1
|
Long T, Li J, Yin T, Liu K, Wang Y, Long J, Wang J, Cheng L. A genetic variant in gene NDUFAF4 confers the risk of non-small cell lung cancer by perturbing hsa-miR-215 binding. Mol Carcinog 2024; 63:145-159. [PMID: 37787384 DOI: 10.1002/mc.23642] [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: 03/20/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023]
Abstract
Hsa-microRNA-215 (hsa-miR-215) plays multiple roles in carcinogenesis through regulating its target genes. Genetic variants in hsa-miR-215 target sites thus may affect hsa-miR-215-mRNA interactions, result in altered expression of target genes and even influence cancer susceptibility. This study aimed to investigate the associations of genetic variants which located in the binding sites of hsa-miR-215 with non-small cell lung cancer (NSCLC) susceptibility in the Chinese population and reveal the potential regulatory mechanism of functional variants in NSCLC development. The candidate genetic variants were predicted and screened through bioinformatics analysis based on the degree of complementarity of hsa-miR-215 sequences. The potential effects of genetic variants on the binding ability of hsa-miR-215 and target genes were also predicted. A case-control study with 932 NSCLC patients and 1036 healthy controls was conducted to evaluate the association of candidate genetic variants with NSCLC susceptibility, and an independent case-control study with 552 NSCLC cases and 571 controls were used to further validate the promising associations. Dual luciferase reporter gene assay was applied to explore the regulation of the genetic variants on transcription activity of target gene. Cell phenotyping experiments in vitro and RNA sequencing (RNA-seq) were then carried out to preliminarily explore the potential regulatory mechanisms of the target genes in NSCLC. A total of five candidate genetic variants located in the binding sites of hsa-miR-215 were screened. The two-stage case-control study showed that a variant rs1854268 A > T, which located in the 3' untranslated (3'UTR) region of NDUFAF4 gene, was associated with decreased risk of NSCLC (additive model, odds ratio [OR] = 0.83, 95% confidence interval [CI]: 0.75-0.92, p < 0.001). Functional annotation displayed that rs1854268 A > T might downregulate the expression of NDUFAF4 by enhancing the binding affinity of hsa-miR-215-5p to NDUFAF4 mRNA. Additionally, transient knockdown of the NDUFAF4 could inhibit lung cancer cell migration and promote lung cancer cell apoptosis. Further RNA-seq analysis revealed that the knockdown of NDUFAF4 may affect NSCLC development by downregulating the nuclear factor kappa B (NF-κB) and phosphoinositide 3 kinase-AKT (PI3K-AKT) signaling pathways. Moreover, the overexpression of CCND1 could partially attenuate the effects of NDUFAF4 knock down on lung cancer cell migration and apoptosis, indicating that CCND1 may be involved in the tumor-promoting effects of NDUFAF4 as a downstream molecule of NDUFAF4 gene. In conclusion, the genetic variant rs1854268 (A > T) on NDUFAF4 confers NSCLC susceptibility by altering the binding affinity of hsa-miR-215-5p, thus regulating the expression of NDUFAF4 and subsequently influencing downstream tumor molecules and pathways such as CCND1, NF kappa B, and PI3K-AKT signaling pathways.
Collapse
Affiliation(s)
- Tingting Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tongxin Yin
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jieyi Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianing Wang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
2
|
Huang CH, Han W, Wu YZ, Shen GL. Identification of aberrantly methylated differentially expressed genes and pro-tumorigenic role of KIF2C in melanoma. Front Genet 2022; 13:817656. [PMID: 35991567 PMCID: PMC9387026 DOI: 10.3389/fgene.2022.817656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Skin Cutaneous Melanoma (SKCM) is known as an aggressive malignant cancer, which could be directly derived from melanocytic nevi. However, the molecular mechanisms underlying the malignant transformation of melanocytes and melanoma tumor progression still remain unclear. Increasing research showed significant roles of epigenetic modifications, especially DNA methylation, in melanoma. This study focused on the identification and analysis of methylation-regulated differentially expressed genes (MeDEGs) between melanocytic nevus and malignant melanoma in genome-wide profiles.Methods: The gene expression profiling datasets (GSE3189 and GSE114445) and gene methylation profiling datasets (GSE86355 and GSE120878) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) were identified via GEO2R. MeDEGs were obtained by integrating the DEGs and DMGs. Then, a functional enrichment analysis of MeDEGs was performed. STRING and Cytoscape were used to describe the protein-protein interaction (PPI) network. Furthermore, survival analysis was implemented to select the prognostic hub genes. Next, we conducted gene set enrichment analysis (GSEA) of hub genes. To validate, SKCM cell culture and lentivirus infection was performed to reveal the expression and behavior pattern of KIF2C. Patients and specimens were collected and then immunohistochemistry (IHC) staining was conducted.Results: We identified 237 hypomethylated, upregulated genes and 182 hypermethylated, downregulated genes. Hypomethylation-upregulated genes were enriched in biological processes of the oxidation-reduction process, cell proliferation, cell division, phosphorylation, extracellular matrix disassembly and protein sumoylation. Pathway enrichment showed selenocompound metabolism, small cell lung cancer and lysosome. Hypermethylation-downregulated genes were enriched in biological processes of positive regulation of transcription from RNA polymerase II promoter, cell adhesion, cell proliferation, positive regulation of transcription, DNA-templated and angiogenesis. The most significantly enriched pathways involved the transcriptional misregulation in cancer, circadian rhythm, tight junction, protein digestion and absorption and Hippo signaling pathway. After PPI establishment and survival analysis, seven prognostic hub genes were CKS2, DTL, KIF2C, KPNA2, MYBL2, TPX2, and FBL. Moreover, the most involved hallmarks obtained by GSEA were E2F targets, G2M checkpoint and mitotic spindle. Importantly, among the 7 hub genes, we found that down-regulated level of KIF2C expression significantly inhibited the proliferative ability of SKCM cells and suppressed the metastasis capacity of SKCM cells.Conclusions: Our study identified potential aberrantly methylated-differentially expressed genes participating in the process of malignant transformation from nevus to melanoma tissues based on comprehensive genomic profiles. Transcription profiles of CKS2, DTL, KIF2C, KPNA2, MYBL2, TPX2, and FBL provided clues of aberrantly methylation-based biomarkers, which might improve the development of precision medicine. KIF2C plays a pro-tumorigenic role and potentially inhibited the proliferative ability in SKCM.
Collapse
Affiliation(s)
- Chun-Hui Huang
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Surgery, Soochow University, Suzhou, China
| | - Wei Han
- Institute of Regenerative Biology and Medicine, Helmholtz Zentrum München, Munich, Germany
| | - Yi-Zhu Wu
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Surgery, Soochow University, Suzhou, China
| | - Guo-Liang Shen
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Surgery, Soochow University, Suzhou, China
- *Correspondence: Guo-Liang Shen,
| |
Collapse
|
3
|
Liang X, Li L, Fan Y. Diagnostic, Prognostic, and Immunological Roles of HELLS in Pan-Cancer: A Bioinformatics Analysis. Front Immunol 2022; 13:870726. [PMID: 35774795 PMCID: PMC9237247 DOI: 10.3389/fimmu.2022.870726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
Background Inappropriate repair of DNA damage drives carcinogenesis. Lymphoid-specific helicase (HELLS) is an important component of the chromatin remodeling complex that helps repair DNA through various mechanisms such as DNA methylation, histone posttranslational modification, and nucleosome remodeling. Its role in human cancer initiation and progression has garnered recent attention. Our study aims to provide a more systematic and comprehensive understanding of the role of HELLS in the development and progression of multiple malignancies through analysis of HELLS in cancers. Methods We explored the role of HELLS in cancers using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database. Multiple web platforms and software were used for data analysis, including R, Cytoscape, HPA, Archs4, TISIDB, cBioPortal, STRING, GSCALite, and CancerSEA. Results High HELLS expression was found in a variety of cancers and differentially expressed across molecular and immune subtypes. HELLS was involved in many cancer pathways. Its expression positively correlated with Th2 and Tcm cells in most cancers. It also correlated with genetic markers of immunomodulators in various cancers. Conclusions Our study elucidates the role HELLS plays in promotion, inhibition, and treatment of different cancers. HELLS is a potential cancer diagnostic and prognostic biomarker with immune, targeted, or cytotoxic therapeutic value. This work is a prerequisite to clinical validation and treatment of HELLS in cancers.
Collapse
Affiliation(s)
- Xiao Liang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Linji Li
- Department of Anesthesiology, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China
| | - Yuchao Fan
- Department of Anesthesiology, Sichuan Cancer Center, Sichuan Cancer Hospital & Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Yuchao Fan,
| |
Collapse
|
4
|
Wang H, Zhang J. Identification of DTL as Related Biomarker and Immune Infiltration Characteristics of Nasopharyngeal Carcinoma via Comprehensive Strategies. Int J Gen Med 2022; 15:2329-2345. [PMID: 35264872 PMCID: PMC8901051 DOI: 10.2147/ijgm.s352330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/02/2022] [Indexed: 11/25/2022] Open
Abstract
Purpose Although considerable progress has been made in basic and clinical research on nasopharyngeal carcinoma (NPC), the biomarkers of the progression of NPC have not been fully studied and described. This study was designed to identify potential novel biomarkers for NPC using integrated analyses and explore the immune cell infiltration in this pathological process. Methods Five GEO data sets were downloaded from gene expression omnibus database (GEO) and analysed to identify differentially expressed genes (DEGs), followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The four algorithms were adopted for screening of novel and key biomarkers for NPC, including random forest (RF) machine learning algorithm, least absolute shrinkage and selection operator (LASSO) logistic regression, support vector machine-recursive feature elimination (SVM-RFE), and weighted gene co-expression network analysis (WGCNA). Lastly, CIBERSORT was used to assess the infiltration of immune cells in NPC, and the correlation between diagnostic markers and infiltrating immune cells was analyzed. Results Herein, we identified 46 DEGs, and enrichment analysis results showed that DEGs and several kinds of signaling pathways might be closely associated with the occurrence and progression of NPC. DTL was recognized as NPC-related biomarker. DTL, also known as retinoic acid-regulated nuclear matrix-associated protein (RAMP), or DNA replication factor 2 (CDT2), is reported to be correlated with the cell proliferation, cell cycle arrest and cell invasion in hepatocellular carcinoma, breast cancer and gastric cancer. Immune infiltration analysis demonstrated that macrophages M0, macrophages M1 and T cells CD4 memory activated were linked to pathogenesis of NPC. Conclusion In summary, we adopted a comprehensive strategy to screen DTL as biomarkers related to NPC and explore the critical role of immune cell infiltration in NPC.
Collapse
Affiliation(s)
- Hehe Wang
- Department of Otolaryngology, Head and Neck Surgery, Ningbo First Hospital, Ningbo, Zhejiang, People’s Republic of China
- Correspondence: Hehe Wang, Department of Otolaryngology Head and Neck Surgery, Ningbo First Hospital, Ningbo, Zhejiang, 315010, People’s Republic of China, Email
| | - Junge Zhang
- Department of Anesthesiology, Ningbo First Hospital, Ningbo, Zhejiang, People’s Republic of China
| |
Collapse
|
5
|
DTL Is a Prognostic Biomarker and Promotes Bladder Cancer Progression through Regulating the AKT/mTOR axis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3369858. [PMID: 35103094 PMCID: PMC8799954 DOI: 10.1155/2022/3369858] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/23/2021] [Indexed: 01/10/2023]
Abstract
Background Denticleless E3 ubiquitin protein ligase homolog (DTL) has been reported to be an important regulator for tumorigenesis and progression. Nonetheless, the biological functions and molecular mechanisms of DTL in BCa remain elusive. Methods We implemented integrative bioinformatics analysis to explore the diagnostic and prognostic values of DTL based on The Cancer Genome Atlas (TCGA), ArrayExpress, and Gene Expression Omnibus (GEO) databases. Then, we utilized qRT-PCR and immunohistochemistry to verify the clinical significance of DTL expression according to clinical specimens and tissue microarray (TMA). Moreover, the biological functions and underlying mechanisms of DTL in BCa were investigated through in vitro and in vivo experiments. Results Integrative bioinformatics analysis revealed that DTL was a key gene associated with BCa progression, and increased DTL expression was correlated with malignant biological behavior and poor prognosis. Experiments on clinical specimens and tissue microarray (TMA) further confirmed our findings. Bioinformatics analysis demonstrated that DTL could be associated with cell cycle- and DNA replication-associated pathways in BCa. The suppression of DTL inhibited BCa cell proliferation, migration, and invasion in vivo and in vitro. Mechanistically, DTL may promote BCa progression through the AKT/mTOR pathway. Conclusions Increased DTL expression was correlated with malignant biological behavior and poor prognosis of BCa patients, and it may promote BCa progression through the AKT/mTOR pathway. Our research provided a potential predictor and therapeutic target for BCa.
Collapse
|
6
|
Bernardes SS, Ferreira I, Elder DE, Nobre AB, Martínez‐Said H, Adams DJ, Robles‐Espinoza CD, Possik PA. More than just acral melanoma: the controversies of defining the disease. J Pathol Clin Res 2021; 7:531-541. [PMID: 34213090 PMCID: PMC8503895 DOI: 10.1002/cjp2.233] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/13/2021] [Accepted: 06/09/2021] [Indexed: 01/17/2023]
Abstract
Acral melanoma (AM) is a malignant cutaneous melanocytic tumour specifically located on the palms, soles, and nail apparatus, which are areas of glabrous (hairless) skin. Acral lentiginous melanoma, a subtype of AM, represents a histopathological subtype diagnosis of cutaneous melanoma with unique morphological and structural features. Despite clear definitions, the misuse of these terms and the inconsistency in reporting the histopathological features of AM cases have become a major obstacle to the study of the disease. In this review, we discuss the epidemiology, histopathological features, prognosis, and genetic profile of AM, highlighting the differences observed when histopathological subtypes are considered. The increasing global effort to characterise AM cases from ethnically diverse populations would benefit greatly from a more consistent classification of the disease.
Collapse
Affiliation(s)
- Sara S Bernardes
- Program of Immunology and Tumour BiologyBrazilian National Cancer InstituteRio de JaneiroBrazil
- Tissue Microenvironment Laboratory, Department of General PathologyFederal University of Minas GeraisBelo HorizonteBrazil
| | - Ingrid Ferreira
- Experimental Cancer GeneticsWellcome Sanger InstituteHinxtonUK
- Université Libre de BruxellesBrusselsBelgium
| | - David E Elder
- Division of Anatomic PathologyHospital of the University of PennsylvaniaPhiladelphiaPAUSA
| | - Aretha B Nobre
- Division of PathologyBrazilian National Cancer InstituteRio de JaneiroBrazil
- Serviço de Patologia, Maternidade EscolaUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Héctor Martínez‐Said
- Servicio de Piel y Partes BlandasInstituto Nacional de CancerologíaCiudad de MéxicoMexico
| | - David J Adams
- Experimental Cancer GeneticsWellcome Sanger InstituteHinxtonUK
| | - Carla Daniela Robles‐Espinoza
- Experimental Cancer GeneticsWellcome Sanger InstituteHinxtonUK
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de MéxicoSantiago de QuerétaroMexico
| | - Patricia A Possik
- Program of Immunology and Tumour BiologyBrazilian National Cancer InstituteRio de JaneiroBrazil
| |
Collapse
|
7
|
Zeng X, Shi G, He Q, Zhu P. Screening and predicted value of potential biomarkers for breast cancer using bioinformatics analysis. Sci Rep 2021; 11:20799. [PMID: 34675265 PMCID: PMC8531389 DOI: 10.1038/s41598-021-00268-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/08/2021] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is the most common cancer and the leading cause of cancer-related deaths in women. Increasing molecular targets have been discovered for breast cancer prognosis and therapy. However, there is still an urgent need to identify new biomarkers. Therefore, we evaluated biomarkers that may aid the diagnosis and treatment of breast cancer. We searched three mRNA microarray datasets (GSE134359, GSE31448 and GSE42568) and identified differentially expressed genes (DEGs) by comparing tumor and non-tumor tissues using GEO2R. Functional and pathway enrichment analyses of the DEGs were performed using the DAVID database. The protein-protein interaction (PPI) network was plotted with STRING and visualized using Cytoscape. Module analysis of the PPI network was done using MCODE. The associations between the identified genes and overall survival (OS) were analyzed using an online Kaplan-Meier tool. The redundancy analysis was conducted by DepMap. Finally, we verified the screened HUB gene at the protein level. A total of 268 DEGs were identified, which were mostly enriched in cell division, cell proliferation, and signal transduction. The PPI network comprised 236 nodes and 2132 edges. Two significant modules were identified in the PPI network. Elevated expression of the genes Discs large-associated protein 5 (DLGAP5), aurora kinase A (AURKA), ubiquitin-conjugating enzyme E2 C (UBE2C), ribonucleotide reductase regulatory subunit M2(RRM2), kinesin family member 23(KIF23), kinesin family member 11(KIF11), non-structural maintenance of chromosome condensin 1 complex subunit G (NCAPG), ZW10 interactor (ZWINT), and denticleless E3 ubiquitin protein ligase homolog(DTL) are associated with poor OS of breast cancer patients. The enriched functions and pathways included cell cycle, oocyte meiosis and the p53 signaling pathway. The DEGs in breast cancer have the potential to become useful targets for the diagnosis and treatment of breast cancer.
Collapse
Affiliation(s)
- Xiaoyu Zeng
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Gaoli Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Qiankun He
- School of Life Sciences, Zhengzhou University, Zhengzhou, China.
| | - Pingping Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China.
| |
Collapse
|
8
|
Ding Y, Li M, Tayier T, Zhang M, Chen L, Feng S. Bioinformatics analysis of lncRNA‑associated ceRNA network in melanoma. J Cancer 2021; 12:2921-2932. [PMID: 33854593 PMCID: PMC8040875 DOI: 10.7150/jca.51851] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/15/2021] [Indexed: 01/06/2023] Open
Abstract
Melanoma is an extremely malignant tumor with early metastasis and high mortality. Little is known about the process of by which melanoma occurs, as its mechanism is very complex and only limited data are available on its long non-coding RNA (lncRNA)-associated competing endogenous RNAs (ceRNAs). The purpose of this study was to screen out potential prognostic molecules and identify a ceRNA network related to the occurrence of melanoma. We screened 169 differentially expressed mRNAs (DEmRNAs) from E-MTAB-1862 and GSE3189; gene ontology (GO) enrichment analysis showed that these genes were closely related to the development of skin. In the protein-protein interaction network, we screened out a total of 19 hub genes. Furthermore, we predicted the microRNAs (miRNAs) that regulate hub genes using the miRWalk database and then intersected these with GSE35579, resulting in nine DEmiRNAs. We also predicted the lncRNAs that regulate the miRNAs using the LncBasev.2 database. According to the ceRNA hypothesis, and based on the intersection of the DElncRNAs with merged GTEx and TCGA data, we obtained 20 DElncRNAs. A total of four DEmRNAs, nine DEmiRNAs, and 20 DElncRNAs were included in the ceRNA network. Based on Cox stepwise regression and survival analysis, we identified five biomarkers, ZSCAN16-AS1, LINC00520, XIST, DTL, and let-7a-5p, and obtained risk scores. The results showed that most of the differentially expressed genes were related to epithelial-mesenchymal transition (EMT) in melanoma. Finally, we obtained a LINC00520/let-7a-5p/DTL molecular regulatory network. These results suggest that ceRNA networks have an important role in evaluating the prognosis of patients with melanoma and provide a new experimental basis for exploring the EMT process in the development of melanoma.
Collapse
Affiliation(s)
- Yi Ding
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Min Li
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Tuersong Tayier
- Department of Pharmacology, Pharmacy College, Xinjiang Medical University, Urumqi, China
| | - MeiLin Zhang
- Xinjiang Urumqi City Center Blood Station, Urumqi, China
| | - Long Chen
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - ShuMei Feng
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, China
| |
Collapse
|
9
|
Nie C, Ma H, Gao Y, Li J, Tang Z, Chen Y, Lu R. RNA Sequencing and Bioinformatic Analysis on Retinoblastoma Revealing that Cell Cycle Deregulation Is a Key Process in Retinoblastoma Tumorigenesis. Ophthalmologica 2020; 244:51-59. [PMID: 32146475 DOI: 10.1159/000506993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/28/2020] [Indexed: 11/19/2022]
Abstract
PURPOSE Retinoblastoma (RB) is a primary pediatric ocular malignancy that can be fatal with inadequate treatment. While multimodal treatments are applied for eye salvage, vision loss and metastasis can occur in some patients. The present study aimed to explore key pathways and factors in RB pathogenesis, which could be potential targets for novel RB treatments. METHODS RNA sequencing was performed on three RB tissues and referenced with three normal retinas. Differentially expressed genes (DEGs) were identified from sequencing data and further analyzed with clustering analysis, function and pathway enrichment, protein-protein interaction (PPI), and data-mining analysis in order to screen for tumorigenic relevancy. RESULTS A total of 331 DEGs were identified by clustering analysis of RB tissues, and the expression patterns were significantly distinguishable from normal retinas. Function and pathway enrichment and PPI analysis together showed that cell cycle was the most prominently upregulated pathway found in RB tissues. Following comprehensive bioinformatic analyses, six key genes relevant to cell cycle regulation were identified, namely BUB1, RRM2, TPX2, UBE2C, NUSAP1, and DTL. CONCLUSIONS Cell cycle pathway and six relevant genes may be potential key factors in RB tumorigenesis and laying the foundation for prospective investigation on development of novel targeted therapies.
Collapse
Affiliation(s)
- Cong Nie
- Department of Orbital Diseases and Ocular Oncology, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Huan Ma
- Department of Orbital Diseases and Ocular Oncology, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Yang Gao
- Department of Orbital Diseases and Ocular Oncology, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Jinmiao Li
- Department of Orbital Diseases and Ocular Oncology, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Zhixin Tang
- Department of Orbital Diseases and Ocular Oncology, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Ying Chen
- Department of Orbital Diseases and Ocular Oncology, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Rong Lu
- Department of Orbital Diseases and Ocular Oncology, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China,
| |
Collapse
|
10
|
Joob B, Wiwanitkit V. Polymorphism within the 3′ untranslated region of denticleless E3 ubiquitin protein ligase homologue and survival in acral melanoma. Eur J Cancer 2020; 124:64. [DOI: 10.1016/j.ejca.2019.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/09/2019] [Indexed: 12/01/2022]
|
11
|
Zhu R, Zhao Y, Xiao T, Wang Q, Liu X. Association between microRNA binding site polymorphisms in immunoinflammatory genes and recurrence risk of ischemic stroke. Genomics 2019; 112:2241-2246. [PMID: 31883451 DOI: 10.1016/j.ygeno.2019.12.020] [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: 09/13/2019] [Revised: 12/14/2019] [Accepted: 12/25/2019] [Indexed: 11/15/2022]
Abstract
MicroRNA binding site polymorphisms in immunoinflammatory genes have been implicated as candidate biomarkers for prediction of complex human diseases. However, the roles of microRNA binding site polymorphisms in stroke onset and prognosis remain unclear. Thus, for the first time, five potential functional polymorphisms in immunoinflammatory genes (CXCR2 rs1126579, TLR4 rs11536889, ADIPOR2 rs12342, MMP-2 rs7201 and MMP-9 rs1056628) were genotyped in 657 patients with ischemic stroke. These five polymorphisms were not related with age onset of ischemic stroke. However, we found that ADIPOR2 rs12342 was significantly associated with a decreased recurrence risk, especially for the patients with small-vessel disease. Moreover, by using multivariate Cox regression, the variant genotype GG/GA of rs12342 was observed as an independent protective factor for stroke recurrence, even after Bonferroni correction. In addition, after the addition of rs12342 in the model with clinical factors, the new model showed the improved discriminatory ability to predict stroke recurrence. In short, our results suggested that ADIPOR2 rs12342 may be a novel genetic biomarker and therapeutic target for ischemic stroke recurrence. Further studies are required to replicate our findings and clarify the potential biological mechanism.
Collapse
Affiliation(s)
- Ruixia Zhu
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yating Zhao
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tongling Xiao
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Qianwen Wang
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xu Liu
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China.
| |
Collapse
|
12
|
Response to: Polymorphism within the 3'-untranslated region of denticleless E3 ubiquitin protein ligase homolog and survival in acral melanoma. Eur J Cancer 2019; 124:65-66. [PMID: 31759293 DOI: 10.1016/j.ejca.2019.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 11/22/2022]
|