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Gu Y, Xu M, Wu W, Ma Z, Liu W. Identification of N6-Methyladenosine-Associated lncRNAs and Analysis of Prognostic Signature in Breast Cancer. Biochem Genet 2024:10.1007/s10528-024-10889-0. [PMID: 39042347 DOI: 10.1007/s10528-024-10889-0] [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: 05/06/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]
Abstract
Breast cancer represents the predominant malignant neoplasm in women, posing significant threats to both life and health. N6-methyladenosine (m6A) methylation, the most prevalent RNA modification, plays a crucial role in cancer development. This study aims to delineate the prognostic implications of m6A-associated long non-coding RNAs (m6AlncRNAs) and identify potential m6AlncRNA candidates as novel therapeutic targets for breast cancer. Through univariate Cox, Least Absolute Shrinkage and Selection Operator and multiple Cox regression analysis, m6AlncRNA was analyzed and a risk-prognosis model was constructed. Kaplan-Meier analysis, principal component analysis and nomogram were used to evaluate the risk model. Finally, we screened candidate lncRNAs and validated them in breast cancer cell lines. m6AlncRNAs were stratified into three subtypes, and their associations with survival outcomes and immune infiltrating capacities were systematically analyzed. Subsequently, breast cancer patients were stratified into high and low-risk groups based on median risk scores, revealing distinct clinical characteristics, tumor immunoinvasive profiles, tumor mutation burden, and survival probabilities. Additionally, a prognostic model was established, highlighting three promising candidate lncRNAs: ECE1-AS1, NDUFA6-DT, and COL4A2-AS1. This study investigated the prognostic implications of m6A-associated long non-coding RNAs (m6AlncRNAs) and developed a prognostic risk model to identify three potential m6AlncRNA candidates. These findings provide valuable insights into the potential application of these m6AlncRNAs in guiding immunotherapeutic strategies for breast cancer.
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Affiliation(s)
- Yun Gu
- Department of Pathology, Nanjing Women and Children's Healthcare Hospital, Women's Hospital of Nanjing Medical University, Tianfei Road 123th, Nanjing, 210004, Jiangsu, China
| | - Min Xu
- Department of Pathology, Nanjing Women and Children's Healthcare Hospital, Women's Hospital of Nanjing Medical University, Tianfei Road 123th, Nanjing, 210004, Jiangsu, China
| | - Wangfei Wu
- Department of Pathology, Nanjing Women and Children's Healthcare Hospital, Women's Hospital of Nanjing Medical University, Tianfei Road 123th, Nanjing, 210004, Jiangsu, China
| | - Zhifang Ma
- Department of Pathology, Nanjing Women and Children's Healthcare Hospital, Women's Hospital of Nanjing Medical University, Tianfei Road 123th, Nanjing, 210004, Jiangsu, China.
| | - Weiguang Liu
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.
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2
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Huang R, Kong Y, Luo Z, Li Q. LncRNA NDUFA6-DT: A Comprehensive Analysis of a Potential LncRNA Biomarker and Its Regulatory Mechanisms in Gliomas. Genes (Basel) 2024; 15:483. [PMID: 38674418 PMCID: PMC11050413 DOI: 10.3390/genes15040483] [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: 03/16/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Gliomas are the most prevalent primary malignant tumors affecting the brain, with high recurrence and mortality rates. Accurate diagnoses and effective treatment challenges persist, emphasizing the need for identifying new biomarkers to guide clinical decisions. Long noncoding RNAs (lncRNAs) hold potential as diagnostic and therapeutic biomarkers in cancer. However, only a limited subset of lncRNAs in gliomas have been explored. Therefore, this study aims to identify lncRNA signatures applicable to patients with gliomas across all grades and explore their clinical significance and potential biological mechanisms. Data used in this study were obtained from TCGA, CGGA, and GEO datasets to identify key lncRNA signatures in gliomas through differential and survival analyses and machine learning algorithms. We examined their associations with the clinical characteristics, gene mutations, diagnosis, and prognosis of gliomas. Functional enrichment analysis was employed to elucidate the potential biological mechanisms associated with these significant lncRNA signatures. We explored competing endogenous RNA (ceRNA) regulatory networks. We found that NDUFA6-DT emerged as a significant lncRNA signature in gliomas, with reduced NDUFA6-DT expression associated with a worse prognosis in gliomas. Nomogram analysis incorporating NDUFA6-DT expression levels exhibited excellent prognostic and predictive capabilities. Functional annotation suggested that NDUFA6-DT might influence immunological responses and synaptic transmission, potentially modifying glioma initiation and progression. The associated ceRNA network revealed the possible presence of the NDUFA6-DT-miR-455-3p-YWHAH/YWHAG axis in low-grade glioma (LGG) and glioblastoma multiforme (GBM), regulating the PI3K-AKT signaling pathway and influencing glioma cell survival and apoptosis. We believe that NDUFA6-DT is a novel lncRNA linked to glioma diagnosis and prognosis, potentially becoming a pivotal biomarker for glioma.
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Affiliation(s)
- Ruiting Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (R.H.); (Y.K.); (Z.L.)
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou 510006, China
| | - Ying Kong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (R.H.); (Y.K.); (Z.L.)
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou 510006, China
| | - Zhiqing Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (R.H.); (Y.K.); (Z.L.)
| | - Quhuan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (R.H.); (Y.K.); (Z.L.)
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou 510006, China
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3
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Zhao S, Wang Q, Liu Y, Zhang P, Ji W, Xie J, Cheng C. Interaction, immune infiltration characteristics and prognostic modeling of efferocytosis-related subtypes in glioblastoma. BMC Med Genomics 2023; 16:248. [PMID: 37853449 PMCID: PMC10583324 DOI: 10.1186/s12920-023-01688-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Efferocytosis is a biological process in which phagocytes remove apoptotic cells and vesicles from tissues. This process is initiated by the release of inflammatory mediators from apoptotic cells and plays a crucial role in resolving inflammation. The signals associated with efferocytosis have been found to regulate the inflammatory response and the tumor microenvironment (TME), which promotes the immune escape of tumor cells. However, the role of efferocytosis in glioblastoma multiforme (GBM) is not well understood and requires further investigation. METHODS In this study, we conducted a comprehensive analysis of 22 efferocytosis-related genes (ERGs) by searching for studies related to efferocytosis. Using bulk RNA-Seq and single-cell sequencing data, we analyzed the expression and mutational characteristics of these ERGs. By using an unsupervised clustering algorithm, we obtained ERG clusters from 549 GBM patients and evaluated the immune infiltration characteristics of each cluster. We then identified differential genes (DEGs) in the two ERG clusters and classified GBM patients into different gene clusters using univariate cox analysis and unsupervised clustering algorithms. Finally, we utilized the Boruta algorithm to screen for prognostic genes and reduce dimensionality, and the PCA algorithm was applied to create a novel efferocytosis-related scoring system. RESULTS Differential expression of ERGs in glioma cell lines and normal cells was analyzed by rt-PCR. Cell function experiments, on the other hand, validated TIMD4 as a tumor risk factor in GBM. We found that different ERG clusters and gene clusters have distinct prognostic and immune infiltration profiles. The ERG signature we developed provides insight into the tumor microenvironment of GBM. Patients with lower ERG scores have a better survival rate and a higher likelihood of benefiting from immunotherapy. CONCLUSIONS Our novel efferocytosis-related signature has the potential to be used in clinical practice for risk stratification of GBM patients and for selecting individuals who are likely to respond to immunotherapy. This can help clinicians design appropriate targeted therapies before initiating clinical treatment.
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Affiliation(s)
- Songyun Zhao
- Department of Neurosurgery, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yuankun Liu
- Department of Neurosurgery, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Pengpeng Zhang
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Ji
- Department of Neurosurgery, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Jiaheng Xie
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, China.
| | - Chao Cheng
- Department of Neurosurgery, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China.
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LncRNA WDR11-AS1 Promotes Extracellular Matrix Synthesis in Osteoarthritis by Directly Interacting with RNA-Binding Protein PABPC1 to Stabilize SOX9 Expression. Int J Mol Sci 2023; 24:ijms24010817. [PMID: 36614257 PMCID: PMC9820994 DOI: 10.3390/ijms24010817] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
Osteoarthritis (OA) is a degenerative disease of articular cartilage that is mainly characterized by chronic and mild inflammation of the joints. Recently, many studies have reported the crucial roles of long noncoding RNAs (lncRNAs) in OA as gene transcriptional regulatory factors, diagnostic biomarkers, or therapeutic targets. However, the exact mechanisms of lncRNAs in the regulation of OA progression remain unclear. In the present study, the lncRNA WDR11 divergent transcript (lncRNA WDR11-AS1) was shown to be downregulated in osteoarthritic cartilage tissues from patients, and to promote extracellular matrix (ECM) synthesis in osteoarthritic chondrocytes with knockdown and overexpression experiments. This function of lncRNA WDR11-AS1 was linked to its ability to interact with the polyadenylate-binding protein cytoplasmic 1 (PABPC1), which was screened by RNA pulldown and mass spectrometry analyses. PABPC1 was discovered to bind ECM-related mRNAs such as SOX9, and the inhibition of PABPC1 improved the mRNA stability of SOX9 to mitigate OA progression. Our results suggest that lncRNA WDR11-AS1 has a promising inhibitory effect on inflammation-induced ECM degradation in OA by directly binding PABPC1, thereby establishing lncRNA WDR11-AS1 and PABPC1 as potential therapeutic targets in the treatment of OA.
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Xu G, Li C, Di Z, Yang Y, Liang L, Yuan Q, Yang Q, Dong X, Xu S, Wu G. Development of the expression and prognostic significance of
m
5
C
‐related
LncRNAs
in breast cancer. Cancer Med 2022; 12:7667-7681. [PMID: 36464884 PMCID: PMC10067052 DOI: 10.1002/cam4.5500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 11/02/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND 5-Methylcytosine (m5C) methylation is a major epigenetic RNA modification and is closely related to tumorigenesis in various cancers. This study aimed to explore the prognostic value of m5C-related lncRNAs in breast cancer. METHODS Clinical characteristics and RNA-seq expression data from TCGA (The Cancer Genome Atlas) were used in the study. First, we performed differentially expressed gene (DEG) analysis and constructed a PPI network for the 12 m5C regulators. Then, we identified the m5C-related LncRNAs by the "cor. test." An m5C-related lncRNA prognostic risk signature was developed using univariate Cox regression and Lasso-penalized Cox regression analyses. The model's performance was determined using Kaplan-Meier (KM) survival analysis and ROC curves. Finally, a nomogram was constructed for clinical application in evaluating patients with BRCA. We also researched the drug sensitivity of signature lncRNAs and immune cell infiltration. Finally, we validated the expression of the signature lncRNAs through qRT-PCR in a breast cancer cell line and a breast epithelial cell line. RESULTS Overall, we constructed an 11-lncRNA risk score signature based on the lncRNAs associated with m5C regulators. According to the median risk score, we divided BRCA patients into high- and low-risk groups. The prognostic risk signature displayed excellent accuracy and demonstrated sufficient independence from other clinical characteristics. The immune cell infiltration analysis showed that the prognostic risk signature was related to the infiltration of immune cell subtypes. Drug sensitivity proved that our prognostic risk signature potentially has therapeutic value. CONCLUSIONS The m5C-related lncRNA signature reliably predicted the prognosis of breast cancer patients and may provide new insight into the breast cancer tumor immune microenvironment.
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Affiliation(s)
- Gaoran Xu
- Department of Thyroid and Breast Surgery Zhongnan Hospital of Wuhan University Wuhan China
| | - Chengxin Li
- Department of Thyroid and Breast Surgery Zhongnan Hospital of Wuhan University Wuhan China
| | - Ziyang Di
- Department of Gastrointestinal Surgery and Department of Gastric and Colorectal Surgical Oncology Zhongnan Hospital of Wuhan University Wuhan China
| | - Yalong Yang
- Department of Thyroid and Breast Surgery Zhongnan Hospital of Wuhan University Wuhan China
| | - Leilei Liang
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
| | - Qianqian Yuan
- Department of Thyroid and Breast Surgery Zhongnan Hospital of Wuhan University Wuhan China
| | - Qian Yang
- Department of Thyroid and Breast Surgery Zhongnan Hospital of Wuhan University Wuhan China
| | - Xingxing Dong
- Department of Thyroid and Breast Surgery Zhongnan Hospital of Wuhan University Wuhan China
| | - Siguang Xu
- Xinxiang Medical College Xinxiang Medical University Xinxiang China
| | - Gaosong Wu
- Department of Thyroid and Breast Surgery Zhongnan Hospital of Wuhan University Wuhan China
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Liu S, Wu S, Xie T, Yeh YY, Li C, Liu T, Sun C, Yang L, Li Z, Yu Y, Hu F, Zhu W, Zhang X. Neuronavigation-Guided Transcortical-Transventricular Endoport-Assisted Endoscopic Resection for Thalamic Lesions: Preliminary Experience. World Neurosurg 2022; 166:19-27. [PMID: 35772710 DOI: 10.1016/j.wneu.2022.06.110] [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: 03/25/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Surgery for thalamic lesions is generally challenging because they are deep-seated lesions surrounded by vital neurovascular structures. Whether neuronavigation-guided transcortical-transventricular endoport-assisted endoscopic resection for thalamic lesions is feasible remains to be further evaluated. METHODS A retrospective review of 8 who patients received neuronavigation-guided transcortical-transventricular endoport-assisted endoscopic resection for thalamic lesions was performed. Preoperative and tumor-related variables and postoperative outcomes were analyzed. RESULTS All lesions were located in the medial part of the thalamus, and most of them expanded forward, downward, or backward. Median size of lesions was 31 mm (range, 16-52 mm). Final pathology results confirmed that 1 case was a cavernous malformation, 3 were pilocytic astrocytomas, and 4 were glioblastomas. None of the patients had postoperative seizures. Gross total resection and long-term postoperative survival were achieved in all patients with benign lesions, while near-total resection (>90%) was achieved in 3 of 4 patients (75%) with glioblastoma, and subtotal resection (<90%) was achieved in 1 patient (25%). Among patients with glioblastoma, 1 patient remained free of recurrence at 16 months of follow-up; the other 3 patients had worse Karnofsky performance scale scores after surgery and died within 6 months. CONCLUSIONS Combining the advantages of neuronavigation, endoscopy, and endoport techniques via the middle frontal gyrus approach can safely and effectively remove benign lesions in the medial part of the thalamus. This procedure can also be performed in well-selected cases of glioblastoma and likely confers a survival advantage for this rapidly and universally fatal disease.
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Affiliation(s)
- Shuang Liu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Silin Wu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tao Xie
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yu Yang Yeh
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Li
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tengfei Liu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chongjing Sun
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Liangliang Yang
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zeyang Li
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yong Yu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fan Hu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Zhu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaobiao Zhang
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China; Digital Medical Research Center, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Key Laboratory of Medical Image Computing and Computer-Assisted Intervention, Shanghai, China.
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Tong S, Xia M, Xu Y, Sun Q, Ye L, Cai J, Ye Z, Tian D. Identification and validation of a 17-gene signature to improve the survival prediction of gliomas. Front Immunol 2022; 13:1000396. [PMID: 36248799 PMCID: PMC9556650 DOI: 10.3389/fimmu.2022.1000396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Gliomas are one of the most frequent types of nervous system tumours and have significant morbidity and mortality rates. As a result, it is critical to fully comprehend the molecular mechanism of glioma to predict prognosis and target gene therapy. The goal of this research was to discover the hub genes of glioma and investigate their prognostic and diagnostic usefulness. In this study, we collected mRNA expression profiles and clinical information from glioma patients in the TCGA, GTEx, GSE68848, and GSE4920 databases. WGCNA and differential expression analysis identified 170 DEGs in the collected datasets. GO and KEGG pathway analyses revealed that DEGs were mainly enriched in gliogenesis and extracellular matrix. LASSO was performed to construct prognostic signatures in the TCGA cohort, and 17 genes were used to build risk models and were validated in the CGGA database. The ROC curve confirmed the accuracy of the prognostic signature. Univariate and multivariate Cox regression analyses showed that all independent risk factors for glioma except gender. Next, we performed ssGSEA to demonstrate a high correlation between risk score and immunity. Subsequently, 7 hub genes were identified by the PPI network and found to have great drug targeting potential. Finally, RPL39, as one of the hub genes, was found to be closely related to the prognosis of glioma patients. Knockdown of RPL39 in vitro significantly inhibited the proliferation and migration of glioma cells, whereas overexpression of RPL39 had the opposite effect. And we found that knockdown of RPL39 inhibited the polarization and infiltration of M2 phenotype macrophages. In conclusion, our new prognosis-related model provides more potential therapeutic strategies for glioma patients.
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Affiliation(s)
- Shiao Tong
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Minqi Xia
- Department of Endocrinology & Metabolism, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yang Xu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qian Sun
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Liguo Ye
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jiayang Cai
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhang Ye
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Daofeng Tian
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Daofeng Tian,
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Hu Y, Li R, Chen H, Chen L, Zhou X, Liu L, Ju M, Chen K, Huang D. Comprehensive analysis of lncRNA-mRNAs co-expression network identifies potential lncRNA biomarkers in cutaneous squamous cell carcinoma. BMC Genomics 2022; 23:274. [PMID: 35392800 PMCID: PMC8988344 DOI: 10.1186/s12864-022-08481-0] [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: 09/11/2021] [Accepted: 03/08/2022] [Indexed: 11/24/2022] Open
Abstract
Background Cutaneous squamous cell carcinoma (cSCC) is the second most common type of skin cancer, the prognosis for patients with metastatic cSCC remains relatively poor. Thus, there is an urgent need to identify new diagnostic, prognostic, and therapeutic targets and pathways in cSCC. Results It detected a total of 37,507 lncRNA probes and 32,825 mRNA probes and found 3593 differentially expressed lncRNAs and 3236 differentially expressed mRNAs. It has been found that mRNAs ACY3, NR1D1, MZB1 has co-expression relationship with six lncRNAs, GXYLT1P3, LINC00348, LOC101928131, A-33-p3340852, A-21-p0003442 and LOC644838. Conclusions The aim of this study is to identify cSCC-specific lncRNAs and indicated that six unstudied lncRNAs may serve an important role in endoplasmic reticulum stress apoptosis, autophagy and the progression of cSCC by modulating ACY3, NR1D1 and MZB1. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08481-0.
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Affiliation(s)
- Yu Hu
- Department of Physiotherapy, Institute of Dermatology, Chinese Academy of Medical Sciences, Peking Union Medical College, 210042, Nanjing, China
| | - Rong Li
- Department of Physiotherapy, Institute of Dermatology, Chinese Academy of Medical Sciences, Peking Union Medical College, 210042, Nanjing, China
| | - Hongyin Chen
- Department of Physiotherapy, Institute of Dermatology, Chinese Academy of Medical Sciences, Peking Union Medical College, 210042, Nanjing, China
| | - Lihao Chen
- Department of Physiotherapy, Institute of Dermatology, Chinese Academy of Medical Sciences, Peking Union Medical College, 210042, Nanjing, China
| | - Xuyue Zhou
- Department of Physiotherapy, Institute of Dermatology, Chinese Academy of Medical Sciences, Peking Union Medical College, 210042, Nanjing, China
| | - Linxi Liu
- Department of Physiotherapy, Institute of Dermatology, Chinese Academy of Medical Sciences, Peking Union Medical College, 210042, Nanjing, China
| | - Mei Ju
- Department of Physiotherapy, Institute of Dermatology, Chinese Academy of Medical Sciences, Peking Union Medical College, 210042, Nanjing, China
| | - Kun Chen
- Department of Physiotherapy, Institute of Dermatology, Chinese Academy of Medical Sciences, Peking Union Medical College, 210042, Nanjing, China.
| | - Dan Huang
- Department of Physiotherapy, Institute of Dermatology, Chinese Academy of Medical Sciences, Peking Union Medical College, 210042, Nanjing, China.,Department of Physiotherapy, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, 12 Jiangwangmiao St, 210042, Nanjing, China
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9
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Wang G, Hu JQ, Liu JY, Zhang XM. Angiogenesis-Related Gene Signature-Derived Risk Score for Glioblastoma: Prospects for Predicting Prognosis and Immune Heterogeneity in Glioblastoma. Front Cell Dev Biol 2022; 10:778286. [PMID: 35372355 PMCID: PMC8971933 DOI: 10.3389/fcell.2022.778286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/15/2022] [Indexed: 12/16/2022] Open
Abstract
Background: Glioblastoma multiforme (GBM) is the most common malignant tumor in the central nervous system with poor prognosis and unsatisfactory therapeutic efficacy. Considering the high correlation between tumors and angiogenesis, we attempted to construct a more effective model with angiogenesis-related genes (ARGs) to better predict therapeutic response and prognosis. Methods: The ARG datasets were downloaded from the NCBI-Gene and Molecular Signatures Database. The gene expression data and clinical information were obtained from TCGA and CGGA databases. The differentially expressed angiogenesis-related genes (DE-ARGs) were screened with the R package “DESeq2”. Univariate Cox proportional hazards regression analysis was used to screen for ARGs related to overall survival. The redundant ARGs were removed by least absolute shrinkage and selection operator (LASSO) regression analysis. Based on the gene signature of DE-ARGs, a risk score model was established, and its effectiveness was estimated through Kaplan–Meier analysis, ROC analysis, etc. Results: A total of 626 DE-ARGs were explored between GBM and normal samples; 31 genes were identified as key DE-ARGs. Then, the risk score of ARG signature was established. Patients with high-risk score had poor survival outcomes. It was proved that the risk score could predict some medical treatments’ response, such as temozolomide chemotherapy, radiotherapy, and immunotherapy. Besides, the risk score could serve as a promising prognostic predictor. Three key prognostic genes (PLAUR, ITGA5, and FMOD) were selected and further discussed. Conclusion: The angiogenesis-related gene signature-derived risk score is a promising predictor of prognosis and treatment response in GBM and will help in making appropriate therapeutic strategies.
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Affiliation(s)
- Gang Wang
- Department of Neurosurgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jin-Qu Hu
- Department of Neurosurgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ji-Yuan Liu
- Department of Neurosurgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiao-Mei Zhang
- Department of Rheumatology and Immunology, ShengJing Hospital of China Medical University, Shenyang, China
- *Correspondence: Xiao-Mei Zhang,
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Xing Z, Liu Z, Fu X, Zhou S, Liu L, Dang Q, Guo C, Ge X, Lu T, Zheng Y, Dai L, Han X, Wang X. Clinical Significance and Immune Landscape of a Pyroptosis-Derived LncRNA Signature for Glioblastoma. Front Cell Dev Biol 2022; 10:805291. [PMID: 35223836 PMCID: PMC8866949 DOI: 10.3389/fcell.2022.805291] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/12/2022] [Indexed: 01/15/2023] Open
Abstract
Introduction: Pyroptosis was recently implicated in the initiation and progression of tumors, including glioblastoma (GBM). This study aimed to explore the clinical significance of pyroptosis-related lncRNAs (PRLs) in GBM. Methods: Three independent cohorts were retrieved from the TCGA and CGGA databases. The consensus clustering and weighted gene coexpression network analysis (WGCNA) were applied to identify PRLs. The LASSO algorithm was employed to develop and validate a pyroptosis-related lncRNA signature (PRLS) in three independent cohorts. The molecular characteristics, clinical significances, tumor microenvironment, immune checkpoints profiles, and benefits of chemotherapy and immunotherapy regarding to PRLS were also explored. Results: In the WGCNA framework, a key module that highly correlated with pyroptosis was extracted for identifying PRLs. Univariate Cox analysis further revealed the associations between PRLs and overall survival. Based on the expression profiles of PRLs, the PRLS was initially developed in TCGA cohort (n = 143) and then validated in two CGGA cohorts (n = 374). Multivariate Cox analysis demonstrated that our PRLS model was an independent risk factor. More importantly, this signature displayed a stable and accurate performance in predicting prognosis at 1, 3, and 5 years, with all AUCs above 0.7. The decision curve analysis also indicated that our signature had promising clinical application. In addition, patients with high PRLS score suggested a more abundant immune infiltration, higher expression of immune checkpoint genes, and better response to immunotherapy but worse to chemotherapy. Conclusion: A novel pyroptosis-related lncRNA signature with a robust performance was constructed and validated in multiple cohorts. This signature provided new perspectives for clinical management and precise treatments of GBM.
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Affiliation(s)
- Zhe Xing
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xudong Fu
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Shaolong Zhou
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoyong Ge
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Taoyuan Lu
- Department of Cerebrovascular Disease, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Youyang Zheng
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lirui Dai
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Correspondence: Xinjun Wang, ; Xinwei Han,
| | - Xinjun Wang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
- Correspondence: Xinjun Wang, ; Xinwei Han,
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11
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Beeraka NM, Gu H, Xue N, Liu Y, Yu H, Liu J, Chen K, Nikolenko VN, Fan R. Testing lncRNAs signature as clinical stage–related prognostic markers in gastric cancer progression using TCGA database. Exp Biol Med (Maywood) 2022; 247:658-671. [PMID: 35068210 DOI: 10.1177/15353702211067173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
LncRNA expression can be conducive to gastric cancer (GC) prognosis. The objective of this study is to ascertain five specific lncRNAs involved in tumor progression of GC and their role as prognostic markers to diagnose clinical stage-wise GC. High-throughput RNA sequencing data were obtained from The Cancer Genome Atlas (TCGA) database and performed genome-wide lncRNA expression analysis using edgeR package, Bioconductor.org , and R-statistical computing to analyze differentially expressed lncRNA analysis. Cutoff parameters were FDR < 0.05 and |Log2FC| > 2. Total 351 tumor samples with differentially expressed lncRNAs were divided into group-1 lncRNAs such as AC019117.2 and LINC00941, and group-2 lncRNAs such as LINC02410, AC012317.2, and AC141273.1 by 2:1. The Spearman correlation coefficients ( p < 0.05) and correlation test function (cor.test ()) were performed for lncRNAs as per clinical stage. Cytoscape software was used to construct lncRNA–mRNA interaction networks. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway ( p < 0.05) analysis were conducted using the clusterProfiler package. Kaplan–Meier survival analysis was performed to determine the overall survival of patients based on the expression of five lncRNAs in different clinical stages of GC. AC019117.2 and LINC00941 of group 1 inferred a positive correlation with clinical stages of stage I to stage IV, and their expressions were higher in tumor tissues than normal tissues. On the contrary, LINC02410, AC012317.2, and AC141273.1 of group 2 exhibited a negative correlation with clinical stage, and they exhibited more expression in normal tissues compared to tumor tissues. GO and KEGG pathway analysis reported that AC019117.2 may interact with LINC00941 via ITGA3 and trophoblast glycoprotein (TPBG) to foster tumor progression. Tumor-specific group-1 lncRNAs were conducive to the poor overall survival and exhibited a positive correlation with the clinical stages of stage I to stage IV in GC as per the lncRNA–mRNA networking analysis. These five lncRNAs could be considered as clinically useful lncRNA-based prognostic markers to predict clinical stage-wise GC progression.
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Affiliation(s)
- Narasimha M Beeraka
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Human Anatomy, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
| | - Hao Gu
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Nannan Xue
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yang Liu
- Department of Radiotherapy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou 450052, China
| | - Huiming Yu
- Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 450052, China
| | - Junqi Liu
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Kuo Chen
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Vladimir N Nikolenko
- Department of Human Anatomy, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
- M.V. Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ruitai Fan
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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12
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Sánchez-Ares M, Cameselle-García S, Abdulkader-Nallib I, Rodríguez-Carnero G, Beiras-Sarasquete C, Puñal-Rodríguez JA, Cameselle-Teijeiro JM. Susceptibility Genes and Chromosomal Regions Associated With Non-Syndromic Familial Non-Medullary Thyroid Carcinoma: Some Pathogenetic and Diagnostic Keys. Front Endocrinol (Lausanne) 2022; 13:829103. [PMID: 35295987 PMCID: PMC8918666 DOI: 10.3389/fendo.2022.829103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/07/2022] [Indexed: 12/05/2022] Open
Abstract
Thyroid cancer is the malignant tumor that is increasing most rapidly in the world, mainly at the expense of sporadic papillary thyroid carcinoma. The somatic alterations involved in the pathogenesis of sporadic follicular cell derived tumors are well recognized, while the predisposing alterations implicated in hereditary follicular tumors are less well known. Since the genetic background of syndromic familial non-medullary carcinoma has been well established, here we review the pathogenesis of non-syndromic familial non-medullary carcinoma emphasizing those aspects that may be useful in clinical and pathological diagnosis. Non-syndromic familial non-medullary carcinoma has a complex and heterogeneous genetic basis involving several genes and loci with a monogenic or polygenic inheritance model. Most cases are papillary thyroid carcinoma (classic and follicular variant), usually accompanied by benign thyroid nodules (follicular thyroid adenoma and/or multinodular goiter). The possible diagnostic and prognostic usefulness of the changes in the expression and/or translocation of various proteins secondary to several mutations reported in this setting requires further confirmation. Given that non-syndromic familial non-medullary carcinoma and sporadic non-medullary thyroid carcinoma share the same morphology and somatic mutations, the same targeted therapies could be used at present, if necessary, until more specific targeted treatments become available.
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Affiliation(s)
- María Sánchez-Ares
- Department of Pathology, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
| | - Soledad Cameselle-García
- Department of Medical Oncology, University Hospital Complex of Ourense, Galician Healthcare Service (SERGAS), Ourense, Spain
| | - Ihab Abdulkader-Nallib
- Department of Pathology, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
- School of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Gemma Rodríguez-Carnero
- Department of Endocrinology and Nutrition, Clinical University Hospital of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
| | - Carolina Beiras-Sarasquete
- Department of Surgery, Clinical University Hospital of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
| | - José Antonio Puñal-Rodríguez
- School of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
- Department of Surgery, Clinical University Hospital of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
| | - José Manuel Cameselle-Teijeiro
- Department of Pathology, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
- School of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
- *Correspondence: José Manuel Cameselle-Teijeiro,
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13
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Yan T, Wang K, Zhao Q, Zhuang J, Shen H, Ma G, Cong L, Du J. Gender specific eRNA TBX5-AS1 as the immunological biomarker for male patients with lung squamous cell carcinoma in pan-cancer screening. PeerJ 2021; 9:e12536. [PMID: 34900441 PMCID: PMC8627656 DOI: 10.7717/peerj.12536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/03/2021] [Indexed: 11/27/2022] Open
Abstract
As an innate feature of human beings, gender differences have an influence on various biological phenotypes, yet it does not attract enough attention in genomics studies. The prognosis of multiple carcinomas usually exhibits a favorable ending for female patients, but the neglect of gender differences can cause serious bias in survival analysis. Enhancer RNAs (eRNAs) are mostly downstream of androgens or estrogen. The present study was aimed to screen eRNAs in patients with non-small-cell lung cancer. The findings revealed that eRNA TBX5-AS1 was expressed differently between female and male patients. Meanwhile, its prognostic significance appeared only in male patients with squamous cell carcinoma (SCC) type. The Gene Set Enrichment Analysis proved that the expression level of TBX5-AS1 increased following the activation of the androgen signaling pathway. In pan-cancer analysis, the prognostic prediction based on gender grouping obtained more meaningful results, and the synergy between TBX5-AS1 and its homologous target was more consistent. Furthermore, immunity variations between sexes prompted us to explore the role that TBX5-AS1 played in tumor microenvironment and immunotherapy. The robust evidence proved that male patients with high expression of TBX5-AS1 possessed a malignant immune microenvironment and urgently needed immune checkpoint inhibitor treatment. In conclusion, TBX5-AS1 may be one of the strongest candidates to predict prognosis for male patients with SCC and provide a reference for immunotherapy.
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Affiliation(s)
- Tao Yan
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Kai Wang
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Healthcare Respiratory Medicine, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qidi Zhao
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Junjie Zhuang
- Institute of Oncology, Shandong Provincial Hospital affiliated to Shandong First Medicine University, Jinan, China
| | - Hongchang Shen
- Department of Oncology, Shandong Provincial Hospital affiliated to Shandong First Medicine University, Jinan, China
| | - Guoyuan Ma
- Department of Thoracic Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lei Cong
- Department of Oncology, Shandong Provincial Hospital affiliated to Shandong First Medicine University, Jinan, China.,Department of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiajun Du
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Thoracic Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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14
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Zhao N, Zhang J, Zhao Q, Chen C, Wang H. Mechanisms of Long Non-Coding RNAs in Biological Characteristics and Aerobic Glycolysis of Glioma. Int J Mol Sci 2021; 22:ijms222011197. [PMID: 34681857 PMCID: PMC8541290 DOI: 10.3390/ijms222011197] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 02/06/2023] Open
Abstract
Glioma is the most common and aggressive tumor of the central nervous system. The uncontrolled proliferation, cellular heterogeneity, and diffusive capacity of glioma cells contribute to a very poor prognosis of patients with high grade glioma. Compared to normal cells, cancer cells exhibit a higher rate of glucose uptake, which is accompanied with the metabolic switch from oxidative phosphorylation to aerobic glycolysis. The metabolic reprogramming of cancer cell supports excessive cell proliferation, which are frequently mediated by the activation of oncogenes or the perturbations of tumor suppressor genes. Recently, a growing body of evidence has started to reveal that long noncoding RNAs (lncRNAs) are implicated in a wide spectrum of biological processes in glioma, including malignant phenotypes and aerobic glycolysis. However, the mechanisms of diverse lncRNAs in the initiation and progression of gliomas remain to be fully unveiled. In this review, we summarized the diverse roles of lncRNAs in shaping the biological features and aerobic glycolysis of glioma. The thorough understanding of lncRNAs in glioma biology provides opportunities for developing diagnostic biomarkers and novel therapeutic strategies targeting gliomas.
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15
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He Y, Chen Y, Tong Y, Long W, Liu Q. Identification of a circRNA-miRNA-mRNA regulatory network for exploring novel therapeutic options for glioma. PeerJ 2021; 9:e11894. [PMID: 34434651 PMCID: PMC8351580 DOI: 10.7717/peerj.11894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/12/2021] [Indexed: 12/19/2022] Open
Abstract
Background Glioma is the most common brain neoplasm with a poor prognosis. Circular RNA (circRNA) and their associated competing endogenous RNA (ceRNA) network play critical roles in the pathogenesis of glioma. However, the alteration of the circRNA-miRNA-mRNA regulatory network and its correlation with glioma therapy haven't been systematically analyzed. Methods With GEO, GEPIA2, circBank, CSCD, CircInteractome, mirWalk 2.0, and mirDIP 4.1, we constructed a circRNA-miRNA-mRNA network in glioma. LASSO regression and multivariate Cox regression analysis established a hub mRNA signature to assess the prognosis. GSVA was used to estimate the immune infiltration level. Potential anti-glioma drugs were forecasted using the cMap database and evaluated with GSEA using GEO data. Results A ceRNA network of seven circRNAs (hsa_circ_0030788/0034182/0000227/ 0018086/0000229/0036592/0002765), 15 miRNAs(hsa-miR-1200/1205/1248/ 1303/3925-5p/5693/581/586/599/607/640/647/6867-5p/767-3p/935), and 46 mRNAs (including 11 hub genes of ARHGAP11A, DRP2, HNRNPA3, IGFBP5, IP6K2, KLF10, KPNA4, NRP2, PAIP1, RCN1, and SEMA5A) was constructed. Functional enrichment showed they influenced majority of the hallmarks of tumors. Eleven hub genes were proven to be decent prognostic signatures for glioma in both TCGA and CGGA datasets. Forty-six LASSO regression significant genes were closely related to immune infiltration. Finally, five compounds (fulvestrant, tanespimycin, mifepristone, tretinoin, and harman) were predicted as potential treatments for glioma. Among them, mifepristone and tretinoin were proven to inhibit the cell cycle and DNA repair in glioma. Conclusion This study highlights the potential pathogenesis of the circRNA-miRNA-mRNA regulatory network and identifies novel therapeutic options for glioma.
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Affiliation(s)
- Yi He
- Neurosurgery Department, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Yihong Chen
- Neurosurgery Department, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Yuxin Tong
- Department of Ophthalmology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, China
| | - Wenyong Long
- Neurosurgery Department, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Qing Liu
- Neurosurgery Department, Xiangya Hospital Central South University, Changsha, Hunan, China
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16
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Zhang X, Cao Y, Chen L. Construction of a prognostic signature of autophagy-related lncRNAs in non-small-cell lung cancer. BMC Cancer 2021; 21:921. [PMID: 34391383 PMCID: PMC8364711 DOI: 10.1186/s12885-021-08654-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/29/2021] [Indexed: 01/18/2023] Open
Abstract
Background Autophagy inhibits tumorigenesis by limiting inflammation. LncRNAs regulate gene expression at various levels as RNAs; thus, both autophagy and lncRNAs are closely related to the occurrence and development of tumours. Methods A total of 232 autophagy-related genes were used to construct a coexpression network to extract autophagy-related lncRNAs. A prognostic signature was constructed by multivariate regression analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was applied to analyse enrichment in cancer-related pathways. Immune infiltration analysis was used to analyse the relationship between the prognostic signature and the tumour microenvironment. Results Nine autophagy-related lncRNAs were used to construct a prognostic model for non-small-cell lung cancer. The median risk score was used to discriminate the high- and low-risk groups, and the low-risk group was found to have better survival. Because KEGG pathway analysis showed that the prognostic signature was enriched in some immune pathways, further analysis of immune infiltration was conducted, and it was found that the prognostic signature did play a unique role in the immune microenvironment. Additionally, the prognostic signature was associated with clinical factors. Conclusion We constructed a prognostic model of autophagy-related lncRNAs that can predict the prognosis of non-small-cell lung cancer.
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Affiliation(s)
- Xinyang Zhang
- Department of Pathology Anatomy, Medical College of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China
| | - Yu Cao
- Third People's Hospital of Nantong, Nantong, 226001, Jiangsu, China
| | - Li Chen
- Department of Pathology Anatomy, Medical College of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China.
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