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Zhu LR, Zheng W, Gao Q, Chen T, Pan ZB, Cui W, Cai M, Fang H. Epigenetics and genetics of hepatoblastoma: Linkage and treatment. Front Genet 2022; 13:1070971. [DOI: 10.3389/fgene.2022.1070971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022] Open
Abstract
Hepatoblastoma is a malignant embryonal tumor with multiple differentiation modes and is the clearest liver malignancy in children. However, little is known about genetic and epigenetic events in Hepatoblastoma. Increased research has recently demonstrated, unique genetic and epigenetic events in Hepatoblastoma, providing insights into its origin and precise treatment. Some genetic disorders and congenital factors are associated with the risk of Hepatoblastoma development, such as the Beckwith-Wiedemann syndrome, Familial Adenomatous polyposis, and Hemihypertrophy. Epigenetic modifications such as DNA modifications, histone modifications, and non-coding RNA regulation are also essential in the development of Hepatoblastoma. Herein, we reviewed genetic and epigenetic events in Hepatoblastoma, focusing on the relationship between these events and cancer susceptibility, tumor growth, and prognosis. By deciphering the genetic and epigenetic associations in Hepatoblastoma, tumor pathogenesis can be clarified, and guide the development of new anti-cancer drugs and prevention strategies.
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Lei S, Cao W, Zeng Z, Zhang Z, Jin B, Tian Q, Wu Y, Zhang T, Li D, Hu C, Lan J, Zhang J, Chen T. JUND/linc00976 promotes cholangiocarcinoma progression and metastasis, inhibits ferroptosis by regulating the miR-3202/GPX4 axis. Cell Death Dis 2022; 13:967. [PMID: 36400758 PMCID: PMC9674662 DOI: 10.1038/s41419-022-05412-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/20/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a novel class of noncoding RNAs that have emerged as critical regulators and biomarkers in various cancers. Nevertheless, the expression profile and mechanistic function of lncRNAs in cholangiocarcinoma (CCA) remain unclear. Herein, we examined the expression levels of linc00976 in clinical specimens and cell lines using reverse transcription-quantitative PCR. In total, 50 patients with CCA were enrolled to analyze the correlation between linc00976 expression and clinical characteristics of CCA. Loss- and gain-of-function experiments were performed to investigate the biological effects of linc00976 on proliferation, ferroptosis, migration, and invasion of CCA cells in vitro and in vivo. In situ hybridization, RNA immunoprecipitation, bioinformatic databases, RNA pull-down assay, a dual-luciferase reporter assay, mRNA sequencing, chromatin immunoprecipitation-PCR, and rescue experiments were performed to elucidate the underlying mechanisms of linc00976-induced competitive endogenous RNA regulatory networks. We characterized a novel and abundant lncRNA, linc00976, that functions as a pro-oncogenic regulator of CCA progression. Compared with normal controls, linc00976 was dramatically upregulated in CCA tissue samples and cell lines. Patients with CCA exhibiting high linc00976 expression had a highly advanced clinical stage, substantial lymph node metastasis, and poor overall survival. Knockdown of linc00976 significantly repressed proliferation and metastasis and promoted ferroptosis of CCA cells both in vitro and in vivo, whereas linc00976 overexpression exerted the opposite effect. Mechanistically, linc00976 competitively interacted with miR-3202 to upregulate GPX4 expression, thus contributing to the malignant biological behavior of CCA cells. Moreover, we demonstrated that JUND specifically interacts with the linc00976 promoter and activates linc00976 transcription. Accordingly, JUND promotes linc00976 transcription, and linc00976 plays a crucial role in accelerating CCA tumorigenesis and metastasis and inhibiting ferroptosis by modulating the miR-3202/GPX4 axis. These findings suggest that targeting linc00976 may afford a promising therapeutic strategy for patients with CCA.
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Affiliation(s)
- Shan Lei
- grid.413458.f0000 0000 9330 9891Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550009 Guizhou China ,grid.413458.f0000 0000 9330 9891Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Wenpeng Cao
- grid.413458.f0000 0000 9330 9891Department of Anatomy, School of Basic Medicine, Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Zhirui Zeng
- grid.413458.f0000 0000 9330 9891Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550009 Guizhou China ,grid.413458.f0000 0000 9330 9891Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Zhixue Zhang
- grid.413458.f0000 0000 9330 9891Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550009 Guizhou China ,grid.413458.f0000 0000 9330 9891Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Bangming Jin
- grid.413458.f0000 0000 9330 9891Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550009 Guizhou China ,grid.413458.f0000 0000 9330 9891Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Qianting Tian
- grid.413458.f0000 0000 9330 9891Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Yingming Wu
- grid.413458.f0000 0000 9330 9891Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550009 Guizhou China ,grid.413458.f0000 0000 9330 9891Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Tuo Zhang
- grid.413458.f0000 0000 9330 9891Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550009 Guizhou China ,grid.413458.f0000 0000 9330 9891Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Dahuan Li
- grid.413458.f0000 0000 9330 9891Digestive Endoscopy Center, the Affiliated of Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Chujiao Hu
- grid.413458.f0000 0000 9330 9891State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Jinzhi Lan
- grid.413458.f0000 0000 9330 9891Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Jinjuan Zhang
- grid.413458.f0000 0000 9330 9891Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, 550009 Guizhou China ,grid.413458.f0000 0000 9330 9891The Functional Science laboratory, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550009 Guizhou China
| | - Tengxiang Chen
- grid.413458.f0000 0000 9330 9891Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550009 Guizhou China ,grid.413458.f0000 0000 9330 9891Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, 550009 Guizhou China
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Li X, Feng C, Peng S. Epigenetics alternation in lung fibrosis and lung cancer. Front Cell Dev Biol 2022; 10:1060201. [PMID: 36420141 PMCID: PMC9676258 DOI: 10.3389/fcell.2022.1060201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/20/2022] [Indexed: 09/10/2023] Open
Abstract
Respiratory disease including interstitial lung diseases (ILDs) and lung cancer is a group of devastating diseases that linked with increased morbidity and healthcare burden. However, respiratory diseases cannot be fully explained by the alternation of genetic information. Genetic studies described that epigenetic mechanisms also participate to transmit genetic information. Recently, many studies demonstrated the role of altered epigenetic modification in the pathogenesis of lung cancer and pulmonary fibrosis. Due to lacking effective medication, the underlying pathophysiological processes and causal relationships of lung diseases with epigenetic mechanisms still need to be better understood. Our present review provided a systematic revision of current knowledge concerning diverse epigenetic aberrations in major lung diseases, with special emphasis on DNA methylation, histone modifications, lncRNAs profiles, telomere patterns, as well as chromatin-remodelling complexes. We believed that a new target therapy for lung disease based on findings of the involved epigenetic pathway is a promising future direction.
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Affiliation(s)
- Xueren Li
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin, China
- Tianjin Institute of Respiratory Diseases, Tianjin, China
| | - Chunjing Feng
- The Institute Includes H&B(Tianjin) Stem Cell Research Institute, Tianjin, China
| | - Shouchun Peng
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin, China
- Tianjin Institute of Respiratory Diseases, Tianjin, China
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154
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Zhou S, Zhang W, Cao W, Jin Q, Jiang X, Jiang X, Yang Y, Yao H, Chen G, Gao W, Zhu Y, Qi J, Tong Z. Development and validation of an autophagy-related long non-coding RNA prognostic signature for cervical squamous cell carcinoma and endocervical adenocarcinoma. Front Oncol 2022; 12:1049773. [DOI: 10.3389/fonc.2022.1049773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
BackgroundIn this study, we aimed to investigate the signature of the autophagy-related lncRNAs (ARLs) and perform integrated analysis with immune infiltration in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC).Methods and resultsThe UCSC Xena and HADb databases provided the corresponding data. The ARLs were selected via constructing a co-expression network of autophagy-related genes (ARGs) and lncRNAs. Univariate Cox regression analysis combined with LASSO regression and multivariate Cox regression analysis were utilized to screen lncRNAs. The ARL risk signature was established by Cox regression and tested if it was an independent element bound up with patient prognosis. We used the xCell algorithm and ssGSEA to clarify the pertinence between immune infiltration and the expression of ARLs. Finally, we predicted the sensitivity of drug treatment as well as the immune response. Results indicated that the three prognostic ARLs (SMURF2P1, MIR9-3HG, and AC005332.4) possessed significant diversity and constituted the ARL signature. Risk score was an individual element (HR = 2.82, 95% CI = 1.87–4.30; p < 0.001). Immune infiltration analysis revealed significant increases in central memory CD8+ T cells, endothelial cells, CD8+ naive T cells, and preadipocytes in the high-risk group (p < 0.05). There were 10 therapeutic agents that varied significantly in their estimated half-maximal inhibitory concentrations in the two groups. According to the experimental validation, we found that SMURF2P1 belongs to the co-stimulatory genes and might assume greater importance in the development of cervical adenocarcinoma. MIR9-3HG and AC005332.4 belonged to the tumor-suppressor genes and they may play a more positive role in cervical squamous cell carcinoma.ConclusionsThis research explored and validated a novel signature of the ARLs, which can be applied to forecast the prognosis of patients with CESC and is closely associated with immune infiltration.
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155
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A 66 amino acid micro-peptide encoded by long non-coding RNA RP11-119F7.5 was identified in hepatocellular carcinoma. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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156
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Chen K, Feng D, Han P. Identification of prognostic cellular senescence related-lncRNAs in bladder cancer via bioinformatics analysis. Asian J Surg 2022; 46:2096-2097. [PMID: 36411162 DOI: 10.1016/j.asjsur.2022.11.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022] Open
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He S, Shi J, Zhou H, Li Q, Wu L. Lnc-ABCA12-8 confers acquired resistance to gefitinib in non-small cell lung cancer by regulating the alternative splicing of fibronectin 1 in the IIICS region. Cancer Gene Ther 2022; 29:1686-1696. [PMID: 35701616 DOI: 10.1038/s41417-022-00483-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/05/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023]
Abstract
Acquired resistance to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs), such as gefitinib, has dramatically impaired the clinical outcomes in non-small cell lung cancer (NSCLC) patients, but the mechanisms are still unclear in substantial cases. In our previous study, we demonstrated that a novel long non-coding RNA (lncRNA), lnc-ABCA12-8, was overexpressed in gefitinib-resistant NSCLC cells, but the exact function is unknown. In this study, we confirmed that lnc-ABCA12-8 was significantly upregulated both in NSCLC cell lines and the plasma samples of NSCLC patients with acquired resistance to gefitinib. Downregulation of lnc-ABCA12-8 could reverse gefitinib resistance both in vitro and in vivo. Mechanistically, lnc-ABCA12-8 interacted with alternative splicing factor/splicing factor 2 (ASF/SF2), promoted the binding of ASF/SF2 to the IIICS exon of fibronectin 1 (FN1) gene and enhanced the IIICS region inclusion during fibronectin 1 (FN1) alternative splicing, resulting in the upregulation of entire IIICS region, and enhanced cell proliferation, migration, invasion, and adhesion. Taken together, our study suggest that lnc-ABCA12-8 is involved in the acquired resistance to gefitinib, and may be a novel biomarker and therapeutic target for monitoring and overcoming gefitinib resistance in NSCLC.
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Affiliation(s)
- Shuai He
- Institute of Life Sciences, Chongqing Medical University, 400016, Chongqing, PR China.,Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, PR China
| | - Jingjing Shi
- Institute of Life Sciences, Chongqing Medical University, 400016, Chongqing, PR China
| | - HongHao Zhou
- Institute of Life Sciences, Chongqing Medical University, 400016, Chongqing, PR China.,Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Central South University, Changsha, PR China
| | - Qingling Li
- Institute of Life Sciences, Chongqing Medical University, 400016, Chongqing, PR China. .,Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, PR China.
| | - Lanxiang Wu
- Institute of Life Sciences, Chongqing Medical University, 400016, Chongqing, PR China. .,Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, PR China.
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158
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Liu Y, Lu F, Li X, Yang Y, Yang J. The silencing of lnc-NONHSAT071210 suppresses the proliferation, fibrosis, migration, and invasion of TGFβ1-treated lung epithelial cells. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1239. [PMID: 36544683 PMCID: PMC9761174 DOI: 10.21037/atm-22-5223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/15/2022] [Indexed: 11/30/2022]
Abstract
Background Pulmonary fibrosis, which is a frequent manifestation of connective tissue disease (CTD), is a leading cause of morbidity and mortality. However, the role of long non-coding ribonucleic acids (lncRNAs) in CTD-associated pulmonary fibrosis requires clarification. This study sought to examine the effects of lnc-NONHSAT071210 on the phenotypes of transforming growth factor β1 (TGFβ1)-treated lung epithelial cells. Methods The GeneChip was used to identify differentially expressed lncRNAs in CTD-associated pulmonary fibrosis patients. After lnc-NONHSAT071210 was knocked down in the TGFβ1-challenged lung epithelial cells, cell viability, cell cycle, migration, and invasion were estimated by Cell Counting Kit-8 assays, a flow cytometry analysis, wound-healing assays, and transwell assays, respectively. The expression and levels of the fibrosis-associated factors were examined by enzyme-linked immunosorbent assays, RT-qPCR, and western blots. Results The expression of the top 7 most significantly upregulated lncRNAs in the CTD-associated pulmonary fibrosis patients was depicted in a heat map and examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The results showed that the expression of lnc-NONHSAT071210 was significantly increased in the tissues of the CTD-associated pulmonary fibrosis patients (P<0.001). The silencing of Lnc-NONHSAT071210 suppressed proliferation, migration, and invasion in the TGFβ1-exposed alveolar epithelial cells (P<0.001). Conclusions Thus, lnc-NONHSAT071210 expression was increased in the tissues of the CTD-associated pulmonary fibrosis patients and TGFβ1-treated lung epithelial cells, and TGFβ1-induced lung epithelial cell injury was alleviated by impeding the expression of lnc-NONHSAT071210.
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Affiliation(s)
- Yuan Liu
- Department of Rheumatology, Liuzhou People’s Hospital, Guangxi Medical University, Liuzhou, China;,Department of Rheumatology, First Affiliated Hospital of Baotou Medical College, Baotou, China
| | - Fuai Lu
- Department of Rheumatology, First Affiliated Hospital of Baotou Medical College, Baotou, China
| | - Xiaofen Li
- Department of Rheumatology, Liuzhou People’s Hospital, Guangxi Medical University, Liuzhou, China
| | - Youguo Yang
- Department of Rheumatology, Liuzhou People’s Hospital, Guangxi Medical University, Liuzhou, China
| | - Jianqing Yang
- Department of General Surgery, Liuzhou People’s Hospital, Guangxi Medical University, Liuzhou, China
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159
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Liu Y, Yang J, Ke RS, Wu L, Hong Z, Guo P, Feng L, Li Z. LINC02875 Upregulation Contributed to Poor Prognosis for the Hepatocellular Carcinoma and Progression for the Cancerous Cells. Horm Metab Res 2022; 54:760-767. [PMID: 36055279 DOI: 10.1055/a-1913-8223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The prognostic implications and physiological effect of LINC02875 are unknown in hepatocellular carcinoma (HCC). We sought to examine the prognostic value of LINC02875 in HCC and assessed its role in HCC cellular function. LINC02875 expression was evaluated by RT-qPCR in HCC specimens and cell lines. LINC02875 expression was subjected to assess the correlation with clinical parameters by Chi-squared test and overall survival by Kaplan - Meier curve and Cox regression analysis. The effects of LINC02875 on the biological characteristics of HCC cells were studied by MTS and Transwell assay. LINC02875 was high-expressed in HCC, and this was associated with unfavorable clinical features and poor prognosis of HCC, especially HBV-related HCC. Knockdown of LINC02875 inhibited the proliferation, migration, and invasion of HCC cells. miR-485-5p was a downstream microRNA of LINC02875. LINC02875 affects the prognosis of HCC patients, especially HBV-related ones. LINC02875 represents a suitable therapeutic target for HCC.
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Affiliation(s)
- Yujian Liu
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jingrui Yang
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Rui-Sheng Ke
- Department of General Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Lupeng Wu
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Zaifa Hong
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Ping Guo
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Liuxing Feng
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Zhimin Li
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
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160
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Zhu W, Tan L, Ma T, Yin Z, Gao J. Long noncoding RNA SNHG8 promotes chemoresistance in gastric cancer via binding with hnRNPA1 and stabilizing TROY expression. Dig Liver Dis 2022; 54:1573-1582. [PMID: 35354542 DOI: 10.1016/j.dld.2022.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 12/30/2022]
Abstract
AIMS To determine SNHG8's function and potential mechanisms in gastric cancer (GC) chemoresistance. METHODS We assessed SNHG8 expression in GC cell lines, GC/CDDP cell lines (cell lines treated with cisplatin), and 42 GC tissues and SNHG8 levels in the lncRNA microarray analysis of AGS/CDDP and AGS cell lines. We also examined GC cell viability in vivo and in vitro and its apoptosis level with Flow cytometry assays. SNHG8 was localized in subcells using fluorescence in situ hybridization (FISH) and cell fraction assays, hnRNPA1's link to SNHG8 was determined utilizing RNA immunoprecipitation (RIP) and FISH assays, gene expression profiles were assessed employing RNA transcriptome sequencing, and hnRNPA1's relationship with TROY was ascertained with the RIP assay. RESULTS SNHG8 increased significantly in GC cell lines and GC tissues. However, a decrease in its expression promoted sensitivity to chemotherapy and inhibited DNA damage repair in vitro and in vivo. SNHG8 appeared to regulate TROY expression via linking with hnRNPA1. Reducing TROY levels considerably stimulated GC cell chemosensitivity, whereas heightening them partially rescued the rate of chemoresistance caused by downregulating SNHG8. CONCLUSION In summary, the "SNHG8/hnRNPA1-TROY" axis is crucial to GC chemoresistance.
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Affiliation(s)
- Wenzhong Zhu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lulu Tan
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Tiantian Ma
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhijie Yin
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jinbo Gao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Yue J, Miao P, Li L, Yan R, Dong WF, Mei Q. Injectable Carbon Dots-Based Hydrogel for Combined Photothermal Therapy and Photodynamic Therapy of Cancer. ACS APPLIED MATERIALS & INTERFACES 2022; 14:49582-49591. [PMID: 36286204 DOI: 10.1021/acsami.2c15428] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Hydrogel has been widely used in modern biotherapeutics due to its excellent biocompatibility, degradability, and high drug loading capacity. Among them, the construction of a phototherapy system including photosensitizer and hydrogel has aroused great interest in tumor therapy. Unfortunately, complex modifications are necessary to integrate different photosensitizers into the hydrogel. In this work, an injectable hydrogel was proposed by the Schiff base reaction between HA-CHO and carbon dots (CDs), which can realize PTT and PTT simultaneously. Notably, the CDs with rich -NH2 can be used not only as a photosensitizer but also as an efficient cross-linking agent for the Schiff base reaction to form a hydrogel network. The CD@Hydrogel with outstanding biosafety showed a high antitumor effect after 660 nm laser irradiation in in vitro and in vivo experiments. In summary, the CD@Hydrogel can not only realize PTT and PDT synergistic treatment under one light source but also act as a cross-linking agent to react with HA-CHO to form hydrogel, which is simple and efficient, providing a new strategy for cancer phototherapy.
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Affiliation(s)
- Juan Yue
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- Department of Clinical Laboratory, Suzhou Science & Technology Town Hospital, Suzhou 215153, China
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China
| | - Peng Miao
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China
| | - Li Li
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China
| | - Ruhong Yan
- Department of Clinical Laboratory, Suzhou Science & Technology Town Hospital, Suzhou 215153, China
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China
| | - Wen-Fei Dong
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China
| | - Qian Mei
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China
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Mo M, Ma X, Luo Y, Tan C, Liu B, Tang P, Liao Q, Liu S, Yu H, Huang D, Zeng X, Qiu X. Liver-specific lncRNA FAM99A may be a tumor suppressor and promising prognostic biomarker in hepatocellular carcinoma. BMC Cancer 2022; 22:1098. [PMID: 36289466 PMCID: PMC9609286 DOI: 10.1186/s12885-022-10186-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/13/2022] [Indexed: 12/17/2022] Open
Abstract
Background Increasing evidence shows that liver-specific long non-coding RNAs (lncRNAs) play important roles in the development of hepatocellular carcinoma (HCC). We identified a novel liver-specific lncRNA, FAM99A, and examined its clinical significance and biological functions in HCC. Methods The expression level and clinical value of FAM99A in HCC were examined using The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO) databases, and were further verified using quantitative real-time polymerase chain reaction (qRT–PCR) in our HCC cohort. Univariate and multivariate Cox proportional hazards regression models were also applied to identify independent prognostic indicators for HCC patients. Cell counting kit-8, colony formation, and Transwell assays were performed to evaluate the effects of FAM99A on the proliferation, migration, and invasion abilities of HCC cells in vitro. A subcutaneous xenograft tumor model was implemented to determine the effect of FAM99A on the tumor growth of HCC cells in vivo. RNA pull-down and mass spectrometry assays were performed to reveal the potential molecular mechanisms of FAM99A in HCC. Results The three public online databases and qRT–PCR data showed that FAM99A was frequently downregulated in HCC tissues and inversely correlated with microvascular invasion and advanced histological grade of HCC patients. Kaplan–Meier survival analysis indicated that decreased FAM99A was significantly associated with poor overall survival of HCC patients based on TCGA database (P = 0.040), ICGC data portal (P < 0.001), and our HCC cohort (P = 0.010). A multivariate Cox proportional hazards regression model based on our HCC cohort suggested that FAM99A was an independent prognostic factor of overall survival for HCC patients (hazard ratio: 0.425, P = 0.039). Upregulation of FAM99A suppressed the proliferation, colony formation, migration, and invasion capacities of HCC cells in vitro, and knockdown of FAM99A had the opposite effects. A subcutaneous xenograft tumor model demonstrated that overexpression of FAM99A significantly inhibited the tumor growth of HCC cells in vivo. Seven tumor-related proteins (PCBP1, SRSF5, SRSF6, YBX1, IGF2BP2, HNRNPK, and HNRNPL) were recognized as possible FAM99A-binding proteins by the RNA pull-down and mass spectrometry assays. Conclusion Our results suggest that FAM99A exerts cancer-inhibiting effects on HCC progression, and it may be a promising prognostic indicator for HCC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-10186-2.
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Affiliation(s)
- Meile Mo
- grid.256607.00000 0004 1798 2653Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi 530021 P.R. China
| | - Xiaoyun Ma
- grid.27255.370000 0004 1761 1174Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012 P.R. China
| | - Yihuan Luo
- grid.412594.f0000 0004 1757 2961Department of Acute Care Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021 P.R. China
| | - Chao Tan
- grid.443385.d0000 0004 1798 9548Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, Guangxi 541004 P.R. China
| | - Bihu Liu
- grid.256607.00000 0004 1798 2653Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi 530021 P.R. China
| | - Peng Tang
- grid.256607.00000 0004 1798 2653Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi 530021 P.R. China
| | - Qian Liao
- grid.256607.00000 0004 1798 2653Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi 530021 P.R. China
| | - Shun Liu
- grid.256607.00000 0004 1798 2653Department of Maternal, Child and Adolescent Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi 530021 P.R. China
| | - Hongping Yu
- grid.256607.00000 0004 1798 2653Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021 P.R. China
| | - Dongping Huang
- grid.256607.00000 0004 1798 2653Department of Sanitary Chemistry, School of Public Health, Guangxi Medical University, Nanning, Guangxi 530021 P.R. China
| | - Xiaoyun Zeng
- grid.256607.00000 0004 1798 2653Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi 530021 P.R. China
| | - Xiaoqiang Qiu
- grid.256607.00000 0004 1798 2653Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi 530021 P.R. China
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Bao Q, Zheng Q, Wang S, Tang W, Zhang B. LncRNA HOTAIR regulates cell invasion and migration in endometriosis through miR-519b-3p/PRRG4 pathway. Front Oncol 2022; 12:953055. [PMID: 36338672 PMCID: PMC9634122 DOI: 10.3389/fonc.2022.953055] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/10/2022] [Indexed: 11/23/2022] Open
Abstract
Endometriosis is a common benign disease in gynecology and has malignant biological behaviors, such as hyperplasia, invasion, metastasis, and recurrence. However, the pathogenesis of endometriosis remains unclear. The present study aimed to investigate whether LncRNA HOTAIR regulates cell invasion and migration in endometriosis by regulating the miR-519b-3p/PRRG4 pathway. The qRT-PCR results showed that the average relative expression of LncRNA HOTAIR was much higher in ectopic endometrial tissues than in eutopic endometrial tissues. Scratch and transwell assays showed that the cell migration and invasion ability of LncRNA HOTAIR overexpression group was significantly higher than those in the control group. Conversely, the LncRNA HOTAIR knockdown group showed the opposite results. Bioinformatics analysis suggested that the downstream target genes of LncRNA HOTAIR were miR-519b-3p and Prrg4. Knockdown of LncRNA HOTAIR can reduce the up-regulation of Prrg4 by miR-519b-3p and then inhibit the invasion and migration ability of endometrial stromal cells. In Conclusion, LncRNA HOTAIR can regulate the ability of invasion and migration of endometrial stromal cells, and its mechanism is proved by regulating the miR-519b-3p/PRRG4 pathway.
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Affiliation(s)
- Qiufang Bao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Obstetrics and Gynecology, The First Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Qiaomei Zheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Obstetrics and Gynecology, The First Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Shaoyu Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Obstetrics and Gynecology, The First Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Wenlu Tang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Obstetrics and Gynecology, The First Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Bin Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Obstetrics and Gynecology, The First Clinical College of Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Bin Zhang,
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Rahmani F, Safavi P, Fathollahpour A, Tanhaye Kalate Sabz F, Tajzadeh P, Arefnezhad M, Ferns GA, Hassanian SM, Avan A. The interplay between non-coding RNAs and Wnt/ß-catenin signaling pathway in urinary tract cancers: from tumorigenesis to metastasis. EXCLI JOURNAL 2022; 21:1273-1284. [PMID: 36483915 PMCID: PMC9727268 DOI: 10.17179/excli2022-5348] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/26/2022] [Indexed: 01/13/2023]
Abstract
Non-coding RNAs (ncRNAs) are emerging as important regulators in various pathological conditions including tumorigenesis, metastasis, and drug resistance in human cancers. Oncogenic or tumor suppressor ncRNAs exert prominent effects on cell proliferation, migration and invasion in cancer cells through modulating various signaling pathways including Wnt/β-catenin. Upregulation of the oncogenic Wnt/β-catenin pathway was reported to be implicated in multiple human cancers including breast, liver, colorectal, and urothelial cancers. Therefore, identifying interactions between ncRNAs and canonical Wnt signaling components may represent novel therapeutic targets for better treatment and management of cancer. In this review, we summarized the recent findings about miRNA/lncRNA-dependent mechanisms that regulate Wnt/β-catenin signaling involved in tumorigenesis and metastasis of urinary tract cancers.
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Affiliation(s)
- Farzad Rahmani
- Kashmar School of Nursing, Mashhad University of Medical Sciences, Mashhad, Iran,Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Pegah Safavi
- Department of Medical Radiation, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | | | - Parastoo Tajzadeh
- Kashmar School of Nursing, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohsen Arefnezhad
- Kashmar School of Nursing, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A. Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex, UK
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,*To whom correspondence should be addressed: Amir Avan, Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran, E-mail:
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165
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The lncRNA KIF9-AS1 Accelerates Hepatocellular Carcinoma Growth by Recruiting DNMT1 to Promote RAI2 DNA Methylation. JOURNAL OF ONCOLOGY 2022; 2022:3888798. [PMID: 36276278 PMCID: PMC9584731 DOI: 10.1155/2022/3888798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/29/2022] [Indexed: 11/18/2022]
Abstract
Background Hepatocellular carcinoma (HCC) is a very common malignant tumor. Long noncoding RNAs (lncRNAs) enable discoveries of new therapeutic tumor targets. We aimed to study the role and potential regulatory mechanisms of the lncRNA KIF9-AS1 in HCC. Methods CCK-8, scratch assay, and flow cytometry were used to detect cell proliferation, migration, and apoptosis, respectively. Bax, Bcl-2, ERK, and pERK expression were measured by western blotting. StarBase predicted KIF9-AS1 expression in HCC and paracancerous tissues. RPISeq predicted the interaction score of KIF9-AS1 and DNMT1, and MethyPrimer revealed the CpG island distribution in the RAI2 promoter. MSP was performed to measure RAI2 methylation. RIP and ChIP were performed to examine lncRNA KIF9-AS1, DNMT1, and RAI2 interactions. Finally, the effect of KIF9-AS1 knockdown on HCC was verified with nude mice. Results We found that KIF9-AS1 expression was increased in HCC tissues. KIF9-AS1 knockdown inhibited the proliferation and migration, and facilitated the apoptosis of HCC cells. lncRNA KIF9-AS1-mediated RAI2 expression led to DNMT1 recruitment and regulated RAI2 DNA methylation. RAI2 overexpression inhibited the proliferation and migration and promoted the apoptosis of HCC cells. KIF9-AS1 knockdown inhibited subcutaneous tumor formation in vivo. Conclusion This study shows that KIF9-AS1 accelerates HCC growth by inducing DNMT1 promotion of RAI2 DNA methylation.
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Lu R, Li Z, Yin S. Constructing a Ferroptosis-related Long Non-coding RNA Signature to Predict the Prognostic of Head and Neck Squamous Cell Carcinoma Patients by Bioinformatic Analysis. Biochem Genet 2022; 60:1825-1844. [PMID: 35098409 PMCID: PMC9470613 DOI: 10.1007/s10528-021-10176-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 12/06/2021] [Indexed: 12/19/2022]
Abstract
Ferroptosis is a novel discovered iron-dependent mode of regulated cell death (RCD) which characterized non-apoptosis. Researches have shown the effect of ferroptosis in the biological activities of tumors. But there is no relevant study showing the relationship between ferroptosis-related genes and head and neck squamous cell carcinoma (HNSCC). In this study, we paid attention to several ferroptosis-related lncRNAs in head and neck squamous cell carcinoma and its clinical features. HNSCC data were obtained from The Cancer Genome Atlas (TCGA) database. Ferroptosis-related lncRNAs were selected by the coexpression network. Then, we identified prognostic ferroptosis-related lncRNAs in HNSCC patients and constructed a ferroptosis-related lncRNAs signature by Lasso cox regression. Besides, GSEA analysis was performed to explore the functional enrichment of ferroptosis-related lncRNAs. Nine ferroptosis-related lncRNAs (AC004687.1, AL450992.2, AC010894.2, AL451085.2, AC104083.1, LIPE-AS1, AC108010.1, CTBP1-DT, and PTCSC2) were identified to have the independent prognostic value in HNSCC patients and the ferroptosis-related lncRNAs signature was constructed based on these nine genes. According to the risk score of the signature, the high-risk group had shorter overall survival (OS) compared with the low-risk group. Risk score showed to be an independent factor for the patients with HNSCC. Additionally, the nomogram was generated and the nine lncRNAs were mainly enriched in phagocytosis, metabolism, and chemokine signaling pathways. The ferroptosis-related lncRNA signature has effects on the prognostic prediction of patients with HNSCC which may serve as potential therapeutic targets for patients with HNSCC.
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Affiliation(s)
- Rui Lu
- Department of Otorhinolaryngology Head and Neck Surgery, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuhan, 430071, People's Republic of China
| | - Zhiyong Li
- Department of Otorhinolaryngology Head and Neck Surgery, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuhan, 430071, People's Republic of China.
| | - Shucheng Yin
- Department of Otorhinolaryngology Head and Neck Surgery, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuhan, 430071, People's Republic of China.
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Jiang F, Li S, Wang X, Deng Y, Peng S. DPP10-AS1-Mediated Downregulation of MicroRNA-324-3p Is Conducive to the Malignancy of Pancreatic Cancer by Enhancing CLDN3 Expression. Pancreas 2022; 51:1201-1210. [PMID: 37078946 DOI: 10.1097/mpa.0000000000002164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
OBJECTIVES Network of long noncoding RNA-microRNA (miRNA)-mRNA is becoming increasingly pivotal roles in carcinogenesis mechanism. Herein, we aim to delineate the mechanistic understanding of dipeptidyl peptidase like 10-antisense RNA 1 (DPP10-AS1)/miRNA-324-3p/claudin 3 (CLDN3) axis in the malignancy of pancreatic cancer (PC). METHODS Microarray profiling and other bioinformatics methods were adopted to predict differentially expressed long noncoding RNA-miRNA-mRNA in PC, followed by verification of expression of DPP10-AS1, microRNA-324-3p (miR-324-3p), and CLDN3 in PC cells. The relationship among DPP10-AS1, miR-324-3p, and CLDN3 were further assessed. The PC cell invasion and migration were evaluated by scratch test and transwell assay. Tumor formation and lymph node metastasis were assessed in nude mice. RESULTS Highly expressed DPP10-AS1 and CLDN3 and poorly expressed miR-324-3p were identified in PC cells. The competitively binding between DPP10-AS1 and miR-324-3p was identified, and CLDN3 was targeted and downregulated by miR-324-3p. In addition, DPP10-AS1 was found to sequester miR-324-3p to release CLDN3 expression. DPP10-AS1 knockdown or miR-324-3p restoration diminished migration, invasion, tumor formation, microvessel density, and lymph node metastasis of PC cells, which was associated with CLDN3 downregulation. CONCLUSIONS Taken together, the study identified the regulatory role of DPP10-AS1/miR-324-3p/CLDN3 axis in PC, offering a mechanistic basis suggesting DPP10-AS1 ablation as a therapeutic target against PC.
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Affiliation(s)
- Fengru Jiang
- From the Clinical Laboratory, Huadu Hospital Affiliated to Southern Medical University
| | - Sumei Li
- From the Clinical Laboratory, Huadu Hospital Affiliated to Southern Medical University
| | - Xiaoyun Wang
- Department of Chronic Non-infectious Disease, Xinhua Community Health Service Center, Guangzhou
| | - Yingzhao Deng
- From the Clinical Laboratory, Huadu Hospital Affiliated to Southern Medical University
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Pan-Cancer Gene Analysis of m6A Modification and Immune Infiltration in Uterine Corpus Endometrial Carcinoma. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:6530884. [PMID: 36199963 PMCID: PMC9529468 DOI: 10.1155/2022/6530884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/21/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022]
Abstract
Objective This investigation was to test the potential role of m6A-related long non-coding RNAs (lncRNAs) and immune infiltration as crucial factors in the diagnosis and treatment of uterine corpus endometrial cancer (UCEC). Method The UCEC RNA-seq data were downloaded in the Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/). There were 587 samples totally, containing 543 UCEC cases and 35 healthy cases. The clinical information of UCEC cases included survival time, survival status, gender, age, stage, and TMN stage. Twenty-three m6A-related genes were found in published journals. The RNA-seq documents of UCEC were downloaded in the Cancer Genome Atlas (TCGA). The hub gene data of UCEC were downloaded from GEPIA2 database. The different packages of R language were applied to calculate and analyze in this research. Results Among 587 cases in our study, we discovered 3039 lncRNAs in the TCGA-UCEC database. After the differential analysis, 23 m6A-associated genetics were screened and twenty-one m6A-associated differential genetics were found. In the end, we obtained 20 m6A-related lncRNAs. LNCTAM34A was considered as a predictive gene through univariate and multivariate Cox regression analysis. In addition to the above, patients with high LNCTAM34A expression had better outcomes than those with low LNCTAM34A expression. The high-risk cohort had greater scores of activated dendritic cells (aDCs), B cells, and T cell regulatory (Tregs) than low-risk cohort; in the meanwhile, high-risk cohort had lower scores of DCs and iDCs. Then, the high-risk cohort displayed greater scores in the immune functions of MHC class I, para-inflammation, and type I IFN response than those of low-risk cohort. Among 27 immune-inducible genes, the level of CD244, KIR3DLI, NRP1, PDCD1LG2, and TNFRSF8 was reduced in UCEC samples and the level of CD27, CD28, CD70, CD80, CD86, HAVCR2, ICOS, IDO1, LAIR1, PDCD1, TIGIT, TNFRSF18, -25, -9, -14, and VTCN1 was increased in UCEC samples. Conclusion The key role of M6A-related lncRNAs in immune microenvironment in high-risk patients of UCEC. The patients with strong expression of LNCTAM34A have a good prognosis, and LNCTAM34A can be used as a prognostic gene for UCEC. m6A-related lncRNAs can be used as a potential treatment for UCEC. Our observations can be used as a hypothetical basis for future in vitro and animal experiments.
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169
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Chen T. Circulating Non-Coding RNAs as Potential Diagnostic Biomarkers in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2022; 9:1029-1040. [PMID: 36132427 PMCID: PMC9484560 DOI: 10.2147/jhc.s380237] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is currently the second leading cause of cancer-related deaths worldwide, with high morbidity and mortality. The clinical diagnosis of HCC mainly depends on imaging technology, such as ultrasound and computed tomography, and serum biomarkers, such as alpha-fetoprotein (AFP). However, HCC is still hard to diagnose at an early stage due to the low sensitivity of the above mentioned traditional methods. Typically, HCC is diagnosed at an advanced stage when limited treatment options are available. It is urgent to identify effective biomarkers for the early diagnosis of HCC. Increasing evidence uncovered ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), could be used in HCC diagnosis. The aim of this review is to summarize our understanding of circulating miRNAs, lncRNAs and circRNAs as fluid-based non-invasive biomarkers, and aiming at providing new insights into the diagnosis of HCC.
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Affiliation(s)
- Tingsong Chen
- The Second Department of Oncology, the Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
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170
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Zhang W, Cao W, Tong Z, Jin Q, Jiang X, Yang Y, Yao H, Chen G, Gao W, Zhu Y, Zhou S. Identification and validation of a novel necroptosis-related prognostic signature in cervical squamous cell carcinoma and endocervical adenocarcinoma. Front Oncol 2022; 12:1011000. [PMID: 36185274 PMCID: PMC9523405 DOI: 10.3389/fonc.2022.1011000] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/30/2022] [Indexed: 12/09/2022] Open
Abstract
BackgroundThe purpose of this study was to investigate the prognostic signature of necroptosis-related lncRNAs (NRLs) and explore their association with immune-related functions and sensitivity of the therapeutic drug in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC).MethodsUCSC Xena provided lncRNA sequencing and clinical data about CESC, and a necroptosis gene list was obtained from the KEGG database. NRLs were selected by structuring a co-expression network of lncRNAs and necroptosis-related genes. To further screen lncRNAs, we used the univariate Cox regression method, Lasso regression, and multivariate Cox regression. Afterward, an NRL signature was established. We used the xCell algorithm and single-sample gene set enrichment analysis (ssGSEA) to clarify the pertinence between immune infiltration and NRL expressions in CESC patients and explored the relationship between the target lncRNAs and immune-related genes. By leveraging the GDSC database, the therapy-sensitive response of the prognostic signature was forecasted and an experimental validation was performed. We performed GSEA with the aim of recognizing the potential pathway related to the individual prognostic signature.ResultsThe two prognostic NRLs (AC009095.1 and AC005332.4) showed significant diversity and constituted the NRL signature. On the grounds of our signature, risk score was an independent element which was bound up with patient outcome (HR = 4.97 CI: 1.87–13.2, P = 0.001). The CESC patients were classified by the median risk score. Immune infiltration analysis revealed significant increases in CD4 + Tcm, eosinophils, epithelial cells, fibroblasts, NKT, plasma cells, platelets, and smooth muscle in the high-risk group (P< 0.05). Target lncRNAs also showed some correlation with NRGs. The estimated IC50 values of bicalutamide, CHIR.99021, and imatinib were lower in the high-risk group. Through the subsequent experimental validation, both AC009095.1 and AC005332.4 were significantly more highly expressed in SiHa than in Hela. AC009095.1 was expressed more highly in SiHa than in HUCEC, but the expression of AC005332.4 was reversed.ConclusionsThis study elucidated that NRLs, as a novel signature, were indispensable factors which can significantly influence the prognosis of patients with CESC and could provide novel clinical evidence to serve as a potential molecular biomarker for future therapeutic targets.
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Affiliation(s)
- Weiyu Zhang
- Department of Gynecology, Anhui Medical University Affiliated Maternity and Child Healthcare Hospital, Hefei, China
- Department of Gynecology, Anhui Province Maternity and Child Healthcare Hospital, Hefei, China
| | - Wujun Cao
- Department of Clinical Laboratory, Anhui Province Maternity and Child Healthcare Hospital, Hefei, China
| | - Zhuting Tong
- Department of Radiation Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qinqin Jin
- Department of Gynecology, Anhui Medical University Affiliated Maternity and Child Healthcare Hospital, Hefei, China
- Department of Gynecology, Anhui Province Maternity and Child Healthcare Hospital, Hefei, China
| | - Xiya Jiang
- Department of Gynecology, Anhui Medical University Affiliated Maternity and Child Healthcare Hospital, Hefei, China
- Department of Gynecology, Anhui Province Maternity and Child Healthcare Hospital, Hefei, China
| | - Yinting Yang
- Department of Gynecology, Anhui Medical University Affiliated Maternity and Child Healthcare Hospital, Hefei, China
- Department of Gynecology, Anhui Province Maternity and Child Healthcare Hospital, Hefei, China
| | - Hui Yao
- Department of Gynecology, Anhui Medical University Affiliated Maternity and Child Healthcare Hospital, Hefei, China
- Department of Gynecology, Anhui Province Maternity and Child Healthcare Hospital, Hefei, China
| | - Guo Chen
- Department of Gynecology, Anhui Medical University Affiliated Maternity and Child Healthcare Hospital, Hefei, China
- Department of Gynecology, Anhui Province Maternity and Child Healthcare Hospital, Hefei, China
| | - Wei Gao
- Department of Gynecology, Anhui Medical University Affiliated Maternity and Child Healthcare Hospital, Hefei, China
- Department of Gynecology, Anhui Province Maternity and Child Healthcare Hospital, Hefei, China
| | - Yuting Zhu
- Department of Gynecology, Anhui Medical University Affiliated Maternity and Child Healthcare Hospital, Hefei, China
- Department of Gynecology, Anhui Province Maternity and Child Healthcare Hospital, Hefei, China
| | - Shuguang Zhou
- Department of Gynecology, Anhui Medical University Affiliated Maternity and Child Healthcare Hospital, Hefei, China
- Department of Gynecology, Anhui Province Maternity and Child Healthcare Hospital, Hefei, China
- *Correspondence: Shuguang Zhou,
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Thymic epithelial tumors: examining the GTF2I mutation and developing a novel prognostic signature with LncRNA pairs to predict tumor recurrence. BMC Genomics 2022; 23:656. [PMID: 36114454 PMCID: PMC9482307 DOI: 10.1186/s12864-022-08880-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Background General transcription factor IIi (GTF2I) mutations are very common in thymic epithelial tumors (TETs) and are related to a more favorable prognosis in TET patients. However, limited research has been conducted on the role of GTF2I in the tumor immune microenvironment (TIME). Further, long non-coding RNAs (lncRNAs) have been associated with the survival of patients with TETs. Therefore, this study aimed to explore the relationship between GTF2I mutations and TIME and build a new potential signature for predicting tumor recurrence in the TETs. Research data was downloaded from The Cancer Genome Atlas database and the CIBERSORT algorithm was used to evaluate TIME differences between GTF2I mutant and wild-type TETs. Relevant differentially expressed lncRNAs based on differentially expressed immune-related genes were identified to establish lncRNA pairs. We constructed a signature using univariate and multivariate Cox regression analyses. Results GTF2I is the most commonly mutated gene in TETs, and is associated with an increased number of early-stage pathological types, as well as no history of myasthenia gravis or radiotherapy treatment. In the GTF2I wild-type group, immune score and immune cell infiltrations with M2 macrophages, activated mast cells, neutrophils, plasma, T helper follicular cells, and activated memory CD4 T cells were higher than the GTF2I mutant group. A risk model was built using five lncRNA pairs, and the 1-, 3-, and 5-year area under the curves were 0.782, 0.873, and 0.895, respectively. A higher risk score was related to more advanced histologic type. Conclusion We can define the GTF2I mutant-type TET as an immune stable type and the GTF2I wild-type as an immune stressed type. A signature based on lncRNA pairs was also constructed to effectively predict tumor recurrence.
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Reactive Oxygen Species and Long Non-Coding RNAs, an Unexpected Crossroad in Cancer Cells. Int J Mol Sci 2022; 23:ijms231710133. [PMID: 36077530 PMCID: PMC9456385 DOI: 10.3390/ijms231710133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/24/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Long non-coding RNAs (lncRNA) have recently been identified as key regulators of oxidative stress in several malignancies. The level of reactive oxygen species (ROS) must be constantly regulated to maintain cancer cell proliferation and chemoresistance and to prevent apoptosis. This review will discuss how lncRNAs alter the ROS level in cancer cells. We will first describe the role of lncRNAs in the nuclear factor like 2 (Nrf-2) coordinated antioxidant response of cancer cells. Secondly, we show how lncRNAs can promote the Warburg effect in cancer cells, thus shifting the cancer cell’s “building blocks” towards molecules important in oxidative stress regulation. Lastly, we explain the role that lncRNAs play in ROS-induced cancer cell apoptosis and proliferation.
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Non-Coding RNAs in Hepatocellular Carcinoma. LIVERS 2022. [DOI: 10.3390/livers2030017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Liver cancer ranks as the fourth leading cause of cancer-related deaths. Despite extensive research efforts aiming to evaluate the biological mechanisms underlying hepatocellular carcinoma (HCC) development, little has been translated towards new diagnostic and treatment options for HCC patients. Historically, the focus has been centered on coding RNAs and their respective proteins. However, significant advances in sequencing and RNA detection technologies have shifted the research focus towards non-coding RNAs (ncRNA), as well as their impact on HCC development and progression. A number of studies reported complex post-transcriptional interactions between various ncRNA and coding RNA molecules. These interactions offer insights into the role of ncRNAs in both the known pathways leading to oncogenesis, such as dysregulation of p53, and lesser-known mechanisms, such as small nucleolar RNA methylation. Studies investigating these mechanisms have identified prevalent ncRNA changes in microRNAs, snoRNAs, and long non-coding RNAs that can both pre- and post-translationally regulate key factors in HCC progression. In this review, we present relevant publications describing ncRNAs to summarize the impact of different ncRNA species on liver cancer development and progression and to evaluate recent attempts at clinical translation.
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McAlarnen LA, Gupta P, Singh R, Pradeep S, Chaluvally-Raghavan P. Extracellular vesicle contents as non-invasive biomarkers in ovarian malignancies. Mol Ther Oncolytics 2022; 26:347-359. [PMID: 36090475 PMCID: PMC9420349 DOI: 10.1016/j.omto.2022.08.005] [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] [Indexed: 11/25/2022] Open
Abstract
Ovarian cancer most commonly presents at an advanced stage where survival is approximately 30% compared with >80% if diagnosed and treated before disease spreads. Diagnostic capabilities have progressed from surgical staging via laparotomy to image-guided biopsies and immunohistochemistry staining, along with advances in technology and medicine. Despite improvements in diagnostic capabilities, population-level screening for ovarian cancer is not recommended. Extracellular vesicles (EVs) are 40–150 nm structures formed when the cellular lipid bilayer invaginates. These structures function in cell signaling, immune responses, cancer progression, and establishing the tumor microenvironment. EVs are found in nearly every bodily fluid, including serum, plasma, ascites, urine, and effusion fluid, and contain molecular cargo from their cell of origin. This cargo can be analyzed to yield information about a possible malignancy. In this review we describe how the cargo of EVs has been studied as biomarkers in ovarian cancer. We bring together studies analyzing evidence for various cargos as ovarian cancer biomarkers. Then, we describe the role of EVs in modulation of the tumor microenvironment. This review also summarizes the therapeutic and translational potential of EVs for their optimal utilization as non-invasive biomarkers for novel treatments against cancer.
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Riahi A, Rajabi A, Sait S, Hussen BM, Tayefeh-Gholami S, Farsad-Akhtar N, Safaralizadeh R. The novel biomarker LUNAR1 overexpression in cervical cancerous tissues specimens and its association with clinicopathological properties. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Regulation of angiogenesis by microRNAs and long non-coding RNAs in endometriosis. REPRODUCTIVE AND DEVELOPMENTAL MEDICINE 2022. [DOI: 10.1097/rd9.0000000000000024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Huang C, Huang H, Xia Z, Yang Y, Jiang X, Yang Y, Wang D, Li X, Chen Z. Sequence Data, Functional Annotation, and Relationship Analysis Between mRNAs and Long Noncoding RNAs from Tea Leaves During Infection by the Fungal Pathogen Epicoccum sorghinum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:875-879. [PMID: 36107196 DOI: 10.1094/mpmi-02-22-0048-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Chen Huang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Hongke Huang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
- College of Tea Science, Guizhou University, Guiyang, Guizhou 550025, China
| | - Zhongqiu Xia
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
- College of Tea Science, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yuqin Yang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
- College of Tea Science, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xinyue Jiang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yuanyou Yang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Delu Wang
- College of Forestry, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xiangyang Li
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Zhuo Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
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The Clinical Value of Long Noncoding RNA DDX11-AS1 as a Biomarker for the Diagnosis and Prognosis of Hepatocellular Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:5735462. [PMID: 36072974 PMCID: PMC9444391 DOI: 10.1155/2022/5735462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
Hepatocellular carcinoma (HCC) is a high-mortality malignant tumor with genetic and phenotypic heterogeneity, making predicting clinical outcomes challenging. The purpose of this investigation was to examine the potential usefulness of lncRNA DDX11 antisense RNA 1 (DDX11-AS1) as a biomarker for diagnosis and prognosis in hepatocellular carcinoma (HCC). The TCGA-LIHC datasets were searched for patients’ clinical information and RNA-seq data, which were then collected. Relative expression levels of DDX11-AS1 in HCC tissues were determined by qRT-PCR. In order to test the sensitivity and specificity of the DDX11-AS1 receiver, receiver operating characteristic curves were utilized. The association of DDX11-AS1 expression with clinicopathological factors or prognosis was statistically analyzed. We found that the levels of DDX11-AS1 were higher in HCC specimens than in normal specimens. ROC analysis showed that DDX11-AS1 was a useful marker for discriminating HCC tissues from normal nontumor specimens. According to the results of clinical tests, a high level of DDX11-AS1 expressions was significantly related to the pathologic stage (
) and the histologic grade (
). Survival studies indicated that patients with higher DDX11-AS1 expression had a significantly poorer overall survival (
) and progression-free interval (
) than those with lower DDX11-AS1 expression. Multivariate survival analysis verified that DDX11-AS1 expression level was an independent predictor for HCC patients. Overall, DDX11-AS1 may serve as a tumor promotor during HCC progression, and its high level may be a potential marker for HCC patients.
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lncRNA TM4SF1-AS1 predicts dismal outcomes and promotes cholangiocarcinoma progression via modulating miR-744-3p. Clin Res Hepatol Gastroenterol 2022; 46:101915. [PMID: 35346892 DOI: 10.1016/j.clinre.2022.101915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is of great malignancy and high mortality. Identification of effective biomarkers could improve the monitoring of CCA development and attenuate patients' outcomes. OBJECTIVE The potential of lncRNA TM4SF1-AS1 (TM4SF1-AS1) serving biomarker of CCA was estimated and the underlying mechanism was also investigated. METHODS A total of 107 pairs of tumor and paracancer tissues were collected from CCA patients. The expression levels of TM4SF1-AS1 and miR-744-3p were analyzed in CCA by PCR, and their clinical significance was estimated by a series of statistical analyses. CCK8 and Transwell assays were used to assess the development-related cellular processes of CCA. The interaction between TM4SF1-AS1 and miR-774-3p was evaluated by cell transfection and dual-luciferase reporter assay. RESULTS The elevated expression of TM4SF1-AS1 and the declined expression of miR-744-3p were observed in CCA. Both TM4SF1-AS1 and miR-744-3p were found to possess a close association with the malignant progression and poor prognosis of CCA patients. TM4SF1-AS1 was suggested to act as a tumor promoter of CCA, where miR-744-3p was found to mediate the function of TM4SF1-AS1. CONCLUSION Both TM4SF1-AS1 and miR-744-3p were identified as prognostic biomarkers of CCA. TM4SF1-AS1 served as tumor promoter of CCA via modulating miR-744-3p.
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Cai J, Ji Z, Wu J, Chen L, Zheng D, Chen Y, Zhang X, Xie W, Huang J, Chen M, Lin R, Lin W, Chen Y, Li Z. Development and validation of a novel endoplasmic reticulum stress-related lncRNA prognostic signature and candidate drugs in breast cancer. Front Genet 2022; 13:949314. [PMID: 36092873 PMCID: PMC9452962 DOI: 10.3389/fgene.2022.949314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/27/2022] [Indexed: 02/05/2023] Open
Abstract
Breast cancer (BC), the most common malignancy in women, has a high cancer-related mortality. Endoplasmic reticulum stress (ERS), a response to the accumulation of unfolded proteins, has emerging roles in tumorigenesis, including invasion, metastasis, immune escape, etc. However, few studies have focused on the correlation between ERS with long non-coding RNAs (lncRNAs) in BC. We attempted to construct an ERS-related lncRNA prognostic signature and study its value in BC from tumor mutational burden (TMB), tumor immune microenvironment (TIME), cluster, clinical treatment, and so on. In the present study, transcriptomic and clinical data of BC patients were extracted from The Cancer Genome Atlas (TCGA) database. Correlation test, Cox regression analysis, least absolute shrinkage, and selection operator (LASSO) method were performed to determine an ERS-related lncRNA prognostic signature. Survival and predictive performance were analyzed according to Kaplan-Meier curves and receiver operating characteristic (ROC) curves, while nomograms and calibration curves were established. Then, an enrichment analysis was performed to study the functions and biological processes of ERS-related lncRNAs. TMB and TIME were also analyzed to assess the mutational status and immune status. Additionally, by using consensus cluster analysis, we compared differences among tumor subtypes. Drug sensitivity analysis and immunologic efficacy evaluations were performed together for further exploration. We identified a novel prognostic signature consisting of 9 ERS-related lncRNAs. High-risk patients had worse prognoses. The signature had a good predictive performance as an independent prognostic indicator and was significantly associated with clinicopathological characteristics. Enrichment analysis showed that metabolic pathways were enriched in high-risk patients, while immune pathways were more active in low-risk patients. Low-risk patients had lower TMB, higher immune scores, and stronger immune functions. Cluster analysis clarified that cluster 2 had the most active immune functions and was sensitive to more drugs, which may have the best clinical immunological efficacy. A clinical efficacy evaluation revealed that patients in the low-risk group may benefit more from chemotherapy, targeted therapy, and immunotherapy. The novel signature has significant clinical implications in prognosis prediction for BC. Our study clarifies that there is a potential connection between the ERS-related lncRNAs and BC, which may provide new treatment guidelines for BC.
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Affiliation(s)
- Jiehui Cai
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Zeqi Ji
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jinyao Wu
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | | | | | | | | | | | | | | | | | | | - Yexi Chen
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Zhiyang Li
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
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Zhao SS, Tao DL, Chen JM, Wu JP, Yang X, Song JK, Zhu XQ, Zhao GH. RNA sequencing reveals dynamic expression of lncRNAs and mRNAs in caprine endometrial epithelial cells induced by Neospora caninum infection. Parasit Vectors 2022; 15:297. [PMID: 35999576 PMCID: PMC9398501 DOI: 10.1186/s13071-022-05405-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background The effective transmission mode of Neospora caninum, with infection leading to reproductive failure in ruminants, is vertical transmission. The uterus is an important reproductive organ that forms the maternal–fetal interface. Neospora caninum can successfully invade and proliferate in the uterus, but the molecular mechanisms underlying epithelial-pathogen interactions remain unclear. Accumulating evidence suggests that host long noncoding RNAs (lncRNAs) play important roles in cellular molecular regulatory networks, with reports that these RNA molecules are closely related to the pathogenesis of apicomplexan parasites. However, the expression profiles of host lncRNAs during N. caninum infection has not been reported. Methods RNA sequencing (RNA-seq) analysis was used to investigate the expression profiles of messenger RNAs (mRNAs) and lncRNAs in caprine endometrial epithelial cells (EECs) infected with N. caninum for 24 h (TZ_24h) and 48 h (TZ_48 h), and the potential functions of differentially expressed (DE) lncRNAs were predicted by using Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of their mRNA targets. Results RNA-seq analysis identified 1280.15 M clean reads in 12 RNA samples, including six samples infected with N. caninum for 24 h (TZ1_24h-TZ3_24h) and 48 h (TZ1_48h-TZ3_48h), and six corresponding control samples (C1_24h-C3_24h and C1_48h-C3_48h). Within the categories TZ_24h-vs-C_24h, TZ_48h-vs-C_48h and TZ_48h-vs-TZ_24h, there were 934 (665 upregulated and 269 downregulated), 1238 (785 upregulated and 453 downregulated) and 489 (252 upregulated and 237 downregulated) DEmRNAs, respectively. GO enrichment and KEGG analysis revealed that these DEmRNAs were mainly involved in the regulation of host immune response (e.g. TNF signaling pathway, MAPK signaling pathway, transforming growth factor beta signaling pathway, AMPK signaling pathway, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway), signaling molecules and interaction (e.g. cytokine-cytokine receptor interaction, cell adhesion molecules and ECM-receptor interaction). A total of 88 (59 upregulated and 29 downregulated), 129 (80 upregulated and 49 downregulated) and 32 (20 upregulated and 12 downregulated) DElncRNAs were found within the categories TZ_24h-vs-C_24h, TZ_48h-vs-C_48h and TZ_48h-vs-TZ_24h, respectively. Functional prediction indicated that these DElncRNAs would be involved in signal transduction (e.g. MAPK signaling pathway, PPAR signaling pathway, ErbB signaling pathway, calcium signaling pathway), neural transmission (e.g. GABAergic synapse, serotonergic synapse, cholinergic synapse), metabolism processes (e.g. glycosphingolipid biosynthesis-lacto and neolacto series, glycosaminoglycan biosynthesis-heparan sulfate/heparin) and signaling molecules and interaction (e.g. cytokine-cytokine receptor interaction, cell adhesion molecules and ECM-receptor interaction). Conclusions This is the first investigation of global gene expression profiles of lncRNAs during N. caninum infection. The results provide valuable information for further studies of the roles of lncRNAs during N. caninum infection. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05405-5.
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Affiliation(s)
- Shan-Shan Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - De-Liang Tao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jin-Ming Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jiang-Ping Wu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jun-Ke Song
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xing-Quan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China. .,Key Laboratory of Veterinary Public Health of Higher Education of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
| | - Guang-Hui Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Wang W, Zhou Z, Dai X, Wang H, Jin J, Min K, Wang Y, Lv M, Liu Y, Zhou Y. LncRNA-ENST00000543604 exerts a tumor-promoting effect via miRNA 564/AEG-1 or ZNF326/EMT and predicts the prognosis of and chemotherapeutic effect in colorectal cancer. Front Oncol 2022; 12:960481. [PMID: 36081570 PMCID: PMC9445881 DOI: 10.3389/fonc.2022.960481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/01/2022] [Indexed: 11/26/2022] Open
Abstract
Objectives Colorectal cancer(CRC) is a common malignant tumor. Recent studies have found that lncRNAs play an important role in the occurrence and development of colorectal cancer. Methods Based on high-throughput sequencing results of fresh CRC tissues and adjacent tissues, we identified lncRNA-ENST00000543604 (lncRNA 604) as the research object by qRT-PCR in CRC tissues and cells. We explored the mechanism of lncRNA 604 action by using luciferin reporter, qRT-PCR and Western blot assays. Kaplan-Meier survival analysis and a Cox regression model were used to analyze the correlation of lncRNA 604 and its regulatory molecules with the prognosis of and chemotherapy efficacy in CRC patients. Results In this study, we found that the expression levels of lncRNA 604 were increased in CRC. LncRNA 604 could promote CRC cell proliferation and metastasis through the miRNA 564/AEG-1 or ZNF326/EMT signaling axis in vivo and in vitro. LncRNA 604 could predict the prognosis of CRC and was an independent negative factor. LncRNA 604 exerted a synergistic effect with miRNA 564 or ZNF326 on the prognosis of CRC. LncRNA 604 could improve chemoresistance by increasing the expression of AEG-1, NF-κB, and ERCC1. Conclusions Our study demonstrated that lncRNA 604 could promote the progression of CRC via the lncRNA 604/miRNA 564/AEG-1/EMT or lncRNA 604/ZNF326/EMT signaling axis. LncRNA 604 could improve chemoresistance by increasing drug resistance protein expression.
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Affiliation(s)
- Weimin Wang
- Institute of Combining Chinese Traditional and Western Medicine, Medical College, Yangzhou University, Jiangsu, China
- Department of Oncology, Yixing Hospital Affiliated to Medical College of Yangzhou University, Yangzhou University, Jiangsu, China
| | - Zhen Zhou
- Institute of Combining Chinese Traditional and Western Medicine, Medical College, Yangzhou University, Jiangsu, China
- Department of Chinese Medicine, Nanjing University of Chinese Medicine, Jiangsu, Nanjing, China
| | - Xiaojun Dai
- Institute of Combining Chinese Traditional and Western Medicine, Medical College, Yangzhou University, Jiangsu, China
| | - Haibo Wang
- Institute of Combining Chinese Traditional and Western Medicine, Medical College, Yangzhou University, Jiangsu, China
| | - Jun Jin
- Department of Oncology, Yixing Hospital Affiliated to Medical College of Yangzhou University, Yangzhou University, Jiangsu, China
| | - Ke Min
- Department of Oncology, Yixing Hospital Affiliated to Medical College of Yangzhou University, Yangzhou University, Jiangsu, China
| | - Yunfan Wang
- Department of Oncology, Yixing Hospital Affiliated to Medical College of Yangzhou University, Yangzhou University, Jiangsu, China
| | - Mengying Lv
- Institute of Combining Chinese Traditional and Western Medicine, Medical College, Yangzhou University, Jiangsu, China
| | - Yanqing Liu
- Institute of Combining Chinese Traditional and Western Medicine, Medical College, Yangzhou University, Jiangsu, China
- Department of Oncology, Yixing Hospital Affiliated to Medical College of Yangzhou University, Yangzhou University, Jiangsu, China
- *Correspondence: Yanqing Liu, ; Yan Zhou,
| | - Yan Zhou
- Institute of Combining Chinese Traditional and Western Medicine, Medical College, Yangzhou University, Jiangsu, China
- Department of Oncology, Yixing Hospital Affiliated to Medical College of Yangzhou University, Yangzhou University, Jiangsu, China
- *Correspondence: Yanqing Liu, ; Yan Zhou,
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Chen Q, Zhou L, Ma D, Hou J, Lin Y, Wu J, Tao M. LncRNA GAS6-AS1 facilitates tumorigenesis and metastasis of colorectal cancer by regulating TRIM14 through miR-370-3p/miR-1296-5p and FUS. J Transl Med 2022; 20:356. [PMID: 35962353 PMCID: PMC9373365 DOI: 10.1186/s12967-022-03550-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/19/2022] [Indexed: 12/24/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are essential regulators of tumorigenesis and the development of colorectal cancer (CRC). Here, we aimed to investigate the role of lncRNA GAS6-AS1 in CRC and its potential mechanisms. Methods Bioinformatics analyses evaluated the level of GAS6-AS1 in colon cancer, its correlation with clinicopathological factors, survival curve and diagnostic value. qRT-PCR were performed to detect the GAS6-AS1 level in CRC samples and cell lines. The CCK8, EdU, scratch healing, transwell assays and animal experiments were conducted to investigate the function of GAS6-AS1 in CRC. RNA immunoprecipitation (RIP) and dual-luciferase reporter gene analyses were carried out to reveal interaction between GAS6-AS1, TRIM14, FUS, and miR-370-3p/miR-1296-5p. Results GAS6-AS1 was greatly elevated in CRC and positively associated with unfavorable prognosis of CRC patients. Functionally, GAS6-AS1 positively regulates CRC proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) in vitro and induces CRC growth and metastasis in vivo. Moreover, GAS6-AS1 exerted oncogenic function by competitively binding to miR-370-3p and miR-1296-5p, thereby upregulating TRIM14. Furthermore, we verified that GAS6-AS1 and TRIM14 both interact with FUS and that GAS6-AS1 stabilized TRIM14 mRNA by recruiting FUS. Besides, rescue experiments furtherly demonstrated that GAS6-AS1 facilitate progression of CRC by regulating TRIM14. Conclusion Collectively, these findings demonstrate that GAS6-AS1 promotes TRIM14-mediated cell proliferation, migration, invasion, and EMT of CRC via ceRNA network and FUS-dependent manner, suggesting that GAS6-AS1 could be utilized as a novel biomarker and therapeutic target for CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03550-0.
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Affiliation(s)
- Qing Chen
- Department of Oncology, Jingjiang People's Hospital, The Seventh Affiliated Hospital of Yangzhou University, Jingjiang, Jiangsu, China.,Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Lin Zhou
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - De Ma
- Department of Oncology, Jingjiang People's Hospital, The Seventh Affiliated Hospital of Yangzhou University, Jingjiang, Jiangsu, China
| | - Juan Hou
- Department of Oncology, Jingjiang People's Hospital, The Seventh Affiliated Hospital of Yangzhou University, Jingjiang, Jiangsu, China
| | - Yuxin Lin
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jie Wu
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China.
| | - Min Tao
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China. .,Department of Oncology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu, China.
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Xie H, Shi M, Liu Y, Cheng C, Song L, Ding Z, Jin H, Cui X, Wang Y, Yao D, Wang P, Yao M, Zhang H. Identification of m6A- and ferroptosis-related lncRNA signature for predicting immune efficacy in hepatocellular carcinoma. Front Immunol 2022; 13:914977. [PMID: 36032107 PMCID: PMC9402990 DOI: 10.3389/fimmu.2022.914977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/13/2022] [Indexed: 12/16/2022] Open
Abstract
Background N6-methyladenosine (m6A) methylation and ferroptosis assist long noncoding RNAs (lncRNAs) in promoting immune escape in hepatocellular carcinoma (HCC). However, the predictive value of m6A- and ferroptosis-related lncRNAs (mfrlncRNAs) in terms of immune efficacy remains unknown. Method A total of 365 HCC patients with complete data from The Cancer Genome Atlas (TCGA) database were used as the training cohort, and half of them were randomly selected as the validation cohort. A total of 161 HCC patients from the International Cancer Genome Consortium (ICGC) database were used as external validation (ICGC cohort). Results We first identified a group of specific lncRNAs associated with both m6A regulators and ferroptosis-related genes and then constructed prognosis-related mfrlncRNA pairs. Based on this, the mfrlncRNA signature was constructed using the least absolute shrinkage and selection operator (LASSO) analysis and Cox regression. Notably, the risk score of patients was proven to be an independent prognostic factor and was better than the TNM stage and tumor grade. Moreover, patients with high-risk scores had lower survival rates, higher infiltration of immunosuppressive cells (macrophages and Tregs), lower infiltration of cytotoxic immune cells (natural killer cells), poorer immune efficacy (both immunophenoscore and score of tumor immune dysfunction and exclusion), higher IC50, and enrichment of the induced Treg pathway, which confirmed that the mfrlncRNA signature contributed to survival prediction and risk stratification of patients with HCC. Conclusions The mfrlncRNA signature, which has great prognostic value, provides new clues for identifying “cold” and “hot” tumors and might have crucial implications for individualized therapy to improve the survival rate of patients with HCC.
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Affiliation(s)
- Hongjun Xie
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, and Medical School of Nantong University, Nantong, China
| | - Muqi Shi
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, and Medical School of Nantong University, Nantong, China
| | - Yifei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Changhong Cheng
- Department of Clinical Laboratory, People’s Hospital of Ganyu District, Lianyungang, China
| | - Lining Song
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, and Medical School of Nantong University, Nantong, China
| | - Zihan Ding
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, and Medical School of Nantong University, Nantong, China
| | - Huanzhi Jin
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, and Medical School of Nantong University, Nantong, China
| | - Xiaohong Cui
- Department of General Surgery, Shanghai Electric Power Hospital, Shanghai, China
| | - Yan Wang
- Department of Emergency, Affiliated Hospital of Nantong University, Nantong, China
| | - Dengfu Yao
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, and Medical School of Nantong University, Nantong, China
| | - Peng Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Min Yao
- Department of Immunology, Medical School of Nantong University, Nantong, China
- *Correspondence: Haijian Zhang, ; Min Yao,
| | - Haijian Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, and Medical School of Nantong University, Nantong, China
- *Correspondence: Haijian Zhang, ; Min Yao,
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Dabi Y, Bendifallah S, Suisse S, Haury J, Touboul C, Puchar A, Favier A, Daraï E. Overview of non-coding RNAs in breast cancers. Transl Oncol 2022; 25:101512. [PMID: 35961269 PMCID: PMC9382556 DOI: 10.1016/j.tranon.2022.101512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/18/2022] [Accepted: 08/02/2022] [Indexed: 12/24/2022] Open
Abstract
Breast cancer in women is the second most common cancer and the fifth leading cause of cancer death worldwide. Although earlier diagnosis and detection of breast cancer has resulted in lower mortality rates, further advances in prevention, detection, and treatment are needed to improve outcomes and survival for women with breast cancer as well as to offer a personalized therapeutic approach. It is now well-established that non-coding RNAs (ncRNAs) represent 98% of the transcriptome but in-depth knowledge about their involvement in the regulation of gene expression is lacking. A growing body of research indicates that ncRNAs are essential for tumorigenesis by regulating the expression of tumour-related genes. In this review, we focus on their implication in breast cancer genesis but also report the latest knowledge of their theragnostic and therapeutic role. We highlight the need for accurate quantification of circulating ncRNAs which is determinant to develop reliable biomarkers. Further studies are mandatory to finally enter the era of personalized medicine for women with breast cancer.
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Affiliation(s)
- Yohann Dabi
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Sorbonne University, 4 rue de la Chine, Paris 75020, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France; INSERM UMR_S_938, Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, Paris 75020, France.
| | - Sofiane Bendifallah
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Sorbonne University, 4 rue de la Chine, Paris 75020, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France; INSERM UMR_S_938, Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, Paris 75020, France
| | | | - Julie Haury
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Sorbonne University, 4 rue de la Chine, Paris 75020, France
| | - Cyril Touboul
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Sorbonne University, 4 rue de la Chine, Paris 75020, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France; INSERM UMR_S_938, Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, Paris 75020, France
| | - Anne Puchar
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Sorbonne University, 4 rue de la Chine, Paris 75020, France
| | - Amélia Favier
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Sorbonne University, 4 rue de la Chine, Paris 75020, France
| | - Emile Daraï
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Sorbonne University, 4 rue de la Chine, Paris 75020, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France; INSERM UMR_S_938, Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, Paris 75020, France
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186
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A somatic mutation-derived LncRNA signatures of genomic instability predicts the prognosis and tumor microenvironment immune characters in hepatocellular carcinoma. Hepatol Int 2022; 16:1220-1233. [PMID: 35947245 DOI: 10.1007/s12072-022-10375-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/04/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is an aggressive carcinoma with genome instability. Long non-coding RNAs (LncRNAs) have been functionally associated with genomic instability in cancers. However, the identification and prognostic value of lncRNAs related to genome instability have not been explored in hepatocellular carcinoma. In this study, we aim to identify a genomic instability-related lncRNA signature for predicting prognosis and the efficacy of immunotherapy in HCC patients. METHODS According to the somatic mutation and transcript data of 364 patients with HCC, we determined differentially expressed genome instability-related lncRNAs (GInLncRNAs). Gene ontology (GO) enrichment analyses and Kyoto Encyclopedia of genes and genomes enrichment analyses revealed the potential functions of genes co-expressed with those lncRNAs involved in cancer development and immune function. We further determined a genome instability-related lncRNA signature (GInLncSig) through Cox regression analysis and LASSO regression analysis. Thereafter, we performed correlation analyses with mutations, clinical stratification analyses, and survival analyses to evaluate GInLncSig predictive function. Subsequently, we construct a nomogram model for prognostic assessments of patients with HCC. Finally, we performed Immunocytes infiltration analysis, gene set enrichment analysis (ssGSEA) of immunity circle-associated pathways, and T cell-inflamed score to explore GInLncSig's potential value in guiding immunotherapy. RESULTS We identified 11 independent prognosis-associated GInLncRNAs (AC002511.2, LINC00501, LINC02055, LINC02714, LINC01508, LOC105371967, RP11_96A15.1, RP11_305F18.1, RP11_342M1.3, RP11_432J24.3, U95743.1) to construct a GInLncSig. According to the risk score calculated by GInLncSig, the high-risk group was characterized by a higher somatic mutation count, significantly poorer clinical prognosis, higher T cell-inflamed score, and specific tumor immune infiltration status compared to the low-risk group. Furthermore, we constructed a nomogram model to improve the reliability and clinical utility of predicting the prognosis of patients with HCC. CONCLUSION Our study established a reliable prognostic prediction signature that could be a tool for prognosis prediction and a promising predictive biomarker of immunotherapy in hepatocellular carcinoma.
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The IncRNA SCIRT Promotes the Proliferative, Migratory, and Invasive Properties of Cervical Cancer Cells by Upregulating MMP-2/-9. JOURNAL OF ONCOLOGY 2022; 2022:3448224. [PMID: 35979035 PMCID: PMC9377974 DOI: 10.1155/2022/3448224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/17/2022] [Indexed: 11/18/2022]
Abstract
Objective. The morbidity and mortality of cervical cancer (CC) rank the fourth-most common among cancers in females, seriously threatening women’s health and affecting their quality of life. However, the molecular mechanism of CC development remains poorly understood. This study investigates the role of lncRNA SCIRT in the development of CC. Methods. The expression profile of long noncoding RNA stem cell inhibitory RNA transcript (lncRNA SCIRT) in CC (n = 34), tumor-adjacent tissue, and CC cell culture was determined through fluorescence quantitative PCR. The knockdown /overexpressed lncRNA SCIRT vectors were constructed and transfected into cells, and the effects of knockdown or overexpression of lncRNA SCIRT on the proliferative, invasive, and migratory properties of CC cells were determined through Cell Counting Kit-8 (CCK-8), colony forming, and Transwell experiments. Western blot was employed to determine the knockdown/overexpression efficiency of SCIRT and its role on the expression of proteins (e-cadherin, n-cadherin, vimentin, matrix metalloproteinase (MMP)-9 and MMP-2) in CC cells. Finally, SCIRT knockdown on the proliferative ability for CC cells was determined through tumorigenic experiment in nude mice. Results. LncRNA SCIRT was highly expressed in CC tissues and cells, and significantly linked with clinical/pathology-based characteristics of patients, including Federation Internationale of Gynecologie and Obstetrigue (FIGO) stage, tumor dimensions, and lymph-node metastasis. SCIRT knockdown markedly reduced CC proliferative, colony forming, and invasive properties, while overexpressing SCIRT promoted the proliferative and invasive properties of CC. Western blotting analysis demonstrated that SCIRT knockdown upregulated e-cadherin and downregulated n-cadherin, vimentin, MMP-9, and MMP-2. Meanwhile, overexpressing SCIRT of lncRNA SCIRT had the opposite effect. Tumorigenic experiment showed that SCIRT knockdown could markedly reduce CC proliferative property the nude mouse. Conclusion. LncRNA SCIRT was highly expressed in CC clinical cases. Knockdown/overexpressing SCIRT affected CC proliferative/invasive properties. Hence, lncRNA SCIRT is a promising drug-target and a new biological diagnostic molecule for CC patients.
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188
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Mirzazadeh S, Sarani H, Nakhaee A, Hashemi SM, Taheri M, Hashemi M, Bahari G. Association between PAX8AS1 (rs4848320 C > T, rs1110839 G > T, and rs6726151 T > G) and MEG3 (rs7158663) gene polymorphisms and non-Hodgkin lymphoma risk. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:1174-1186. [PMID: 35938744 DOI: 10.1080/15257770.2022.2104870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 06/06/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Long non-coding RNA (lncRNA) PAX8 antisense RNA 1 (PAX8AS1) and Maternal-expressed gene 3 (MEG3) contribute to the pathogenesis of various malignancies including non-Hodgkin lymphoma (NHL). In this study, we aimed to examine the possible association of polymorphisms of PAX8 and MEG3 and the risk NHL. A total of 175 patients and 175 healthy subjects were genotyped by PCR-RFLP and Tetra-Arms PCR assays. Results demonstrated rs4848320 C > T and rs6726151 T > G of PAX8AS1 and rs7158663 of MEG3 play a potential role in the susceptibility of NHL and PAX8AS1 rs1110839 T > G variant was associated with decreased risk of NHL. Haplotype analysis of rs1110839, rs4848320, and rs6726151 demonstrated GCG haplotype is associated with increased risk of lymphoma and TTG, TTT, and GTT haplotypes are related to decreased lymphoma susceptibility.
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Affiliation(s)
- Samaneh Mirzazadeh
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hosna Sarani
- Children and Adolescent Health Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
- Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Alireza Nakhaee
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Seyed-Mehdi Hashemi
- Department of Internal Medicine, Clinical Immunology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohsen Taheri
- Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohammad Hashemi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Gholamreza Bahari
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Children and Adolescent Health Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
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The Expression of the Long Noncoding RNA AFAP1-AS1 in Laryngeal Carcinoma Affects the Proliferation, Invasion, Migration, and Apoptosis of TU212 Cell Line. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2337447. [PMID: 35968243 PMCID: PMC9371880 DOI: 10.1155/2022/2337447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
Abstract
Background. lncRNA AFAP1-AS1 has been linked to the pathogenesis of a wide range of tumors. Nevertheless, whether it plays a role in laryngeal carcinoma (LC) remains unclear. Methods. Twenty-nine pairs of LC and related normal tissues were collected for the detection of lncRNA AFAP1-AS1 using qRT-PCR. Correlation of lncRNA AFAP1-AS1 level and clinicopathological characters was assessed by the chi-square test. Impacts of lncRNA AFAP1-AS1 silencing on LC phenotypes were tested in vitro via CCK-8, clone formation, EdU staining, wound healing, flow cytometry, and Transwell assay. Results. Herein, a remarkable elevation of lncRNA AFAP1-AS1 was observed in LC patients. And higher lncRNA AFAP1-AS1 level was correlated to worse clinical pathological characteristics. Moreover, lncRNA AFAP1-AS1 silencing was revealed to repress TU212 malignant phenotypes. Conclusion. Our data suggested that lncRNA AFAP1-AS1 acts as an oncogene of LC in vitro.
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Peña-Flores JA, Bermúdez M, Ramos-Payán R, Villegas-Mercado CE, Soto-Barreras U, Muela-Campos D, Álvarez-Ramírez A, Pérez-Aguirre B, Larrinua-Pacheco AD, López-Camarillo C, López-Gutiérrez JA, Garnica-Palazuelos J, Estrada-Macías ME, Cota-Quintero JL, Barraza-Gómez AA. Emerging role of lncRNAs in drug resistance mechanisms in head and neck squamous cell carcinoma. Front Oncol 2022; 12:965628. [PMID: 35978835 PMCID: PMC9376329 DOI: 10.3389/fonc.2022.965628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 12/12/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) originates in the squamous cell lining the mucosal surfaces of the head and neck region, including the oral cavity, nasopharynx, tonsils, oropharynx, larynx, and hypopharynx. The heterogeneity, anatomical, and functional characteristics of the patient make the HNSCC a complex and difficult-to-treat disease, leading to a poor survival rate and a decreased quality of life due to the loss of important physiologic functions and aggressive surgical injury. Alteration of driver-oncogenic and tumor-suppressing lncRNAs has recently been recently in HNSCC to obtain possible biomarkers for diagnostic, prognostic, and therapeutic approaches. This review provides current knowledge about the implication of lncRNAs in drug resistance mechanisms in HNSCC. Chemotherapy resistance is a major therapeutic challenge in HNSCC in which lncRNAs are implicated. Lately, it has been shown that lncRNAs involved in autophagy induced by chemotherapy and epithelial–mesenchymal transition (EMT) can act as mechanisms of resistance to anticancer drugs. Conversely, lncRNAs involved in mesenchymal–epithelial transition (MET) are related to chemosensitivity and inhibition of invasiveness of drug-resistant cells. In this regard, long non-coding RNAs (lncRNAs) play a pivotal role in both processes and are important for cancer detection, progression, diagnosis, therapy response, and prognostic values. As the involvement of more lncRNAs is elucidated in chemoresistance mechanisms, an improvement in diagnostic and prognostic tools could promote an advance in targeted and specific therapies in precision oncology.
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Affiliation(s)
- José A. Peña-Flores
- Faculty of Odontology, Autonomous University of Chihuahua, Chihuahua, Mexico
| | - Mercedes Bermúdez
- Faculty of Odontology, Autonomous University of Chihuahua, Chihuahua, Mexico
- *Correspondence: Mercedes Bermúdez,
| | - Rosalío Ramos-Payán
- Faculty of Biological and Chemical Sciences, Autonomous University of Sinaloa, Culiacán, Mexico
| | | | - Uriel Soto-Barreras
- Faculty of Odontology, Autonomous University of Chihuahua, Chihuahua, Mexico
| | | | | | | | | | | | - Jorge A. López-Gutiérrez
- Faculty of Biological and Chemical Sciences, Autonomous University of Sinaloa, Culiacán, Mexico
- Faculty of Biology, Autonomous University of Sinaloa, Culiacán, Mexico
| | | | | | - Juan L. Cota-Quintero
- Faculty of Biology, Autonomous University of Sinaloa, Culiacán, Mexico
- Faculty of Odontology , Autonomous University of Sinaloa, Culiacán, Mexico
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191
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Relationship Between the MicroRNAs and PI3K/AKT/mTOR Axis: Focus on Non-Small Cell Lung Cancer. Pathol Res Pract 2022; 239:154093. [DOI: 10.1016/j.prp.2022.154093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/21/2022]
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192
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Luo Y, Li T, Zhao H, Chen A. A novel 7‑hypoxia‑related long non‑coding RNA signature associated with prognosis and proliferation in melanoma. Mol Med Rep 2022; 26:255. [PMID: 35703357 PMCID: PMC9218734 DOI: 10.3892/mmr.2022.12771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/12/2022] [Indexed: 11/05/2022] Open
Abstract
Hypoxia‑related long non‑coding RNAs (lncRNAs) are important indicators of the poor prognosis of cancers. The present study aimed to explore the potential relationship between melanoma and hypoxia‑related lncRNAs. The transcriptome and clinical data of patients with melanoma were downloaded from The Cancer Genome Atlas database. The prognostic hypoxia‑related lncRNAs were screened out using Pearson's correlation test and univariate Cox analysis. As a result, a hypoxia‑related‑lncRNA signature based on the expression of 7 lncRNAs was constructed, with one unfavourable [MIR205 host gene (MIR205HG)] and six favourable (T cell receptor β variable 11‑2, HLA‑DQB1 antisense RNA 1, AL365361.1, AC004847.1, ubiquitin specific peptidase 30 antisense RNA 1 and AC022706.1) lncRNAs as prognostic factors for melanoma. Patients with melanoma were divided into high‑ and low‑risk groups based on the risk score obtained. Survival analyses were performed to assess the prognostic value of the present risk model. Potential tumour‑associated biological pathways associated with the present signature were explored using gene set enrichment analysis. The CIBERSORT algorithm demonstrated the important role of the hypoxia‑related lncRNAs in regulating tumour‑infiltrating immune cells. Clinical samples collected from our center partly confirmed our findings. Cell Counting Kit‑8 and flow cytometry assays indicated the suppression of proliferation of melanoma cells following inhibition of MIR205HG expression. Indicators of the canonical Wnt/β‑catenin signalling pathway were detected by western blotting. The present study demonstrated that MIR205HG could promote melanoma cell proliferation partly via the canonical Wnt/β‑catenin signalling pathway. These findings indicated a 7‑hypoxia‑related‑lncRNA signature that can serve as a novel predictor of melanoma prognosis.
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Affiliation(s)
- Yi Luo
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Tinghao Li
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Hengguang Zhao
- Department of Dermatology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, P.R. China
| | - Aijun Chen
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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193
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Zhou L, Ma J. MIR99AHG/miR-204-5p/TXNIP/Nrf2/ARE Signaling Pathway Decreases Glioblastoma Temozolomide Sensitivity. Neurotox Res 2022; 40:1152-1162. [PMID: 35904670 DOI: 10.1007/s12640-022-00536-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 10/16/2022]
Abstract
Glioblastoma (GBM) is the most prevalent primary cerebral tumor in adults with high aggressiveness. Temozolomide (TMZ) is considered as the most widely used chemotherapy for GBM patients. Accumulating studies have proved that long non-coding RNAs (lncRNAs) participate in the pathogenesis of tumors. The aim of our study is to disclose the role of mir-99a-let-7c cluster host gene (MIR99AHG) in GBM. MIR99AHG expression was discovered to be elevated in GBM cells through quantitative real-time polymerase chain reaction (RT-qPCR) analysis. Loss-of-function experiments demonstrated that MIR99AHG silencing enhanced TMZ sensitivity of GBM both in vitro and in vivo. RNA pull down, RNA-binding protein immunoprecipitation (RIP), and luciferase reporter assays were implemented to unveil the underlying mechanism of MIR99AHG in GBM. The results of the mechanism assays implied that MIR99AHG interacted with microRNA-204-5p (miR-204-5p) and enhanced thioredoxin interacting protein (TXNIP) expression to inactivate the Nrf2/ARE signaling pathway. MIR99AHG/miR-204-5p/TXNIP regulatory axis was verified by rescue experiments in GBM. To summarize, MIR99AHG plays a promoting role in the TMZ resistance of GBM cells. The findings in this study might provide novel sight for the treatment for GBM.
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Affiliation(s)
- Liang Zhou
- Department of Neurosurgery, Shanghai Fifth People's Hospital, Fudan University, No.801, Heqing Road, Minhang District, Shanghai, 200240, China
| | - Junfeng Ma
- Department of Neurosurgery, Shanghai Fifth People's Hospital, Fudan University, No.801, Heqing Road, Minhang District, Shanghai, 200240, China.
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194
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LncRNA ANRIL mediates endothelial dysfunction through BDNF downregulation in chronic kidney disease. Cell Death Dis 2022; 13:661. [PMID: 35906216 PMCID: PMC9338026 DOI: 10.1038/s41419-022-05068-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 01/21/2023]
Abstract
Endothelial dysfunction is common in patients with chronic kidney disease (CKD), but the mechanism is unknown. In this study, we found that the circulating ANRIL level was increased and correlated with vascular endothelial dysfunction in patients with CKD, also negatively correlated with plasma brain-derived neurotrophic factor (BDNF) concentration. We constructed the ANRIL knockout mice model, and found that ANRIL deficiency reversed the abnormal expression of BDNF, along with endothelial nitric oxide synthase (eNOS), vascular adhesion molecule 1 (VCAM-1) and Von Willebrand factor (vWF). Meanwhile, mitochondrial dynamics-related proteins, Dynamin-related protein 1 (Drp1) and mitofusins (Mfn2) level were also recovered. In addition, in vitro, serum derived from CKD patients and uremia toxins induced abnormal expression of ANRIL. By making use of the gain- and loss-of-function approaches, we observed that ANRIL mediated endothelial dysfunction through BDNF downregulation. To explore the specific mechanism, RNA pull-down and RNA-binding protein immunoprecipitation (RIP) were used to explore the binding of ANRIL to histone methyltransferase Enhancer of zeste homolog 2 (EZH2). Further experiments found increased EZH2 and histone H3 lysine 27 trimethylation (H3K27me3) levels at the BDNF promoter region. Collectively, we demonstrated that ANRIL mediate BDNF transcriptional suppression through recruitment of EZH2 to the BDNF promoter region, then regulated the proteins expression related to endothelial function and mitochondrial dynamics. This study provides new insights for the study of endothelial dysfunction in CKD.
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195
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Jiao X, Wang R, Ding X, Yan B, Lin Y, Liu Q, Wu Y, Zhou C. LncRNA-84277 is involved in chronic pain-related depressive behaviors through miR-128-3p/SIRT1 axis in central amygdala. Front Mol Neurosci 2022; 15:920216. [PMID: 35959106 PMCID: PMC9362774 DOI: 10.3389/fnmol.2022.920216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Long-term chronic pain can lead to depression. However, the mechanism underlying chronic pain-related depression remains unclear. Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylase (HDAC). Our previous studies have demonstrated that SIRT1 in the central nucleus of the amygdala (CeA) is involved in the development of chronic pain-related depression. In addition, increasing studies have indicated that long non-coding RNAs (lncRNAs) play a vital role in the pathogenesis of pain or depression. However, whether lncRNAs are involved in SIRT1-mediated chronic pain-related depression remains largely unknown. In this study, we identified that a novel lncRNA-84277 in CeA was the upstream molecule to regulate SIRT1 expression. Functionally, lncRNA-84277 overexpression in CeA significantly alleviated the depression-like behaviors in spared nerve injury (SNI)-induced chronic pain rats, whereas lncRNA-84277 knockdown in CeA induced the depression-like behaviors in naïve rats. Mechanically, lncRNA-84277 acted as a competing endogenous RNA (ceRNA) to upregulate SIRT1 expression by competitively sponging miR-128-3p, and therefore improved chronic pain-related depression-like behaviors. Our findings reveal the critical role of lncRNA-84277 in CeA specifically in guarding against chronic pain-related depression via a ceRNA mechanism and provide a potential therapeutic target for chronic pain-related depression.
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Affiliation(s)
- Xiaowei Jiao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Ruiyao Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Xiaobao Ding
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Binbin Yan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Yuwen Lin
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Qiang Liu
- Jiangsu Province Key Laboratory of Anesthesiology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Yuqing Wu
- Jiangsu Province Key Laboratory of Anesthesiology, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
- Yuqing Wu,
| | - Chenghua Zhou
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Chenghua Zhou,
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196
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Qi X, Chen X, Zhao Y, Chen J, Niu B, Shen B. Prognostic Roles of ceRNA Network-Based Signatures in Gastrointestinal Cancers. Front Oncol 2022; 12:921194. [PMID: 35924172 PMCID: PMC9339642 DOI: 10.3389/fonc.2022.921194] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/15/2022] [Indexed: 01/19/2023] Open
Abstract
Gastrointestinal cancers (GICs) are high-incidence malignant tumors that seriously threaten human health around the world. Their complexity and heterogeneity make the classic staging system insufficient to guide patient management. Recently, competing endogenous RNA (ceRNA) interactions that closely link the function of protein-coding RNAs with that of non-coding RNAs, such as long non-coding RNA (lncRNA) and circular RNA (circRNA), has emerged as a novel molecular mechanism influencing miRNA-mediated gene regulation. Especially, ceRNA networks have proven to be powerful tools for deciphering cancer mechanisms and predicting therapeutic responses at the system level. Moreover, abnormal gene expression is one of the critical breaking events that disturb the stability of ceRNA network, highlighting the role of molecular biomarkers in optimizing cancer management and treatment. Therefore, developing prognostic signatures based on cancer-specific ceRNA network is of great significance for predicting clinical outcome or chemotherapy benefits of GIC patients. We herein introduce the current frontiers of ceRNA crosstalk in relation to their pathological implications and translational potentials in GICs, review the current researches on the prognostic signatures based on lncRNA or circRNA-mediated ceRNA networks in GICs, and highlight the translational implications of ceRNA signatures for GICs management. Furthermore, we summarize the computational approaches for establishing ceRNA network-based prognostic signatures, providing important clues for deciphering GIC biomarkers.
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Affiliation(s)
- Xin Qi
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Xingqi Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Yuanchun Zhao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Jiajia Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Bairong Shen,
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Alba J, Barcia R, Gutiérrez-Berzal J, Ramos-Martínez JI. Could inhibition of metalloproteinases be used to block the process of metastasis? Cell Biochem Funct 2022; 40:600-607. [PMID: 35789101 PMCID: PMC9544369 DOI: 10.1002/cbf.3730] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 12/14/2022]
Abstract
Metastasis is a multisequential process that allows tumor cells to migrate to tissues distant from the primary tumor. Only a small number of cells escape from the primary tumor; however, the metastases generated are responsible for more than 90% of cancer deaths. Many metastatic processes initially require the total or partial start‐up of a program for the transformation of tumor epithelial cells into mesenchymal cells (EMT). The launching of the EMT program is stimulated by cytokines and other elements produced by the diverse types of cells composing the tumor stroma. In parallel, a process of destabilization of the extracellular matrix (ECM) takes place by means of the synthesis of proteases of the matrix metalloproteinases (MMPs) family. EMC degradation allows the exportation of some tumor cells as mesenchymal cells to the circulatory system and their subsequent implantation in a tissue distant from the primary tumor. The blocking of these both processes appears as a hypothetical stop point in the metastatic mechanism. The present review deals with the different options to achieve the inhibition of MMPs, focusing on MMP7 as a target given its involvement in the metastatic processes of a wide variety of tumors. The simultaneous implantation of the epithelial–mesenchymal program and the synthesis and activation of matrix metalloproteinases during the first phases of the metastasis process is known. The inhibition of proteases could constitute a possible blockage of the process. The review describes the evolution of the different inhibition mechanisms that could inform applicable therapeutic mechanisms for the paralysis of the metastatic process.
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Affiliation(s)
- Jesús Alba
- Histobiomol, Hospital POLUSA, Lugo, Spain
| | - Ramiro Barcia
- Faculty of Sciences, University of Santiago de Compostela, Lugo, Spain
| | | | - Juan I Ramos-Martínez
- Department of Biochemistry and Molecular Biology, School of Veterinary, University of Santiago de Compostela, Lugo, Spain
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198
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Xu D, Xu Z, Bi X, Cai J, Cao M, Zheng D, Chen L, Li P, Wang H, Wu D, Yang J, Li K. Identification and functional analysis of N6-methyladenine (m 6 A)-related lncRNA across 33 cancer types. Cancer Med 2022; 12:2104-2116. [PMID: 35789547 PMCID: PMC9883401 DOI: 10.1002/cam4.5001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/12/2022] [Accepted: 06/20/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6 A) plays an essential role in tumorigenesis and cancer progression. Long noncoding RNAs (lncRNAs) are discovered to be important targets of m6 A modification, and they play fundamental roles in diverse biological processes. However, there is still a lack of knowledge with regards to the association between m6 A and lncRNAs in human tumors. METHODS The relationship between lncRNAs and 21 m6 A regulators was comprehensively explored, through the integration of multi-omics data from M6A2Target, m6A-Atlas, and TCGA (The Cancer Genome Atlas). In order to explore the potential roles of m6A-related lncRNAs in human tumors, three applicable methods were introduced, which include the construction of ceRNA networks, drug sensitivity estimation, and survival analysis. RESULTS A substantial number of positive correlation events across 33 cancer types were found. Moreover, cancer-specific lncRNAs were associated with tissue specificity, and cancer-common lncRNAs were conserved in cancer-related biological function. In particular, the m6 A-related lncRNA FGD5-AS1 was found to be associated with cancer treatment, through its influence on cisplatin resistance in breast cancer patients. Finally, a user-friendly interface Lnc2m6A, which is enriched with various browsing sections resource for the exhibition of relationships and putative biogenesis between lncRNAs and m6 A modifications, is offered in http://hainmu-biobigdata.com/Lnc2m6A. CONCLUSIONS In summary, the results from this paper will provide a valuable resource that guides both mechanistic and therapeutic roles of m6 A-related lncRNAs in human tumors.
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Affiliation(s)
- Dahua Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of EducationCollege of Biomedical Information and Engineering, Hainan General Hospital, Hainan Medical UniversityHaikouChina
| | - Zhizhou Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of EducationCollege of Biomedical Information and Engineering, Hainan General Hospital, Hainan Medical UniversityHaikouChina
| | - Xiaoman Bi
- Key Laboratory of Tropical Translational Medicine of Ministry of EducationCollege of Biomedical Information and Engineering, Hainan General Hospital, Hainan Medical UniversityHaikouChina
| | - Jiale Cai
- Key Laboratory of Tropical Translational Medicine of Ministry of EducationCollege of Biomedical Information and Engineering, Hainan General Hospital, Hainan Medical UniversityHaikouChina
| | - Meng Cao
- Key Laboratory of Tropical Translational Medicine of Ministry of EducationCollege of Biomedical Information and Engineering, Hainan General Hospital, Hainan Medical UniversityHaikouChina
| | - Dehua Zheng
- Key Laboratory of Tropical Translational Medicine of Ministry of EducationCollege of Biomedical Information and Engineering, Hainan General Hospital, Hainan Medical UniversityHaikouChina
| | - Liyang Chen
- Key Laboratory of Tropical Translational Medicine of Ministry of EducationCollege of Biomedical Information and Engineering, Hainan General Hospital, Hainan Medical UniversityHaikouChina
| | - Peihu Li
- Key Laboratory of Tropical Translational Medicine of Ministry of EducationCollege of Biomedical Information and Engineering, Hainan General Hospital, Hainan Medical UniversityHaikouChina
| | - Hong Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of EducationCollege of Biomedical Information and Engineering, Hainan General Hospital, Hainan Medical UniversityHaikouChina
| | - Deng Wu
- School of Life Sciences, Faculty of ScienceThe Chinese University of Hong KongHong Kong
| | - Jun Yang
- Key Laboratory of Tropical Translational Medicine of Ministry of EducationCollege of Biomedical Information and Engineering, Hainan General Hospital, Hainan Medical UniversityHaikouChina
| | - Kongning Li
- Key Laboratory of Tropical Translational Medicine of Ministry of EducationCollege of Biomedical Information and Engineering, Hainan General Hospital, Hainan Medical UniversityHaikouChina
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199
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Li H, Gao J, Liu L, Zhang S. LINC00958: A promising long non-coding RNA related to cancer. Biomed Pharmacother 2022; 151:113087. [PMID: 35569349 DOI: 10.1016/j.biopha.2022.113087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/27/2022] [Accepted: 05/04/2022] [Indexed: 11/02/2022] Open
Abstract
Long non-coding RNAs (lncRNAs), a class of RNA transcripts longer than 200 nucleotides, do not encode proteins; however, they encode small peptides and micropeptides that act as bioactive peptides with notable effects in regulating the progression of malignant tumors, such as lung and colorectal cancers, and affecting patient prognosis. lncRNAs are important intracellular regulators, particularly in tumorigenesis and tumor progression. Long intergenic non-protein coding RNA958 (LINC00958), which has received increasing attention in recent years, is highly expressed in various malignancies, including head and neck squamous cell carcinoma (HNSC), non-small-cell lung cancer (NSCLC), gastric cancer, hepatocellular carcinoma (HCC), colorectal cancer, bladder cancer, and breast cancer. Here, we reviewed the recent studies on LINC00958 as well as its closely related clinical features and functional regulation in cancers. We systematically expounded the molecular mechanisms underlying the biological functions of LINC00958 in inhibiting cell apoptosis and enhancing the chemoradiotherapy resistance of tumor cells. The upregulation of LINC00958 enhances the resistance of tumor cells to radiotherapy and chemotherapy and induces lymphangiogenesis. Moreover, it is involved in tumor glycolytic metabolism, which plays a crucial role in facilitating the proliferation, invasion, and migration of tumor cells. Additionally, analysis of various studies revealed that LINC00958 acts as an endogenous competitive RNA (ceRNA) and regulates the malignant behavior of tumor cells through the miRNA-mRNA axis. Collectively, the use of LINC00958 as a novel biomarker and therapeutic target for the clinical diagnosis and treatment of different cancers has bright prospects in the future.
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Affiliation(s)
- Hongxu Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ, Transplantation at Henan Universities, Zhengzhou 450052, China; Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou 450052, China
| | - Jie Gao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ, Transplantation at Henan Universities, Zhengzhou 450052, China; Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou 450052, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ, Transplantation at Henan Universities, Zhengzhou 450052, China; Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou 450052, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ, Transplantation at Henan Universities, Zhengzhou 450052, China; Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou 450052, China.
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Singh D, Assaraf YG, Gacche RN. Long Non-coding RNA Mediated Drug Resistance in Breast Cancer. Drug Resist Updat 2022; 63:100851. [DOI: 10.1016/j.drup.2022.100851] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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