1
|
Naicker D, Rhoda C, Sunda F, Arowolo A. Unravelling the Intricate Roles of FAM111A and FAM111B: From Protease-Mediated Cellular Processes to Disease Implications. Int J Mol Sci 2024; 25:2845. [PMID: 38474092 DOI: 10.3390/ijms25052845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Proteases are critical enzymes in cellular processes which regulate intricate events like cellular proliferation, differentiation and apoptosis. This review highlights the multifaceted roles of the serine proteases FAM111A and FAM111B, exploring their impact on cellular functions and diseases. FAM111A is implicated in DNA replication and replication fork protection, thereby maintaining genome integrity. Additionally, FAM111A functions as an antiviral factor against DNA and RNA viruses. Apart from being involved in DNA repair, FAM111B, a paralog of FAM111A, participates in cell cycle regulation and apoptosis. It influences the apoptotic pathway by upregulating anti-apoptotic proteins and modulating cell cycle-related proteins. Furthermore, FAM111B's association with nucleoporins suggests its involvement in nucleo-cytoplasmic trafficking and plays a role in maintaining normal telomere length. FAM111A and FAM111B also exhibit some interconnectedness and functional similarity despite their distinct roles in cellular processes and associated diseases resulting from their dysfunction. FAM111A and FAM111B dysregulation are linked to genetic disorders: Kenny-Caffey Syndrome type 2 and Gracile Bone Dysplasia for FAM111A and POIKTMP, respectively, and cancers. Therefore, the dysregulation of these proteases in diseases emphasizes their potential as diagnostic markers and therapeutic targets. Future research is essential to unravel the intricate mechanisms governing FAM111A and FAM111B and explore their therapeutic implications comprehensively.
Collapse
Affiliation(s)
- Danielle Naicker
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Cenza Rhoda
- Hair and Skin Research Unit, Division of Dermatology, Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Falone Sunda
- Hair and Skin Research Unit, Division of Dermatology, Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Afolake Arowolo
- Hair and Skin Research Unit, Division of Dermatology, Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town 7500, South Africa
| |
Collapse
|
2
|
Pu J, Xu Z, Huang Y, Nian J, Yang M, Fang Q, Wei Q, Huang Z, Liu G, Wang J, Wu X, Wei H. N 6 -methyladenosine-modified FAM111A-DT promotes hepatocellular carcinoma growth via epigenetically activating FAM111A. Cancer Sci 2023; 114:3649-3665. [PMID: 37400994 PMCID: PMC10475779 DOI: 10.1111/cas.15886] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 07/05/2023] Open
Abstract
As an epitranscriptomic modulation manner, N6 -methyladenosine (m6 A) modification plays important roles in various diseases, including hepatocellular carcinoma (HCC). m6 A modification affects the fate of RNAs. The potential contributions of m6 A to the functions of RNA still need further investigation. In this study, we identified long noncoding RNA FAM111A-DT as an m6 A-modified RNA and confirmed three m6 A sites on FAM111A-DT. The m6 A modification level of FAM111A-DT was increased in HCC tissues and cell lines, and increased m6 A level was correlated with poor survival of HCC patients. m6 A modification increased the stability of FAM111A-DT transcript, whose expression level showed similar clinical relevance to that of the m6 A level of FAM111A-DT. Functional assays found that only m6 A-modified FAM111A-DT promoted HCC cellular proliferation, DNA replication, and HCC tumor growth. Mutation of m6 A sites on FAM111A-DT abolished the roles of FAM111A-DT. Mechanistic investigations found that m6 A-modified FAM111A-DT bound to FAM111A promoter and also interacted with m6 A reader YTHDC1, which further bound and recruited histone demethylase KDM3B to FAM111A promoter, leading to the reduction of the repressive histone mark H3K9me2 and transcriptional activation of FAM111A. The expression of FAM111A was positively correlated with the m6 A level of FAM111A-DT, and the expression of methyltransferase complex, YTHDC1, and KDM3B in HCC tissues. Depletion of FAM111A largely attenuated the roles of m6 A-modified FAM111A-DT in HCC. In summary, the m6 A-modified FAM111A-DT/YTHDC1/KDM3B/FAM111A regulatory axis promoted HCC growth and represented a candidate therapeutic target for HCC.
Collapse
Affiliation(s)
- Jian Pu
- Department of Hepatobiliary SurgeryAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Zuoming Xu
- Department of Hepatobiliary SurgeryAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Youguan Huang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Jiahui Nian
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Meng Yang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Quan Fang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Qing Wei
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Zihua Huang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Guoman Liu
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Jianchu Wang
- Department of Hepatobiliary SurgeryAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Xianjian Wu
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Huamei Wei
- Department of PathologyAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| |
Collapse
|
3
|
He Y, Døssing KBV, Sloth AB, He X, Rossing M, Kjaer A. Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets. Cancers (Basel) 2023; 15. [PMID: 36900348 DOI: 10.3390/cancers15051557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/17/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Targeting glioblastoma (GBM) stem-like cells (GSCs) is a common interest in both the laboratory investigation and clinical treatment of GBM. Most of the currently applied GBM stem-like markers lack validation and comparison with common standards regarding their efficiency and feasibility in various targeting methods. Using single-cell RNA sequencing datasets from 37 GBM patients, we obtained a large pool of 2173 GBM stem-like marker candidates. To evaluate and select these candidates quantitatively, we characterized the efficiency of the candidate markers in targeting the GBM stem-like cells by their frequencies and significance of being the stem-like cluster markers. This was followed by further selection based on either their differential expression in GBM stem-like cells compared with normal brain cells or their relative expression level compared with other expressed genes. The cellular location of the translated protein was also considered. Different combinations of selection criteria highlight different markers for different application scenarios. By comparing the commonly used GSCs marker CD133 (PROM1) with markers selected by our method regarding their universality, significance, and abundance, we revealed the limitations of CD133 as a GBM stem-like marker. Overall, we propose BCAN, PTPRZ1, SOX4, etc. for laboratory-based assays with samples free of normal cells. For in vivo targeting applications that require high efficiency in targeting the stem-like subtype, the ability to distinguish GSCs from normal brain cells, and a high expression level, we recommend the intracellular marker TUBB3 and the surface markers PTPRS and GPR56.
Collapse
|
4
|
Ji X, Liu Z, Gao J, Bing X, He D, Liu W, Wang Y, Wei Y, Yin X, Zhang F, Han M, Lu X, Wang Z, Liu Q, Xin T. N 6-Methyladenosine-modified lncRNA LINREP promotes Glioblastoma progression by recruiting the PTBP1/HuR complex. Cell Death Differ 2023; 30:54-68. [PMID: 35871232 PMCID: PMC9883516 DOI: 10.1038/s41418-022-01045-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
Glioblastoma multiforme (GBM) is acknowledged as the most aggressive primary brain tumor in adults. It is typically characterized by the high heterogeneity which corresponds to extensive genetic mutations and complex alternative splicing (AS) profiles. Known as a major repressive splicing factor in AS, polypyrimidine tract-binding protein 1 (PTBP1) is involved in the exon skipping events of multiple precursor mRNAs (pre-mRNAs) in GBM. However, precise mechanisms that modulate the expression and activity of PTBP1 remain to be elucidated. In present study, we provided evidences for the role of a long intergenic noncoding RNA (LINREP) implicated in the regulation of PTBP1-induced AS. LINREP interacted with PTBP1 and human antigen R (HuR, ELAVL1) protein complex and protected PTBP1 from the ubiquitin-proteasome degradation. Consequently, a broad spectrum of PTBP1-induced spliced variants was generated by exon skipping, especially for the skipping of reticulon 4 (RTN4) exon 3. Interestingly, LINREP also promoted the dissociation of nuclear UPF1 from PTBP1, which increased the binding of PTBP1 to RTN4 transcripts, thus enhancing the skipping of RTN4 exon 3 to some extent. Besides, HuR recruitment was essential for the stabilization of LINREP via a manner dependent on N6-methyladenosine (m6A) formation and identification. Taken together, our results demonstrated the functional significance of LINREP in human GBM for its dual regulation of PTBP1-induced AS and its m6A modification modality, implicating that HuR/LINREP/PTBP1 axis might serve as a potential therapeutic target for GBM.
Collapse
Affiliation(s)
- Xiaoshuai Ji
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China
| | - Zihao Liu
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Jiajia Gao
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China
| | - Xin Bing
- Department of Otolaryngology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Dong He
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Wenqing Liu
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China
| | - Yunda Wang
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan, 250014, China
| | - Yanbang Wei
- Department of Histology and Embryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Xianyong Yin
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan, 250014, China
| | - Fenglin Zhang
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China
| | - Min Han
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan, 250014, China
| | - Xiangdong Lu
- Department of Neurosurgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Zixiao Wang
- Department of Histology and Embryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Qian Liu
- Department of Histology and Embryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
| | - Tao Xin
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250014, China.
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan, 250014, China.
- Department of Neurosurgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, 330006, Jiangxi, China.
| |
Collapse
|
5
|
Cha J, Lavi M, Kim J, Shomron N, Lee I. Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis. Comput Struct Biotechnol J 2023; 21:2296-2304. [PMID: 37035549 PMCID: PMC10073994 DOI: 10.1016/j.csbj.2023.03.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Single-cell transcriptome data provide a unique opportunity to explore the gene networks of a particular cell type. However, insufficient capture rate and high dimensionality of single-cell RNA sequencing (scRNA-seq) data challenge cell-type-specific gene network (CGN) reconstruction. Here, we demonstrated that the imputation of scRNA-seq data enables reconstruction of CGNs by effective retrieval of gene functional associations. We reconstructed CGNs for seven primary and nine metastatic breast cancer cell lines using scRNA-seq data with imputation. Key genes for primary or metastatic cell lines were prioritized based on network centrality measures and CGN hub genes that were presumed to be the major determinant of cell type characteristics. To identify novel genes in breast cancer metastasis, we used the average rank difference of centrality between the primary and metastatic cell lines. Genes predicted using CGN centrality analysis were more enriched for known breast cancer metastatic genes than those predicted using differential expression. The molecular chaperone CCT2 was identified as a novel gene for breast metastasis during knockdown assays of several candidate genes. Overall, our study demonstrated an effective CGN reconstruction technique with imputation of scRNA-seq data and the feasibility of identifying key genes for particular cell subsets using single-cell network analysis.
Collapse
Affiliation(s)
- Junha Cha
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Michael Lavi
- Faculty of Medicine and Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Junhan Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Noam Shomron
- Faculty of Medicine and Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding author.
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- Corresponding author at: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
| |
Collapse
|
6
|
Ge Y, Xia J, He C, Liu S. Identification of circRNA-lncRNA-miRNA-mRNA competitive endogenous RNA networks as prognostic bio-markers in head and neck squamous cell carcinoma. Technol Health Care 2023; 31:2193-2212. [PMID: 37522233 DOI: 10.3233/thc-230083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is one of the most prevalent neoplasms of malignancy. The pathogenesis of HNSCC is involved in the change of gene expression and the abnormal interaction between genes. OBJECTIVE The purpose of our research is to find genes that affect the survival time of patients and construct circRNA-lncRNA-miRNA-mRNA network. This paper aims to reveal the development mechanism of HNSCC and provide new ideas for clinical prognosis prediction. METHODS Transcriptome data were obtained from TCGA and GEO databases. A total of 556 samples were included. We screened the differentially expressed lncRNAs, circRNAs and mRNAs to predict interactions between lncRNA-miRNA, circRNA-miRNA and miRNA-mRNA. Then, we selected the hub mRNAs to predict the prognosis of patients. RESULTS We identified 8 hub prognostic mRNAs (FAM111A, IFIT2, CAV1, KLF9, OCIAD2, SLCO3A1, S100A16 and APOL3) by a series of bioinformatics analyses and established the prognostic ceRNA network of 8 mRNAs, 3 miRNAs, 2 circRNAs and 1 lncRNAs according to the targeting relationship by using databases. CONCLUSION We established the circRNA-lncRNA-miRNA-mRNA gene interaction network in HNSCC. We illuminated the molecular mechanism underlying the gene regulation associated with the pathogenesis of HNSCC and predicted the biomarkers related to prognosis.
Collapse
|
7
|
He D, Qin Z, Liu Z, Ji X, Gao J, Guo H, Yang F, Fan H, Wei Y, Wang Z, Liu Q, Pang Q. Comprehensive Analysis of the Prognostic Value and Immune Infiltration of Butyrophilin Subfamily 2/3 (BTN2/3) Members in Pan-Glioma. Front Oncol 2022; 12:816760. [PMID: 36033440 PMCID: PMC9399357 DOI: 10.3389/fonc.2022.816760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/15/2022] [Indexed: 11/13/2022] Open
Abstract
The BTN2/3 subfamilies are overexpressed in many cancers, including pan-glioma (low- and high-grade gliomas). However, the expression and prognosis of BTN2/3 subfamilies and tumor-infiltrating lymphocytes in pan-glioma remain unknown. In the present study, we systematically explored and validated the expression and prognostic value of BTN2/3 subfamily members in pan-glioma [The Cancer Genome Atlas–glioblastoma and low-grade glioma (TCGA-GBMLGG) merge cohort] using multiple public databases. We used clinical specimens for high-throughput verification and cell lines for qRT-PCR verification, which confirmed the expression profiles of BTN2/3 subfamilies. In addition, the function of the BTN2/3 subfamily members and the correlations between BTN2/3 subfamily expression and pan-glioma immune infiltration levels were investigated. We found that BTN2/3 subfamily members were rarely mutated. BTN2/3 subfamilies were overexpressed in pan-glioma; high expression of BTN2/3 subfamily members was correlated with poor prognosis. In addition, BTN2/3 subfamilies might positively regulate proliferation, and the overexpression of BTN2/3 subfamilies influenced cell cycle, differentiation, and glioma stemness. In terms of immune infiltrating levels, BTN2/3 subfamily expression was positively associated with CD4+ T-cell, B-cell, neutrophil, macrophage, and dendritic cell infiltrating levels. These findings suggest that BTN2/3 subfamily expression is correlated with prognosis and immune infiltration levels in glioma. Therefore, the BTN2/3 subfamilies can be used as biomarkers for pan-glioma and prognostic biomarkers for determining the prognosis and immune infiltration levels in pan-glioma.
Collapse
Affiliation(s)
- Dong He
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
| | - Zhen Qin
- Department of Clinical Laboratory, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zihao Liu
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
| | - Xiaoshuai Ji
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiajia Gao
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hua Guo
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fan Yang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Haitao Fan
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yanbang Wei
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
| | - Zixiao Wang
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
| | - Qian Liu
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
- *Correspondence: Qian Liu, ; Qi Pang,
| | - Qi Pang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Qian Liu, ; Qi Pang,
| |
Collapse
|
8
|
Deng ZL, Zhou DZ, Cao SJ, Li Q, Zhang JF, Xie H. Development and Validation of an Inflammatory Response-Related Gene Signature for Predicting the Prognosis of Pancreatic Adenocarcinoma. Inflammation 2022; 45:1732-1751. [PMID: 35322324 DOI: 10.1007/s10753-022-01657-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 11/05/2022]
Abstract
Pancreatic adenocarcinoma (PAAD) is a highly dangerous malignant tumor of the digestive tract, and difficult to diagnose, treat, and predict the prognosis. As we all know, tumor and inflammation can affect each other, and thus the inflammatory response in the microenvironment can be used to affect the prognosis. So far, the prognostic value of inflammatory response-related genes in PAAD is still unclear. Therefore, this study aimed to explore the inflammatory response-related genes for predicting the prognosis of PAAD. In this study, the mRNA expression profiles of PAAD patients and the corresponding clinical characteristics data of PAAD patients were downloaded from the public database. The least absolute shrinkage and selection operator (LASSO) Cox analysis model was used to identify and construct the prognostic gene signature in The Cancer Genome Atlas (TCGA) cohort. The PAAD patients used for verification are from the International Cancer Genome Consortium (ICGC) cohort. The Kaplan-Meier method was used to compare the overall survival (OS) between the high- and low-risk groups. Univariate and multivariate Cox analyses were performed to identify the independent predictors of OS. Gene set enrichment analysis (GSEA) was performed to obtain gene ontology (GO) terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and the correlation between gene expression and immune infiltrates was investigated via single sample gene set enrichment analysis (ssGSEA). The GEPIA database was performed to examine prognostic genes in PAAD. LASSO Cox regression analysis was used to construct a model of inflammatory response-related gene signature. Compared with the low-risk group, patients in the high-risk group had significantly lower OS. The receiver operating characteristic curve (ROC) analysis confirmed the signature's predictive capacity. Multivariate Cox analysis showed that risk score is an independent predictor of OS. Functional analysis shows that the immune status between the two risk groups is significantly different, and the cancer-related pathways were abundant in the high-risk group. Moreover, the risk score is significantly related to tumor grade, stage, and immune infiltration types. It was also obtained that the expression level of prognostic genes was significantly correlated with the sensitivity of cancer cells to anti-tumor drugs. In addition, there are significant differences in the expression of PAAD tissues and adjacent non-tumor tissues. The novel signature constructed from five inflammatory response-related genes can be used to predict prognosis and affect the immune status of PAAD. In addition, suppressing these genes may be a treatment option.
Collapse
Affiliation(s)
- Zu-Liang Deng
- Department of Radiation Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China
| | - Ding-Zhong Zhou
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China
| | - Su-Juan Cao
- Department of Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China
| | - Qing Li
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China
| | - Jian-Fang Zhang
- Department of Physical Examination, Beihu Centers for Disease Control and Prevention, Chenzhou, 423000, People's Republic of China
| | - Hui Xie
- Department of Radiation Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China.
| |
Collapse
|
9
|
Dong X, Zhang P, Liu L, Li H, Cheng S, Li S, Wang Y, Zheng C, Dong J, Zhang L. The Circ_0001367/miR-545-3p/LUZP1 Axis Regulates Cell Proliferation, Migration and Invasion in Glioma Cells. Front Oncol 2021; 11:781471. [PMID: 34869035 PMCID: PMC8637337 DOI: 10.3389/fonc.2021.781471] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/01/2021] [Indexed: 01/05/2023] Open
Abstract
Glioma is the most common primary intracranial malignant tumour in adults. It has a high incidence and poses a serious threat to human health. Circular RNA is a hotspot of cancer research. In this study, we aimed to explore the role of circ_0001367 in gliomagenesis and the underlying mechanism. First, qRT-PCR was conducted, which showed that circ_0001367 level was downregulated in glioma tissues and cells. Next, gain-of-function and loss-of-function assays were performed, which indicated that circ_0001367 inhibited the proliferation, migration and invasion of glioma cells. Subsequent bioinformatics analysis, dual-luciferase reporter assays, RNA immunoprecipitation assays and cell function assays demonstrated that circ_0001367 inhibited the proliferation, migration and invasion of glioma cells by absorbing miR-545-3p and thereby regulating the expression of leucine zipper protein (LUZP1). Finally, an in vivo experiment was conducted, which demonstrated that circ_0001367 inhibited glioma growth in vivo by modulating miR-545-3p and LUZP1. Taken together, the results of this study demonstrate that the circ_0001367/miR-545-3p/LUZP1 axis may be a novel target for glioma therapy.
Collapse
Affiliation(s)
- Xuchen Dong
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China.,Medical College of Soochow University, Suzhou, China
| | - Peng Zhang
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China.,Department of Neurosurgery, Rugao Hospital Affiliated to Nantong University, Nantong, China
| | - Liang Liu
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Haoran Li
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Shan Cheng
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Suwen Li
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuan Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Chaonan Zheng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Jun Dong
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| |
Collapse
|