665. The fixed-effects model was used to analyze the combined HR values and 95% CI when the studies had no significant heterogeneity (P > 0.1 for the Chi-square test or I2 < 50%). Begg's test and sensitivity analysis were also conducted. This study was registered in The International Prospective Register of Systematic Reviews (PROSPERO registration number: CRD42021290123). RESULTS A total of 710 patients from 10 eligible studies were enrolled in this meta-analysis, which was based on China population. The pooled results of this analysis revealed that high-level expression of LINC00665 was notably correlated with poor overall survival (HR = 2.08, 95% CI = 1.57-2.75) and recurrence-free survival (HR = 2.49, 95% CI = 1.63-3.80) in human cancers. Elevated LINC00665 expression was also correlated with more advanced clinical stage, earlier lymph node metastasis, lower tumor differentiation, earlier distant metastasis and larger tumor size. CONCLUSION LINC00665 expression was critically related to the cancer prognosis, which has important prognostic implications for clinical prediction.
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Affiliation(s)
- Ze Jin
- Division of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ya-Jun Meng
- Division of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu-Shuang Xu
- Division of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng-Meng Wang
- Division of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Di Chen
- Division of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Jiang
- Division of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhi-Fan Xiong
- Division of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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11
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Liangyu Z, Bochao Z, Guoquan Y, Yuan Z, Heng L, Hanyu Z. Bioinformatics prediction and experimental verification identify cuproptosis-related lncRNA as prognosis biomarkers of hepatocellular carcinoma. Biochem Biophys Rep 2023; 35:101502. [PMID: 37426702 PMCID: PMC10322676 DOI: 10.1016/j.bbrep.2023.101502] [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: 12/01/2022] [Revised: 04/29/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
Cuproptosis is a form of cell death caused by intracellular copper excess, which plays an important regulatory role in the development and progression of cancers, including hepatocellular carcinoma (HCC), a prevalent malignancy with high morbidity and mortality. This study aimed to create a cuproptosis associated long non-coding RNAs (CAlncRNAs)signature to predict HCC patient survival and immunotherapy response. Firstly, we identified 509 CAlncRNAs using Pearson correlation analysis in The Cancer Genome Atlas (TCGA) datasets, before the three CAlncRNAs (MKLN1-AS, FOXD2-AS1, LINC02870) with the most prognostic value were further screened. Then, we constructed a prognostic risk model for HCCwas using univariate and LASSO Cox regression analyses. Multivariate Cox regression analyses illustrated that this model was an independent prognostic factor for overall survival (OS) prediction, outperforming traditional clinicopathological factors. And the risk score not only could be prognostic factors independent of other factors but also suited for patients with diverse ages, stages, and grades. The 1-, 3-, and 5- years areas under the curves (AUC) values of the model were 0.759, 0.668 and 0.674 respectively. Pathway analyses showed that the high-risk groupenriched in immune-related pathways. Importantly, patients with higher risk scores exhibited higher mutation frequency, higher TMB scores, and lower TIDE scores. Besides, we screened for two chemical drugs (A-443654 and Pyrimethamine) with the greatest value for high-risk HCC patients. Finally, the abnormal high expression of the three CAlncRNAs were confirmed in HCC tissues and cells by Real Time Quantitative PCR (RT-qPCR). And proliferative, migratory and invasion abilities of HCC cell were restrained via silencing CAlncRNAs expression in vitro. In summary, we built a CAlncRNAs-based risk score model, which can be a candidate for HCC patients prognostic prediction and offer some useful information for immunotherapies.
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Affiliation(s)
- Zhu Liangyu
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Zhang Bochao
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Yin Guoquan
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Zhang Yuan
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Li Heng
- Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China
| | - Zhou Hanyu
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
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12
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Xing S, Zhu Y, You Y, Wang S, Wang H, Ning M, Jin H, Liu Z, Zhang X, Yu C, Lu ZJ. Cell-free RNA for the liquid biopsy of gastrointestinal cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1791. [PMID: 37086051 DOI: 10.1002/wrna.1791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/22/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Gastrointestinal (GI) cancer includes many cancer types, such as esophageal, liver, gastric, pancreatic, and colorectal cancer. As the cornerstone of personalized medicine for GI cancer, liquid biopsy based on noninvasive biomarkers provides promising opportunities for early diagnosis and dynamic treatment management. Recently, a growing number of studies have demonstrated the potential of cell-free RNA (cfRNA) as a new type of noninvasive biomarker in body fluids, such as blood, saliva, and urine. Meanwhile, transcriptomes based on high-throughput RNA detection technologies keep discovering new cfRNA biomarkers. In this review, we introduce the origins and applications of cfRNA, describe its detection and qualification methods in liquid biopsy, and summarize a comprehensive list of cfRNA biomarkers in different GI cancer types. Moreover, we also discuss perspective studies of cfRNA to overcome its current limitations in clinical applications. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Institute for Precision Medicine, Tsinghua University, Beijing, China
| | - Yumin Zhu
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Population Health and Aristogenics, Department of Maternal & Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Yaxian You
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Siqi Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongke Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Meng Ning
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Heyue Jin
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Population Health and Aristogenics, Department of Maternal & Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Zhengxia Liu
- Department of General Surgery, SIR RUN RUN Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Geriatrics, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xinhua Zhang
- Department of Health Care, Jiangsu Women and Children Health Hospital, the First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, Jiangsu, China
| | - Chunzhao Yu
- Department of General Surgery, SIR RUN RUN Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Geriatrics, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Institute for Precision Medicine, Tsinghua University, Beijing, China
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13
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Chen W, Ruan M, Zou M, Liu F, Liu H. Clinical Significance of Non-Coding RNA Regulation of Programmed Cell Death in Hepatocellular Carcinoma. Cancers (Basel) 2023; 15:4187. [PMID: 37627215 PMCID: PMC10452865 DOI: 10.3390/cancers15164187] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/02/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a widely prevalent and malignantly progressive tumor. Most patients are typically diagnosed with HCC at an advanced stage, posing significant challenges in the execution of curative surgical interventions. Non-coding RNAs (ncRNAs) represent a distinct category of RNA molecules not directly involved in protein synthesis. However, they possess the remarkable ability to regulate gene expression, thereby exerting significant regulatory control over cellular processes. Notably, ncRNAs have been implicated in the modulation of programmed cell death (PCD), a crucial mechanism that various therapeutic agents target in the fight against HCC. This review summarizes the clinical significance of ncRNA regulation of PCD in HCC, including patient diagnosis, prognosis, drug resistance, and side effects. The aim of this study is to provide new insights and directions for the diagnosis and drug treatment strategies of HCC.
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Affiliation(s)
| | | | | | - Fuchen Liu
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai 200438, China; (W.C.); (M.R.)
| | - Hui Liu
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai 200438, China; (W.C.); (M.R.)
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14
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Zhu L, Zhang XP, Xu S, Hu MG, Zhao ZM, Zhao GD, Xiao ZH, Liu R. Identification of a CD4+ conventional T cells-related lncRNAs signature associated with hepatocellular carcinoma prognosis, therapy, and tumor microenvironment. Front Immunol 2023; 13:1111246. [PMID: 36700197 PMCID: PMC9868629 DOI: 10.3389/fimmu.2022.1111246] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related death worldwide, and CD4+ T lymphocytes can inhibit hepatocarcinogenesis and mediate tumor regression. However, few studies have focused on the prognostic power of CD4+ Tconv-related lncRNAs in HCC patients. Method We obtained data from TCGA and GEO databases and identified CD4+Tconv-related lncRNAs in HCC. The risk score was constructed using lasso regression and the model was validated using two validation cohorts. The RS was also assessed in different clinical subgroups, and a nomogram was established to further predict the patients' outcomes. Furthermore, we estimated the immune cell infiltration and cancer-associated fibroblasts (CAFs) through TIMER databases and assessed the role of RS in immune checkpoint inhibitors response. Results We constructed a CD4+ Tconv-related lncRNAs risk score, including six lncRNAs (AC012073.1, AL031985.3, LINC01060, MKLN1-AS, MSC-AS1, and TMCC1-AS1), and the RS had good predictive ability in validation cohorts and most clinical subgroups. The RS and the T stage were included in the nomogram with optimum prediction and the model had comparable OS prediction power compared to the AJCC. Patients in the high-risk group had a poor immune response phenotype, with high infiltrations of macrophages, CAFs, and low infiltrations of NK cells. Immunotherapy and chemotherapy response analysis indicated that low-risk group patients had good reactions to immune checkpoint inhibitors. Conclusion We constructed and validated a novel CD4+ Tconv-related lncRNAs RS, with the potential predictive value of HCC patients' survival and immunotherapy response.
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Affiliation(s)
- Lin Zhu
- Medical School of Chinese PLA, Beijing, China,Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China,The First Clinical Medical School, Lanzhou University, Lanzhou, China
| | - Xiu-Ping Zhang
- Medical School of Chinese PLA, Beijing, China,Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China
| | - Shuai Xu
- Department of Liver Transplantation and Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ming-Gen Hu
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China
| | - Zhi-Ming Zhao
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China
| | - Guo-Dong Zhao
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China
| | - Zhao-Hui Xiao
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China
| | - Rong Liu
- Medical School of Chinese PLA, Beijing, China,Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Centre, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China,Institute of Hepatobiliary Surgery of Chinese PLA, Beijing, China,Key Laboratory of Digital Hepatobiliary Surgery, PLA, Beijing, China,The First Clinical Medical School, Lanzhou University, Lanzhou, China,*Correspondence: Rong Liu,
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15
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Zhu Y, Sun W, Jiang X, Bai R, Luo Y, Gao Y, Li S, Huang Z, Gong Y, Xie C. Differential effects of WRAP53 transcript variants on non-small cell lung cancer cell behaviors. PLoS One 2023; 18:e0281132. [PMID: 36706151 PMCID: PMC9882892 DOI: 10.1371/journal.pone.0281132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The WD40-encoding RNA antisense to p53 (WRAP53) is an antisense gene of TP53 with three transcriptional start sites producing three transcript variants involved in the progression of non-small cell lung cancer. However, the mechanism by which these different transcript variants regulate non-small cell lung cancer cell behaviors is to be elucidated. METHODS Two non-small cell lung cancer cell lines, A549 cells with wild-type p53 and H1975 with mutated p53, were transfected with WRAP53-1α and WRAP53-1β siRNA. The biological effects were assessed via colony formation, cell viability, apoptosis, cell cycle, wound healing and cell invasion assays, as well as immunoblotting. RESULTS Knockdown of WRAP53-1α increased the mRNA and protein levels of p53; suppressed colony formation and proliferation of A549 cells but promoted them in H1975 cells; increased the proportion of cells in the G0/G1 phase in A549 cells but decreased that in H1975 cells; and suppressed migration and invasion in A549 cells but not in H1975 cells. Conversely, knockdown of WRAP53-1β had no effect on p53 expression; promoted the growth of A549 cells but not of H1975 cells; decreased the proportion of cells in the G0/G1 phase in A549 cells but not in H1975 cells; and promoted migration and invasion in A549 cells but not in H1975 cells. Knockdown of both WRAP53-1α and WRAP53-1β promoted apoptosis in A549 cells but not in H1975 cells. CONCLUSIONS WRAP53 transcript variants exerted different functions in non-small cell lung cancer cells and regulated non-small cell lung cancer cell behaviors depending on the p53 expression.
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Affiliation(s)
- Yan Zhu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Department of Oncology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Wenjie Sun
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xueping Jiang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Rui Bai
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yuan Luo
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yanping Gao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Shuying Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhengrong Huang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- * E-mail: (CX); (YG)
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Key Laboratory of Tumour Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- * E-mail: (CX); (YG)
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16
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Li R, Jin C, Zhao W, Liang R, Xiong H. Development of a novel immune-related lncRNA prognostic signature for patients with hepatocellular carcinoma. BMC Gastroenterol 2022; 22:450. [PMID: 36344926 PMCID: PMC9639314 DOI: 10.1186/s12876-022-02540-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common neoplasm and the major cause of cancer-associated death worldwide. The high mortality rate of HCC is mainly attributed to its widespread prevalence and the lack of effective treatment. Immunotherapy as a promising, innovative approach has revolutionised the treatment of solid tumours. However, owing to the heterogeneity and complex tumour microenvironment of HCC, an efficient biomarker for immunotherapy has yet to be identified. We investigated the role of immune-related long non-coding RNAs (lncRNAs) as prognostic biomarkers in patients with HCC from The Cancer Genome Atlas (TCGA) database. Spearman correlation, univariate and multivariate Cox, and lasso regression analyses were utilised to screen lncRNAs associated with prognosis. Four lncRNAs were filtered out to develop an immune-associated lncRNA prognostic signature in TCGA training as well as validation cohorts. Patients with HCC were then categorised into low- and high-risk groups according to the median value of the risk scores to evaluate the ability of the prognostic model between training and validation cohorts. A nomogram (based on risk score and stage) was constructed to appraise the general overall survival (OS) of patients with HCC. Differences in immune cell infiltration, immune checkpoint inhibitor (ICI) treatment response, gene mutation, and drug sensitivity were observed between the two groups. Thus, the lncRNA prognostic signature can serve as a sensitive prognostic biomarker with potential in individualised immunotherapy for HCC patients.
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Affiliation(s)
- Rui Li
- grid.33199.310000 0004 0368 7223Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Chen Jin
- grid.268099.c0000 0001 0348 3990Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang China
| | - Weiheng Zhao
- grid.33199.310000 0004 0368 7223Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Rui Liang
- grid.190737.b0000 0001 0154 0904Biological Engineering Academy, Chongqing University, Chongqing, China
| | - Huihua Xiong
- grid.33199.310000 0004 0368 7223Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei China
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17
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Gadelha RB, Machado CB, Pessoa FMCDP, Pantoja LDC, Barreto IV, Ribeiro RM, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira-Nunes CA. The Role of WRAP53 in Cell Homeostasis and Carcinogenesis Onset. Curr Issues Mol Biol 2022; 44:5498-5515. [PMID: 36354684 PMCID: PMC9688736 DOI: 10.3390/cimb44110372] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/30/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2023] Open
Abstract
The WD repeat containing antisense to TP53 (WRAP53) gene codifies an antisense transcript for tumor protein p53 (TP53), stabilization (WRAP53α), and a functional protein (WRAP53β, WDR79, or TCAB1). The WRAP53β protein functions as a scaffolding protein that is important for telomerase localization, telomere assembly, Cajal body integrity, and DNA double-strand break repair. WRAP53β is one of many proteins known for containing WD40 domains, which are responsible for mediating a variety of cell interactions. Currently, WRAP53 overexpression is considered a biomarker for a diverse subset of cancer types, and in this study, we describe what is known about WRAP53β's multiple interactions in cell protein trafficking, Cajal body formation, and DNA double-strand break repair and its current perspectives as a biomarker for cancer.
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Affiliation(s)
- Renan Brito Gadelha
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Caio Bezerra Machado
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Flávia Melo Cunha de Pinho Pessoa
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Laudreísa da Costa Pantoja
- Department of Pediatrics, Octávio Lobo Children’s Hospital, Belém 60430-275, PA, Brazil
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
| | - Igor Valentim Barreto
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | | | - Manoel Odorico de Moraes Filho
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Maria Elisabete Amaral de Moraes
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
| | - Caroline Aquino Moreira-Nunes
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
- Northeast Biotechnology Network (RENORBIO), Itaperi Campus, Ceará State University, Fortaleza 60740-903, CE, Brazil
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18
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Chen W, Chen F, Gong M, Jin Z, Shu L, Wang ZW, Wang J. Comprehensive analysis of lncRNA-mediated ceRNA networkfor hepatocellular carcinoma. Front Oncol 2022; 12:1042928. [PMID: 36338699 PMCID: PMC9634570 DOI: 10.3389/fonc.2022.1042928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/30/2022] [Indexed: 11/25/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a high-burden cancer. The molecular mechanism of HCC has not been fully elucidated. Notably, current research has revealed a significant function for long non-coding RNAs (lncRNAs) in the prognosis of patients with HCC. Here, this study aims to construct a regulated lncRNA-mediated ceRNA network and find biological targets for the treatment of HCC. Methods Based on the RNA expression patterns from the TCGA, we did an analysis to determine which genes were expressed differently between liver tumor tissues and noncancerous tissues. Then, using bioinformatic tools, we built a lncRNA-miRNA-mRNA ceRNA network and used GO and KEGG functional analyses on the DEmRNAs connected to ceRNA networks. The main lncRNAs in the subnetwork were chosen, and we next looked at the relationships between these lncRNAs and the clinical characteristics of patients with HCC. The prognosis-related genes and immune cells were identified using Kaplan-Meier and Cox proportional hazard analyses, and CIBERSORT was utilized to separate the 22 immune cell types. CCK8 assay was performed to measure cell viability in HCC cells after lncRNA HOTTIP modulation. Results Differentially expressed mRNA and lncRNAs in HCC and paracancerous tissues were identified. There are 245 lncRNAs, 126 miRNAs, and 1980 mRNAs that are expressed differently in liver tumour tissues than in noncancerous cells. Function analysis showed that mRNAs in ceRNA network were significantly enriched in G1/S transition of mototiv cell cycle, positive regulation of cell cycle process, hepatocellular carcinoma, and cancer related pathways. CD8 T cells and T follicular helper cells had a favourable link with a 0.65 correlation coefficient. Additionally, there was a strong correlation between Eosinophils, activated NK cells, and B memory cells. Strikingly, depletion of lncRNA HOTTIP inhibited viability of HCC cells. In addition, miR-205 upregulation suppressed viability of HCC cells, while miR-205 downregulation repressed viability of HCC cells. Notably, miR-205 depletion rescued HOTTIP depletion-mediated suppression of cell viability in HCC. Conclusion A ceRNA network was created by examining the lncRNA, miRNA, and mRNA expression profiles of liver tumours from the TCGA database. LncRNA HOTTIP promoted cell viability via inhibition of miR-205 in HCC cells.
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Affiliation(s)
- Weiqing Chen
- First People’s Hospital of Hangzhou Lin’an District, Affiliated Lin’an People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Feihua Chen
- First People’s Hospital of Hangzhou Lin’an District, Affiliated Lin’an People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Mouchun Gong
- First People’s Hospital of Hangzhou Lin’an District, Affiliated Lin’an People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Zhaoqing Jin
- First People’s Hospital of Hangzhou Lin’an District, Affiliated Lin’an People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Lilu Shu
- Department of Research and Development, Zhejiang Zhongwei Medical Research Center, Hangzhou, China
| | - Zhi-wei Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Jianjiang Wang, ; Zhi-wei Wang,
| | - Jianjiang Wang
- First People’s Hospital of Hangzhou Lin’an District, Affiliated Lin’an People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Jianjiang Wang, ; Zhi-wei Wang,
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19
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Han Q, Wang M, Dong X, Wei F, Luo Y, Sun X. Non-coding RNAs in hepatocellular carcinoma: Insights into regulatory mechanisms, clinical significance, and therapeutic potential. Front Immunol 2022; 13:985815. [PMID: 36300115 PMCID: PMC9590653 DOI: 10.3389/fimmu.2022.985815] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/23/2022] [Indexed: 01/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a complex and heterogeneous malignancy with high incidence and poor prognosis. In addition, owing to the lack of diagnostic and prognostic markers, current multimodal treatment options fail to achieve satisfactory outcomes. Tumor immune microenvironment (TIME), angiogenesis, epithelial-mesenchymal transition (EMT), invasion, metastasis, metabolism, and drug resistance are important factors influencing tumor development and therapy. The intercellular communication of these important processes is mediated by a variety of bioactive molecules to regulate pathophysiological processes in recipient cells. Among these bioactive molecules, non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), account for a large part of the human transcriptome, and their dysregulation affects the progression of HCC. The purpose of this review is to evaluate the potential regulatory mechanisms of ncRNAs in HCC, summarize novel biomarkers from somatic fluids (plasma/serum/urine), and explore the potential of some small-molecule modulators as drugs. Thus, through this review, we aim to contribute to a deeper understanding of the regulatory mechanisms, early diagnosis, prognosis, and precise treatment of HCC.
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Affiliation(s)
- Qin Han
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory for Research and Evaluation of Pharmacovigilance, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Mengchen Wang
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory for Research and Evaluation of Pharmacovigilance, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xi Dong
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory for Research and Evaluation of Pharmacovigilance, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Wei
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory for Research and Evaluation of Pharmacovigilance, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yun Luo
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory for Research and Evaluation of Pharmacovigilance, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Yun Luo, ; Xiaobo Sun,
| | - Xiaobo Sun
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory for Research and Evaluation of Pharmacovigilance, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Yun Luo, ; Xiaobo Sun,
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20
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Chen T. Circulating Non-Coding RNAs as Potential Diagnostic Biomarkers in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2022; 9:1029-1040. [PMID: 36132427 PMCID: PMC9484560 DOI: 10.2147/jhc.s380237] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is currently the second leading cause of cancer-related deaths worldwide, with high morbidity and mortality. The clinical diagnosis of HCC mainly depends on imaging technology, such as ultrasound and computed tomography, and serum biomarkers, such as alpha-fetoprotein (AFP). However, HCC is still hard to diagnose at an early stage due to the low sensitivity of the above mentioned traditional methods. Typically, HCC is diagnosed at an advanced stage when limited treatment options are available. It is urgent to identify effective biomarkers for the early diagnosis of HCC. Increasing evidence uncovered ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), could be used in HCC diagnosis. The aim of this review is to summarize our understanding of circulating miRNAs, lncRNAs and circRNAs as fluid-based non-invasive biomarkers, and aiming at providing new insights into the diagnosis of HCC.
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Affiliation(s)
- Tingsong Chen
- The Second Department of Oncology, the Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
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21
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Machida K. HCV and tumor-initiating stem-like cells. Front Physiol 2022; 13:903302. [PMID: 36187761 PMCID: PMC9520593 DOI: 10.3389/fphys.2022.903302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/11/2022] [Indexed: 12/24/2022] Open
Abstract
Neoplasms contain tumor-initiating stem-like cells (TICs) that are characterized by increased drug resistance. The incidence of many cancer types have trended downward except for few cancer types, including hepatocellular carcinoma (HCC). Therefore mechanism of HCC development and therapy resistance needs to be understood. These multiple hits by hepatitis C virus (HCV) eventually promotes transformation and TIC genesis, leading to HCC development. This review article describes links between HCV-associated HCC and TICs. This review discusses 1) how HCV promotes genesis of TICs and HCC development; 2) how this process avails itself as a novel therapeutic target for HCC treatment; and 3) ten hall marks of TIC oncogenesis and HCC development as targets for novel therapeutic modalities.
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22
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Su C, Wang W, Mo J, Liu F, Zhang H, Liu Y, Chen X, Liao Z, Zhang B, Zhu P. Long noncoding RNA HOXC-AS3 interacts with CDK2 to promote proliferation in hepatocellular carcinoma. Biomark Res 2022; 10:65. [PMID: 36031658 PMCID: PMC9420287 DOI: 10.1186/s40364-022-00411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/09/2022] [Indexed: 11/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a type of cancer that affects the liver and has a high mortality rate. Long non-coding RNAs (lncRNAs) dysregulation can contribute to cancer occurrence and progression, although the underlying molecular pathways are mostly unclear. HOXC-AS3 was found to be considerably overexpressed in HCC in this investigation. The goal of this work was to look into the involvement of HOXC-AS3 in HCC and the various molecular pathways that underpin it. Methods Normal liver and paired HCC tissues from HCC patients were used to evaluate HOXC-AS3 expression by qRT-PCR. The role of HOXC-AS3 in HCC was assessed both in vitro and in vivo. RNA pulldown, RIP and co-IP were used to demonstrate the potential mechanism by which HOXC-AS3 regulates the progression of HCC. Results Using qRT-PCR, it was discovered that HOXC-AS3 was substantially expressed in HCC. In vitro and in vivo, overexpression of HOXC-AS3 aided proliferation and cell cycle progression. HOXC-AS3 interacted with CDK2 to facilitate CDK2’s decreased binding to p21, resulting in enhanced CDK2 activity, which promoted the phosphorylation of Rb and the progression of HCC. Conclusions HOXC-AS3 is highly expressed in HCC and can promote the progression of HCC by interacting with CDK2. Therefore, targeting HOXC-AS3 is very likely to provide a new strategy for the treatment of HCC and for improving patient prognosis. Supplementary Information The online version contains supplementary material available at 10.1186/s40364-022-00411-2.
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23
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Function of the Long Noncoding RNAs in Hepatocellular Carcinoma: Classification, Molecular Mechanisms, and Significant Therapeutic Potentials. Bioengineering (Basel) 2022; 9:bioengineering9080406. [PMID: 36004931 PMCID: PMC9405066 DOI: 10.3390/bioengineering9080406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common and serious type of primary liver cancer. HCC patients have a high death rate and poor prognosis due to the lack of clear signs and inadequate treatment interventions. However, the molecular pathways that underpin HCC pathogenesis remain unclear. Long non-coding RNAs (lncRNAs), a new type of RNAs, have been found to play important roles in HCC. LncRNAs have the ability to influence gene expression and protein activity. Dysregulation of lncRNAs has been linked to a growing number of liver disorders, including HCC. As a result, improved understanding of lncRNAs could lead to new insights into HCC etiology, as well as new approaches for the early detection and treatment of HCC. The latest results with respect to the role of lncRNAs in controlling multiple pathways of HCC were summarized in this study. The processes by which lncRNAs influence HCC advancement by interacting with chromatin, RNAs, and proteins at the epigenetic, transcriptional, and post-transcriptional levels were examined. This critical review also highlights recent breakthroughs in lncRNA signaling pathways in HCC progression, shedding light on the potential applications of lncRNAs for HCC diagnosis and therapy.
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24
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Kunadirek P, Pinjaroen N, Nookaew I, Tangkijvanich P, Chuaypen N. Transcriptomic Analyses Reveal Long Non-Coding RNA in Peripheral Blood Mononuclear Cells as a Novel Biomarker for Diagnosis and Prognosis of Hepatocellular Carcinoma. Int J Mol Sci 2022; 23:ijms23147882. [PMID: 35887228 PMCID: PMC9324406 DOI: 10.3390/ijms23147882] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 02/06/2023] Open
Abstract
Novel biomarkers are highly required for the diagnosis and predicting prognosis of hepatocellular carcinoma (HCC). In this study, we investigated the profiles of long non-coding RNAs (lncRNAs) obtained from the peripheral blood mononuclear cells (PBMCs) of patients with HCC and PBMCs from a co-culture model using transcriptomic analysis. The differentially expressed lncRNAs (DElncRNAs) were then characterized and integrated as cancer-induced lncRNAs. Among them, three up-regulating DElncRNAs including MIR4435-2HG, SNHG9 and lnc-LCP2-1 and one down-regulating, lnc-POLD3-2, were identified. The functional analysis showed that these enriched lncRNAs were mainly associated with carcinogenesis and immune responses. Following further validation in PBMCs samples (100 HBV-related HCC, 100 chronic hepatitis B and 100 healthy controls), MIR4435-2HG, lnc-POLD3-2 and their combination were revealed to be sensitive biomarkers in discriminating HCC from non-HCC (AUROC = 0.78, 0.80, and 0.87, respectively), particularly among individuals with normal serum alpha-fetoprotein levels. Additionally, high circulating SNHG9 expression was shown to be an independent prognostic factor of overall survival in patients with HCC. These results indicate that determining these lncRNAs in PBMCs could serve as novel diagnostic and prognostic biomarkers for HBV-related HCC.
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Affiliation(s)
- Pattapon Kunadirek
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Nutcha Pinjaroen
- Department of Radiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
- Correspondence: (P.T.); (N.C.); Tel.: +66-2-256-4482 (N.C.)
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
- Correspondence: (P.T.); (N.C.); Tel.: +66-2-256-4482 (N.C.)
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25
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Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. NPJ Precis Oncol 2022; 6:40. [PMID: 35729321 PMCID: PMC9213432 DOI: 10.1038/s41698-022-00283-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
Cancer ranks as one of the deadliest diseases worldwide. The high mortality rate associated with cancer is partially due to the lack of reliable early detection methods and/or inaccurate diagnostic tools such as certain protein biomarkers. Cell-free nucleic acids (cfNA) such as circulating long noncoding RNAs (lncRNAs) have been proposed as a new class of potential biomarkers for cancer diagnosis. The reported correlation between the presence of tumors and abnormal levels of lncRNAs in the blood of cancer patients has notably triggered a worldwide interest among clinicians and oncologists who have been actively investigating their potentials as reliable cancer biomarkers. In this report, we review the progress achieved (“the Good”) and challenges encountered (“the Bad”) in the development of circulating lncRNAs as potential biomarkers for early cancer diagnosis. We report and discuss the diagnostic performance of more than 50 different circulating lncRNAs and emphasize their numerous potential clinical applications (“the Beauty”) including therapeutic targets and agents, on top of diagnostic and prognostic capabilities. This review also summarizes the best methods of investigation and provides useful guidelines for clinicians and scientists who desire conducting their own clinical studies on circulating lncRNAs in cancer patients via RT-qPCR or Next Generation Sequencing (NGS).
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26
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Amer RG, Ezz El Arab LR, Abd El Ghany D, Saad AS, Bahie-Eldin N, Swellam M. Prognostic utility of lncRNAs (LINC00565 and LINC00641) as molecular markers in glioblastoma multiforme (GBM). J Neurooncol 2022; 158:435-444. [PMID: 35668225 PMCID: PMC9256564 DOI: 10.1007/s11060-022-04030-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022]
Abstract
Background and aim Glioblastoma multiforme (GBM) is primary brain tumor grade IV characterized by fast cell proliferation, high mortality and morbidity and most lethal gliomas. Molecular approaches underlying its pathogenesis and progression with diagnostic and prognostic value have been an area of interest. Long-non coding RNAs (lncRNAs) aberrantly expressed in GBM have been recently studied. The aim is to investigate the clinical role of lncRNA565 and lncRNA641 in GBM patients. Patients and methods Blood samples were withdrawn from 35 newly diagnosed GBM cases with 15 healthy individuals, then lncRNA565 and lncRNA641 expression were evaluated using real time-PCR. Their diagnostic efficacy was detected using receiver operating characteristic curve. Progression free survival (PFS) and overall survival (OS) were studied using Kaplan–Meier curves. Results lncRNAs expressions were increased significantly among GBM as compared to control group. Their expressions were correlated with clinico-pathological data and survival pattern for the studied GBM patients. Higher levels of both lncRNAs were correlated to worse performance status. Expression of lncRNA565 was increased with large tumor size (≥ 5 cm). Survival analysis showed that both investigated lncRNA were increased with worse PFS and OS. Conclusion Expression of lncRNA565 and lncRNA641 in a liquid biopsy sample can be used as prognostic biomarker for GBM patients.
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Affiliation(s)
- Rehab G Amer
- Clinical Oncology Department, Ain Shams University, Cairo, Egypt
| | | | | | - Amr S Saad
- Clinical Oncology Department, Ain Shams University, Cairo, Egypt
| | | | - Menha Swellam
- Biochemistry Department, Biotechnology Research Institute, High Throughput Molecular and Genetic laboratory, Central Laboratories Network and the Centers of Excellence, National Research Centre, Dokki, Giza, Egypt.
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27
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Huang Y, Jiang L, Liu Y, Liu L, Wang J, Shi L. Long non-coding RNAs in virus-related cancers. Rev Med Virol 2022; 32:e2364. [PMID: 35607835 DOI: 10.1002/rmv.2364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/30/2022] [Accepted: 05/06/2022] [Indexed: 12/12/2022]
Abstract
Some viral infections lead to tumourigenesis explained by a variety of underlying molecular mechanisms. Long non-coding RNAs (lncRNAs) have the potential to be added to this list due to their diverse mechanisms in biological functions and disease processes via gene alternation, transcriptional regulation, protein modification, microRNA sponging and interaction with RNA/DNA/proteins. In this review, we summarise the dysregulation and mechanism of lncRNAs in virus-related cancers focussing on Hepatitis B virus, Epstein-Barr virus, Human Papillomavirus. We will also discuss the potential implications of lncRNAs in COVID-19.
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Affiliation(s)
- Yushan Huang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Longchang Jiang
- Department of Vascular Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yang Liu
- Gansu Provincial People's Hospital, Lanzhou, China
| | - Lixian Liu
- Shijiangzhuang City Zoo, Shijiazhuang, China
| | - Junling Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Lei Shi
- School of Public Health, Lanzhou University, Lanzhou, China
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28
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Han Y, Jiang W, Wang Y, Zhao M, Li Y, Ren L. Serum long non-coding RNA SCARNA10 serves as a potential diagnostic biomarker for hepatocellular carcinoma. BMC Cancer 2022; 22:431. [PMID: 35443674 PMCID: PMC9022341 DOI: 10.1186/s12885-022-09530-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 04/11/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Circulating long non-coding RNAs (lncRNAs) have been demonstrated to serve as diagnostic or prognosis biomarkers for various disease. We aimed to elucidate the diagnostic efficacy of serum lncRNA SCARNA10 for the hepatocellular carcinoma (HCC). METHODS In this study, a total of 182 patients with HCC, 105 patients with benign liver disease (BLD), and 149 healthy controls (HC) were enrolled. According to different classifications, the levels of serum SCARNA10 were assessed by quantitative real-time polymerase chain reaction (qPCR). The correlations between serum SCARNA10 and clinicopathological characteristics were further analyzed. The receiver operating characteristic (ROC) curve and area under curve (AUC) were utilized to estimate the diagnostic capacity of serum SCARNA10 and its combination with AFP for HCC. RESULTS The results demonstrated that the levels of serum SCARNA10 were significantly higher in HCC patients than in patients with BLD and healthy controls, and significantly increased in HCC patients with hepatitis B or C infection, or with liver cirrhosis. Furthermore, positive correlations were noted between serum SCARNA10 level and some clinicopathological characteristics, including tumor size, differentiation degrees, tumor stage, vascular invasion, tumor metastasis and complications. ROC analysis revealed that SCARNA10 had a significantly predictive value for HCC (Sensitivity = 0.70, Specificity = 0.77, and AUC = 0.82), the combination of SCARNA10 and AFP gained the higher sensitivity (AUCSCARNA10 + AFP = 0.92 vs AUCAFP = 0.83, p < 0.01). SCARNA10 retained significant diagnosis capabilities for AFP-negative HCC patients. CONCLUSIONS In summary, lncRNA SCARNA10 may serve as a novel and non-invasive biomarker with relatively high sensitivity and specificity for HCC diagnosis.
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Affiliation(s)
- Yawei Han
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China
| | - Wenna Jiang
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China
| | - Yu Wang
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China.,College of Inspection, Tianjin Medical University, Tianjin, China
| | - Meng Zhao
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China
| | - Yueguo Li
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China.
| | - Li Ren
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China.
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Li D, Fan X, Li Y, Yang J, Lin H. The paradoxical functions of long noncoding RNAs in hepatocellular carcinoma: Implications in therapeutic opportunities and precision medicine. Genes Dis 2022; 9:358-369. [PMID: 35224152 PMCID: PMC8843871 DOI: 10.1016/j.gendis.2020.11.014] [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: 06/03/2020] [Revised: 10/22/2020] [Accepted: 11/24/2020] [Indexed: 11/20/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is among the most aggressive and lethal diseases with poor prognosis, worldwide. However, the mechanisms underlying HCC have not been comprehensively elucidated. With the recent application of high-throughput sequencing techniques, a diverse catalogue of differentially expressed long non-coding RNAs (lncRNA) in cancer have been shown to participate in HCC. Rather than being "transcriptional noise," they are emerging as important regulators of many biological processes, including chromatin remodelling, transcription, alternative splicing, translational and post-translational modification. Moreover, lncRNAs have dual effects in the development and progression of HCC, including oncogenic and tumour-suppressive roles. Collectively, recently data point to lncRNAs as novel diagnostic and prognostic biomarkers with satisfactory sensitivity and specificity, as well as being therapeutic targets for HCC patients. In this review, we highlight recent progress of the molecular patterns of lncRNAs and discuss their potential clinical application in human HCC.
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Affiliation(s)
- Duguang Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Xiaoxiao Fan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Yirun Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Jing Yang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Hui Lin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
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Circulating MicroRNA-21 As A Novel Noninvasive Biomarker for Hepatocellular Carcinoma Compared with Alpha Fetoprotein Gold Test. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the greatest traditional kind of pre-eminent cancer worldwide, which happens mainly in chronic liver disease and cirrhotic patients. The available surveillance strategies for suspected HCC patients include serum alpha-fetoprotein (AFP) and liver imaging have been mainly recommended. However, the sensitivity and selectivity of these diagnostic strategies especially in the early stages of HCC have many obstacles. MicroRNAs (miRNAs) are non-coding RNAs that are 18–25 nucleotides in length. Plasma miRNAs may be a promising new biomarker for cancer detection and prognosis in the early stages. Assessment of Plasma MicroRNA-21 (miRNA-21) significance as a noninvasive Hepatocellular carcinoma marker compared with AFP gold standard test to improve HCC early diagnostic power. This is a prospective research project that included 90 patients in total, split into three classes., liver cirrhosis patients (LC) without any malignancies and (HCC) patients in addition to the healthy control group. Patients and controls were subjected to the clinical studies, routine investigations, imaging studies, and detection of plasma miRNA-21 & AFP. miRNA-21 showed a highly significant difference in the 3 studied groups. Control group with LC group, control group with HCC group, and LC group with HCC group P value (P 0.0001, P1 0.0001, P2 0.0001and P3 0.0001) respectively. Also, a highly significant difference was observed between pre-TACE and post-TACE miRNA-21 in the HCC group P value (0.0001). Circulating miRNA-21 may be used as a noninvasive co biomarker with AFP to increase HCC diagnostic accuracy in its early stages.
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The Expression and Function of Circadian Rhythm Genes in Hepatocellular Carcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:4044606. [PMID: 34697563 PMCID: PMC8541861 DOI: 10.1155/2021/4044606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/07/2021] [Accepted: 09/25/2021] [Indexed: 12/25/2022]
Abstract
Hepatocellular carcinoma (HCC) is among the most common and lethal form of cancer worldwide. However, its diagnosis and treatment are still dissatisfactory, due to limitations in the understanding of its pathogenic mechanism. Therefore, it is important to elucidate the molecular mechanisms and identify novel therapeutic targets for HCC. Circadian rhythm-related genes control a variety of biological processes. These genes play pivotal roles in the initiation and progression of HCC and are potential diagnostic markers and therapeutic targets. This review gives an update on the research progress of circadian rhythms, their effects on the initiation, progression, and prognosis of HCC, in a bid to provide new insights for the research and treatment of HCC.
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Upregulation of a novel LncRNA AC104958.2 stabilized by PCBP2 promotes proliferation and microvascular invasion in hepatocellular carcinoma. Exp Cell Res 2021; 407:112791. [PMID: 34418457 DOI: 10.1016/j.yexcr.2021.112791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) were reported to be involved in tumorigenesis and progression of hepatocellular carcinoma (HCC). Microvascular invasion (MVI) is an independent predictor for early recurrence and overall survival in postoperative patients with HCC. However, the mechanisms how lncRNAs affect HCC and MVI remain elusive. By RNA sequencing (RNA-seq) in a series of 65 HCC samples and 30 paired adjacent non-tumor liver tissue, we identified a novel lncRNA AC104958.2 that was significantly upregulated in HCC tissues and associated with MVI. Overexpression of AC104958.2 obviously elevated cell viability, metastasis, invasion and epithelial-mesenchymal transition (EMT), while knockout of AC104958.2 mediated by CRISPR/Cas9 technique showed the opposite effects. In addition, the interaction between AC104958.2 and Poly (rC) binding protein 2 (PCBP2) was identified by RNA pull down and mass spectrometry (MS), which was further validated by RNA immunoprecipitation (RIP). PCBP2 was also upregulated in HCC and associated with MVI. High expression of both AC104958.2 and PCBP2 was correlated with tumor size, TNM stage and MVI in HCC. Overexpression of PCBP2 greatly increased the cell viability, metastasis, invasion and EMT. Moreover, actinomycin D assay showed that overexpression of PCBP2 enhanced the RNA stability of AC104958.2. In conclusion, our study showed that a novel lncRNA AC104958.2 exerted oncogenic roles in HCC and might be a promising biomarker and therapeutic target.
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The Role of Long Non-Coding RNA and microRNA Networks in Hepatocellular Carcinoma and Its Tumor Microenvironment. Int J Mol Sci 2021; 22:ijms221910630. [PMID: 34638971 PMCID: PMC8508708 DOI: 10.3390/ijms221910630] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a common liver malignancy with high morbidity and poor prognosis. Long non-coding RNAs (lncRNAs) are involved in crucial biological processes of tumorigenesis and progression, and play four major regulatory roles, namely signal, decoy, guide, and scaffold, to regulate gene expression. Through these processes, lncRNAs can target microRNAs (miRNAs) to form lncRNA and miRNA networks, which regulate cancer cell proliferation, metastasis, drug resistance, and the tumor microenvironment. Here, we summarize the multifaceted functions of lncRNA and miRNA networks in the pathogenesis of HCC, the potential use of diagnostic or prognostic biomarkers, and novel therapeutic targets in HCC. This review also highlights the regulatory effects of lncRNA and miRNA networks in the tumor microenvironment of HCC.
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Guo T, He K, Wang Y, Sun J, Chen Y, Yang Z. Prognostic Signature of Hepatocellular Carcinoma and Analysis of Immune Infiltration Based on m6A-Related lncRNAs. Front Oncol 2021; 11:691372. [PMID: 34527575 PMCID: PMC8435865 DOI: 10.3389/fonc.2021.691372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
The relationship between m6A-related lncRNAs and prognosis in hepatocellular carcinoma (HCC) is not yet clear. We used Lasso regression to establish a prognostic signature based on m6A-related lncRNAs using a training set from TCGA, and then verified the signature efficacy in a test set. Fluorescence quantitative real-time PCR (qPCR), Survival analysis, clinical risk difference analysis, immune-related analysis, and drug-sensitivity analysis were conducted. The results revealed that 1,651 lncRNAs were differentially expressed in HCC tissues, among which, 163 were m6A-related. Univariate analysis showed that 87 lncRNAs were associated with the overall survival. Six differential m6A-related lncRNAs were validated and selected via Lasso regression to construct a prognostic signature which demonstrated a satisfactory predictive efficacy. In the clinically relevant pathologic stage, histologic grade, and T stage, the risk scores obtained based on this signature showed a statistically significant difference. The high- and low-risk groups exhibited a difference in the tumor immune infiltrating cells, immune checkpoint gene expression, and sensitivity to chemotherapy. In summary, the prognostic signature based on the m6A-related lncRNAs can effectively predict the prognosis of patients and might provide a new vista for the chemotherapy and immunotherapy of HCC.
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Affiliation(s)
- Ting Guo
- Department of Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Kun He
- Department of Hepatobiliary Surgery, Xi Jing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yifei Wang
- Department of Hepatobiliary Surgery, Xi Jing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jingjing Sun
- Department of Hepatobiliary Surgery, Xi Jing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yong Chen
- Department of Hepatobiliary Surgery, Xi Jing Hospital, Fourth Military Medical University, Xi'an, China
| | - Zelong Yang
- Department of Hepatobiliary Surgery, Xi Jing Hospital, Fourth Military Medical University, Xi'an, China
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Huang JY, Wang SY, Lin Y, Yi HC, Niu JJ. The Diagnostic Performance of lncRNAs from Blood Specimens in Patients with Hepatocellular Carcinoma: A Meta-Analysis. Lab Med 2021; 52:64-73. [PMID: 32700735 DOI: 10.1093/labmed/lmaa050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE Long noncoding RNAs (lncRNAs) are widely involved in the carcinogenesis and development of cancers. We conducted a meta-analysis to evaluate the diagnostic performance of lncRNAs in hepatocellular carcinoma (HCC). METHODS After the inclusion and exclusion process, relevant information was extracted. Heterogeneity between studies was evaluated, and data synthesis was conducted by employing a bivariate random-effects model. RESULTS In total, 20 eligible studies were enrolled. The pooled sensitivity and specificity were 0.86 (95% confidence interval [CI], 0.80-0.90) and 0.88 (95% CI, 0.82-0.92), respectively. The pooled positive likelihood ratio, pooled negative likelihood ratio, and pooled diagnostic odds ratio were 7.1 (95% CI, 4.9-10.2), 0.16 (95% CI, 0.11-0.23), and 44 (95% CI, 25-79), respectively. The results of the linear regression method and visual inspection of the Deeks funnel plot did not indicate significant publication bias. CONCLUSION Our meta-analysis suggested that lncRNAs have high diagnostic performance for HCC and have the potential for clinical application.
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Affiliation(s)
- Jing-Yi Huang
- Clinical Laboratory, Xiamen Branch of Zhongshan Hospital, Fudan University, Xiamen, Fujian Province, China
| | - Si-Yu Wang
- Center of Clinical Laboratory, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Province, China
| | - Yong Lin
- Center of Clinical Laboratory, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Province, China
| | - Huo-Chun Yi
- Center of Clinical Laboratory, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Province, China
| | - Jian-Jun Niu
- Center of Clinical Laboratory, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Province, China
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Matboli M, Kamel MM, Essawy N, Bekhit MM, Abdulrahman B, Mohamed GF, Eissa S. Identification of Novel Insulin Resistance Related ceRNA Network in T2DM and Its Potential Editing by CRISPR/Cas9. Int J Mol Sci 2021; 22:ijms22158129. [PMID: 34360895 PMCID: PMC8348752 DOI: 10.3390/ijms22158129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/11/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Type 2 diabetes mellitus is one of the leading causes of morbidity and mortality worldwide and is derived from an accumulation of genetic and epigenetic changes. In this study, we aimed to construct Insilco, a competing endogenous RNA (ceRNA) network linked to the pathogenesis of insulin resistance followed by its experimental validation in patients’, matched control and cell line samples, as well as to evaluate the efficacy of CRISPR/Cas9 as a potential therapeutic strategy to modulate the expression of this deregulated network. By applying bioinformatics tools through a two-step process, we identified and verified a ceRNA network panel of mRNAs, miRNAs and lncRNA related to insulin resistance, Then validated the expression in clinical samples (123 patients and 106 controls) and some of matched cell line samples using real time PCR. Next, two guide RNAs were designed to target the sequence flanking LncRNA/miRNAs interaction by CRISPER/Cas9 in cell culture. Gene editing tool efficacy was assessed by measuring the network downstream proteins GLUT4 and mTOR via immunofluorescence. Results: LncRNA-RP11-773H22.4, together with RET, IGF1R and mTOR mRNAs, showed significant upregulation in T2DM compared with matched controls, while miRNA (i.e., miR-3163 and miR-1) and mRNA (i.e., GLUT4 and AKT2) expression displayed marked downregulation in diabetic samples. CRISPR/Cas9 successfully knocked out LncRNA-RP11-773H22.4, as evidenced by the reversal of the gene expression of the identified network at RNA and protein levels to the normal expression pattern after gene editing. Conclusions: The present study provides the significance of this ceRNA based network and its related target genes panel both in the pathogenesis of insulin resistance and as a therapeutic target for gene editing in T2DM.
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Affiliation(s)
- Marwa Matboli
- Medicinal Biochemistry and Molecular Biology Department, School of Medicine, Ain Shams University, Cairo 11566, Egypt;
- Correspondence: (M.M.); (S.E.)
| | - Marwa Mostafa Kamel
- Medicinal Biochemistry and Molecular Biology Department, School of Medicine, Ain Shams University, Cairo 11566, Egypt;
| | - Nada Essawy
- Institut Pasteur, CEDEX 15, 75724 Paris, France;
| | - Meram Mohamed Bekhit
- Internal Medicine, Endocrinology and Diabetes Department, School of Medicine, Ain Shams University, Cairo 11566, Egypt;
| | - Basant Abdulrahman
- Calgary Prion Research Unit, University of Calgary, Calgary, AB T2N 4Z6, Canada;
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
| | - Ghada F. Mohamed
- Department of Histology, School of Medicine, Ain Shams University, Cairo 11566, Egypt;
| | - Sanaa Eissa
- Medicinal Biochemistry and Molecular Biology Department, School of Medicine, Ain Shams University, Cairo 11566, Egypt;
- Correspondence: (M.M.); (S.E.)
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Zhou P, Lu Y, Zhang Y, Wang L. Construction of an Immune-Related Six-lncRNA Signature to Predict the Outcomes, Immune Cell Infiltration, and Immunotherapy Response in Patients With Hepatocellular Carcinoma. Front Oncol 2021; 11:661758. [PMID: 34277410 PMCID: PMC8283691 DOI: 10.3389/fonc.2021.661758] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/08/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the world's most lethal malignant tumors with a poor prognosis. Growing evidence has been demonstrating that immune-related long non-coding RNAs (lncRNAs) are relevant to the tumor microenvironment (TME) and can help assess the effects of immunotherapy and evaluate one's prognosis. This study aims to identify an immune-related lncRNA signature for the prospective assessment of the immunotherapy and prognosis in HCC. METHOD We downloaded HCC RNA-seq data and clinical information from The Cancer Genome Atlas (TCGA) project database. We first used ESTIMATE to evaluate the TME. Then, we conducted a cox regression analysis to construct a prognostic signature and the riskScore. We then applied the univariate Cox regression, multivariate Cox regression, principal components analysis (PCA), receiver operating characteristic (ROC) curve, and stratification analyses to confirm our previous assessments. Afterward, we employed a gene set enrichment analysis (GSEA) to explore the biological processes and pathways. Besides, we used CIBERSORT to estimate the abundance of tumor-infiltrating immune cells (TIICs). Furthermore, we investigated the relationship between the immune-related lncRNA signature and immune checkpoint genes. Finally, we used the quantitative real-time polymerase chain reaction (qRT-PCR) assays to demonstrate the expression of the six lncRNAs. RESULTS We identified six immune-related lncRNAs - MSC-AS1, AC145207.5, SNHG3, AL365203.2, AL031985.3, NRAV - which show the ability to stratify patients into high-risk and low-risk groups with significantly different survival rates. The univariate Cox regression, multivariate Cox regression, ROC, and stratification analyses confirmed that the immune-related six-lncRNA signature was a novel independent prognostic factor in HCC patients. The high-risk group and low-risk group illustrated contrasting distributions in PCA. The GSEA suggested that the immune-related six-lncRNA signature was involved in the immune-related biological processes and pathways. Besides, the immune-related six-lncRNA signature was associated with the infiltration of immune cells. Furthermore, it was linked with the expression of critical immune genes and could predict immunotherapy's clinical response. Finally, the qRT-PCR demonstrated that the six lncRNAs were significantly differentially expressed in HCC cell lines and normal hepatic cell lines. CONCLUSION In summary, we identified an immune-related six-lncRNA signature that can predict the outcomes, immune cell infiltration, and immunotherapy response in patients with hepatocellular carcinoma.
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Affiliation(s)
| | - Yuhua Lu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Yewei Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Southeast University Zhongda Hospital, Nanjing, China
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lei Wang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Nantong, China
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Alfano V, Zeisel MB, Levrero M, Guerrieri F. The lncRNAs in HBV-Related HCCs: Targeting Chromatin Dynamics and Beyond. Cancers (Basel) 2021; 13:3115. [PMID: 34206504 PMCID: PMC8268133 DOI: 10.3390/cancers13133115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) represents the fourth leading and fastest rising cause of cancer death (841,000 new cases and 782,000 deaths annually), and hepatitis B (HBV), with 250 million people chronically infected at risk of developing HCC, accounts for >50% of the cases worldwide. Long non-coding RNAs (lncRNAs), untranslated transcripts longer than 200 nucleotides, are implicated in gene regulation at the transcriptional and post-transcriptional levels, exerting their activities both in the nuclear and cytoplasmic compartments. Thanks to high-throughput sequencing techniques, several lncRNAs have been shown to favor the establishment of chronic HBV infection, to change the host transcriptome to establish a pro-carcinogenic environment, and to directly participate in HCC development and progression. In this review, we summarize current knowledge on the role of lncRNAs in HBV infection and HBV-related liver carcinogenesis and discuss the potential of lncRNAs as predictive or diagnostic biomarkers.
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Affiliation(s)
- Vincenzo Alfano
- Cancer Research Center of Lyon (CRCL), UMR Inserm 1052 CNRS 5286 Mixte CLB, Université de Lyon 1 (UCBL1), 69003 Lyon, France; (V.A.); (M.B.Z.)
| | - Mirjam B. Zeisel
- Cancer Research Center of Lyon (CRCL), UMR Inserm 1052 CNRS 5286 Mixte CLB, Université de Lyon 1 (UCBL1), 69003 Lyon, France; (V.A.); (M.B.Z.)
| | - Massimo Levrero
- Cancer Research Center of Lyon (CRCL), UMR Inserm 1052 CNRS 5286 Mixte CLB, Université de Lyon 1 (UCBL1), 69003 Lyon, France; (V.A.); (M.B.Z.)
- Hospices Civils de Lyon, Hôpital Croix Rousse, Service d’Hépato-Gastroentérologie, 69004 Lyon, France
- Department of Medicine SCIAC, University of Rome La Sapienza, 00161 Rome, Italy
| | - Francesca Guerrieri
- Cancer Research Center of Lyon (CRCL), UMR Inserm 1052 CNRS 5286 Mixte CLB, Université de Lyon 1 (UCBL1), 69003 Lyon, France; (V.A.); (M.B.Z.)
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Unfried JP, Sangro P, Prats-Mari L, Sangro B, Fortes P. The Landscape of lncRNAs in Hepatocellular Carcinoma: A Translational Perspective. Cancers (Basel) 2021; 13:2651. [PMID: 34071216 PMCID: PMC8197910 DOI: 10.3390/cancers13112651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
LncRNAs are emerging as relevant regulators of multiple cellular processes involved in cell physiology as well as in the development and progression of human diseases, most notably, cancer. Hepatocellular carcinoma (HCC) is a prominent cause of cancer-related death worldwide due to the high prevalence of causative factors, usual cirrhotic status of the tumor-harboring livers and the suboptimal benefit of locoregional and systemic therapies. Despite huge progress in the molecular characterization of HCC, no oncogenic loop addiction has been identified and most genetic alterations remain non-druggable, underscoring the importance of advancing research in novel approaches for HCC treatment. In this context, long non-coding RNAs (lncRNAs) appear as potentially useful targets as they often exhibit high tumor- and tissue-specific expression and many studies have reported an outstanding dysregulation of lncRNAs in HCC. However, there is a limited perspective of the potential role that deregulated lncRNAs may play in HCC progression and aggressiveness or the mechanisms and therapeutic implications behind such effects. In this review, we offer a clarifying landscape of current efforts to evaluate lncRNA potential as therapeutic targets in HCC using evidence from preclinical models as well as from recent studies on novel oncogenic pathways that show lncRNA-dependency.
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Affiliation(s)
- Juan Pablo Unfried
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, Universidad de Navarra (UNAV), 31008 Pamplona, Spain; (L.P.-M.); (P.F.)
| | - Paloma Sangro
- Liver Unit, Clínica Universidad de Navarra (CUN), 31008 Pamplona, Spain;
| | - Laura Prats-Mari
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, Universidad de Navarra (UNAV), 31008 Pamplona, Spain; (L.P.-M.); (P.F.)
| | - Bruno Sangro
- Liver Unit, Clínica Universidad de Navarra (CUN), 31008 Pamplona, Spain;
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), 31008 Pamplona, Spain
| | - Puri Fortes
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, Universidad de Navarra (UNAV), 31008 Pamplona, Spain; (L.P.-M.); (P.F.)
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), 31008 Pamplona, Spain
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Guo C, Zhou S, Yi W, Yang P, Li O, Liu J, Peng C. Long non-coding RNA muskelin 1 antisense RNA (MKLN1-AS) is a potential diagnostic and prognostic biomarker and therapeutic target for hepatocellular carcinoma. Exp Mol Pathol 2021; 120:104638. [PMID: 33878313 DOI: 10.1016/j.yexmp.2021.104638] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/21/2021] [Accepted: 04/13/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUNDS/AIMS Hepatocellular carcinoma is recognized as the most common subtype of hepatic cancer. Muskelin 1 antisense RNA (MKLN1-AS) shows prognostic value in hepatitis B virus-hepatocellular carcinoma. The aim of this study is to investigate the detailed biological role of MKLN1-AS and Yes-associated transcriptional regulator 1 (YAP1)-related mechanisms. METHODS Based on online databases (GEPIA, TCGA, and GEO), the expression of MKLN1-AS and YAP1 in patients with hepatocellular carcinoma was analyzed. The IntaRNA algorithm was used to predict complementary sites between MKLN1-AS and YAP1 mRNA. Hepatocellular carcinoma tumor tissues and cells were collected for the quantification of MKLN1-AS and YAP1. FISH was performed to explore the location of MKLN1-AS in cells. The effects of MKLN1-AS and YAP1 on proliferation, migration and invasionof hepatocellular carcinoma were determined in vitro and in vivo. Actinomycin D and RNA immunoprecipitation were resorted to confirm the regulatory role of MKLN1-AS in YAP1 expression. RESULTS The up-regulation of MKLN1-AS contributed to the poor prognosis of patients with hepatocellular carcinoma. MKLN1-AS and YAP1 were overexpressed in hepatocellular carcinoma tissues and cells. MKLN1-AS positively modulated YAP1 expression through targeting and stabilizing YAP1 mRNA.MKLN1-AS was predominantly located in the cytoplasm of the cells. MKLN1-AS intensified proliferation, migration and invasion of hepatocellular carcinoma cells via YAP1. MKLN1-AS also caused hepatocarcinogenesis through inducing YAP1 expression in vivo. CONCLUSIONS MKLN1-AS overexpression enhances the stability of YAP1 mRNA, which is necessary for the oncogenic activity of MKLN1-AS. MKLN1-AS can be utilized in the diagnosis and prognosis of hepatocellular carcinoma as an upstream factor of YAP1.
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Affiliation(s)
- Chao Guo
- Department of hepatobiliary surgery, the First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, No.61 Jiefang West Road, Changsha City, Hunan Province 410005, China
| | - Shuhuang Zhou
- Department of hepatobiliary surgery, the First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, No.61 Jiefang West Road, Changsha City, Hunan Province 410005, China
| | - Weimin Yi
- Department of hepatobiliary surgery, the First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, No.61 Jiefang West Road, Changsha City, Hunan Province 410005, China
| | - Pingzhou Yang
- Department of hepatobiliary surgery, the First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, No.61 Jiefang West Road, Changsha City, Hunan Province 410005, China
| | - Ou Li
- Department of hepatobiliary surgery, the First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, No.61 Jiefang West Road, Changsha City, Hunan Province 410005, China
| | - Jianming Liu
- Department of hepatobiliary surgery, the First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, No.61 Jiefang West Road, Changsha City, Hunan Province 410005, China
| | - Chuang Peng
- Department of hepatobiliary surgery, the First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, No.61 Jiefang West Road, Changsha City, Hunan Province 410005, China.
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Ramli S, Sim MS, Guad RM, Gopinath SCB, Subramaniyan V, Fuloria S, Fuloria NK, Choy KW, Rana S, Wu YS. Long Noncoding RNA UCA1 in Gastrointestinal Cancers: Molecular Regulatory Roles and Patterns, Mechanisms, and Interactions. JOURNAL OF ONCOLOGY 2021; 2021:5519720. [PMID: 33936199 PMCID: PMC8055404 DOI: 10.1155/2021/5519720] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/15/2021] [Accepted: 03/26/2021] [Indexed: 02/08/2023]
Abstract
The rising trend of gastrointestinal (GI) cancer has become a global burden due to its aggressive nature and poor prognosis. Long noncoding RNAs (lncRNAs) have recently been reported to be overexpressed in different GI cancers and may contribute to cancer progression and chemoresistance. They are featured with more than 200 nucleotides, commonly polyadenylated, and lacking an open reading frame. LncRNAs, particularly urothelial carcinoma-associated 1 (UCA1), are oncogenes involved in regulating cancer progression, such as cell proliferation, invasion, migration, and chemoresistance, particularly in GI cancer. This review was aimed to present an updated focus on the molecular regulatory roles and patterns of lncRNA UCA1 in progression and chemoresistance of different GI cancers, as well as deciphering the underlying mechanisms and its interactions with key molecules involved, together with a brief presentation on its diagnostic and prognostic values. The regulatory roles of lncRNA UCA1 are implicated in esophageal cancer, gastric cancer, pancreatic cancer, hepatobiliary cancer, and colorectal cancer, where they shared similar molecular mechanisms in regulating cancer phenotypes and chemoresistance. Comparatively, gastric cancer is the most intensively studied type in GI cancer. LncRNA UCA1 is implicated in biological roles of different GI cancers via interactions with various molecules, particularly microRNAs, and signaling pathways. In conclusion, lncRNA UCA1 is a potential molecular target for GI cancer, which may lead to the development of a novel chemotherapeutic agent. Hence, it also acts as a potential diagnostic and prognostic marker for GI cancer patients.
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Affiliation(s)
- Suaidah Ramli
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Maw Shin Sim
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Rhanye M. Guad
- Department of Biomedical Science and Therapeutics, Faculty of Medicine and Health Science, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Subash C. B Gopinath
- School of Bioprocess Engineering, Universiti Malaysia Perlis, Arau 02600, Perlis, Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar 01000, Perlis, Malaysia
| | - Vetriselvan Subramaniyan
- Department of Pharmacology, School of Medicine, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom, Selangor 42610, Malaysia
| | - Shivkanya Fuloria
- Faculty of Pharmacy, AIMST University, Bedong, Kedah 08100, Malaysia
| | - Neeraj K. Fuloria
- Faculty of Pharmacy, AIMST University, Bedong, Kedah 08100, Malaysia
| | - Ker Woon Choy
- Department of Anatomy, Faculty of Medicine, Universiti Teknologi MARA, Shah Alam, Sungai Buloh 47000, Selangor, Malaysia
| | - Sohel Rana
- Department of Pharmacy, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore-7400, Bangladesh
| | - Yuan Seng Wu
- Department of Biochemistry, School of Medicine, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom, Selangor 42610, Malaysia
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Song T, Li L, Wu S, Liu Y, Guo C, Wang W, Dai L, Zhang T, Wu H, Su B. Peripheral Blood Genetic Biomarkers for the Early Diagnosis of Hepatocellular Carcinoma. Front Oncol 2021; 11:583714. [PMID: 33777736 PMCID: PMC7991745 DOI: 10.3389/fonc.2021.583714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/18/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and has high mortality. Biomarkers related to HCC, such as alpha-fetoprotein, and imaging technology, such as ultrasound and computed tomography, have been used to screen and monitor HCC, but HCC is still difficult to diagnose effectively in the early stage due to the low sensitivity of the above mentioned traditional methods. There is an urgent need for noninvasive biomarkers to facilitate the screening and early diagnosis of HCC. With the advancement of next-generation sequencing, genetic biomarkers are becoming the core of cancer diagnosis. Genetic biomarkers such as peripheral blood circulating tumor DNA, microRNAs, long noncoding RNAs, circular RNAs, and exosomes have become the focus of early HCC diagnostics. HCC genetic biomarkers have been implemented in clinical practice. In this review, we describe the available literature on peripheral blood genetic biomarkers in the diagnosis of early HCC.
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Affiliation(s)
- Ting Song
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China.,Department of Hepatology, The Sixth People's Hospital of Qingdao, Qingdao, China
| | - Li Li
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Shaobo Wu
- Center of Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences (CAMS), Chengdu, China
| | - Yan Liu
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Caiping Guo
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wen Wang
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Lili Dai
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Tong Zhang
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Hao Wu
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Bin Su
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
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Aboughaleb IH, Matboli M, Shawky SM, El-Sharkawy YH. Integration of transcriptomes analysis with spectral signature of total RNA for generation of affordable remote sensing of Hepatocellular carcinoma in serum clinical specimens. Heliyon 2021; 7:e06388. [PMID: 33748469 PMCID: PMC7972971 DOI: 10.1016/j.heliyon.2021.e06388] [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: 07/29/2020] [Revised: 01/08/2021] [Accepted: 02/25/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a major global health problem with about 841,000 new cases and 782,000 deaths annually, due to lacking early biomarker/s, and centralized diagnosis. Transcriptomes research despite its infancy has proved excellence in its implementation in identifying a coherent specific cancer RNAs differential expression. However, results are sometimes overlapped by other cancer types which negatively affecting specificity, plus the high cost of the equipment used. Hyperspectral imaging (HSI) is an advanced tool with unique, spectroscopic features, is an emerging tool that has widely been used in cancer detection. Herein, a pilot study has been performed for HCC diagnosis, by exploiting HIS properties and the analysis of the transcriptome for the development of non-invasive remote HCC sensing. HSI data cube images of the sera extracted total RNA have been analyzed in HCC, normal subject, liver benign tumor, and chronic HCV with cirrhotic/non-cirrhotic liver groups. Data analyses have revealed a specific spectral signature for all groups and can be easily discriminated; at the computed optimum wavelength. Moreover, we have developed a simple setup based on a commercial laser pointer for sample illumination and a Smartphone CCD camera, with HSI consistent data output. We hypothesized that RNA differential expression and its spatial organization/folding are the key players in the obtained spectral signatures. To the best of our knowledge, we are the first to use HSI for sensing cancer based on total RNA in serum, using a Smartphone CCD camera/laser pointer. The proposed biosensor is simple, rapid (2 min), and affordable with specificity and sensitivity of more than 98% and high accuracy.
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Affiliation(s)
| | - Marwa Matboli
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Sherif M. Shawky
- Center of Genomics, Helmy Medical Institute, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 6th of October City, 12578 Giza, Egypt
- Misr University for Science and Technology, Faculty of Pharmacy, Biochemistry Department, Al-Motamayez District. P.O.BOX: 77, 6thOctober City, Giza, Egypt
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Sukowati CHC, Cabral LKD, Tiribelli C, Pascut D. Circulating Long and Circular Noncoding RNA as Non-Invasive Diagnostic Tools of Hepatocellular Carcinoma. Biomedicines 2021; 9:90. [PMID: 33477833 PMCID: PMC7832835 DOI: 10.3390/biomedicines9010090] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death worldwide, partially due to late diagnosis of the disease. Growing evidence in the field of biomarker discovery has shown the promising use of nucleic acid in the early detection of many cancers, including HCC. Here, we review data on how various long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) could be used as a diagnostic tool for HCC being differentially expressed in HCC compared to non-HCC patients. These non-coding RNAs (ncRNAs) showed high stability in the blood being present as free-circulating molecules or encapsulated into exosomes. This review reports some recent evidence on the use of lncRNAs and circRNAs as possible diagnostic biomarkers for HCC. Further, their pathophysiological mechanism in liver carcinogenesis was also described, elucidating the complex regulatory networks making these ncRNAs of particular relevance for the study of liver malignancy cancer.
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Affiliation(s)
- Caecilia H. C. Sukowati
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, SS14, km 163.5, 34149 Trieste, Italy; (C.H.C.S.); (L.K.D.C.); (C.T.)
| | - Loraine Kay D. Cabral
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, SS14, km 163.5, 34149 Trieste, Italy; (C.H.C.S.); (L.K.D.C.); (C.T.)
- Doctoral School in Molecular Biomedicine, University of Trieste, 34100 Trieste, Italy
| | - Claudio Tiribelli
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, SS14, km 163.5, 34149 Trieste, Italy; (C.H.C.S.); (L.K.D.C.); (C.T.)
| | - Devis Pascut
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, SS14, km 163.5, 34149 Trieste, Italy; (C.H.C.S.); (L.K.D.C.); (C.T.)
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Wu X, Liu J, Zhu C, Ma M, Chen X, Liu Y, Xia N, Dong Q. Identification of Potential Biomarkers of Prognosis-Related Long Non-Coding RNA (lncRNA) in Pediatric Rhabdoid Tumor of the Kidney Based on ceRNA Networks. Med Sci Monit 2020; 26:e927725. [PMID: 33328429 PMCID: PMC7754694 DOI: 10.12659/msm.927725] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Long non-coding RNA (lncRNA) can act as competing endogenous RNA (ceRNA) during tumor development. However, no study has elucidated the ceRNA network in pediatric rhabdoid tumor of the kidney (RTK) and its prognostic-related lncRNAs. The goal of the present study was to identify potential biomarkers of prognostic-related lncRNAs. MATERIAL AND METHODS RNA sequencing and clinical data were procured from the TARGET database. The "EdgeR" package was used to obtain differentially expressed lncRNA (DElncRNA), differentially expressed messenger RNAs (DEmRNA), and differentially expressed microRNAs (DEmiRNA). Cytoscape software was used to construct a ceRNA network. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were conducted on the ceRNA network-related DEmRNA. The Kaplan-Meier method was used for predicting survival with ceRNA network-related DElncRNA. Univariate and multivariate Cox analyses were used to identify prognosis-related lncRNAs in the ceRNA network, and an RTK prognostic signature was constructed. RESULTS We identified 1109 DElncRNAs, 215 DEmiRNAs, and 3436 DEmRNAs; and 107 DElncRNAs, 21 DEmiRNAs, and 74 DEmRNAs were included in the ceRNA regulatory network. GO enrichment analysis and KEGG pathway enrichment indicated that the DEmRNAs were mainly related to the regulation of phospholipase C activity and the MAPK signaling pathway. Survival analysis showed that 9 of 107 DElncRNAs were correlated with prognosis (P<0.05). Univariate and multivariate Cox analysis identified 4 DElncRNAs (HNF1A-AS1, TPTEP1, SNHG6, and ZNF503-AS2) to establish a predictive model and can be used as independent prognostic biomarkers. CONCLUSIONS We constructed a ceRNA network that reveals potential lncRNA biomarkers for pediatric RTK.
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Affiliation(s)
- Xiongwei Wu
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Jie Liu
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Chengzhan Zhu
- Shandong Key Laboratory of Digital Medicine and Computer Assisted Surgery, Qingdao, Shandong, China (mainland)
| | - Mingdi Ma
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Xin Chen
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Yusheng Liu
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Nan Xia
- Shandong Key Laboratory of Digital Medicine and Computer Assisted Surgery, Qingdao, Shandong, China (mainland)
| | - Qian Dong
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland).,Shandong Key Laboratory of Digital Medicine and Computer Assisted Surgery, Qingdao, Shandong, China (mainland)
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46
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Abstract
Liver cancer is a global problem and hepatocellular carcinoma (HCC) accounts for about 85% of this cancer. In the USA, etiologies and risk factors for HCC include chronic hepatitis C virus (HCV) infection, diabetes, non-alcoholic steatohepatitis (NASH), obesity, excessive alcohol drinking, exposure to tobacco smoke, and genetic factors. Chronic HCV infection appears to be associated with about 30% of HCC. Chronic HCV infection induces multistep changes in liver, involving metabolic disorders, steatosis, cirrhosis and HCC. Liver carcinogenesis requires initiation of neoplastic clones, and progression to clinically diagnose malignancy. Tumor progression associates with profound exhaustion of tumor-antigen-specific CD8+T cells, and accumulation of PD-1hi CD8+T cells and Tregs. In this chapter, we provide a brief description of HCV and environmental/genetic factors, immune regulation, and highlight mechanisms of HCV associated HCC. We also underscore HCV treatment and recent paradigm of HCC progression, highlighted the current treatment and potential future therapeutic opportunities.
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Fang X, Wang D, Pu K, Zhang Z, Wang H, Wang H, Zheng Y, Wang Y, Guan Q, Zhou Y. Diagnostic value of circulating lncRNAs as biomarkers of digestive system cancers: A systematic review and meta-analysis. Expert Rev Mol Diagn 2020; 20:1051-1062. [PMID: 33138648 DOI: 10.1080/14737159.2020.1822169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 09/08/2020] [Indexed: 12/23/2022]
Abstract
OBJECTIVE This meta-analysis aims to explore the diagnostic value and accuracy of circulating lncRNAs as biomarkers of digestive system tumors. METHODS PubMed, Embase, Cochrane Library, and Web of science were searched for relevant articles that were published before April 2019, and a meta-analysis was conducted. RESULTS 52 studies with 63 lncRNAs were discussed in the meta-analysis. The pooled sensitivity and specificity of diagnosis were 0.80 (95% CI: 0.79-0.81) and 0.76 (95% CI: 0.75-0.77), respectively. The pooled DOR (the diagnostic odds ratio) was 15.63 (95% CI: 12.77-19.12), and the overall AUC (the area under the curve) was 0.87. Besides, subgroup analyzes showed that the DOR and AUC of large sample sizes (>80), multiple lncRNAs, serum-based lncRNAs, and downregulation group were superior to those of small sample sizes (≤80), single lncRNA, plasma-based lncRNAs, and upregulation group, respectively. The current data also highlight that the diagnostic accuracy of circulating lncRNAs in the case of colorectal cancer was higher than gastric cancer, hepatocellular carcinoma, esophageal carcinoma, and pancreatic cancer. And there is no difference in the perspective of geographical regions. CONCLUSION The circulating lncRNAs have high diagnostic value and accuracy in digestive system cancers and may serve as potential biomarkers.
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Affiliation(s)
- Xidong Fang
- The First Clinical Medical College, Lanzhou University , Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University , Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, Lanzhou University , Lanzhou, China
| | - Dongke Wang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China
| | - Ke Pu
- The First Clinical Medical College, Lanzhou University , Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University , Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, Lanzhou University , Lanzhou, China
| | - Zhaoyu Zhang
- Department of Physiology and Pathophysiology, Peking University Health Science Center , Beijing, China
| | - Huiying Wang
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University , Changsha, Hunan, China
- National Clinical Research Center for Metabolic Diseases , Changsha, Hunan, China
| | - Haojia Wang
- The First Clinical Medical College, Lanzhou University , Lanzhou, China
| | - Ya Zheng
- The First Clinical Medical College, Lanzhou University , Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University , Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, Lanzhou University , Lanzhou, China
| | - Yuping Wang
- The First Clinical Medical College, Lanzhou University , Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University , Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, Lanzhou University , Lanzhou, China
| | - Quanlin Guan
- The First Clinical Medical College, Lanzhou University , Lanzhou, China
- Department of Oncology Surgery, The First Hospital of Lanzhou University , Lanzhou, China
| | - Yongning Zhou
- The First Clinical Medical College, Lanzhou University , Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University , Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, Lanzhou University , Lanzhou, China
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Cao P, Jin Q, Feng L, Li H, Qin G, Zhou G. Emerging roles and potential clinical applications of noncoding RNAs in hepatocellular carcinoma. Semin Cancer Biol 2020; 75:136-152. [PMID: 32931952 DOI: 10.1016/j.semcancer.2020.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma(HCC) is one of the most common forms of cancer, and accounts for a high proportion of cancer-associated deaths. Growing evidences have demonstrated that non- protein-coding regions of the genome could give rise to transcripts, termed noncoding RNA (ncRNA), that form novel functional layers of the cellular activity. ncRNAs are implicated in different molecular mechanisms and functions at transcriptional, translational and post-translational levels. An increasing number of studies have demonstrated a complex array of molecular and cellular functions of ncRNAs in different stages of the HCC tumorigenesis, either in an oncogenic or tumor-suppressive manner. As a result, several pre-clinical studies have highlighted the great potentials of ncRNAs as novel biomarkers for cancer diagnosis or therapeutics in targeting HCC progression. In this review, we briefly described the characteristics of several representative ncRNAs and summarized the latest findings of their roles and mechanisms in the development of HCC, in order to better understand the cancer biology and their potential clinical applications in this malignancy.
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Affiliation(s)
- Pengbo Cao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Qian Jin
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Lan Feng
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Haibei Li
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, Tianjin City, China
| | - Geng Qin
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun City, China
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China; Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, China; Medical College, Guizhou University, Guiyang City, China.
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Kim SS, Baek GO, Ahn HR, Sung S, Seo CW, Cho HJ, Nam SW, Cheong JY, Eun JW. Serum small extracellular vesicle-derived LINC00853 as a novel diagnostic marker for early hepatocellular carcinoma. Mol Oncol 2020; 14:2646-2659. [PMID: 32525601 PMCID: PMC7530776 DOI: 10.1002/1878-0261.12745] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/25/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
This study aimed to identify novel long noncoding RNA (lncRNA) biomarkers for hepatocellular carcinoma (HCC) using publicly available tissue genomic datasets and validate their diagnostic utility for early-stage HCC. Differentially expressed lncRNAs between 371 HCC and 50 nontumor tissues were obtained from The Cancer Genome Atlas liver hepatocellular carcinoma (TCGA_LIHC) project. Subsequently, the expression of the serum- and extracellular vesicle (EV)-derived lncRNA was assessed in 10 patients with HCC and 10 healthy controls using RT-qPCR. The candidate lncRNAs were validated in 90 HCC and 92 non-HCC (29 healthy control, 28 chronic hepatitis, 35 liver cirrhosis) patients. The sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were calculated for the candidate lncRNAs and the current HCC biomarker, alpha-fetoprotein (AFP). SFTA1P, HOTTIP, HAGLROS, LINC01419, HAGLR, CRNDE, and LINC00853 were markedly upregulated in HCC in TCGA_LIHC dataset. Among them, LINC00853 has not been reported in relation to HCC before. In patients with HCC, only expression of small EV-derived LINC00853 (EV-LINC00853) was increased. EV-LINC00853 showed excellent discriminatory ability in the diagnosis of all-stage HCC (AUC = 0.934, 95% confidence interval = 0.887-0.966). Moreover, using a 14-fold increase and 20 ng·mL-1 as cutoffs for EV-LINC00853 expression and AFP level, respectively, EV-LINC00853 was found to have a sensitivity of 93.75% and specificity of 89.77%, while AFP showed only 9.38% sensitivity and 72.73% specificity for the diagnosis of early-stage HCC (mUICC stage I). EV-LINC00853 had a positivity of 97% and 67% in AFP-negative and AFP-positive early HCC, respectively. Serum EV-derived LINC00853 may be a novel potential diagnostic biomarker for early HCC, especially for AFP-negative HCC.
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Affiliation(s)
- Soon Sun Kim
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, South Korea
| | - Geum Ok Baek
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, South Korea
| | - Hye Ri Ahn
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, South Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, South Korea
| | - Suna Sung
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, South Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, South Korea
| | - Chul Won Seo
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, South Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, South Korea
| | - Hyo Jung Cho
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, South Korea
| | - Suk Woo Nam
- Functional RNomics Research Center, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine & Health Sciences, Graduate School of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jae Youn Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, South Korea
| | - Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, South Korea
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A Circulating Long Noncoding RNA Panel Serves as a Diagnostic Marker for Hepatocellular Carcinoma. DISEASE MARKERS 2020; 2020:5417598. [PMID: 32733618 PMCID: PMC7376401 DOI: 10.1155/2020/5417598] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 06/26/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023]
Abstract
Background Circulating long noncoding RNAs (lncRNAs) have been demonstrated to serve as diagnostic biomarkers for various cancers. We aimed to elucidate the diagnostic efficacy of eight serum lncRNAs HULC, MALAT1, Linc00152, PTENP1, PTTG3P, SPRY4-IT1, UBE2CP3, and UCA1 and their combinations for the diagnosis of hepatocellular carcinoma (HCC). Methods A total of 129 patients with HCC, 49 patients with liver cirrhosis, 27 patients with chronic hepatitis B, and 93 healthy controls were enrolled in this study. The levels of serum lncRNAs were assessed by quantitative real-time polymerase chain reaction. The correlations between serum lncRNAs and clinicopathological characteristics were further analyzed. The receiver operating characteristic (ROC) curve and area under curve (AUC) were utilized to estimate the diagnostic capacity of serum lncRNAs and their combination with AFP for HCC. A logistic regression model was performed to establish a multiple-lncRNA panel. Results The levels of serum HULC, MALAT1, Linc00152, PTTG3P, SPRY4-IT1, UBE2CP3, and UCA1 were significantly higher in HCC patients than in patients with benign liver diseases and healthy controls, whereas serum PTENP1 was significantly decreased in HCC patients compared with healthy participants. Positive correlations between serum Linc00152 and GGT, serum PTTG3P and GGT, and serum SPRY4-IT1 and ALT were noted in HCC patients. ROC analysis revealed that all these lncRNAs had a significantly predictive value for HCC except for PTENP1. The best performance of single lncRNA was obtained by Linc00152 with an AUC of 0.877. When combined with AFP, the combination of Linc00152 and AFP gained the highest accuracy, yielding an AUC of 0.906. Through logistic regression analysis, the panel consisting of serum linc00152, UCA1, and AFP provided the greatest predictive ability, obtaining an AUC of 0.912 with 82.9% sensitivity and 88.2% specificity. Conclusion The panel of serum Linc00152, UCA1, and AFP demonstrates a novel and noninvasive biomarker with relatively high sensitivity and specificity for HCC diagnosis.
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