1
|
Mishra SK, Wang H. SUDAZFLNC - a curated and searchable online database for zebrafish lncRNAs, mRNAs, miRNAs, and circadian expression profiles. Comput Struct Biotechnol J 2024; 23:1844-1853. [PMID: 38707541 PMCID: PMC11067007 DOI: 10.1016/j.csbj.2024.04.026] [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: 12/30/2023] [Revised: 03/29/2024] [Accepted: 04/09/2024] [Indexed: 05/07/2024] Open
Abstract
The zebrafish (Danio rerio) has emerged as a model organism for investigating lncRNAs-driven fundamental biological processes, such as circadian rhythms, physiology, metabolism, and various diseases. While state-of-the-art sequencing technologies have identified an increasing number of lncRNAs in zebrafish, their annotations are far from complete. In this study, we collect 28,925 lncRNAs from both the published studies and our own RNA-seq analyses and establish a novel webserver-based database called SUDAZFLNC (https://sudarna.website/). The database, containing 28,925 lncRNAs, 25,432 mRNAs, and 368 miRNAs, provides several crucial features and annotations for the zebrafish RNAs, such as sequence identifiers (IDs), sequence length, hexamer score, coding probabilities, GO and KEGG annotations, and micropeptides. SUDAZFLNC also includes time-course expression profiles of 3288 lncRNAs, 25,432 mRNAs, and 342 miRNAs generated from our RNA-seq experiments, and 149, 4407, and 43 rhythmically expressed lncRNAs, mRNAs, and miRNAs, respectively. Based on the peak expression patterns, we classified these RNAs into morning RNAs, evening RNAs, and night RNAs. Users of the database can access the RNA sequences and their expression profiles by searching the corresponding IDs from the Graphical User Interface (GUI) of the database. The database supports several features to investigate RNA sequences and expression profiles, including BLAST, search of sequence and data, ID conversion, and RNA-RNA interaction prediction. This is the largest curated database of zebrafish RNAs and their expression profiles to date.
Collapse
Affiliation(s)
- Shital Kumar Mishra
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| |
Collapse
|
2
|
Mishra SK, Liu T, Wang H. Thousands of oscillating LncRNAs in the mouse testis. Comput Struct Biotechnol J 2024; 23:330-346. [PMID: 38205156 PMCID: PMC10776378 DOI: 10.1016/j.csbj.2023.11.046] [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: 09/20/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 01/12/2024] Open
Abstract
The long noncoding RNAs (lncRNAs) are involved in numerous fundamental biological processes, including circadian regulation. Although recent studies have revealed insights into the functions of lncRNAs, how the lncRNAs regulate circadian rhythms still requires a deeper investigation. In this study, we generate two datasets of RNA-seq profiles of the mouse (Mus musculus) testis under light-dark (LD) cycle. The first dataset included 18,613 unannotated transcripts measured at 12 time points, each with duplicate samples, under LD conditions; while the second dataset included 21,414 unannotated transcripts measured at six time points, each with three replicates, under desynchronized and control conditions. We identified 5964 testicular lncRNAs in each dataset by BLASTing these transcripts against the known mouse lncRNAs from the NONCODE database. MetaCycle analyses were performed to identify 519, 475, and 494 rhythmically expressed mouse testicular lncRNAs in the 12-time-point dataset, the six-time-point control dataset, and the six-time-point desynchronized dataset, respectively. A comparison of the expression profiles of the lncRNAs under desynchronized and control conditions revealed that 427 rhythmically expressed lncRNAs from the control condition became arrhythmic under the desynchronized condition, suggesting a possible loss of rhythmicity. In contrast, 446 arrhythmic lncRNAs from the control condition became rhythmic under the desynchronized condition, suggesting a possible gain of rhythmicity. Interestingly, 48 lncRNAs were rhythmically expressed under both desynchronized and control conditions. These oscillating lncRNAs were divided into morning lncRNAs, evening lncRNAs, and night lncRNAs based on their time-course expression patterns. We interrogated the promoter regions of these rhythmically expressed mouse testicular lncRNAs to predict their possible regulation by the E-box, D-box, or RORE promoter motifs. GO and KEGG analyses were performed to identify the possible biological functions of these rhythmically expressed mouse testicular lncRNAs. Further, we conducted conservation analyses of the rhythmically expressed mouse testicular lncRNAs with lncRNAs from humans, rats, and zebrafish, and uncovered three mouse testicular lncRNAs conserved across these four species. Finally, we computationally predicted the conserved lncRNA-encoded peptides and their 3D structures from each of the four species. Taken together, our study revealed thousands of rhythmically expressed lncRNAs in the mouse testis, setting the stage for further computational and experimental validations.
Collapse
Affiliation(s)
- Shital Kumar Mishra
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Taole Liu
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| |
Collapse
|
3
|
Shah M, Sarkar D. HCC-Related lncRNAs: Roles and Mechanisms. Int J Mol Sci 2024; 25:597. [PMID: 38203767 PMCID: PMC10779127 DOI: 10.3390/ijms25010597] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatocellular carcinoma (HCC) presents a significant global health threat, particularly in regions endemic to hepatitis B and C viruses, and because of the ongoing pandemic of obesity causing metabolic-dysfunction-related fatty liver disease (MAFLD), a precursor to HCC. The molecular intricacies of HCC, genetic and epigenetic alterations, and dysregulated signaling pathways facilitate personalized treatment strategies based on molecular profiling. Epigenetic regulation, encompassing DNA methyltion, histone modifications, and noncoding RNAs, functions as a critical layer influencing HCC development. Long noncoding RNAs (lncRNAs) are spotlighted for their diverse roles in gene regulation and their potential as diagnostic and therapeutic tools in cancer. In this review, we explore the pivotal role of lncRNAs in HCC, including MAFLD and viral hepatitis, the most prevalent risk factors for hepatocarcinogenesis. The dysregulation of lncRNAs is implicated in HCC progression by modulating chromatin regulation and transcription, sponging miRNAs, and influencing structural functions. The ongoing studies on lncRNAs contribute to a deeper comprehension of HCC pathogenesis and offer promising routes for precision medicine, highlighting the utility of lncRNAs as early biomarkers, prognostic indicators, and therapeutic targets.
Collapse
Affiliation(s)
- Mimansha Shah
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Massey Comprehensive Cancer Center, and VCU Institute of Molecular Medicine (VIMM), Virginia Commonwealth University, Richmond, VA 23298, USA
| |
Collapse
|
4
|
Tian T, Li S, Luo H, Li Y, Chen H, Yang Y, Chen G, Xie B, Yan Z, Wang Z, Li L, Jiang Y. LILAR, a novel long noncoding RNA regulating autophagy in the liver tissues of endotoxemic mice through a competing endogenous RNA mechanism. MedComm (Beijing) 2023; 4:e398. [PMID: 37829506 PMCID: PMC10565381 DOI: 10.1002/mco2.398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/07/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
Sepsis is an often-deadly complication of infection that can lead to multiple organ failure. Previous studies have demonstrated that autophagy has a protective effect on liver injury in sepsis. Here, we report a novel long noncoding RNA (lncRNA), named lipopolysaccharide (LPS)-induced liver autophagy regulator (LILAR), which was highly induced in the liver tissues of endotoxemic mice. LILAR deficiency significantly increased the susceptibility of mice to LPS. In contrast, LILAR overexpression rescued the liver injury mediated by LILAR deficiency and increased the survival of LILAR knockout mice with endotoxemia. Autophagy-related protein 13 (Atg13) is a potential downstream target gene of LILAR. LILAR deficiency notably decreased Atg13 expression and suppressed autophagy in the livers of mice challenged with LPS. A reporter gene assay showed that LILAR competitively adsorbed miR-705 to increase the expression of Atg13 in cultured cells, indicating that LILAR participates in the regulation of the autophagy in the liver tissues of endotoxemic mice through a competitive endogenous RNA mechanism. In summary, we identified a novel lncRNA, LILAR, as a hepatic autophagy regulator, which not only promotes our understanding of liver pathophysiology but also provides a potential therapeutic target and/or diagnostic biomarker for liver injury in endotoxemia.
Collapse
Affiliation(s)
- Tian Tian
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| | - Shan Li
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| | - Haihua Luo
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| | - Yijing Li
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| | - Hanghang Chen
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| | - Ying Yang
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| | - Guangqin Chen
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| | - Bingyao Xie
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| | - Zhengzheng Yan
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| | - Zhenqi Wang
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| | - Lei Li
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| | - Yong Jiang
- Guangdong Provincial Key Laboratory of ProteomicsState Key Laboratory of Organ Failure ResearchDepartment of PathophysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdongChina
| |
Collapse
|
5
|
Guo Y, Zhang Y, Yu J, Dong Y, Chen Z, Zhu C, Hong X, Xie Z, Zhang M, Wang S, Liang Y, He X, Ju W, Chen M. Novel ceRNA network construction associated with programmed cell death in acute rejection of heart allograft in mice. Front Immunol 2023; 14:1184409. [PMID: 37753085 PMCID: PMC10518384 DOI: 10.3389/fimmu.2023.1184409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/28/2023] [Indexed: 09/28/2023] Open
Abstract
Background T cell-mediated acute rejection(AR) after heart transplantation(HT) ultimately results in graft failure and is a common indication for secondary transplantation. It's a serious threat to heart transplant recipients. This study aimed to explore the novel lncRNA-miRNA-mRNA networks that contributed to AR in a mouse heart transplantation model. Methods The donor heart from Babl/C mice was transplanted to C57BL/6 mice with heterotopic implantation to the abdominal cavity. The control group was syngeneic heart transplantation with the same kind of mice donor. The whole-transcriptome sequencing was performed to obtain differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs) and lncRNAs (DElncRNAs) in mouse heart allograft. The biological functions of ceRNA networks was analyzed by GO and KEGG enrichment. Differentially expressed ceRNA involved in programmed cell death were further verified with qRT-PCR testing. Results Lots of DEmRNAs, DEmiRNAs and DElncRNAs were identified in acute rejection and control after heart transplantation, including up-regulated 4754 DEmRNAs, 1634 DElncRNAs, 182 DEmiRNAs, and down-regulated 4365 DEmRNAs, 1761 DElncRNAs, 132 DEmiRNAs. Based on the ceRNA theory, lncRNA-miRNA-mRNA regulatory networks were constructed in allograft acute rejection response. The functional enrichment analysis indicate that the down-regulated mRNAs are mainly involved in cardiac muscle cell contraction, potassium channel activity, etc. and the up-regulated mRNAs are mainly involved in T cell differentiation and mononuclear cell migration, etc. The KEGG pathway enrichment analysis showed that the down-regulated DEmRNAs were mainly enriched in adrenergic signaling, axon guidance, calcium signaling pathway, etc. The up-regulated DEmRNAs were enriched in the adhesion function, chemokine signaling pathway, apoptosis, etc. Four lncRNA-mediated ceRNA regulatory pathways, Pvt1/miR-30c-5p/Pdgfc, 1700071M16Rik/miR-145a-3p/Pdgfc, 1700071M16Rik/miR-145a-3p/Tox, 1700071M16Rik/miR-145a-3p/Themis2, were finally validated. In addition, increased expression of PVT1, 1700071M16Rik, Tox and Themis2 may be considered as potential diagnostic gene biomarkers in AR. Conclusion We speculated that Pvt1/miR-30c-5p/Pdgfc, 1700071M16Rik/miR-145a-3p/Pdgfc, 1700071M16Rik/miR-145a-3p/Tox and 1700071M16Rik/miR-145a-3p/Themis2 interaction pairs may serve as potential biomarkers in AR after HT.
Collapse
Affiliation(s)
- Yiwen Guo
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Yixi Zhang
- Liver Transplantation Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jia Yu
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Yuqi Dong
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Zhitao Chen
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Chuchen Zhu
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Xitao Hong
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Zhonghao Xie
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Min Zhang
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Shuai Wang
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Yichen Liang
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Xiaoshun He
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Weiqiang Ju
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Maogen Chen
- The First Affiliated Hospital, Sun Yat-Sen University, Organ Transplant Centre, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| |
Collapse
|
6
|
Li Q, Zhu Z, Zhang H, Wu X, Yang H, Li X, Li W, Zhao Y, Du F, Chen Y, Shen J, Xiao Z, Chen M, Wang F, Gu L, Sun Y, Lu L, Jia Y, Li M. LncRNA RP11-93B14.5 promotes gastric cancer cell growth through PI3K/AKT signaling pathway. Mol Biotechnol 2023:10.1007/s12033-023-00844-6. [PMID: 37682457 DOI: 10.1007/s12033-023-00844-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/29/2023] [Indexed: 09/09/2023]
Abstract
OBJECTIVE Emerging evidence indicates that long non-coding RNA (lncRNA) RP11-93B14.5 facilitates tumor progression in variety of malignancies. The present study proposed to study the functional effect of lncRNA RP11-93B14.5 in gastric cancer (GC) as well as the underlying mechanism. METHODS Bioinformatics analysis was utilized to analyze lncRNA expression in GC tissues. siRNA was used for knockdown of RP11-93B14.5 in GC cells MKN45 and KATO III. The stable knockdown cell lines were constructed by CRISPR-Cas9. Cell counting kit-8 (CCK-8) assay and soft agar colony formation assay were used to analyze GC cell viability. Flow cytometry analysis was performed to analyze the cell cycle distribution of MKN45 and KATO III. RNA sequencing (RNA-seq) was employed to detect differential genes after transfection with siRP11-93B14.5. Quantitative PCR (Q-PCR) was used to examine gene expression in GC cell lines. Western-blot assay was used to measure protein levels. RNA fluorescent in situ hybridization (FISH) was conducted for lncRNA cellular location and expression. RESULTS Based on the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database, RP11-93B14.5 was upregulated in GC tissue, which was also verified in GC cell lines in comparison to the normal gastric epithelial HFE145 cells. Knockdown of RP11-93B14.5 decreased cell viability and the colony number of MKN45 and KATO III cells, and altered cell cycle distribution in vitro. RNA-seq analysis revealed RP11-93B14.5 may modulate genes expression of S100A2 and TIMP2 in MKN45 and KATO III cells. Mechanistically, RP11-93B14.5 may drive the progression of GC via S100A2 related-PI3K/AKT signaling pathway. CONCLUSIONS LncRNA RP11-93B14.5 knockdown alleviated the malignant phenotypes of GC cells through regulating PI3K/AKT. Our results provide evidence for the role of lncRNAs in regulating tumor progression.
Collapse
Affiliation(s)
- Qianxiu Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Zhongxiu Zhu
- The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, 250000, Shandong, China
| | - Hanyu Zhang
- Nanchong Key Laboratory of Individualized Drug Therapy, Department of Pharmacy, The Second Clinical Medical College, Nanchong Central Hospital, North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Huan Yang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Xiaobing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Wanping Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Meijuan Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Fang Wang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Li Gu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Yuhong Sun
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Lan Lu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, 610106, Sichuan, China
| | - Yuliang Jia
- Department of Gastroenterology, The first affiliated hospital of Wannan Medical College, Wuhu, 241000, Anhui, China.
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China.
| |
Collapse
|
7
|
Zhang Z, Gao W, Tan X, Deng T, Zhou W, Jian H, Zeng P. Construction and verification of a novel circadian clock related long non-coding RNA model and prediction of treatment for survival prognosis in patients with hepatocellular carcinoma. BMC Cancer 2023; 23:57. [PMID: 36647032 PMCID: PMC9843932 DOI: 10.1186/s12885-023-10508-y] [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: 05/14/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Circadian clock genes are significant in the occurrence and development of HCC and long-non coding RNAs (lncRNAs) are closely related to HCC progression. In this study, we aimed to establish a prognostic risk model for HCC. Circadian clock-related lncRNAs expressed in HCC were extracted from The Cancer Genome Atlas. A nomogram was established to predict individual survival rate. Biological processes enriched for risk model transcripts were investigated by Gene Set Enrichment Analysis. Further, we evaluated the relationship between risk score and immune-checkpoint inhibitor-related gene expression level. The Genomics of Drug Sensitivity in Cancer (GDSC) database was used to assess the sensitivity of tumors in high- and low-risk score groups to different drugs. A total of 11 circadian clock-related lncRNAs were included in multi-Cox proportional hazards model analysis to establish a risk model. Univariate and multivariate Cox regression analysis showed that the risk model was an independent risk factor in HCC. The risk model was a significantly associated with the immune signature. Further GDSC analysis indicated that patients in each risk score group may be sensitive to different anti-cancer drugs. QRT-PCR analysis results showed that C012073.1, PRRT3-AS1, TMCC1-AS1, LINC01138, MKLN1-AS, KDM4A-AS1, AL031985.3, POLH-AS1, LINC01224, and AC099850.3 were more highly expressed in Huh-7 and HepG2, compared to LO2, while AC008549.1 were lower expressed. Our work established a prognostic model for HCC. Risk score analysis indicated that the model is significantly associated with modulation tumor immunity and could be used to guide more effective therapeutic strategies in the future.
Collapse
Affiliation(s)
- Zhen Zhang
- grid.489633.3Department of Oncology, Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, 410006 Changsha, P.R. China
| | - Wenhui Gao
- grid.488482.a0000 0004 1765 5169School of Chinese Medicine, Hunan University of Chinese Medicine, 410208 Changsha, P.R. China
| | - Xiaoning Tan
- grid.489633.3Department of Oncology, Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, 410006 Changsha, P.R. China
| | - Tianhao Deng
- grid.489633.3Department of Oncology, Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, 410006 Changsha, P.R. China
| | - Wanshuang Zhou
- grid.489633.3Department of Oncology, Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, 410006 Changsha, P.R. China
| | - Huiying Jian
- grid.488482.a0000 0004 1765 5169School of Chinese Medicine, Hunan University of Chinese Medicine, 410208 Changsha, P.R. China
| | - Puhua Zeng
- grid.489633.3Department of Oncology, Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, 410006 Changsha, P.R. China
| |
Collapse
|
8
|
Qu M, Zhang G, Qu H, Vu A, Wu R, Tsukamoto H, Jia Z, Huang W, Lenz HJ, Rich JN, Kay SA. Circadian regulator BMAL1::CLOCK promotes cell proliferation in hepatocellular carcinoma by controlling apoptosis and cell cycle. Proc Natl Acad Sci U S A 2023; 120:e2214829120. [PMID: 36595671 PMCID: PMC9926257 DOI: 10.1073/pnas.2214829120] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/06/2022] [Indexed: 01/05/2023] Open
Abstract
Hepatocellular carcinoma (HCC) remains a global health challenge whose incidence is growing worldwide. Previous evidence strongly supported the notion that the circadian clock controls physiological homeostasis of the liver and plays a key role in hepatocarcinogenesis. Despite the progress, cellular and molecular mechanisms underpinning this HCC-clock crosstalk remain unknown. Addressing this knowledge gap, we show here that although the human HCC cells Hep3B, HepG2, and Huh7 displayed variations in circadian rhythm profiles, all cells relied on the master circadian clock transcription factors, BMAL1 and CLOCK, for sustained cell growth. Down-regulating Bmal1 or Clock in the HCC cells induced apoptosis and arrested cell cycle at the G2/M phase. Mechanistically, we found that inhibiting Bmal1/Clock induced dysregulation of the cell cycle regulators Wee1 and p21 which cooperatively contribute to tumor cell death. Bmal1/Clock knockdown caused downregulation of Wee1 that led to apoptosis activation and upregulation of p21 which arrested the cell cycle at the G2/M phase. Collectively, our results suggest that the circadian clock regulators BMAL1 and CLOCK promote HCC cell proliferation by controlling Wee1 and p21 levels, thereby preventing apoptosis and cell cycle arrest. Our findings shed light on cellular impact of the clock proteins for maintaining HCC oncogenesis and provide proof-of-principle for developing cancer therapy based on modulation of the circadian clock.
Collapse
Affiliation(s)
- Meng Qu
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang322000, China
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| | - Guoxin Zhang
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA15232
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA15232
| | - Han Qu
- Department of Botany and Plant Sciences, University of California, Riverside, CA92521
| | - Alexander Vu
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| | - Raymond Wu
- Southern California Research Center for Alcoholic Liver and Pancreatic Diseases and Cirrhosis and Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
| | - Hidekazu Tsukamoto
- Southern California Research Center for Alcoholic Liver and Pancreatic Diseases and Cirrhosis and Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, CA92521
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA92521
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA91010
| | - Heinz-Josef Lenz
- Division of Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA90032
| | - Jeremy N. Rich
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA15232
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA15232
| | - Steve A. Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| |
Collapse
|
9
|
Akkaya C, Karadag M, Hangul Z, Sahin E, Isbilen E. Evaluation of the Regulatory Role of Circadian Rhythm Related Long Non-Coding RNAs in ADHD Etiogenesis. J Atten Disord 2023; 27:201-213. [PMID: 36254757 DOI: 10.1177/10870547221130113] [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] [Indexed: 11/17/2022]
Abstract
OBJECTIVE ADHD is associated with increased sleep problems and circadian rhythm disturbances. This study aimed to examine ADHD patients and healthy controls in terms of chronotypic features and expression levels of CLOCK, PER1, lncRNA HULC, lncRNA UCA1. METHOD Eighty-three children were included (43 ADHD). Conner's Parent Rating Scale-Revised Short Form, Childhood Chronotype Questionnaire, Children's Sleep Disorders Scale were administered. Gene expression levels were studied from peripheral blood. RESULTS Evening chronotype, sleep initiation/maintenance disorder, sleep-wake transition disorder, excessive sleepiness disorder were higher in the ADHD group compared to the controls in the scales reported by the parents. Expression levels of all examined genes were statistically significantly higher in the ADHD group. There was no significant relationship between genes and sleep parameters in the ADHD group. CONCLUSION Our study provides the first evidence that lncRNA HULC and lncRNA UCA1 might have a role in the etiology of ADHD.
Collapse
|
10
|
Brooks R, Monzy J, Aaron B, Zhang X, Kossenkov A, Hayden J, Keeney F, Speicher DW, Zhang L, Dang CV. Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis. Cell Rep 2022; 41:111514. [PMID: 36261012 PMCID: PMC9652615 DOI: 10.1016/j.celrep.2022.111514] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 05/25/2022] [Accepted: 09/26/2022] [Indexed: 11/20/2022] Open
Abstract
We identify ADIRF-AS1 circadian long non-coding RNA (lncRNA). Deletion of ADIRF-AS1 in U2OS cells alters rhythmicity of clock-controlled genes and expression of extracellular matrix genes. ADIRF-AS1 interacts with all components of the PBAF (PBRM1/BRG1) complex in U2OS cells. Because PBRM1 is a tumor suppressor mutated in over 40% of clear cell renal carcinoma (ccRCC) cases, we evaluate ADIRF-AS1 in ccRCC cells. Reducing ADIRF-AS1 expression in ccRCC cells decreases expression of some PBAF-suppressed genes. Expression of these genes is partially rescued by PBRM1 loss, consistent with ADIRF-AS1 acting in part to modulate PBAF. ADIRF-AS1 expression correlates with survival in human ccRCC, particularly in PBRM1 wild-type, but not mutant, tumors. Loss of ADIRF-AS1 eliminates in vivo tumorigenesis, partially rescued by concurrent loss of PBRM1 only when co-injected with Matrigel, suggesting a PBRM1-independent function of ADIRF-AS1. Our findings suggest that ADIRF-AS1 functions partly through PBAF to regulate specific genes as a BMAL1-CLOCK-regulated, oncogenic lncRNA.
Collapse
Affiliation(s)
- Rebekah Brooks
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | - Judith Monzy
- The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | - Bailey Aaron
- The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | - Xue Zhang
- The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | | | - James Hayden
- The Ludwig Institute for Cancer Research, New York, NY, USA
| | | | | | - Lin Zhang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chi V Dang
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA.
| |
Collapse
|
11
|
Morphofunctional State and Circadian Rhythms of the Liver of Female Rats under the Influence of Chronic Alcohol Intoxication and Constant Lighting. Int J Mol Sci 2022; 23:ijms231810744. [PMID: 36142658 PMCID: PMC9502101 DOI: 10.3390/ijms231810744] [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: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
A separate and combined effect of constant illumination and chronic alcohol intoxication (CAI) on diurnal dynamics of micromorphometric parameters of hepatocytes in female Wistar rats and p53, Ki-67, PER2, BMAL1, and ADH5 expression in these cells were studied. The increase in apoptotic activity and proliferation in all animals under the action of chronodestructors is shown. All experimental animals showed a decrease in BMAL1 expression and increase in PER2 expression; ADH5 is overexpressed under the influence of ethanol. Circadian rhythms (CRs) of BMAL1, PER2, p53, and Ki-67 expression persist in all groups, except combined action of chronodestructors, and ADH5 CRs persist in all groups—thus, these rhythms in females are quite stable. CRs of the hepatocyte nuclei area are preserved in all the studied groups, although they undergo a significant shift. At the same time, the CRs of the hepatocyte area are destroyed under the action of light, both independently and in combination with CAI, and the CR of the nuclear-cytoplasmic ratio (NCR) is destroyed by exposure to CAI. It can be assumed that CRs of the hepatocyte area are significantly affected by dark deprivation and NCR rhythm is sensitive to ethanol consumption, while the stability of studied genes’ expression rhythms at separate influences of studied chronodestructors is maintained by yet unknown adaptation mechanisms. It is necessary to note that, according to our previous studies of male rats, rat females show significantly greater stability of the studied CRs.
Collapse
|
12
|
Buel SM, Debopadhaya S, De los Santos H, Edwards KM, David AM, Dao UH, Bennett KP, Hurley JM. The PAICE suite reveals circadian posttranscriptional timing of noncoding RNAs and spliceosome components in Mus musculus macrophages. G3 (BETHESDA, MD.) 2022; 12:6649694. [PMID: 35876788 PMCID: PMC9434326 DOI: 10.1093/g3journal/jkac176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/27/2022] [Indexed: 01/07/2023]
Abstract
Circadian rhythms broadly regulate physiological functions by tuning oscillations in the levels of mRNAs and proteins to the 24-h day/night cycle. Globally assessing which mRNAs and proteins are timed by the clock necessitates accurate recognition of oscillations in RNA and protein data, particularly in large omics data sets. Tools that employ fixed-amplitude models have previously been used to positive effect. However, the recognition of amplitude change in circadian oscillations required a new generation of analytical software to enhance the identification of these oscillations. To address this gap, we created the Pipeline for Amplitude Integration of Circadian Exploration suite. Here, we demonstrate the Pipeline for Amplitude Integration of Circadian Exploration suite's increased utility to detect circadian trends through the joint modeling of the Mus musculus macrophage transcriptome and proteome. Our enhanced detection confirmed extensive circadian posttranscriptional regulation in macrophages but highlighted that some of the reported discrepancy between mRNA and protein oscillations was due to noise in data. We further applied the Pipeline for Amplitude Integration of Circadian Exploration suite to investigate the circadian timing of noncoding RNAs, documenting extensive circadian timing of long noncoding RNAs and small nuclear RNAs, which control the recognition of mRNA in the spliceosome complex. By tracking oscillating spliceosome complex proteins using the PAICE suite, we noted that the clock broadly regulates the spliceosome, particularly the major spliceosome complex. As most of the above-noted rhythms had damped amplitude changes in their oscillations, this work highlights the importance of the PAICE suite in the thorough enumeration of oscillations in omics-scale datasets.
Collapse
Affiliation(s)
| | | | | | - Kaelyn M Edwards
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Alexandra M David
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Uyen H Dao
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Kristin P Bennett
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA,Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA,Institute for Data Exploration and Applications, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jennifer M Hurley
- Corresponding author: Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| |
Collapse
|
13
|
Qiao C, Qiao T, Yang S, Liu L, Zheng M. SNHG17/miR-384/ELF1 axis promotes cell growth by transcriptional regulation of CTNNB1 to activate Wnt/β-catenin pathway in oral squamous cell carcinoma. Cancer Gene Ther 2022; 29:122-132. [PMID: 33531646 DOI: 10.1038/s41417-021-00294-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/29/2020] [Accepted: 01/05/2021] [Indexed: 01/29/2023]
Abstract
Increasing evidence proved the abnormal expression of long non-coding RNAs (lncRNAs) in various human malignancies, including oral squamous cell carcinoma (OSCC). Nevertheless, limited explorations concern the role of lncRNA small nucleolar RNA host gene 17 (SNHG17) in OSCC. Herein, SNHG17 was disclosed to be remarkably upregulated in OSCC cell lines and promoted OSCC cell growth. Further mechanistic studies, including DNA/RNA pull down, RIP, ChIP, and luciferase reporter gene assays, were conducted. It was confirmed that Wnt/β-catenin signaling pathway was involved in the SNHG17-mediated OSCC cell growth. Moreover, E74 like ETS transcription factor 1 (ELF1) was identified as the transcription activator of CTNNB1 (β-catenin mRNA) in OSCC. Inspired by competing for endogenous RNAs (ceRNAs) network, we were pleasantly surprised to find that SNHG17 and ELF1 functioned as ceRNAs in OSCC via competitively binding to microRNA-384 (miR-384). By using rescue assays, we revealed that SNHG17 facilitated OSCC cell growth through modulating miR-384/ELF1 axis. Importantly, we certified that ELF1 was indispensable for SNHG17-affected OSCC progression. Collectively, it can be concluded that SNHG17/miR-384/ELF1 axis contributed to OSCC cell growth via promoting CTNNB1 expression, thus activating Wnt/β-catenin signaling pathway.
Collapse
Affiliation(s)
- Chunyan Qiao
- Department of Pathology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China.
| | - Tianyi Qiao
- Department of Gastroenterology, the First Clinical Medical College and Hospital of Jilin University, Changchun, 130012, Jilin, China
| | - Shihui Yang
- Department of Dental Implantology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China
| | - Lili Liu
- Department of Pathology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China
| | - Mengdan Zheng
- Department of Pathology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China
| |
Collapse
|
14
|
Hundreds of LncRNAs Display Circadian Rhythmicity in Zebrafish Larvae. Cells 2021; 10:cells10113173. [PMID: 34831396 PMCID: PMC8620895 DOI: 10.3390/cells10113173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/06/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been shown to play crucial roles in various life processes, including circadian rhythms. Although next generation sequencing technologies have facilitated faster profiling of lncRNAs, the resulting datasets require sophisticated computational analyses. In particular, the regulatory roles of lncRNAs in circadian clocks are far from being completely understood. In this study, we conducted RNA-seq-based transcriptome analysis of zebrafish larvae under both constant darkness (DD) and constant light (LL) conditions in a circadian manner, employing state-of-the-art computational approaches to identify approximately 3220 lncRNAs from zebrafish larvae, and then uncovered 269 and 309 lncRNAs displaying circadian rhythmicity under DD and LL conditions, respectively, with 30 of them are coexpressed under both DD and LL conditions. Subsequently, GO, COG, and KEGG pathway enrichment analyses of all these circadianly expressed lncRNAs suggested their potential involvement in numerous biological processes. Comparison of these circadianly expressed zebrafish larval lncRNAs, with rhythmically expressed lncRNAs in the zebrafish pineal gland and zebrafish testis, revealed that nine (DD) and twelve (LL) larval lncRNAs are coexpressed in the zebrafish pineal gland and testis, respectively. Intriguingly, among peptides encoded by these coexpressing circadianly expressed lncRNAs, three peptides (DD) and one peptide (LL) were found to have the known domains from the Protein Data Bank. Further, the conservation analysis of these circadianly expressed zebrafish larval lncRNAs with human and mouse genomes uncovered one lncRNA and four lncRNAs shared by all three species under DD and LL conditions, respectively. We also investigated the conserved lncRNA-encoded peptides and found one peptide under DD condition conserved in these three species and computationally predicted its 3D structure and functions. Our study reveals that hundreds of lncRNAs from zebrafish larvae exhibit circadian rhythmicity and should help set the stage for their further functional studies.
Collapse
|
15
|
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.
Collapse
|
16
|
Carbone A, De Santis E, Cela O, Giambra V, Miele L, Marrone G, Grieco A, Buschbeck M, Capitanio N, Mazza T, Mazzoccoli G. The Histone Variant MacroH2A1 Impacts Circadian Gene Expression and Cell Phenotype in an In Vitro Model of Hepatocellular Carcinoma. Biomedicines 2021; 9:biomedicines9081057. [PMID: 34440260 PMCID: PMC8391426 DOI: 10.3390/biomedicines9081057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/21/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. A foremost risk factor for HCC is obesity/metabolic syndrome-related non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), which is prompted by remarkable changes in transcription patterns of genes enriching metabolic, immune/inflammatory, and circadian pathways. Epigenetic mechanisms play a role in NAFLD-associated HCC, and macroH2A1, a variant of histone H2A, is involved in the pathogenesis modulating the expression of oncogenes and/or tumor suppressor genes and interacting with SIRT1, which crucially impacts the circadian clock circuitry. Hence, we aimed to appraise if and how macroH2A1 regulated the expression patterns of circadian genes in the setting of NAFLD-associated HCC. We took advantage of an in vitro model of liver cancer represented by HepG2 (human hepatocarcinoma) cells stably knocked down for macroH2A1 and conducted whole transcriptome profiling and deep phenotyping analysis. We found up-regulation of PER1 along with several deregulated circadian genes, enriching several important pathways and functions related to cancer onset and progression, such as epithelial-to-mesenchymal transition, cell cycle deregulation, and DNA damage. PER1 silencing partially mitigated the malignant phenotype induced by the loss of macroH2A1 in HCC cells. In conclusion, our findings suggest a modulatory role for the core circadian protein PER1 in liver carcinogenesis in the context of a lack of the macroH2A1 epigenetic and transcriptional landscape.
Collapse
Affiliation(s)
- Annalucia Carbone
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
| | - Elisabetta De Santis
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (E.D.S.); (V.G.)
| | - Olga Cela
- Department of Clinical and Experimental Medicine, University of Foggia, 71100 Foggia, Italy; (O.C.); (N.C.)
| | - Vincenzo Giambra
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (E.D.S.); (V.G.)
| | - Luca Miele
- Fondazione Policlinico Universitario A. Gemelli-IRCCS, Catholic University of the Sacred Heart, 00168 Rome, Italy; (L.M.); (G.M.); (A.G.)
| | - Giuseppe Marrone
- Fondazione Policlinico Universitario A. Gemelli-IRCCS, Catholic University of the Sacred Heart, 00168 Rome, Italy; (L.M.); (G.M.); (A.G.)
| | - Antonio Grieco
- Fondazione Policlinico Universitario A. Gemelli-IRCCS, Catholic University of the Sacred Heart, 00168 Rome, Italy; (L.M.); (G.M.); (A.G.)
| | - Marcus Buschbeck
- Josep Carreras Leukaemia Research Institute, IJC Building, Can Ruti Campus Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Spain;
| | - Nazzareno Capitanio
- Department of Clinical and Experimental Medicine, University of Foggia, 71100 Foggia, Italy; (O.C.); (N.C.)
| | - Tommaso Mazza
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
| | - Gianluigi Mazzoccoli
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
- Correspondence: ; Tel./Fax: +39-(0882)-410-255
| |
Collapse
|
17
|
Qin F, Cao H, Feng C, Zhu T, Zhu B, Zhang J, Tong J, Pei H. Microarray profiling of LncRNA expression in the testis of pubertal mice following morning and evening exposure to 1800 MHz radiofrequency fields. Chronobiol Int 2021; 38:1745-1760. [PMID: 34369206 DOI: 10.1080/07420528.2021.1962902] [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] [Indexed: 10/20/2022]
Abstract
In this paper, the chronotoxicity of radiofrequency fields (RF) in the pubertal testis development and the involved molecular pathways were investigated by exposing four-week-old mice to RF (1800 MHz, SAR, 0.50 W/kg) in the morning and evening of each day for three weeks. Then, pathological changes and functional indices within the testis were determined. We also used a long non-coding RNA (lncRNA) microarray and GO/KEGG pathway analyses to determine lncRNA expression profiles and predict their potential functions. The cis and trans regulation of lncRNAs were investigated, and an interaction network was constructed using Cytoscape software. RF exposure led to a range of pathological changes in the testes of adolescent mice, as testicular weights and daily sperm productions decreased, and the testosterone secretion reduced. Furthermore, RF induced dysregulation in the expression of testicular lncRNAs. We identified 615 and 183 differentially expressed lncRNAs that were associated with morning and evening exposure to RF, respectively. From 15 differential expression lncRNAs both in morning RF group and evening RF group, we selected 6 lncRNAs to be validated by quantitative reverse transcription PCR (qRT-PCR). The differentially expressed lncRNAs induced by morning RF exposure were highly correlated with many different pathways, including Fanconi syndrome, metabolic processes, cell cycle, DNA damage, and DNA replication. Trans-regulation analyses further showed that differentially expressed lncRNAs were involved in multiple transcription factor-regulated pathways, such as TCFAP4, NFkB, HINFP, TFDP2, FoxN1, and PAX5. These transcription factors have all been shown to be involved in the modulation of testis development, cell cycle progression, and spermatogenesis. These findings suggest that the extent to which 1800 MHz RF induced toxicity in the testes and changed the expression of lncRNAs showed differences between morning exposure and evening exposure. These data indicate that differentially expressed lncRNAs play crucial roles in the RF exposure damage to the developing pubertal testis. Collectively, our findings provide a better understanding of the mechanisms underlying the toxic effects of RF exposure on testicular development.
Collapse
Affiliation(s)
- Fenju Qin
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, China.,School of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Honglong Cao
- School of Electronics & Information Engineering, Soochow University, Suzhou, China
| | - Chuhan Feng
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, China
| | - Tianyuan Zhu
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, China
| | - Bingxu Zhu
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, China
| | - Jie Zhang
- School of Public Health, Soochow University, Suzhou, China
| | - Jian Tong
- School of Public Health, Soochow University, Suzhou, China
| | - Hailong Pei
- School of Radiation Medicine and Protection, Soochow University, Suzhou, China
| |
Collapse
|
18
|
Mishra SK, Liu T, Wang H. Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis. Int J Mol Sci 2021; 22:7810. [PMID: 34360576 PMCID: PMC8346003 DOI: 10.3390/ijms22157810] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/14/2022] Open
Abstract
Noncoding RNAs have been known to contribute to a variety of fundamental life processes, such as development, metabolism, and circadian rhythms. However, much remains unrevealed in the huge noncoding RNA datasets, which require further bioinformatic analysis and experimental investigation-and in particular, the coding potential of lncRNAs and the functions of lncRNA-encoded peptides have not been comprehensively studied to date. Through integrating the time-course experimentation with state-of-the-art computational techniques, we studied tens of thousands of zebrafish lncRNAs from our own experiments and from a published study including time-series transcriptome analyses of the testis and the pineal gland. Rhythmicity analysis of these data revealed approximately 700 rhythmically expressed lncRNAs from the pineal gland and the testis, and their GO, COG, and KEGG pathway functions were analyzed. Comparative and conservative analyses determined 14 rhythmically expressed lncRNAs shared between both the pineal gland and the testis, and 15 pineal gland lncRNAs as well as 3 testis lncRNAs conserved among zebrafish, mice, and humans. Further, we computationally analyzed the conserved lncRNA-encoded peptides, and revealed three pineal gland and one testis lncRNA-encoded peptides conserved among these three species, which were further investigated for their three-dimensional (3D) structures and potential functions. Our computational findings provided novel annotations and regulatory mechanisms for hundreds of rhythmically expressed pineal gland and testis lncRNAs in zebrafish, and set the stage for their experimental studies in the near future.
Collapse
Affiliation(s)
- Shital Kumar Mishra
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China; (S.K.M.); (T.L.)
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China
| | - Taole Liu
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China; (S.K.M.); (T.L.)
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China; (S.K.M.); (T.L.)
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China
| |
Collapse
|
19
|
Mosig RA, Kojima S. Timing without coding: How do long non-coding RNAs regulate circadian rhythms? Semin Cell Dev Biol 2021; 126:79-86. [PMID: 34116930 DOI: 10.1016/j.semcdb.2021.04.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a new class of regulatory RNAs that play important roles in disease development and a variety of biological processes. Recent studies have underscored the importance of lncRNAs in the circadian clock system and demonstrated that lncRNAs regulate core clock genes and the core clock machinery in mammals. In this review, we provide an overview of our current understanding of how lncRNAs regulate the circadian clock without coding a protein. We also offer additional insights into the challenges in understanding the functions of lncRNAs and other unresolved questions in the field. We do not cover other regulatory ncRNAs even though they also play important roles; readers are highly encouraged to refer to other excellent reviews on this topic.
Collapse
Affiliation(s)
- Rebecca A Mosig
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech 1015 Life Science Circle, Blacksburg, VA 24061, USA.
| |
Collapse
|
20
|
Ray I, Goswami S. Circadian rhythm genes in cancer: insight into their functions and regulation involving noncoding RNAs. Chronobiol Int 2021; 38:1231-1243. [PMID: 34024245 DOI: 10.1080/07420528.2021.1928157] [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: 12/20/2022]
Abstract
The 24-h circadian rhythm handles a wide variety of physiological needs. Clock genes, in coordination with other tissue-specific factors regulate various processes and often turns responsible for the pathological conditions when altered. Cancer is one such disease where the clock genes have been shown to contribute at multiple levels modulating key hallmarks of cancer. Most importantly, adding to this complication, noncoding RNAs (ncRNAs) have emerged as one of the major post-transcriptional regulators of gene expression and many recent studies have indicated about involvement of microRNAs or long noncoding RNAs in the process. In this review, we have described how do circadian pathway genes participated in oncogenesis and also updated the latest status of ncRNA involvement. We also try to address the existing gaps to have a more comprehensive understanding of the phenomenon in future.Abbreviations: HIFs: hypoxia-inducible factors; VEGF: Vascular endothelial growth factor; Mdm2: Mouse double minute 2 homolog; ATM: Ataxia telangiectasia mutated; Chk2: Checkpoint kinase 2; Bcl-Xl: B-cell lymphoma-extra-large; Bcl-2: B-cell lymphoma 2; DGCR8: DiGeorge syndrome chromosomal region 8; PPAR-γ: Peroxisome proliferator-activated receptor gamma.
Collapse
Affiliation(s)
- Indrani Ray
- National Institute of Biomedical Genomics, Kalyani, India
| | | |
Collapse
|
21
|
Huang X, Sun L, Wen S, Deng D, Wan F, He X, Tian L, Liang L, Wei C, Gao K, Fu Q, Li Y, Jiang J, Zhai R, He M. RNA sequencing of plasma exosomes revealed novel functional long noncoding RNAs in hepatocellular carcinoma. Cancer Sci 2020; 111:3338-3349. [PMID: 32506598 PMCID: PMC7469810 DOI: 10.1111/cas.14516] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/21/2022] Open
Abstract
Exosomal long noncoding RNA (lncRNA) has been found to be associated with the development of cancers. However, the expression characteristics and the biological roles of exosomal lncRNAs in hepatocellular carcinoma (HCC) remain unknown. Here, by RNA sequencing, we found 9440 mRNAs and 8572 lncRNAs were differentially expressed (DE-) in plasma exosomes between HCC patients and healthy controls. Exosomal DE-lncRNAs displayed higher expression levels and tissue specificity, lower expression variability and splicing efficiency than DE-mRNAs. Six candidate DE-lncRNAs (fold change 6 or more, P ≤ .01) were high in HCC cells and cell exosomes. The knockdown of these candidate DE-lncRNAs significantly affected the migration, proliferation, and apoptosis in HCC cells. In particular, a novel DE-lncRNA, RP11-85G21.1 (lnc85), promoted HCC cellular proliferation and migration by targeted binding and regulating of miR-324-5p. More importantly, the level of serum lnc85 was highly expressed in both Alpha-fetoprotein (AFP)-positive and AFP-negative HCC patients and allowed distinguishing AFP-negative HCC from healthy control and liver cirrhosis (area under the receiver operating characteristic curve, 0.869; sensitivity, 80.0%; specificity, 76.5%) with high accuracy. Our finding offers a new insight into the association between the dysregulation of exosomal lncRNA and HCC, suggesting that lnc85 could be a potential biomarker of HCC.
Collapse
Affiliation(s)
- Xuejing Huang
- School of Public HealthGuangxi Medical UniversityNanningChina
- Guangxi Medical University Laboratory Animal CenterNanningChina
| | - Liyuan Sun
- Guangdong Key laboratory for Genome Stability and Disease PreventionShenzhen University Health Science CentreShenzhenChina
| | - Sha Wen
- Guangxi Medical University Laboratory Animal CenterNanningChina
| | - Deli Deng
- Department of Infectious DiseasesThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Fengjie Wan
- School of Public HealthGuangxi Medical UniversityNanningChina
| | - Xiao He
- School of Public HealthGuilin Medical UniversityGuilinChina
| | - Li Tian
- Guangdong Key laboratory for Genome Stability and Disease PreventionShenzhen University Health Science CentreShenzhenChina
| | - Lifang Liang
- School of Public HealthGuangxi Medical UniversityNanningChina
| | - Chunmeng Wei
- School of Public HealthGuangxi Medical UniversityNanningChina
| | - Kaiping Gao
- Guangdong Key laboratory for Genome Stability and Disease PreventionShenzhen University Health Science CentreShenzhenChina
| | - Qiang Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐ BioresourcesNanningChina
| | - Yasi Li
- School of Global Public HealthNew York UniversityNew YorkNYUSA
| | - Jianning Jiang
- Department of Infectious DiseasesThe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Rihong Zhai
- Guangdong Key laboratory for Genome Stability and Disease PreventionShenzhen University Health Science CentreShenzhenChina
- Carson Cancer CenterShenzhen UniversityShenzhenChina
| | - Min He
- School of Public HealthGuangxi Medical UniversityNanningChina
- Guangxi Medical University Laboratory Animal CenterNanningChina
- Key Laboratory of High‐Incidence Tumor Prevention and Treatment (Guangxi Medical University)Ministry of EducationNanningChina
| |
Collapse
|
22
|
Zhang H, Li S, Xu H, Sun L, Zhu Z, Yao Z. Interference of miR-107 with Atg12 is inhibited by HULC to promote metastasis of hepatocellular carcinoma. MedComm (Beijing) 2020; 1:165-177. [PMID: 34766115 PMCID: PMC8491224 DOI: 10.1002/mco2.25] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 01/13/2023] Open
Abstract
Highly upregulated in liver cancer (HULC) had a significant predictive effect on tumor growth and metastasis of hepatocellular carcinoma (HCC); however, the mechanisms of HULC on HCC still need to be clarified. We attempted to determine the roles of HULC and miR-107 in autophagy and invasion of HCC. HULC siRNA reduced the level of autophagy. The impact of HULC siRNA on invasion can be reversed by activating autophagy in HCC cell lines. Further studies on HULC and autophagy were conducted. An interacting sequence between HULC and miR-107, as well as miR-107 and Atg12, was predicted by software. The relationship of each pair of molecules was confirmed by luciferase reporter assays. The negative impacts of miR-107 on autophagy and invasion were proved in HCC cell lines. The inhibitor of miR-107-promoted invasion can also be reversed by Atg12 siRNA. The changes of miR-107, Atg12, epithelial-mesenchymal transition, and autophagy in transplanted tumors of mouse models also confirmed the results in HCC cell lines. Finally, we find that HULC acts as an endogenous sponge, which abolishes the binding of miR-107 on the Atg12 3'-UTR and promotes autophagy and metastasis of HCC.
Collapse
Affiliation(s)
- Haiming Zhang
- Liver Transplantation CenterNational Clinical Research Center for Digestive Diseases and Beijing Key Laboratory of Tolerance Induction and Organ Protection in TransplantationBeijing Friendship HospitalCapital Medical UniversityBeijingChina
| | - Shipeng Li
- Department of General SurgeryJiaozuo People's HospitalXinxiang Medical UniversityJiaozuoChina
| | - Haixu Xu
- Department of ImmunologyTianjin Key Laboratory of Cellular and Molecular ImmunologyTianjin Medical UniversityTianjinChina
| | - Liying Sun
- Liver Transplantation CenterNational Clinical Research Center for Digestive Diseases and Beijing Key Laboratory of Tolerance Induction and Organ Protection in TransplantationBeijing Friendship HospitalCapital Medical UniversityBeijingChina
| | - Zhijun Zhu
- Liver Transplantation CenterNational Clinical Research Center for Digestive Diseases and Beijing Key Laboratory of Tolerance Induction and Organ Protection in TransplantationBeijing Friendship HospitalCapital Medical UniversityBeijingChina
| | - Zhi Yao
- Department of ImmunologyTianjin Key Laboratory of Cellular and Molecular ImmunologyTianjin Medical UniversityTianjinChina
| |
Collapse
|
23
|
Qi F, Jiang Z, Hou W, Peng B, Cheng S, Zhang X, Luo Z, Dai Z, Wang Y, Liu Y, Wang Y, Wang Z. The Clock-Controlled lncRNA-AK028245 Participates in the Immune Response via Immune Response Factors OTUD7B and A20. J Biol Rhythms 2020; 35:542-554. [PMID: 32748687 DOI: 10.1177/0748730420944328] [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] [Indexed: 11/15/2022]
Abstract
Emerging evidence has demonstrated that long noncoding RNAs (lncRNAs) play critical roles in the epigenetic and transcriptional regulation of mammalian circadian systems. Circadian rhythmicity regulates many aspects of our immune system, and perturbation of the circadian clock can augment the inflammatory response. However, knowledge of the precise functions of lncRNAs in the regulation of immune functions within the circadian system is relatively limited. In this study, differentially expressed lncRNAs induced by Clock knockdown were screened via mRNA/lncRNA microarray and bioinformatic prediction analysis. We identified a Clock-regulated lncRNA, AK028245, which was correlated with the activation of the immune response. The expression levels of AK028245 were decreased in the spleen of immunosuppressed mice and elevated in immune-activated mice treated with lipopolysaccharide (LPS). Further, Clock knockdown decreased the expression of OTUD7B and A20, 2 early immune response factors acting on the NF-κB signaling pathway. Interestingly, inhibition of AK028245 increased their expression, mitigating the effects of Clock knockdown. In addition, inhibition of AK028245 downregulated the expression of tumor necrosis factor-α and interleukin-6 in the late stages of LPS stimulation and the expression of interferon-γ and Cxcl12 in the peak stages. We conclude that this newly identified lncRNA plays a role in the crosstalk between Clock and immune response regulators, likely resulting in a proinflammatory response targeting OTUD7B and A20. The lncRNA AK028245 has revealed a new mechanism of the immune response and provided new targets for the treatment of immune disorders.
Collapse
Affiliation(s)
- Fang Qi
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Zhou Jiang
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Wang Hou
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Bo Peng
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Shuting Cheng
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Xiaolong Zhang
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Zhihan Luo
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Zeyong Dai
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yumeng Wang
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yanyou Liu
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yuhui Wang
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Zhengrong Wang
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| |
Collapse
|
24
|
Lee T, Cho CH, Kim WR, Moon JH, Kim S, Geum D, In HP, Lee HJ. Development of model based on clock gene expression of human hair follicle cells to estimate circadian time. Chronobiol Int 2020; 37:993-1001. [PMID: 32654537 DOI: 10.1080/07420528.2020.1777150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Considering the effects of circadian misalignment on human pathophysiology and behavior, it is important to be able to detect an individual's endogenous circadian time. We developed an endogenous Clock Estimation Model (eCEM) based on a machine learning process using the expression of 10 circadian genes. Hair follicle cells were collected from 18 healthy subjects at 08:00, 11:00, 15:00, 19:00, and 23:00 h for two consecutive days, and the expression patterns of 10 circadian genes were obtained. The eCEM was designed using the inverse form of the circadian gene rhythm function (i.e., Circadian Time = F(gene)), and the accuracy of eCEM was evaluated by leave-one-out cross-validation (LOOCV). As a result, six genes (PER1, PER3, CLOCK, CRY2, NPAS2, and NR1D2) were selected as the best model, and the error range between actual and predicted time was 3.24 h. The eCEM is simple and applicable in that a single time-point sampling of hair follicle cells at any time of the day is sufficient to estimate the endogenous circadian time.
Collapse
Affiliation(s)
- Taek Lee
- Department of Convergence Security Engineering, Sungshin University , Seoul, Republic of Korea
| | - Chul-Hyun Cho
- Department of Psychiatry, Chungnam National University , Daejeon, Republic of Korea
| | | | - Joung Ho Moon
- Department of Psychiatry.,Chronobiology Institute, Korea University College of Medicine
| | | | | | - Hoh Peter In
- Department of Computer Science, Korea University College of Information , Seoul, Republic of Korea
| | - Heon-Jeong Lee
- Department of Biomedical Sciences.,Department of Psychiatry.,Chronobiology Institute, Korea University College of Medicine
| |
Collapse
|
25
|
Advances in DNA Repair-Emerging Players in the Arena of Eukaryotic DNA Repair. Int J Mol Sci 2020; 21:ijms21113934. [PMID: 32486270 PMCID: PMC7313471 DOI: 10.3390/ijms21113934] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic DNA is constantly damaged by factors produced during natural metabolic processes as well as agents coming from the external environment. Considering such a wide array of damaging agents, eukaryotic cells have evolved a DNA damage response (DRR) that opposes the influence of deleterious factors. Despite the broad knowledge regarding DNA damage and repair, new areas of research are emerging. New players in the field of DDR are constantly being discovered. The aim of this study is to review current knowledge regarding the roles of sirtuins, heat shock proteins, long-noncoding RNAs and the circadian clock in DDR and distinguish new agents that may have a prominent role in DNA damage response and repair.
Collapse
|
26
|
Non-Coding RNAs: Regulating Disease Progression and Therapy Resistance in Hepatocellular Carcinoma. Cancers (Basel) 2020; 12:cancers12051243. [PMID: 32429062 PMCID: PMC7281199 DOI: 10.3390/cancers12051243] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC), the primary liver cancer arising from hepatocytes, is a universal health problem and one of the most common malignant tumors. Surgery followed by chemotherapy as well as tyrosine kinase inhibitors (TKIs), such as sorafenib, are primary treatment procedures for HCC, but recurrence of disease because of therapy resistance results in high mortality. It is necessary to identify novel regulators of HCC for developing effective targeted therapies that can significantly interfere with progression of the disease process. Non-coding RNAs (ncRNAs) are an abundant group of versatile RNA transcripts that do not translate into proteins, rather serve as potentially functional RNAs. The role of ncRNAs in regulating diverse aspects of the carcinogenesis process are gradually being elucidated. Recent advances in RNA sequencing technology have identified a plethora of ncRNAs regulating all aspects of hepatocarcinogenesis process and serving as potential prognostic or diagnostic biomarkers. The present review provides a comprehensive description of the biological roles of ncRNAs in disease process and therapy resistance, and potential clinical application of these ncRNAs in HCC.
Collapse
|
27
|
Role of Non-Coding RNAs in Lung Circadian Clock Related Diseases. Int J Mol Sci 2020; 21:ijms21083013. [PMID: 32344623 PMCID: PMC7215637 DOI: 10.3390/ijms21083013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
Circadian oscillations are regulated at both central and peripheral levels to maintain physiological homeostasis. The central circadian clock consists of a central pacemaker in the suprachiasmatic nucleus that is entrained by light dark cycles and this, in turn, synchronizes the peripheral clock inherent in other organs. Circadian dysregulation has been attributed to dysregulation of peripheral clock and also associated with several diseases. Components of the molecular clock are disrupted in lung diseases like chronic obstructive pulmonary disease (COPD), asthma and IPF. Airway epithelial cells play an important role in temporally organizing magnitude of immune response, DNA damage response and acute airway inflammation. Non-coding RNAs play an important role in regulation of molecular clock and in turn are also regulated by clock components. Dysregulation of these non-coding RNAs have been shown to impact the expression of core clock genes as well as clock output genes in many organs. However, no studies have currently looked at the potential impact of these non-coding RNAs on lung molecular clock. This review focuses on the ways how these non-coding RNAs regulate and in turn are regulated by the lung molecular clock and its potential impact on lung diseases.
Collapse
|
28
|
LncRNAs Act as a Link between Chronic Liver Disease and Hepatocellular Carcinoma. Int J Mol Sci 2020; 21:ijms21082883. [PMID: 32326098 PMCID: PMC7216144 DOI: 10.3390/ijms21082883] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important contributors to the biological processes underlying the pathophysiology of various human diseases, including hepatocellular carcinoma (HCC). However, the involvement of these molecules in chronic liver diseases, such as nonalcoholic fatty liver disease (NAFLD) and viral hepatitis, has only recently been considered in scientific research. While extensive studies on the pathogenesis of the development of HCC from hepatic fibrosis have been conducted, their regulatory molecular mechanisms are still only partially understood. The underlying mechanisms related to lncRNAs leading to HCC from chronic liver diseases and cirrhosis have not yet been entirely elucidated. Therefore, elucidating the functional roles of lncRNAs in chronic liver disease and HCC can contribute to a better understanding of the molecular mechanisms, and may help in developing novel diagnostic biomarkers and therapeutic targets for HCC, as well as in preventing the progression of chronic liver disease to HCC. Here, we comprehensively review and briefly summarize some lncRNAs that participate in both hepatic fibrosis and HCC.
Collapse
|
29
|
Chen L, Wu X, Zeb F, Huang Y, An J, Jiang P, Chen A, Xu C, Feng Q. Acrolein-induced apoptosis of smooth muscle cells through NEAT1-Bmal1/Clock pathway and a protection from asparagus extract. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113735. [PMID: 31864078 DOI: 10.1016/j.envpol.2019.113735] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/08/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Apoptosis of vascular smooth muscle cells (VSMCs) accelerates manifestation of plaque vulnerability in atherosclerosis. Long noncoding RNA NEAT1 participates in the proliferation and apoptosis of cells. In addition, circadian clock genes play a significant role in cell apoptosis. However, whether acrolein, an environmental pollutant, affects the apoptosis of VSMCs by regulating NEAT1 and clock genes is still elusive. We established VSMCs as an atherosclerotic cell model in vitro. Acrolein exposure reduced survival rate of VSMCs, and raised apoptosis percentage through upregulating the expression of Bax, Cytochrome c and Cleaved caspase-3 and downregulating Bcl-2. Asparagus extract (AE), as a dietary supplementation, was able to protect VSMCs against acrolein-induced apoptosis. Expression of NEAT1, Bmal1 and Clock was decreased by acrolein, while was ameliorated by AE. Knockdown of NEAT1, Bmal1 or Clock promoted VSMCs apoptosis by regulating Bax, Bcl-2, Cytochrome c and Caspase-3 levels. Correspondingly, overexpression of NEAT1 inhibited the apoptosis. We also observed that silence of NEAT1 repressed the expression of Bmal1/Clock and vice versa. In this study, we demonstrated that VSMCs apoptosis induced by acrolein was associated with downregulation of NEAT1 and Bmal1/Clock. AE alleviated the effects of proapoptotic response and circadian disorders caused by acrolein, which shed a new light on cardiovascular protection.
Collapse
Affiliation(s)
- Lijun Chen
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xiaoyue Wu
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Falak Zeb
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yunxiang Huang
- Hebei Province Asparagus Industry Technology Research Institute, Qinhuangdao, 066004, China
| | - Jing An
- Hebei Province Asparagus Industry Technology Research Institute, Qinhuangdao, 066004, China
| | - Pan Jiang
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Aochang Chen
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Chuyue Xu
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Qing Feng
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| |
Collapse
|
30
|
Song W, Zhang J, Zhang J, Sun M, Xia Q. Overexpression of lncRNA PIK3CD-AS1 promotes expression of LATS1 by competitive binding with microRNA-566 to inhibit the growth, invasion and metastasis of hepatocellular carcinoma cells. Cancer Cell Int 2019; 19:150. [PMID: 31624469 PMCID: PMC6784333 DOI: 10.1186/s12935-019-0857-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/10/2019] [Indexed: 12/20/2022] Open
Abstract
Background This study is conducted to investigate the effect of lncRNA PIK3CD-AS1 on the growth and metastasis of hepatocellular carcinoma (HCC) and its potential mechanism. Methods Hepatocellular carcinoma tissues and adjacent normal tissues together with HCC cells and normal liver cells were obtained for detecting expression of PIK3CD-AS1, microRNA-566 (miR-566) and LATS1. Additionally, a series of experiments were performed to determine cell proliferation, migration, invasion, cell cycle distribution and apoptosis of HCC cells. The xenograft tumor model of HCC was established and the growth rate and weight of xenograft tumor in nude mice were compared. Furthermore, the binding site between PIK3CD-AS1 and miR-566 as well as between miR-566 and LATS1 were verified. Results LncRNA PIK3CD-AS1 was downregulated in HCC tissues and cells, and mainly located in cytoplasm. Overexpression of PIK3CD-AS1 inhibited proliferation, colony formation, invasion, migration, epithelial–mesenchymal transition (EMT) and cell cycle progression and promoted apoptosis of HCC cells. Overexpression of PIK3CD-AS1 decreased the growth rate and weight of xenograft tumor in nude mice PIK3CD-AS1 competitively combined with miR-566 to regulate expression of LAST1. Conclusion Collectively, our study suggests that the expression of PIK3CD-AS1 was down-regulated in HCC, and overexpression of PIK3CD-AS1 promoted the expression of LATS1 by competitive binding of miR-566 to inhibit the growth, invasion and metastasis of HCC cells.
Collapse
Affiliation(s)
- Wei Song
- 1Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University, No. 127 Dongming Road, Zhengzhou, 450000 People's Republic of China
| | - Jingjing Zhang
- 2Department of Cardiovascularology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450000 People's Republic of China
| | - Jianbo Zhang
- 1Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University, No. 127 Dongming Road, Zhengzhou, 450000 People's Republic of China
| | - Miaomiao Sun
- 1Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University, No. 127 Dongming Road, Zhengzhou, 450000 People's Republic of China
| | - Qingxin Xia
- 1Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University, No. 127 Dongming Road, Zhengzhou, 450000 People's Republic of China
| |
Collapse
|
31
|
Yuan W, Liu L, Wei C, Li X, Sun D, Dai C, Li S, Peng S, Jiang L. Identification and meta-analysis of copy number variation-driven circadian clock genes for colorectal cancer. Oncol Lett 2019; 18:4816-4824. [PMID: 31611992 PMCID: PMC6781691 DOI: 10.3892/ol.2019.10830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
Both copy number variation (CNV) and circadian clock genes play a critical role in the etiology and pathogenesis of colorectal cancer (CRC); however, a comprehensive analysis of CNV-driven circadian clock genes is urgently required. The present study aimed to investigate the systematic associations between somatic cell CNVs and circadian clock gene expression in patients with CRC. Using somatic CNV, legacy clinical information and gene expression data from The Cancer Genome Atlas, 295 genes that were significantly differentially expressed and with significantly different CNV were obtained, and the expression of the genes, among which 15 were circadian clock genes, was significantly associated with CNV. Further analysis revealed that aryl hydrocarbon receptor nuclear translocator-like 2 (ARNTL2) expression and CNV in these circadian clock genes were significantly associated with survival time in patients with CRC, and the expression of ARNTL2 was also significantly associated with the pathological stage of CRC. Gene set enrichment analysis found that ARNTL2 is enriched for gene sets associated with CRC pathogenesis such as the p53 signaling pathway. These results suggest that ARNTL2 may be a promising prognostic biomarker for patients with CRC, and that circadian clock genes play an important role in CRC through CNV.
Collapse
Affiliation(s)
- Wenliang Yuan
- School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, P.R. China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China.,College of Mathematics and Computer Science, Chizhou University, Chizhou, Anhui 247000, P.R. China
| | - Li Liu
- College of Mathematics and Computer Science, Chizhou University, Chizhou, Anhui 247000, P.R. China
| | - Cai Wei
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China
| | - Xiaobo Li
- Institute of Biomedical Informatics, Lishui University, Lishui, Zhejiang 323000, P.R. China.,College of Engineering, Lishui University, Lishui, Zhejiang 323000, P.R. China
| | - Dan Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China
| | - Chaoxu Dai
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China
| | - Sicong Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China
| | - Sihua Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China
| | - Linhua Jiang
- School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, P.R. China
| |
Collapse
|
32
|
Mai H, Zhou B, Liu L, Yang F, Conran C, Ji Y, Hou J, Jiang D. Molecular pattern of lncRNAs in hepatocellular carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:198. [PMID: 31097003 PMCID: PMC6524221 DOI: 10.1186/s13046-019-1213-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/07/2019] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most notable lethal malignancies worldwide. However, the molecular mechanisms involved in the initiation and progression of this disease remain poorly understood. Over the past decade, many studies have demonstrated the important regulatory roles of long non-coding RNAs (lncRNAs) in HCC. Here, we comprehensively review recent discoveries regarding HCC-associated lncRNA functions, which we have classified and described according to their mechanism models.
Collapse
Affiliation(s)
- Haoming Mai
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institute of Liver Diseases Research of Guangdong Province, Guangzhou, China.,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Bin Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institute of Liver Diseases Research of Guangdong Province, Guangzhou, China.,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Li Liu
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institute of Liver Diseases Research of Guangdong Province, Guangzhou, China.,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Fu Yang
- Department of Medical Genetics, Second Military Medical University, Shanghai, 200433, China
| | - Carly Conran
- University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Yuan Ji
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institute of Liver Diseases Research of Guangdong Province, Guangzhou, China.,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Deke Jiang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institute of Liver Diseases Research of Guangdong Province, Guangzhou, China. .,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| |
Collapse
|
33
|
LncRNAs with miRNAs in regulation of gastric, liver, and colorectal cancers: updates in recent years. Appl Microbiol Biotechnol 2019; 103:4649-4677. [PMID: 31062053 DOI: 10.1007/s00253-019-09837-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 12/15/2022]
Abstract
Long noncoding RNA (lncRNA) is a kind of RNAi molecule composed of hundreds to thousands of nucleotides. There are several major types of functional lncRNAs which participate in some important cellular pathways. LncRNA-RNA interaction controls mRNA translation and degradation or serves as a microRNA (miRNA) sponge for silencing. LncRNA-protein interaction regulates protein activity in transcriptional activation and silencing. LncRNA guide, decoy, and scaffold regulate transcription regulators of enhancer or repressor region of the coding genes for alteration of expression. LncRNA plays a role in cellular responses including the following activities: regulation of chromatin structural modification and gene expression for epigenetic and cell function control, promotion of hematopoiesis and maturation of immunity, cell programming in stem cell and somatic cell development, modulation of pathogen infection, switching glycolysis and lipid metabolism, and initiation of autoimmune diseases. LncRNA, together with miRNA, are considered the critical elements in cancer development. It has been demonstrated that tumorigenesis could be driven by homeostatic imbalance of lncRNA/miRNA/cancer regulatory factors resulting in biochemical and physiological alterations inside the cells. Cancer-driven lncRNAs with other cellular RNAs, epigenetic modulators, or protein effectors may change gene expression level and affect the viability, immortality, and motility of the cells that facilitate cancer cell cycle rearrangement, angiogenesis, proliferation, and metastasis. Molecular medicine will be the future trend for development. LncRNA/miRNA could be one of the potential candidates in this category. Continuous studies in lncRNA functional discrepancy between cancer cells and normal cells and regional and rational genetic differences of lncRNA profiles are critical for clinical research which is beneficial for clinical practice.
Collapse
|
34
|
Yang Y, Wang F, Huang H, Zhang Y, Xie H, Men T. lncRNA SLCO4A1-AS1 promotes growth and invasion of bladder cancer through sponging miR-335-5p to upregulate OCT4. Onco Targets Ther 2019; 12:1351-1358. [PMID: 30863101 PMCID: PMC6389014 DOI: 10.2147/ott.s191740] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Background Bladder cancer (BC) is among the most frequently occurring cancer types in the urinary system. In recent years, the importance of lncRNAs in BC has been acknowledged. SLCO4A1-AS1 is an oncogene in colorectal cancer. However, the role of SLCO4A1-AS1 in BC remains unknown. Materials and methods The expression levels of SLCO4A1-AS1 in BC tissues were analyzed by qRT-PCR. The effects of SLCO4A1-AS1 knockdown on proliferation were determined by CCK8 assay. Transwell assay was used to evaluate the role of SLCO4A1-AS1 on migration and invasion. Furthermore, xenograft assay was utilized to test the effect of SLCO4A1-AS1 on BC growth in vivo. Results SLCO4A1-AS1 expression was more upregulated in BC tissues than in adjacent normal tissues. Moreover, SLCO4A1-AS1 level was positively correlated with the advanced stage and metastasis in BC. The upregulation of SLCO4A1-AS1 indicates poor prognosis in BC patients. The knockdown of SLCO4A1-AS1 downregulated the proliferation, migration, and invasion of EJ and T24 cells in vitro. In addition, the loss of SLCO4A1-AS1 prevented BC growth in vivo. Mechanistic investigation showed that SLCO4A1-AS1 was the sponge for miR-335-5p, and miR-335-5p modulated OCT4 expression. Conclusion High SLCO4A1-AS1 expression level was associated with the progression of BC, and SLCO4A1-AS1 promoted the malignant phenotypes of BC cells through the miR-335-5p/OCT4 axis.
Collapse
Affiliation(s)
- Yu Yang
- Department of Urology, Qianfoshan Hospital Affiliated to Shandong University, Jinan 250014, China,
| | - Feng Wang
- Department of Urology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Hang Huang
- Department of Urology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Yan Zhang
- Transplant Section, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Hui Xie
- Department of Urology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Tongyi Men
- Department of Urology, Qianfoshan Hospital Affiliated to Shandong University, Jinan 250014, China,
| |
Collapse
|
35
|
Singh K, Jha NK, Thakur A. Spatiotemporal chromatin dynamics - A telltale of circadian epigenetic gene regulation. Life Sci 2019; 221:377-391. [PMID: 30721705 DOI: 10.1016/j.lfs.2019.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/27/2019] [Accepted: 02/01/2019] [Indexed: 01/08/2023]
Abstract
Over the course of evolution, nature has forced organisms under selection pressure to hardwire an internal time keeping device that defines 24 h of a daily cycle of physiological and behavioral rhythms, known as circadian rhythms. At the cellular level, the cycle is governed by significant fractions of transcriptomes, which are under the control of transcriptional and translational feedback loop of clock genes. Intriguingly, this feedback loop is regulated at multiple stratums such as at the transcriptional and translational levels, which direct a cell towards producing a robust rhythm by sustaining the repeated stoichiometry of protein products. Moreover, with the advent of state of the art paradigms, epigenetic regulation of circadian rhythms has been becoming more evident at present time. Light-induced recurring fluctuations in chromatin acetylation concurrent with the binding of RNA Pol II and integration of miRNAs monitor the chromatin modifiers or clock genes expression to drive temporal rhythmicity. Furthermore, CLOCK protein intrinsic histone acetyl transferase activity, the interaction of CLOCK-BMAL-1 with HAT enzymes, and the involvement of many histone deacetylases also maintain the rhythmic protein profile. Additionally, the critical role of the rhythmic methylation pattern of clock genes in battery of cancer and metabolic disorders also defines its importance. Therefore, in this review, we focused on accumulating all the present data available on epigenetics and circadian rhythms. Interestingly, we also gathered evidence from the available literature pinpointing towards the dynamic nature of chromatin architecture governed by long and short-range regulatory elements DNA contacts arising daily, that was thought to be steady otherwise.
Collapse
Affiliation(s)
- Kunal Singh
- Department of Biotechnology, Noida Institute of Engineering & Technology (NIET), Greater Noida, India.
| | - Niraj Kumar Jha
- Department of Biotechnology, Noida Institute of Engineering & Technology (NIET), Greater Noida, India
| | - Abhimanyu Thakur
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, India
| |
Collapse
|
36
|
Li N, Zhu Y. Targeting liver cancer stem cells for the treatment of hepatocellular carcinoma. Therap Adv Gastroenterol 2019; 12:1756284818821560. [PMID: 30719075 PMCID: PMC6348509 DOI: 10.1177/1756284818821560] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 11/15/2018] [Indexed: 02/04/2023] Open
Abstract
Liver cancer is one of the most common malignant tumors and prognosis remains poor. It has been increasingly recognized that liver cancer stem cells (LCSCs) are responsible for the carcinogenesis, recurrence, metastasis and chemoresistance of hepatocellular carcinoma (HCC). Targeting LCSCs is promising to be a new direction for the treatment of HCC. Herein, we summarize the potentially therapeutic targets in LCSCs at the level of genes, molecules and cells, such as knockout of oncogenes or oncoproteins, restoring the silent tumor suppressor genes, inhibition of the transcription factors and regulation of noncoding RNAs (including microRNAs and long noncoding RNAs) in LCSCs at the genetic level; inhibition of markers and blockade of the key signaling pathways of LCSCs at the molecular level; and inhibiting autophagy and application of oncolytic adenoviruses in LCSCs at the cellular level. Moreover, we analyze the potential targets in LCSCs to eliminate chemoresistance of HCC. Thereinto, the suppression of autophagy and Nanog by chloroquine and shRNA respectively may be the most promising targeting approaches. These targets may provide novel therapeutic strategies for the treatment of HCC by targeting LCSCs.
Collapse
Affiliation(s)
- Na Li
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | | |
Collapse
|
37
|
Huang H, Bu Y, Zhang X, Liu J, Zhu L, Fang Y. LINC01433 promotes hepatocellular carcinoma progression via modulating the miR‐1301/STAT3 axis. J Cell Physiol 2018; 234:6116-6124. [PMID: 30317567 DOI: 10.1002/jcp.27366] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 08/14/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Haijin Huang
- Department of General Surgery Hongze District People's Hospital Hongze China
| | - Yan‐Zhi Bu
- Department of General Surgery Lianshui County People's Hospital Huai'an China
| | - Xiao‐Yu Zhang
- Division of Gastrointestinal Surgery, Department of General Surgery Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University Huai'an China
| | - Juan Liu
- Operating Room, Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University Huai'an China
| | - Li‐Yao Zhu
- Department of Hepatology The Fourth People's Hospital of Huai'an Huai'an China
| | - Yong Fang
- Department of General Surgery Jiangwan Hospital of Shanghai Hongkou District, No. 22 Changzhong Road Hongkou District Shanghai China
| |
Collapse
|
38
|
Tao SC, Guo SC. Extracellular Vesicles: Potential Participants in Circadian Rhythm Synchronization. Int J Biol Sci 2018; 14:1610-1620. [PMID: 30416375 PMCID: PMC6216034 DOI: 10.7150/ijbs.26518] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/15/2018] [Indexed: 12/14/2022] Open
Abstract
The circadian rhythm (CR) is a set of autonomous endogenous oscillators. Exposure to the 24-hour day-night cycle synchronizes our CR system, maintaining homeostasis and human health. Several mechanisms for the CR system have been proposed, including those underlying the function (transcriptional-translational negative-feedback loops, or TTFLs), mechanisms regulating the TTFLs, and the mechanism by which the "server clock" is synchronized to environmental time. Several pathways downstream of the "server clock" perform well-characterized biological functions. However, the synchronization between the "server clock" (the endogenous master clock seated in the suprachiasmatic nucleus within the hypothalamus) and the "client clock" (imbedded in nearly every cell in the form of interlocking TTFLs) is difficult to explain with current theories. Extracellular vesicles (EVs), which are involved in intercellular communication and have recently been found to participate in regulation of the "client clock", might be the answer to this question. In this review, we summarize the current knowledge of CRs, TTFLs, and EVs, examine research findings about the functions of EVs in the CR system, and discuss the issues requiring attention in future research.
Collapse
Affiliation(s)
- Shi-Cong Tao
- Department of Orthopaedic Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Shang-Chun Guo
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| |
Collapse
|
39
|
Xin X, Wu M, Meng Q, Wang C, Lu Y, Yang Y, Li X, Zheng Q, Pu H, Gui X, Li T, Li J, Jia S, Lu D. Long noncoding RNA HULC accelerates liver cancer by inhibiting PTEN via autophagy cooperation to miR15a. Mol Cancer 2018; 17:94. [PMID: 29895332 PMCID: PMC5998602 DOI: 10.1186/s12943-018-0843-8] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 06/01/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Long noncoding RNA HULC is highly up-regulation in human hepatocellular carcinoma (HCC). However, the functions of HULC in hepatocarcinogenesis remains unclear. METHODS RT-PCR, Western blotting, Chromatin immunoprecipitation (CHIP) assay, RNA Immunoprecipitation (RIP) and tumorignesis test in vitro and in vivo were performed. RESULTS HULC is negatively associated with expression of PTEN or miR15a in patients of human liver cancer. Moreover, HULC accelerates malignant progression of liver cancer cells in vitro and in vivo. Mechanistically, HULC increasesthe expression of P62 via decreasing mature miR15a. On the other hand, excessive HULC increases the expression of LC3 on the level of transcription and then activates LC3 through Sirt1 (a deacetylase). Notably, HULC enhanced the interplay between LC3 and ATG3. Furthermore, HULC also increases the expression of becline-1(autophagy related gene). Therefore, HULC increases the cellular autophagy by increasing LC3II dependent on Sirt1.Noteworthy, excessive HULC reduces the expression of PTEN, β-catenin and enhances the expression of SAPK/JUNK, PKM2, CDK2, NOTCH1, C-Jun in liver cancer cells. Of significance, our observations also revealed that HULC inhibited PTEN through ubiquitin-proteasome system mediated by autophagy-P62.Ultimately,HULC activates AKT-PI3K-mTOR pathway through inhibiting PTEN in human liver cancer cells. CONCLUSIONS This study elucidates a novel mechanism that lncRNA HULC produces a vital function during hepatocarcinogenesis.
Collapse
Affiliation(s)
- Xiaoru Xin
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Mengying Wu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Qiuyu Meng
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Chen Wang
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Yanan Lu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Yuxin Yang
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Xiaonan Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Qidi Zheng
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Hu Pu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Xin Gui
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Tianming Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Jiao Li
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Song Jia
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Dongdong Lu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China. .,Tongji University School of Life Science and Technology, Shanghai, 200092, China.
| |
Collapse
|
40
|
The association of lncRNA-HULC polymorphisms with hepatocellular cancer risk and prognosis. Gene 2018; 670:148-154. [PMID: 29803923 DOI: 10.1016/j.gene.2018.05.096] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/10/2018] [Accepted: 05/23/2018] [Indexed: 02/09/2023]
Abstract
BACKGROUND Genetic polymorphisms in lncRNA HULC may affect the susceptibility and clinical outcome of cancer. We aimed to investigate the association of HULC tagSNPs with the risk and prognosis of hepatocellular cancer, as well as the influence of the SNPs on lncRNA expression level. METHODS A total of 1338 samples were recruited in the risk study. Among them, 351 HCC patients were involved in the prognosis study. SNP genotyping was performed using KASP method and lncRNA expression was detected by Real-time PCR. RESULTS We found a promoter SNP, rs1041279, was associated with a 1.41-fold increased HCC risk (P = 0.032). In the stratified analysis, rs1041279 had greater ORs for the increased HCC risk in the male subgroup (P = 0.014, OR = 1.54). Furthermore, multi-logistic regression analysis revealed a two-way interaction effect of smoking-rs2038540 SNP on HCC risk (OR = 4.20). And MDR analysis consistently demonstrated a SNP-environmental interaction among smoking-drinking-rs2038540 SNP as the best model for predicting HCC risk (P = 0.0107). In our study, no significant association was found between HULC SNPs and the overall survival (P > 0.05), and no significant effect was observed of rs1041279 SNP on lncRNA-HULC expression (P > 0.05). CONCLUSION lncRNA-HULC rs1041279 SNP and the interaction of rs2038540 SNP with environmental factors could enhance HCC risk.
Collapse
|
41
|
Li Y, Ge C, Feng G, Xiao H, Dong J, Zhu C, Jiang M, Cui M, Fan S. Low dose irradiation facilitates hepatocellular carcinoma genesis involving HULC. Mol Carcinog 2018; 57:926-935. [PMID: 29573465 DOI: 10.1002/mc.22813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 03/12/2018] [Accepted: 03/20/2018] [Indexed: 12/27/2022]
Abstract
Irradiation exposure positive correlates with tumor formation, such as breast cancer and lung cancer. However, whether low dose irradiation induces hepatocarcinogenesis and the underlying mechanism remain poorly defined. In the present study, we reported that low dose irradiation facilitated the proliferation of hepatocyte through up-regulating HULC in vitro and in vivo. Low dose irradiation exposure elevated HULC expression level in hepatocyte. Deletion of heightened HULC erased the cells growth accelerated following low dose irradiation exposure. CDKN1, the neighbor gene of HULC, was down-regulated by overexpression of HULC following low dose irradiation exposure via complementary base pairing, resulting in promoting cell cycle process. Thus, our findings provide new insights into the mechanism of low dose irradiation-induced hepatocarcinogenesis through HULC/CDKN1 signaling, and shed light on the potential risk of low dose irradiation for the development of hepatocellular carcinoma in pre-clinical settings.
Collapse
Affiliation(s)
- Yuan Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Chang Ge
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Guoxing Feng
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Huiwen Xiao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jiali Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Changchun Zhu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Mian Jiang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Ming Cui
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| |
Collapse
|
42
|
Jiang Z, Liu H. Metformin inhibits tumorigenesis in HBV-induced hepatocellular carcinoma by suppressing HULC overexpression caused by HBX. J Cell Biochem 2018; 119:4482-4495. [PMID: 29231260 DOI: 10.1002/jcb.26555] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 11/30/2017] [Indexed: 02/06/2023]
Abstract
We aimed to understand whether metformin imposes the inhibitory effect on the HBV-associated tumorigenesis by regulating the HULC and its downstream signaling pathway. Luciferase assay, RT-PCR, and Western-blot, MTT and flow cytometry analysis were performed to understand and the mechanism, by which metformin enhance the inhibitory effect on the HBV-associated tumorigenesis by regulating the HULC and its downstream signaling pathway. HBX promoted viability of three types of cell lines, while metformin inhibited apoptosis of above two cells. ZEB1 was a direct downstream of miR-200a, which was further confirmed that miR-200a reduced luciferase activity of wild-type but not mutant ZEB1 3'UTR, and HULC was bound to region of miR-200a-3p using alignment prediction, but can't affect ZEB1 level. HULC transcription ability, HULC, ZEB1, and p18 levels were much higher in cell treated with HBX, while notably lower in cell treated with metformin, furthermore miR-200a level in cell showed an opposite trend as HULC, ZEB1, and p18 levels. HULC siRNA and miR-200a had no effect on HULC transcription ability, but decreased HULC, ZEB1, and p18 levels, and increased miR-200a expression. HBV (+) HCC +metformin exhibited a higher survival ratio and a lower recurrence rates than HBV (+) HCC group, HBV (-) HCC displayed an even higher survival ratio and an even lower recurrence rates than HBV (+) HCC + metformin groups. This study indicated that metformin imposed inhibitory effect on the HBV-associated HCC by negatively regulating the HULC/p18/miR-200a/ZEB1 signaling pathway.
Collapse
Affiliation(s)
- Zhen Jiang
- Department of Gastroenterology, the First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Haichao Liu
- Department of Hepatopancreatobiliary Surgery, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
43
|
Wang X, Peng J, Wang J, Li M, Wu D, Wu S, Liao J, Dou J. Hepatitis C virus core impacts expression of miR122 and miR204 involved in carcinogenic progression via regulation of TGFBRAP1 and HOTTIP expression. Onco Targets Ther 2018. [PMID: 29535540 PMCID: PMC5841326 DOI: 10.2147/ott.s149254] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Despite the breadth of understanding the noncoding RNAs' function in molecular biology, their functional roles in hepatocellular carcinoma (HCC) is poorly understood. In this study, we investigated the effect of hepatitis C virus (HCV) core upon the expression of noncoding RNAs. Methods The lncRNAs, mRNAs, and circRNAs were employed for identification of HCV core protein gene expression in human Huh7 hepatoma (Huh7) cell line. In data analysis, we applied a threshold that eliminated all genes that were not increased or decreased by at least a 2-fold change in a comparison between transfected and control cells. Hierarchical Clustering and the Kyoto encyclopedia of genes and genome pathway analyses were performed to show the distinguishable lncRNA, mRNAs, and circRNAs expression pattern among samples. Results The array data showed that 4,851 lncRNAs, 4,785 mRNAs, and 823 circRNAs were 2-fold up-regulated but 3,569 lncRNAs, 3,192 mRNAs, and 419 circRNAs were 2-fold down-regulated in Huh 7-core cells. The genes in the enriched set were associated with macromolecule and nucleic acid metabolic processes, DNA damage response and regulation of voltage-gated calcium channel. We identified 10 genes from the selected 14 genes that were higher or lower expression in Huh7-core cells than that of Huh7-vector cells by quantitative real-time polymerase chain reaction. Interestingly, overexpression of miR122 and miR204 partly abrogated the expression of TGFBRAP1 and HOTTIP, and increased the HPCAL1 expression in the predicted carcinogenic pathways. Conclusion Our data suggests that the pathways of miR204-HPCAL1-lncRNAHOTTIP and miR122-TGFBRAP1 were likely involved in the carcinogenic progress due to the presence of HCV core, and that overexpression of miR122 and miR204 might inhibit the HCC progress by down-regulation of TGFBRAP1 and HOTTIP expression.
Collapse
Affiliation(s)
- Xiaoying Wang
- Department of Basis Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, People's Republic of China.,Department of Pathogenic Biology and Immunology, School of Medicine, Southeast University, Nanjing, People's Republic of China
| | - Jiefu Peng
- Department of Pathogenic Biology and Immunology, School of Medicine, Southeast University, Nanjing, People's Republic of China.,Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, People's Republic of China
| | - Jing Wang
- Department of Gynecology & Obstetrics, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, People's Republic of China
| | - Miao Li
- Department of Pathogenic Biology and Immunology, School of Medicine, Southeast University, Nanjing, People's Republic of China
| | - Di Wu
- Department of Pathogenic Biology and Immunology, School of Medicine, Southeast University, Nanjing, People's Republic of China
| | - Songyan Wu
- Department of Pathogenic Biology and Immunology, School of Medicine, Southeast University, Nanjing, People's Republic of China
| | - Jipei Liao
- Department of Pathogenic Biology and Immunology, School of Medicine, Southeast University, Nanjing, People's Republic of China
| | - Jun Dou
- Department of Pathogenic Biology and Immunology, School of Medicine, Southeast University, Nanjing, People's Republic of China
| |
Collapse
|
44
|
The Role of Long Non-Coding RNAs in Hepatocarcinogenesis. Int J Mol Sci 2018; 19:ijms19030682. [PMID: 29495592 PMCID: PMC5877543 DOI: 10.3390/ijms19030682] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 02/23/2018] [Accepted: 02/24/2018] [Indexed: 02/07/2023] Open
Abstract
Whole-transcriptome analyses have revealed that a large proportion of the human genome is transcribed in non-protein-coding transcripts, designated as long non-coding RNAs (lncRNAs). Rather than being “transcriptional noise”, increasing evidence indicates that lncRNAs are key players in the regulation of many biological processes, including transcription, post-translational modification and inhibition and chromatin remodeling. Indeed, lncRNAs are widely dysregulated in human cancers, including hepatocellular carcinoma (HCC). Functional studies are beginning to provide insights into the role of oncogenic and tumor suppressive lncRNAs in the regulation of cell proliferation and motility, as well as oncogenic and metastatic potential in HCC. A better understanding of the molecular mechanisms and the complex network of interactions in which lncRNAs are involved could reveal novel diagnostic and prognostic biomarkers. Crucially, it may provide novel therapeutic opportunities to add to the currently limited number of therapeutic options for HCC patients. In this review, we summarize the current status of the field, with a focus on the best characterized dysregulated lncRNAs in HCC.
Collapse
|
45
|
El Khodiry A, Afify M, El Tayebi HM. Behind the curtain of non-coding RNAs; long non-coding RNAs regulating hepatocarcinogenesis. World J Gastroenterol 2018; 24:549-572. [PMID: 29434445 PMCID: PMC5799857 DOI: 10.3748/wjg.v24.i5.549] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/17/2018] [Accepted: 01/23/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common and aggressive cancers worldwide. HCC is the fifth common malignancy in the world and the second leading cause of cancer death in Asia. Long non-coding RNAs (lncRNAs) are RNAs with a length greater than 200 nucleotides that do not encode proteins. lncRNAs can regulate gene expression and protein synthesis in several ways by interacting with DNA, RNA and proteins in a sequence specific manner. They could regulate cellular and developmental processes through either gene inhibition or gene activation. Many studies have shown that dysregulation of lncRNAs is related to many human diseases such as cardiovascular diseases, genetic disorders, neurological diseases, immune mediated disorders and cancers. However, the study of lncRNAs is challenging as they are poorly conserved between species, their expression levels aren’t as high as that of mRNAs and have great interpatient variations. The study of lncRNAs expression in cancers have been a breakthrough as it unveils potential biomarkers and drug targets for cancer therapy and helps understand the mechanism of pathogenesis. This review discusses many long non-coding RNAs and their contribution in HCC, their role in development, metastasis, and prognosis of HCC and how to regulate and target these lncRNAs as a therapeutic tool in HCC treatment in the future.
Collapse
Affiliation(s)
- Aya El Khodiry
- Genetic Pharmacology Research Group, Clinical Pharmacy Unit, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Menna Afify
- Genetic Pharmacology Research Group, Clinical Pharmacy Unit, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Hend M El Tayebi
- Genetic Pharmacology Research Group, Clinical Pharmacy Unit, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| |
Collapse
|
46
|
Abstract
Self-sustained and synchronized to environmental stimuli, circadian clocks are under genetic and epigenetic regulation. Recent findings have greatly increased our understanding of epigenetic plasticity governed by circadian clock. Thus, the link between circadian clock and epigenetic machinery is reciprocal. Circadian clock can affect epigenetic features including genomic DNA methylation, noncoding RNA, mainly miRNA expression, and histone modifications resulted in their 24-h rhythms. Concomitantly, these epigenetic events can directly modulate cyclic system of transcription and translation of core circadian genes and indirectly clock output genes. Significant findings interlocking circadian clock, epigenetics, and cancer have been revealed, particularly in breast, colorectal, and blood cancers. Aberrant methylation of circadian gene promoter regions and miRNA expression affected circadian gene expression, together with 24-h expression oscillation pace have been frequently observed.
Collapse
|
47
|
Zeng T, Wang D, Chen J, Chen K, Yu G, Chen Q, Liu Y, Yan S, Zhu L, Zhou H, Huang A, Tang H. AF119895 regulates NXF3 expression to promote migration and invasion of hepatocellular carcinoma through an interaction with miR-6508-3p. Exp Cell Res 2017; 363:129-139. [PMID: 29274323 DOI: 10.1016/j.yexcr.2017.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/15/2017] [Accepted: 12/16/2017] [Indexed: 12/25/2022]
Abstract
Various studies revealed that numerous long noncoding RNAs (lncRNAs) have been found dysregulated in HCC and played important role in hepatocarcinogenesis, although the underlying mechanism still remains unclear. Herein, we reported AF119895, a new lncRNA which was identified from microarray and amplified in HCC. Functionally, AF119895 promoted migration and invasion of HCC cells both in vitro and in vivo. Furthermore, we identified that NXF3 was a downstream target of AF119895. NXF3 depletion could decrease HCC cells migration and invasion. In addition, AF119895 could act as an endogenous sponge by binding to miR-6508-3p and reduce miR-6508-3p expression. And miR-6508-3p could regulate NXF3 by interacting with its 3'UTR. These observations collectively demonstrate that AF119895 modulates the repression of NXF3 by binding to miR-6508-3p. Our results outline a novel signaling pathway mediated by AF119895 and suggest its candidacy as a new prognostic biomarker and therapeutic target of HCC.
Collapse
Affiliation(s)
- Tao Zeng
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Dan Wang
- Department of Clinical Laboratory, The People's Hospital of Rongchang, Chongqing, China
| | - Juan Chen
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ke Chen
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Gangfeng Yu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Qiuxu Chen
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yuyang Liu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Shaoyin Yan
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Liying Zhu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Huihao Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ailong Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China.
| | - Hua Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
| |
Collapse
|
48
|
Ma J, Li T, Han X, Yuan H. Knockdown of LncRNA ANRIL suppresses cell proliferation, metastasis, and invasion via regulating miR-122-5p expression in hepatocellular carcinoma. J Cancer Res Clin Oncol 2017; 144:205-214. [PMID: 29127494 DOI: 10.1007/s00432-017-2543-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/07/2017] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Previous studies reported that lncRNA antisense non-coding RNA in the INK4 locus (ANRIL) was upregulated in hepatocellular carcinoma (HCC) tissues and decreased expression of ANRIL could suppress cell proliferation, metastasis, and invasion and induce apoptosis of HCC cells. However, the molecular mechanism of ANRIL involved in HCC tumorigenesis is still unknown. METHODS The expressions of ANRIL and miR-122-5p in HCC tissues and cells were quantified by qRT-PCR. MTT assay, colony formation assay, wound healing assay, and transwell invasion assay were performed to evaluate cell growth, metastasis, and invasion, respectively. RNA immunoprecipitation (RIP) assay and luciferase reporter assay were performed to determine whether ANRIL could directly bind to miR-122-5p in HCC cells. Xenograft tumor experiment was conducted to confirm the biological role and underlying mechanism of ANRIL in vivo. RESULTS The results showed that ANRIL was upregulated and miR-122-5p was downregulated in HCC tissues and cells. ANRIL was negatively correlated with miR-122-5p expression in HCC tissues. Knockdown of ANRIL or miR-122-5p overexpression suppressed HCC cell viability, colony formation ability, metastasis, and invasion. ANRIL was demonstrated to directly bind to miR-122-5p and inhibit its expression. Forced expression of ANRIL abolished the inhibitory effect of miR-122-5p overexpression on HCC progression. In vivo experiment demonstrated that ANRIL knockdown impeded tumor growth in vivo and increased miR-122-5p expression. CONCLUSION Our finding suggested that knockdown of ANRIL suppressed cell proliferation, metastasis and invasion via regulating miR-122-5p expression in HCC, illustrating the underlying mechanism of the oncogenic role of ANRIL in HCC.
Collapse
Affiliation(s)
- Ji Ma
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Νo. 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Tengfei Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Νo. 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Νo. 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China.
| | - Huifeng Yuan
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Νo. 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| |
Collapse
|
49
|
Epigenetic reprogramming in liver fibrosis and cancer. Adv Drug Deliv Rev 2017; 121:124-132. [PMID: 29079534 PMCID: PMC5716427 DOI: 10.1016/j.addr.2017.10.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 10/10/2017] [Accepted: 10/17/2017] [Indexed: 12/18/2022]
Abstract
Novel insights into the epigenetic control of chronic liver diseases are now emerging. Recent advances in our understanding of the critical roles of DNA methylation, histone modifications and ncRNA may now be exploited to improve management of fibrosis/cirrhosis and cancer. Furthermore, improved technologies for the detection of epigenetic markers from patients' blood and tissues will vastly improve diagnosis, treatment options and prognostic tracking. The aim of this review is to present recent findings from the field of liver epigenetics and to explore their potential for translation into therapeutics to prevent disease promoting epigenome reprogramming and reverse epigenetic changes.
Collapse
|
50
|
Tang WG, Hu B, Sun HX, Sun QM, Sun C, Fu PY, Yang ZF, Zhang X, Zhou CH, Fan J, Ren N, Xu Y. Long non-coding RNA00364 represses hepatocellular carcinoma cell proliferation via modulating p-STAT3-IFIT2 signaling axis. Oncotarget 2017; 8:102006-102019. [PMID: 29254221 PMCID: PMC5731931 DOI: 10.18632/oncotarget.22039] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 08/28/2017] [Indexed: 12/24/2022] Open
Abstract
The effects of long non-coding RNAs (lncRNAs) on hepatocellular carcinoma (HCC) remain largely unclear. In this study, we identified an interferon (IFN)-γ-induced LncRNA, LncRNA00364, in HCC by microarray. LncRNA00364 displays lower expression in HCC tumor samples compared to paired normal controls. Overexpression of LncRNA00364 inhibits cell proliferation, G1/S cell cycle progression and promotes apoptosis in HCC cell lines. Consistently, LncRNA00364 overexpression leads to decreased HCC tumor formation in vivo. Mechanistically, LncRNA00364 specifically binds with STAT3, resulting in inhibition of STAT3 phosphorylation and therefore leads to upregulation of IFIT2. In a clinical setting, LncRNA00364 shows an independent prognostic indicator for overall survival and cumulative recurrence in HCC patients, and correlates with IFIT2. Therefore, our study provides new insights into a novel therapeutic avenue targeting the LncRNA00364 signaling axis in HCC.
Collapse
Affiliation(s)
- Wei-Guo Tang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China.,Department of Surgery, Minhang Branch of Zhongshan Hospital, Fudan University, Shanghai 201199, P. R. China.,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai 201199, P. R. China
| | - Bo Hu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China
| | - Hai-Xiang Sun
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China
| | - Qi-Man Sun
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China
| | - Chao Sun
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China
| | - Pei-Yao Fu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China
| | - Zhang-Fu Yang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China
| | - Xin Zhang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China
| | - Chen-Hao Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China
| | - Jia Fan
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China
| | - Ning Ren
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China.,Department of Surgery, Minhang Branch of Zhongshan Hospital, Fudan University, Shanghai 201199, P. R. China.,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai 201199, P. R. China
| | - Yang Xu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P. R. China
| |
Collapse
|