1
|
Zhang S, Wu Q, Cheng W, Dong W, Kou B. YTHDC1-Mediated lncRNA MSC-AS1 m6A Modification Potentiates Laryngeal Squamous Cell Carcinoma Development via Repressing ATXN7 Transcription. Mol Biotechnol 2024:10.1007/s12033-024-01150-5. [PMID: 38637450 DOI: 10.1007/s12033-024-01150-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024]
Abstract
Laryngeal squamous cell carcinoma (LSCC) has the highest mortality rate among head and neck squamous cell carcinoma. This study was designed to investigate the biological effect of long noncoding RNA (lncRNA) MSC antisense RNA 1 (MSC-AS1) on LSCC development and the underlying mechanism. The expression and prognostic value of lncRNAs in head and neck squamous cell carcinoma were predicted in the bioinformatics tools. The overexpression of MSC-AS1 in LSCC patients predicted a poor prognosis. Depletion of MSC-AS1 using shRNA repressed the malignant phenotype of AMC-HN-8 and TU-177 cells. MSC-AS1, mainly localized in the nucleus, interacted closely with the transcription factor CCCTC-binding factor (CTCF). CTCF played anti-tumor effects in vitro and in vivo. Ataxin-7 (ATXN7) was predicted to be a downstream target of CTCF, whose expression was negatively controlled by MSC-AS1. MSC-AS1 was found to block the expression of CTCF, thereby repressing ATXN7. Finally, MSC-AS1 overexpression in LSCC was governed by YTH domain-containing protein 1 (YTHDC1)-mediated m6A modification. In summary, our research identified the YTHDC1/MSC-AS1/CTCF/ATXN7 axis in LSCC development, which indicated that MSC-AS1 is an attractive biomarker in the LSCC treatment.
Collapse
Affiliation(s)
- Shu Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, 710061, Shaanxi, People's Republic of China
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, People's Republic of China
| | - Qun Wu
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Wei Cheng
- Department of General Surgery, Danfeng County Hospital, Shangluo, 726200, Shaanxi, People's Republic of China
| | - Weijiang Dong
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Bo Kou
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, 710061, Shaanxi, People's Republic of China.
| |
Collapse
|
2
|
Liu Y, Meng J, Ruan X, Wei F, Zhang F, Qin X. A disulfidptosis-related lncRNAs signature in hepatocellular carcinoma: prognostic prediction, tumor immune microenvironment and drug susceptibility. Sci Rep 2024; 14:746. [PMID: 38185671 PMCID: PMC10772085 DOI: 10.1038/s41598-024-51459-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/05/2024] [Indexed: 01/09/2024] Open
Abstract
Disulfidptosis, a novel type of programmed cell death, has attracted researchers' attention worldwide. However, the role of disulfidptosis-related lncRNAs (DRLs) in liver hepatocellular carcinoma (LIHC) not yet been studied. We aimed to establish and validate a prognostic signature of DRLs and analyze tumor microenvironment (TME) and drug susceptibility in LIHC patients. RNA sequencing data, mutation data, and clinical data were obtained from the Cancer Genome Atlas Database (TCGA). Lasso algorithm and cox regression analysis were performed to identify a prognostic DRLs signature. Kaplan-Meier curves, principal component analysis (PCA), nomogram and calibration curve, function enrichment, TME, immune dysfunction and exclusion (TIDE), tumor mutation burden (TMB), and drug sensitivity analyses were analyzed. External datasets were used to validate the predictive value of DRLs. qRT-PCR was also used to validate the differential expression of the target lncRNAs in tissue samples and cell lines. We established a prognostic signature for the DRLs (MKLN1-AS and TMCC1-AS1) in LIHC. The signature could divide the LIHC patients into low- and high-risk groups, with the high-risk subgroup associated with a worse prognosis. We observed discrepancies in tumor-infiltrating immune cells, immune function, function enrichment, and TIDE between two risk groups. LIHC patients in the high-risk group were more sensitive to several chemotherapeutic drugs. External datasets, clinical tissue, and cell lines confirmed the expression of MKLN1-AS and TMCC1-AS1 were upregulated in LIHC and associated with a worse prognosis. The novel signature based on the two DRLs provide new insight into LIHC prognostic prediction, TME, and potential therapeutic strategies.
Collapse
Affiliation(s)
- Yanqiong Liu
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jiyu Meng
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xuelian Ruan
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Fangyi Wei
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Fuyong Zhang
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xue Qin
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.
| |
Collapse
|
3
|
Huang M, Wang X, Botchway BOA, Zhang Y, Liu X. The role of long noncoding ribonucleic acids in the central nervous system injury. Mol Cell Biochem 2023:10.1007/s11010-023-04875-0. [PMID: 37898578 DOI: 10.1007/s11010-023-04875-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/05/2023] [Indexed: 10/30/2023]
Abstract
Central nervous system (CNS) injury involves complex pathophysiological molecular mechanisms. Long noncoding ribonucleic acids (lncRNAs) are an important form of RNA that do not encode proteins but take part in the regulation of gene expression and various biological processes. Multitudinous studies have evidenced lncRNAs to have a significant role in the process of progression and recovery of various CNS injuries. Herein, we review the latest findings pertaining to the role of lncRNAs in CNS, both normal and diseased state. We aim to present a comprehensive clinical application prospect of lncRNAs in CNS, and thus, discuss potential strategies of lncRNAs in treating CNS injury.
Collapse
Affiliation(s)
- Min Huang
- Department of Histology and Embryology, School of Medicine, Shaoxing University, Shaoxing City, 312000, China
| | - Xizhi Wang
- Department of Histology and Embryology, School of Medicine, Shaoxing University, Shaoxing City, 312000, China
- Department of Cardiology, Lihuili Hospital Affiliated to Ningbo University, Ningbo City, China
| | | | - Yong Zhang
- Department of Histology and Embryology, School of Medicine, Shaoxing University, Shaoxing City, 312000, China
| | - Xuehong Liu
- Department of Histology and Embryology, School of Medicine, Shaoxing University, Shaoxing City, 312000, China.
| |
Collapse
|
4
|
Lu S, Liu X, Wu C, Zhang J, Stalin A, Huang Z, Tan Y, Wu Z, You L, Ye P, Fu C, Zhang X, Wu J. Identification of an immune-related 6-lncRNA panel with a good performance for prognostic prediction in hepatocellular carcinoma by integrated bioinformatics analysis. Medicine (Baltimore) 2023; 102:e33990. [PMID: 37478241 PMCID: PMC10662904 DOI: 10.1097/md.0000000000033990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/23/2023] [Indexed: 07/23/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most malignant tumors with a poor prognosis. The long non-coding RNA (lncRNA) has been found to have great potential as a prognostic biomarker or therapeutic target for cancer patients. However, the prognostic value and tumor immune infiltration of lncRNAs in HCC has yet to be fully elucidated. To identify prognostic biomarkers of lncRNA in HCC by integrated bioinformatics analysis and explore their functions and relationship with tumor immune infiltration. The prognostic risk assessment model for HCC was constructed by comprehensively using univariate/multivariate Cox regression analysis, Kaplan-Meier survival analysis, and the least absolute shrinkage and selection operator regression analysis. Subsequently, the accuracy, independence, and sensitivity of our model were evaluated, and a nomogram for individual prediction in the clinic was constructed. Tumor immune microenvironment (TIME), immune checkpoints, and human leukocyte antigen alleles were compared in high- and low-risk patients. Finally, the functions of our lncRNA signature were examined using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and gene set enrichment analysis. A 6-lncRNA panel of HCC consisting of RHPN1-AS1, LINC01224, CTD-2510F5.4, RP1-228H13.5, LINC01011, and RP11-324I22.4 was eventually identified, and show good performance in predicting the survivals of patients with HCC and distinguishing the immunomodulation of TIME of high- and low-risk patients. Functional analysis also suggested that this 6-lncRNA panel may play an essential role in promoting tumor progression and immune regulation of TIME. In this study, 6 potential lncRNAs were identified as the prognostic biomarkers in HCC, and the regulatory mechanisms involved in HCC were initially explored.
Collapse
Affiliation(s)
- Shan Lu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xinkui Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Chao Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jingyuan Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Antony Stalin
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhihong Huang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yingying Tan
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Zhishan Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Leiming You
- Department of Immunology and Microbiology, School of Life Science, Beijing University of Chinese Medicine, Beijing, China
| | - Peizhi Ye
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Changgeng Fu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaomeng Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jiarui Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| |
Collapse
|
5
|
Hua T, Liu DX, Zhang XC, Li ST, Yan P, Zhao Q, Chen SB. CD4+ conventional T cells-related genes signature is a prognostic indicator for ovarian cancer. Front Immunol 2023; 14:1151109. [PMID: 37063862 PMCID: PMC10104164 DOI: 10.3389/fimmu.2023.1151109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/16/2023] [Indexed: 04/18/2023] Open
Abstract
Introduction It is believed that ovarian cancer (OC) is the most deadly form of gynecological cancer despite its infrequent occurrence, which makes it one of the most salient public health concerns. Clinical and preclinical studies have revealed that intratumoral CD4+ T cells possess cytotoxic capabilities and were capable of directly killing cancer cells. This study aimed to identify the CD4+ conventional T cells-related genes (CD4TGs) with respect to the prognosis in OC. Methods We obtained the transcriptome and clinical data from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. CD4TGs were first identified from single-cell datasets, then univariate Cox regression was used to screen prognosis-related genes, LASSO was conducted to remove genes with coefficient zero, and multivariate Cox regression was used to calculate riskscore and to construct the CD4TGs risk signature. Kaplan-Meier analysis, univariate Cox regression, multivariate Cox regression, time-dependent receiver operating characteristics (ROC), decision curve analysis (DCA), nomogram, and calibration were made to verify and evaluate the risk signature. Gene set enrichment analyses (GSEA) in risk groups were conducted to explore the tightly correlated pathways with the risk group. The role of riskscore has been further explored in the tumor microenvironment (TME), immunotherapy, and chemotherapy. A risk signature with 11 CD4TGs in OC was finally established in the TCGA database and furtherly validated in several GEO cohorts. Results High riskscore was significantly associated with a poorer prognosis and proven to be an independent prognostic biomarker by multivariate Cox regression. The 1-, 3-, and 5-year ROC values, DCA curve, nomogram, and calibration results confirmed the excellent prediction power of this model. Compared with the reported risk models, our model showed better performance. The patients were grouped into high-risk and low-risk subgroups according to the riskscore by the median value. The low-risk group patients tended to exhibit a higher immune infiltration, immune-related gene expression and were more sensitive to immunotherapy and chemotherapy. Discussion Collectively, our findings of the prognostic value of CD4TGs in prognosis and immune response, provided valuable insights into the molecular mechanisms and clinical management of OC.
Collapse
Affiliation(s)
- Tian Hua
- Department of Gynecology, Affiliated Xingtai People Hospital of Hebei Medical University, Xingtai, China
| | - Deng-xiang Liu
- Department of Oncology, Affiliated Xingtai People Hospital of Hebei Medical University, Xingtai, China
| | - Xiao-chong Zhang
- Department of Oncology, Affiliated Xingtai People Hospital of Hebei Medical University, Xingtai, China
| | - Shao-teng Li
- Department of Oncology, Affiliated Xingtai People Hospital of Hebei Medical University, Xingtai, China
| | - Peng Yan
- Department of Oncology, The Second Affiliated Hospital Of Xingtai Medical College, Xingtai, China
| | - Qun Zhao
- Department of Oncology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, China
- *Correspondence: Shu-bo Chen, ; Qun Zhao,
| | - Shu-bo Chen
- Department of Oncology, Affiliated Xingtai People Hospital of Hebei Medical University, Xingtai, China
- *Correspondence: Shu-bo Chen, ; Qun Zhao,
| |
Collapse
|