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Azim R, Wang S, Dipu SA, Islam N, Ala Muid MR, Elahe MF. A patient-specific functional module and path identification technique from RNA-seq data. Comput Biol Med 2023; 158:106871. [PMID: 37030265 DOI: 10.1016/j.compbiomed.2023.106871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/12/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023]
Abstract
With the advancement of new technologies, a huge amount of high dimensional data is being generated which is opening new opportunities and challenges to the study of cancer and diseases. In particular, distinguishing the patient-specific key components and modules which drive tumorigenesis is necessary to analyze. A complex disease generally does not initiate from the dysregulation of a single component but it is the result of the dysfunction of a group of components and networks which differs from patient to patient. However, a patient-specific network is required to understand the disease and its molecular mechanism. We address this requirement by constructing a patient-specific network by sample-specific network theory with integrating cancer-specific differentially expressed genes and elite genes. By elucidating patient-specific networks, it can identify the regulatory modules, driver genes as well as personalized disease networks which can lead to personalized drug design. This method can provide insight into how genes are associating with each other and characterized the patient-specific disease subtypes. The results show that this method can be beneficial for the detection of patient-specific differential modules and interaction between genes. Extensive analysis using existing literature, gene enrichment and survival analysis for three cancer types STAD, PAAD and LUAD shows the effectiveness of this method over other existing methods. In addition, this method can be useful for personalized therapeutics and drug design. This methodology is implemented in the R language and is available at https://github.com/riasatazim/PatientSpecificRNANetwork.
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Expression and Prognostic Value of Chromobox Family Proteins in Esophageal Cancer. Genes (Basel) 2022; 13:genes13091582. [PMID: 36140750 PMCID: PMC9498422 DOI: 10.3390/genes13091582] [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: 07/05/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Esophageal cancer (EC) is one of the most common human malignant tumors worldwide. Chromobox (CBX) family proteins are significant components of epigenetic regulatory complexes. It is reported that CBXs play critical roles in the oncogenesis and development of various tumors. Nonetheless, their functions and specific roles in EC remain vague and obscure. Methods and Materials: We used multiple bioinformatics tools, including Oncomine, Gene Expression Profiling Interactive Analysis 2 (GEPIA2), UALCAN, Kaplan–Meier plotter, cBioPortal, Metascape, TIMER2 and TISIDB, to investigate the expression profile, gene alterations and prognostic roles of CBX family proteins, as well as their association with clinicopathologic parameters, immune cells and immune regulators. In addition, RT-qPCR, Western blot, CCK8, colony formation, wound healing and transwell assays were performed to investigate the biological functions of CBX3 in EC cells. Results: CBX3 and CBX5 were overexpressed in EC compared to normal tissues. Survival analysis revealed that high expression of CBX1 predicted worse disease-free survival (DFS) in EC patients. Functionally, CBXs might participate in mismatch repair, spliceosome, cell cycle, the Fanconi anemia pathway, tight junction, the mRNA surveillance pathway and the Hippo signaling pathway in EC development. Furthermore, CBXs were related to distinct immune cells infiltration and immune regulators. Additionally, depletion of CBX3 inhibited the proliferation, migration and invasion abilities of EC cells. Conclusions: Our study comprehensively investigated the expression pattern, prognostic value, and gene alterations of CBXs in EC, as well as their relationships with clinicopathologic variables, immune cells infiltration and immune regulators. These results suggested that CBX family proteins, especially CBX3, might be potential biomarkers in the progression of EC.
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Hu K, Yao L, Xu Z, Yan Y, Li J. Prognostic Value and Therapeutic Potential of CBX Family Members in Ovarian Cancer. Front Cell Dev Biol 2022; 10:832354. [PMID: 35155439 PMCID: PMC8829121 DOI: 10.3389/fcell.2022.832354] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/12/2022] [Indexed: 02/05/2023] Open
Abstract
Background: Ovarian cancer (OV) is one of the common malignant tumors and has a poor prognosis. Chromobox (CBX) family proteins are critical components of epigenetic regulation complexes that repress target genes transcriptionally via chromatin modification. Some studies have investigated the function specifications among several CBXs members in multiple cancer types, however, little is known about the functions and prognostic roles of distinct CBXs family proteins in ovarian cancer. Methods: In this study, several bioinformatics databases and in vitro experiments were used to analyze the expression profiles, prognostic values, and therapeutic potential of the CBXs family (CBX1-8) in ovarian cancer. Results: It was found that higher expression of CBX3/8 and lower expression of CBX1/6/7 were detected in OV tissues. CBX2/4/5/8 were significantly correlated with individual cancer stages of OV. The expression of CBX1/2/3 were all significantly associated with worse overall survival (OS) and progression-free survival (PFS) for OV patients, whereas the expression of other five CBXs members showed either irrelevant (CBX5 and CBX8) or inconsistent (CBX4, CBX6, and CBX7) results for both OS and PFS in OV. These results showed that only CBX3 had consistent results in expression and prognosis. Further cell experiments also showed that CBX3 promoted the proliferation of ovarian cancer cells. CBX3 was highly expressed in chemoresistant OV tissues. These results indicated that CBX3 was the most likely prognostic indicator and new therapeutic target in OV. Furthermore, gene enrichment analysis suggests that the CBXs family was primarily involved in mast cell activation and mast cell mediated immunity. Individual CBXs members were associated with varying degrees of the infiltration of immune cells, especially B cells. Finally, a high genetic alteration rate of CBXs family (39%) was observed in OV. The low methylation status of CBX3/8 in OV may be associated with their high expression levels. Conclusions: Taken together, these findings exhibited the pivotal value of CBXs family members (especially CBX3) in the prognosis and chemoresistance of ovarian cancer. Our results may provide new insight to explore new prognostic biomarkers and therapeutic targets for ovarian cancer.
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Affiliation(s)
- Kuan Hu
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Lei Yao
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Juanni Li, ; Yuanliang Yan,
| | - Juanni Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Juanni Li, ; Yuanliang Yan,
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Mao G, Zheng Y, Lin S, Ma L, Zhou Z, Zhang S. Bioinformatic Analysis of Prognostic Value, Genetic Interaction, and Immune Infiltration of Chromobox Family Proteins in Breast Cancer. Int J Gen Med 2021; 14:9181-9191. [PMID: 34880657 PMCID: PMC8647335 DOI: 10.2147/ijgm.s343948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/23/2021] [Indexed: 11/23/2022] Open
Abstract
Introduction Breast cancer (BC) has become the malignant tumor with the highest incidence worldwide. As a critical components of epigenetic regulation complexes, chromobox (CBX) family members inhibit the transcription of target genes through chromatin modification, leading to the progression of various human diseases and cancers. So far, little is known about the role of different CBX members in BC, especially their association with immune cells. Methods We conducted the analysis of differential expression of CBXs using Oncomine and GEPIA, prognostic value of CBXs using GEPIA and Kaplan-Meier, genetic interaction of CBXs using cBioPortal and GeneMANIA, and immune cell infiltration of CBXs in BC patients using TIMER. Results The CBX2/3/4/8 expression levels were increased significantly, while the CBX6/7 expression levels were decreased. We found that CBX3 was significantly correlated with clinicopathological staging and short DFS in BC patients. High CBX3/5 expression was correlated with short OS in BC patients, while high expression of CBX4 was correlated with long OS in BC patients. In addition, the functions of CBXs family members mainly focus on methylated histone residue binding and chromatin organization. The CBXs expressions were closely related to the infiltration level of a variety of immune cells, including CD4/8+ T cells, B cells, neutrophils, macrophages and dendritic cells in BC cancers. The correlation between CBXs and immune cell infiltration was more common in Luminal BC than in Basal and Her-2 type. Conclusion This study may provide a new understanding for selection of molecular typing, therapeutic and prognostic biomarkers of CBX family in BC.
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Affiliation(s)
- Guochao Mao
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710000, People's Republic of China
| | - Yi Zheng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710000, People's Republic of China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710000, People's Republic of China
| | - Li Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710000, People's Republic of China
| | - Zhangjian Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710000, People's Republic of China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710000, People's Republic of China
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5
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Hu CY, Li X, Zeng T, Ye DM, Li YK, Yan HX. Significance of chromobox protein (CBX) expression in diffuse LBCL. Gene 2021; 813:146092. [PMID: 34896523 DOI: 10.1016/j.gene.2021.146092] [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: 06/08/2021] [Revised: 10/24/2021] [Accepted: 11/23/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is the main pathological type of non-Hodgkin lymphoma (NHL). Chromobox (CBX) family proteins are classical components of polycomb group (PcG) complexes in many cancer types, resulting in accelerated carcinogenesis. Nevertheless, the prognostic, functional and expression significance of these CBX family members in DLBCL remain unclear and elusive. METHODS CBX transcriptional levels were confirmed using Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA) and Cancer Cell Line Encyclopedia (CCLE) databases. The protein levels of CBX family members were analysed using The Human Protein Atlas (HPA) database. Information on the PPI network, functional enrichment, drug sensitivity, prognostic value, miRNA network, protein structure, genetic alteration and immune cell infiltration were generated using the GeneMANIA, Metascape, GSCALite, GEPIA, PDB, cBioPortal, and TIMER databases, and the correlation of these factors with CBX expression levels in DLBCL was assessed. RESULTS CBX1/2/3/5/6/8 mRNA levels were significantly enhanced in DLBCL tissues compared to corresponding normal tissues. CBX1/3/4/5/8 protein expression levels were obviously increased, whereas CBX7 was obviously decreased. This difference might be attributed to miRNA regulation based on the miRNA network. Overall survival (OS) analysis showed that CBX levels were not correlated with prognosis in DLBCL patients, indicating that CBXs are not good biomarkers for DLBCL patients. Furthermore, functional enrichment analyses indicated that CBXs were closely related to DNA duplex unwinding, covalent chromatin modification, and histone lysine methylation. The levels of CBXs were also significantly associated with diverse immune cell infiltration in DLBCL. CONCLUSIONS This study reveals that dysregulated CBXs are involved in DLBCL development and might represent potential therapeutic targets for DLBCL.
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Affiliation(s)
- Chun-Yan Hu
- Department of Pediatrics, The Second Affiliated Hospital of University of South China, Hengyang, Hunan 421001, PR China
| | - Xuan Li
- Department of Embryo Laboratory, Changsha Reproductive Medical Hospital, Changsha, Hunan 410000, PR China
| | - Tian Zeng
- Hengyang Medical College & Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study & Department of Pharmacy and Pharmacology, University of South China, Hengyang 421001, PR China
| | - Dong-Mei Ye
- Department of Pathology, The First Hospital of Nanchang City, Nanchang, Jiangxi 330008, PR China
| | - Yu-Kun Li
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of University of South China, Hengyang, Hunan 421001, PR China
| | - Hong-Xia Yan
- Department of Pediatrics, The Second Affiliated Hospital of University of South China, Hengyang, Hunan 421001, PR China.
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Zhu Y, Pu Z, Li Z, Lin Y, Li N, Peng F. Comprehensive Analysis of the Expression and Prognosis Value of Chromobox Family Members in Clear Cell Renal Cell Carcinoma. Front Oncol 2021; 11:700528. [PMID: 34395271 PMCID: PMC8357267 DOI: 10.3389/fonc.2021.700528] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) accounts for 80% of all renal cancers and has a poor prognosis. Chromobox (CBX) family protein expression has been reported in a variety of human malignancies, but the roles of CBXs in ccRCC remain unclear. In this study, by using ONCOMINE, UALCAN, GEPIA, Kaplan-Meier Plotter, cBioPortal, and TIMER, we found the transcriptional levels of CBX3 and CBX4 in ccRCC tissues were significantly higher than those in normal kidney tissues, whereas the transcriptional levels of CBX1, CBX5, CBX6, and CBX7 were significantly reduced in ccRCC tissues. The promoters of CBX2, CBX3, CBX4, CBX5, CBX6, CBX7, and CBX8 were hypermethylated, whereas the CBX1 promoter was hypomethylated in ccRCC. The expression of CBX1, CBX3, CBX4, CBX5, CBX6, and CBX7 was significantly associated with clinicopathological parameters in ccRCC patients. ccRCC patients with high expression levels of CBX3, CBX4, and CBX8 and low expression levels of CBX1, CBX5, CBX6, and CBX7 showed a strong association with poor overall survival. Genetic alterations in CBXs were correlated with poor overall survival and disease-free survival in patients with ccRCC. Moreover, we found significant associations between the expression of CBXs and infiltration of immune cells (B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells). Our results provide novel insights into the development of CBX-based biomarkers and therapeutic targets for ccRCC.
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Affiliation(s)
- Yuanyuan Zhu
- Department of Blood Transfusion, Xiangya Hospital, Central South University, Changsha, China.,National Health Commission (NHC) Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhangya Pu
- Department of Infectious Diseases and Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenfen Li
- National Health Commission (NHC) Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, China
| | - Ying Lin
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Ning Li
- Department of Blood Transfusion, Xiangya Hospital, Central South University, Changsha, China
| | - Fang Peng
- Department of Blood Transfusion, Xiangya Hospital, Central South University, Changsha, China.,National Health Commission (NHC) Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, China
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Sun Y, Wang X, Bu X. LINC02381 contributes to cell proliferation and hinders cell apoptosis in glioma by transcriptionally enhancing CBX5. Brain Res Bull 2021; 176:121-129. [PMID: 34274429 DOI: 10.1016/j.brainresbull.2021.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/25/2021] [Accepted: 07/12/2021] [Indexed: 01/11/2023]
Abstract
Glioma, featured with high incidence and low survival rate, is the most common type of primary brain tumor, severely affecting human life worldwide. LINC02381 is an interesting lncRNA functioning as oncogenic lncRNA in some cancers but as tumor-suppressor in others, but no report demonstrates its association with and function in glioma. Intriguingly, we found in a bioinformatics website LncRNADisease that LINC02381 was closely related to malignant glioma, so this study aimed to figure out the expression and function of LINC02381 in glioma. By RT-qPCR, we confirmed LINC02381 upregulation in glioma cells. Functional experiments demonstrated that LINC02381 knockdown repressed glioma cell proliferation and induced apoptosis. Boinformatics tools and RT-qPCR revealed the positive correlation between LINC02381 and CBX5 in glioma cells. More importantly, we confirmed that LINC02381 could interact and work synergistically with CEBPβ to bind to CBX5 promoter and activate CBX5 transcriptionally. Additionally, rescue experiments indicated that CBX5 up-regulation reversed the decline in cell proliferation and the augment in cell apoptosis caused by LINC02381 knockdown. To conclude, LINC02381 could facilitate CBX5 transcription via interaction with CEBPβ, thus exerting its oncogenic role in glioma cells, which could contribute to better understanding of glioma.
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Affiliation(s)
- Yong Sun
- Department of Neurosurgery, Henan Provincial People's Hospital, No.7 Weiwu Road, Jinshui District, Zhengzhou, 450003, Henan, China
| | - Xinjun Wang
- Department of Neurosurgery, Fifth Affiliated Hospital of Zhengzhou University, No.3 Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450052, China
| | - Xingyao Bu
- Department of Neurosurgery, Henan Provincial People's Hospital, No.7 Weiwu Road, Jinshui District, Zhengzhou, 450003, Henan, China.
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Qiang F, Li J. CircCSNK1G1 Contributes to the Tumorigenesis of Gastric Cancer by Sponging miR-758 and Regulating ZNF217 Expression. Cancer Manag Res 2021; 13:5027-5038. [PMID: 34234548 PMCID: PMC8253995 DOI: 10.2147/cmar.s305767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/07/2021] [Indexed: 12/29/2022] Open
Abstract
Background Increasing evidence indicates that circular RNAs (circRNAs) act as vital regulators in various cancers. Nevertheless, the effect of circCSNK1G1 on gastric cancer (GC) is still unknown. Methods The mRNA levels of circCSNK1G1, miR-758, and ZNF217 were measured by RT-qPCR. The protein levels of ZNF217 were evaluated by Western blotting. Cell migration, invasion, proliferation, and apoptosis were detected by Transwell, CCK-8, and flow cytometry assays. The association between miR-758 and circCSNK1G1/ZNF217 was confirmed by RIP and luciferase reporter assays. Xenograft assay was employed for in vivo experiment. Results In the current study, it was demonstrated that the expression levels of circCSNK1G1 and ZNF217 were upregulated in GC tissues and cells, while the level of miR-758 was declined. Furthermore, functional assays indicated that circCSNK1G1 depletion suppressed GC progression in vitro and in vivo. In addition, circCSNK1G1 directly interacted with miR-758, and the supplementation of miR-758 suppressed the development of GC, which was abolished following pcDNA3.1-circCSNK1G1 transfection. Then, we explored the downstream mechanism of miR-758 and found that miR-758 could target the 3'UTR of ZNF217 mRNA. The overexpression of miR-758 neutralized the ZNF217-mediated effects on facilitating the progression of GC. Finally, we revealed that circCSNK1G1 could upregulate ZNF217 expression by sponging miR-758 in GC cells. Conclusion Our study revealed that circCSNK1G1 accelerated GC progression via the miR-758/ZNF217 axis, suggesting that circCSNK1G1 might be a potential biomarker for GC diagnosis and treatment.
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Affiliation(s)
- Feng Qiang
- Department of Gastroenterology, the First People's Hospital of Huzhou, Huzhou, 313000, People's Republic of China
| | - Jingjing Li
- Department of Gastroenterology, the First People's Hospital of Huzhou, Huzhou, 313000, People's Republic of China
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Yu L, Zhang W, Wang P, Zhang Q, Cong A, Yang X, Sang K. LncRNA SNHG11 aggravates cell proliferation and migration in triple-negative breast cancer via sponging miR-2355-5p and targeting CBX5. Exp Ther Med 2021; 22:892. [PMID: 34257707 PMCID: PMC8243335 DOI: 10.3892/etm.2021.10324] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/06/2021] [Indexed: 12/24/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most common malignances worldwide. Concurrently, the incidence of TNBC has continued to rise in recent years. It is reported that long non-coding RNAs (lncRNAs) are involved in biological processes in numerous cancers including TNBC. Small nucleolar RNA host gene 11 (SNHG11) has already been studied and reported in some cancers. However, the role of SNHG11 in TNBC remains unknown. RT-qPCR was used to measure gene expression in the current study. CCK-8, colony formation, flow cytometry, Transwell and western blotting experiments were also performed to determine the biological function of SNHG11 in TNBC cells. Luciferase reporter and RIP assays were performed to measure relationship between genes. In the present study, the results indicated SNHG11 was highly expressed in TNBC tissues and cell lines. Moreover, SNHG11 aggravated cell proliferation and migration, and whereas it attenuated cell apoptosis in TNBC. Furthermore, SNHG11 sponged microRNA 2355-5p (miR-2355-5p) in TNBC. Silencing SNHG11 increased miR-2355-5p expression. In addition, chromobox 5 (CBX5) was identified to be targeted by miR-2355-5p in TNBC. It was also suggested that CBX5 silencing suppressed cell proliferation and migration. Furthermore, overexpressed CBX5 recovered the inhibitive influence of SNHG11 silencing on proliferative and migrative abilities of TNBC cells. Overall, SNHG11 acted as a tumor promoter in TNBC and regulated TNBC cell growth by modulating the miR-2355-5p/CBX5 axis, which indicated that it may be used as a biomarker for TNBC treatment.
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Affiliation(s)
- Lei Yu
- Department of Oncology, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu 225300, P.R. China
| | - Wei Zhang
- Department of Infectious Diseases, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu 225300, P.R. China
| | - Peng Wang
- Department of Oncology, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu 225300, P.R. China
| | - Qi Zhang
- Department of Oncology, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu 225300, P.R. China
| | - Aihua Cong
- Department of Oncology, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu 225300, P.R. China
| | - Xiuyuan Yang
- Department of Oncology, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu 225300, P.R. China
| | - Kai Sang
- Department of Breast Surgery, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu 225300, P.R. China
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He M, Yue L, Wang H, Yu F, Yu M, Ni P, Zhang K, Chen S, Duan G, Zhang R. Evaluation of the prognostic value of CBXs in gastric cancer patients. Sci Rep 2021; 11:12375. [PMID: 34117289 PMCID: PMC8196000 DOI: 10.1038/s41598-021-91649-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 04/26/2021] [Indexed: 12/23/2022] Open
Abstract
Chromobox (CBX) proteins were suggested to exert epigenetic regulatory and transcriptionally repressing effects on target genes and might play key roles in the carcinogenesis of a variety of carcinomas. Nevertheless, the functions and prognostic significance of CBXs in gastric cancer (GC) remain unclear. The current study investigated the roles of CBXs in the prognosis of GC using the Oncomine, The Gene Expression Profiling Interactive Analysis (GEPIA), UALCAN, The Cancer Genome Atlas (TCGA), and cBioPortal databases. CBX1/2/3/4/5 were significantly upregulated in GC tissues compared with normal tissues, and CBX7 was downregulated. Multivariate analysis showed that high mRNA expression levels of CBX3/8 were independent prognostic factors for prolonged OS in GC patients. In addition, the genetic mutation rate of CBXs was 37% in GC patients, and genetic alterations in CBXs showed no association with OS or disease-free survival (DFS) in GC patients. These results indicated that CBX3/8 can be prognostic biomarkers for the survival of GC patients.
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Affiliation(s)
- Mengya He
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Limin Yue
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China.
| | - Haiyan Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Feiyan Yu
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Mingyang Yu
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Peng Ni
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Ke Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China.
| | - Rongguang Zhang
- Department of Epidemiology, College of Public Health, Hainan Medical University, Longhua District, No.3 Xueyuan Road, Haikou, 570216, China. .,Department of Experimentation Center, College of Public Health, Zhengzhou University, No.100 Kexue Avenue, Zhengzhou, 450001, China.
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11
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Zhu ZJ, Pang Y, Jin G, Zhang HY, Wang WH, Liu JW, Tuo GX, Wu P, Yang Y, Wang ZQ, Wang K. Hypoxia induces chemoresistance of esophageal cancer cells to cisplatin through regulating the lncRNA-EMS/miR-758-3p/WTAP axis. Aging (Albany NY) 2021; 13:17155-17176. [PMID: 34081626 PMCID: PMC8312407 DOI: 10.18632/aging.203062] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/14/2021] [Indexed: 04/10/2023]
Abstract
Hypoxia contributes significantly to the development of chemoresistance of many malignancies including esophageal cancer (EC). Accumulating studies have indicated that long non-coding RNAs play important roles in chemotherapy resistance. Here, we identified a novel lncRNA-EMS/miR-758-3p/WTAP axis that was involved in hypoxia-mediated chemoresistance to cisplatin in human EC. Hypoxia induced the expressions of lncRNA EMS and WTAP, and reduced the expression of miR-758-3p in EC cell line ECA-109. In addition, the expressions of EMS and WTAP were required for the hypoxia-induced drug resistance to cisplatin in EC cells, while overexpression of miR-758-3p reversed such chemoresistance. The targeting relationships between EMS and miR-758-3p, as well as miR-758-3p and WTAP, were verified by luciferase-based reporter assays and multiple quantitative assays after gene overexpression/knockdown. Moreover, we found significant correlations between tumor expressions of these molecules. Notably, higher levels of EMS/WTAP, or lower levels of miR-758-3p in tumors predicted worse survivals of EC patients. Furthermore, in a xenograft mouse model, targeted knockdown of EMS and WTAP in ECA-109 cells markedly attenuated the resistance of tumors to cisplatin treatments. Our study uncovers a critical lncRNA-EMS/miR-758-3p/WTAP axis in regulating hypoxia-mediated drug resistance to cisplatin in EC.
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Affiliation(s)
- Zi-Jiang Zhu
- Department of Thoracic Surgery 2, Gansu Provincial People's Hospital, Lanzhou 730000, China
| | - Yao Pang
- Department of Thoracic Surgery 2, Gansu Provincial People's Hospital, Lanzhou 730000, China
| | - Gang Jin
- Department of Thoracic Surgery 2, Gansu Provincial People's Hospital, Lanzhou 730000, China
| | - Hong-Yi Zhang
- Department of Thoracic Surgery 2, Gansu Provincial People's Hospital, Lanzhou 730000, China
| | - Wen-Hao Wang
- Department of Thoracic Surgery 2, Gansu Provincial People's Hospital, Lanzhou 730000, China
| | - Jia-Wei Liu
- Department of Thoracic Surgery 2, Gansu Provincial People's Hospital, Lanzhou 730000, China
| | - Guang-Xin Tuo
- School of Clinical Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou 730000, China
| | - Peng Wu
- School of Clinical Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou 730000, China
| | - Yi Yang
- School of Clinical Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou 730000, China
| | - Ze-Quan Wang
- School of Clinical Medicine, Ningxia Medical University, Ningxia 750004, China
| | - Kui Wang
- School of Clinical Medicine, Ningxia Medical University, Ningxia 750004, China
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Biagioni A, Chillà A, Del Rosso M, Fibbi G, Scavone F, Andreucci E, Peppicelli S, Bianchini F, Calorini L, Li Santi A, Ragno P, Margheri F, Laurenzana A. CRISPR/Cas9 uPAR Gene Knockout Results in Tumor Growth Inhibition, EGFR Downregulation and Induction of Stemness Markers in Melanoma and Colon Carcinoma Cell Lines. Front Oncol 2021; 11:663225. [PMID: 34055629 PMCID: PMC8163229 DOI: 10.3389/fonc.2021.663225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
uPAR is a globular protein, tethered to the cell membrane by a GPI-anchor involved in several cancer-related properties and its overexpression commonly correlates with poor prognosis and metastasis. We investigated the consequences of uPAR irreversible loss in human melanoma and colon cancer cell lines, knocking out its expression by CRISPR/Cas9. We analyzed through flow cytometry, western blotting and qPCR, the modulation of the most known cancer stem cells-associated genes and the EGFR while we observed the proliferation rate exploiting 2D and 3D cellular models. We also generated uPAR “rescue” expression cell lines as well as we promoted the expression of only its 3’UTR to demonstrate the involvement of uPAR mRNA in tumor progression. Knocking out PLAUR, uPAR-encoding gene, we observed an inhibited growth ratio unexpectedly coupled with a significant percentage of cells acquiring a stem-like phenotype. In vivo experiments demonstrated that uPAR loss completely abrogates tumorigenesis despite the gained stem-like profile. Nonetheless, we proved that the reintroduction of the 3’UTR of PLAUR gene was sufficient to restore the wild-type status validating the hypothesis that such a region may act as a “molecular sponge”. In particular miR146a, by binding PLAUR 3’ UTR region might be responsible for uPAR-dependent inhibition of EGFR expression.
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Affiliation(s)
- Alessio Biagioni
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, Italy
| | - Anastasia Chillà
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, Italy
| | - Mario Del Rosso
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, Italy
| | - Gabriella Fibbi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, Italy
| | - Francesca Scavone
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, Italy
| | - Elena Andreucci
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, Italy
| | - Silvia Peppicelli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, Italy
| | - Francesca Bianchini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, Italy
| | - Lido Calorini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, Italy
| | - Anna Li Santi
- Department of Chemistry and Biology, University of Salerno, Fisciano, Italy
| | - Pia Ragno
- Department of Chemistry and Biology, University of Salerno, Fisciano, Italy
| | - Francesca Margheri
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, Italy
| | - Anna Laurenzana
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Firenze, Italy
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13
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Zhou J, Chen Z, Zou M, Wan R, Wu T, Luo Y, Wu G, Wang W, Liu T. Prognosis and Immune Infiltration of Chromobox Family Genes in Sarcoma. Front Oncol 2021; 11:657595. [PMID: 34046352 PMCID: PMC8147558 DOI: 10.3389/fonc.2021.657595] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/13/2021] [Indexed: 12/16/2022] Open
Abstract
Background Chromobox family genes (CBXs) are known to play roles in numerous modifications of the chromatin in order to inhibit the transcription of target genes. CBXs have been shown to be expressed at high levels in many types of cancer and can also serve as a target gene for therapeutic purposes. However, little is known about the expression and prognostic value of CBXs in human sarcomas. Methods The transcription level of CBXs was analyzed using the Oncomine dataset, and the differential expression of CBXs in sarcoma was reported by the Gene Expression Profiling Interactive Analysis (GEPIA) dataset. We also used the CCLE dataset to evaluate the expression of CBXs in a sarcoma cell line. The prognostic value of CBXs was analyzed using GEPIA and Kaplan–Meier analysis. In addition, the corrections between CBXs and their co-expressed genes were reported using Oncomine and GEPIA datasets. DAVID was used to perform GO function enrichment analysis for the CBXs and their co-expression genes. Finally, TIMER was used to analyze the immune cell infiltration of CBXs in patients with sarcoma. Results HP1-α/β/γ (CBX1/3/5) and CBX4/6/8 were found to be overexpressed in human sarcoma, and CBXs were upregulated in almost all the sarcoma cell line. The expression levels of HP1-α/β/γ (CBX1/3/5) and CBX7 were associated with overall survival (OS) in patients with sarcoma, while high expression levels of CBX7 were related to disease-free survival (DFS). In addition, the expression levels of CBX2/6/7 were related to recurrence-free survival (RFS). We also found that the CBX family was positively correlated with the infiltration of immune cells, including CD8+ T cells, CD4+ T cells, B cells, macrophages, neutrophils, and dendritic cells, in sarcoma. Conclusions The results from the present study indicated that CBXs were significantly associated with prognosis and immunological status in sarcoma. These data suggest that CBXs could serve as potential biomarkers for prognosis and immune infiltration in human sarcoma.
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Affiliation(s)
- Jian Zhou
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ziyuan Chen
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ming Zou
- Department of Orthopedics, Brain Hospital of Hunan Province (The Second People's Hospital of Hunan Province), Changsha, China
| | - Rongjun Wan
- Department of Respiratory and Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Tong Wu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yingquan Luo
- Department of General Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Gen Wu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Clinical Medicine Eight-Year Program, Central South University, Changsha, China
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
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14
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Li H, Wu N, Liu ZY, Chen YC, Cheng Q, Wang J. Development of a novel transcription factors-related prognostic signature for serous ovarian cancer. Sci Rep 2021; 11:7207. [PMID: 33785763 PMCID: PMC8010122 DOI: 10.1038/s41598-021-86294-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/12/2021] [Indexed: 12/20/2022] Open
Abstract
Growing evidence suggest that transcription factors (TFs) play vital roles in serous ovarian cancer (SOC). In the present study, TFs mRNA expression profiles of 564 SOC subjects in the TCGA database, and 70 SOC subjects in the GEO database were screened. A 17-TFs related prognostic signature was constructed using lasso cox regression and validated in the TCGA and GEO cohorts. Consensus clustering analysis was applied to establish a cluster model. The 17-TFs related prognostic signature, risk score and cluster models were effective at accurately distinguishing the overall survival of SOC. Analysis of genomic alterations were used to elaborate on the association between the 17-TFs related prognostic signature and genomic aberrations. The GSEA assay results suggested that there was a significant difference in the inflammatory and immune response pathways between the high-risk and low-risk score groups. The potential immune infiltration, immunotherapy, and chemotherapy responses were analyzed due to the significant difference in the regulation of lymphocyte migration and T cell-mediated cytotoxicity between the two groups. The results indicated that patients with low-risk score were more likely to respond anti-PD-1, etoposide, paclitaxel, and veliparib but not to gemcitabine, doxorubicin, docetaxel, and cisplatin. Also, the prognostic nomogram model revealed that the risk score was a good prognostic indicator for SOC patients. In conclusion, we explored the prognostic values of TFs in SOC and developed a 17-TFs related prognostic signature to predict the survival of SOC patients.
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Affiliation(s)
- He Li
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Nayiyuan Wu
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Zhao-Yi Liu
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Yong-Chang Chen
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
| | - Jing Wang
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, Changsha, 410008, Hunan, People's Republic of China.
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15
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van Wijnen AJ, Bagheri L, Badreldin AA, Larson AN, Dudakovic A, Thaler R, Paradise CR, Wu Z. Biological functions of chromobox (CBX) proteins in stem cell self-renewal, lineage-commitment, cancer and development. Bone 2021; 143:115659. [PMID: 32979540 DOI: 10.1016/j.bone.2020.115659] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/02/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023]
Abstract
Epigenetic regulatory proteins support mammalian development, cancer, aging and tissue repair by controlling many cellular processes including stem cell self-renewal, lineage-commitment and senescence in both skeletal and non-skeletal tissues. We review here our knowledge of epigenetic regulatory protein complexes that support the formation of inaccessible heterochromatin and suppress expression of cell and tissue-type specific biomarkers during development. Maintenance and formation of heterochromatin critically depends on epigenetic regulators that recognize histone 3 lysine trimethylation at residues K9 and K27 (respectively, H3K9me3 and H3K27me3), which represent transcriptionally suppressive epigenetic marks. Three chromobox proteins (i.e., CBX1, CBX3 or CBX5) associated with the heterochromatin protein 1 (HP1) complex are methyl readers that interpret H3K9me3 marks which are mediated by H3K9 methyltransferases (i.e., SUV39H1 or SUV39H2). Other chromobox proteins (i.e., CBX2, CBX4, CBX6, CBX7 and CBX8) recognize H3K27me3, which is deposited by Polycomb Repressive Complex 2 (PRC2; a complex containing SUZ12, EED, RBAP46/48 and the methyl transferases EZH1 or EZH2). This second set of CBX proteins resides in PRC1, which has many subunits including other polycomb group factors (PCGF1, PCGF2, PCGF3, PCGF4, PCGF5, PCGF6), human polyhomeotic homologs (HPH1, HPH2, HPH3) and E3-ubiquitin ligases (RING1 or RING2). The latter enzymes catalyze the subsequent mono-ubiquitination of lysine 119 in H2A (H2AK119ub). We discuss biological, cellular and molecular functions of CBX proteins and their physiological and pathological activities in non-skeletal cells and tissues in anticipation of new discoveries on novel roles for CBX proteins in bone formation and skeletal development.
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Affiliation(s)
- Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America; Biochemistry & Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America; Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - Leila Bagheri
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - Amr A Badreldin
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - A Noelle Larson
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America; Biochemistry & Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - Christopher R Paradise
- Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, United States of America; Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, United States of America
| | - Zhong Wu
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America
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16
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Identification of the Roles of Chromobox Family Members in Gastric Cancer: A Study Based on Multiple Datasets. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5306509. [PMID: 33344640 PMCID: PMC7732380 DOI: 10.1155/2020/5306509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/05/2020] [Accepted: 10/16/2020] [Indexed: 12/24/2022]
Abstract
Background As the important components in polycomb repressive complexes 1 (PRC1) and heterochromatin protein 1 (HP1), Chromobox (CBX) family members are involved in epigenetic regulatory function, transcriptional repression, and other cellular metabolisms. Increasing studies have indicated significant associations between CBX and tumorigenesis, which is a progression in different types of cancers. However, the information about the roles of each CBX in gastric cancer is extremely limited. Methods We explored CBX mRNA expression, corrections with clinicopathological parameters, protein expression, prognostic values, enrichment analysis with several databases including Oncomine, Human Protein Atlas, UALCAN, Kaplan-Meier plotter, cBioPortal, GeneMANIA, and Enrichr. Results In our study, comparing to the normal tissues, higher mRNA expression of CBX1/2/3/4/5/8 and lower mRNA expression of CBX7 were found in GC tissues while upregulations of CBX1/2/3/4/5/8 and downregulations of CBX7 were indicated to be significantly correlated to the nodal metastasis status and individual cancer stages in GC patients. As for protein level, the expression of CBX2/3/4/5/6 was higher and the expression of CBX7 was lower in the GC tissues than those in the normal. What is more, higher mRNA expression of CBX1/5/6/8 and lower mRNA expression of CBX7 were markedly correlated to poor outcomes of OS and FP in GC patients. Besides, high mutation rate of CBXs (42%) was observed in GC patients. Conclusions We suggest that CBX5/7 may serve as potential therapeutic targets for GC while CBX1/8 may serve as potential prognostic indicators for GC.
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17
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Lin K, Zhu J, Hu C, Bu F, Luo C, Zhu X, Zhu Z. Comprehensive analysis of the prognosis for chromobox family in gastric cancer. J Gastrointest Oncol 2020; 11:932-951. [PMID: 33209489 DOI: 10.21037/jgo-20-208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Chromobox (CBX) family proteins are a class of transcriptional repressors involved in epigenetic regulation and developmental processes of various tumors, including gastric cancer. However, the function and prognosis of different CBXs in gastric cancer remain unknown. Methods This study addresses this issue by synthesizing several mainstream databases (Oncomine, GEPIA2, cBioportal, and Kaplan-Meier plotter, among others) that currently contain many tumor samples and provide very reliable analysis results, investigating the role of CBXs in the prognosis of gastric cancer. Results The mRNA of CBX1/2/3/4/5/8 was highly expressed in gastric cancer, the mRNA of CBX7 was lowly expressed in gastric cancer, and the mRNA expression of CBX6 was not significantly different in CRC. Besides, high and low CBXs mRNA expression correlated with cancer stage, node metastasis status, H. pylori infection status, and tumor grade in CRC patients. We found that high mRNA expression of CBX4/5/6/7/8 was significantly associated with worse overall survival (OS), progression-free survival (FP), and post-progression survival (PPS) in a large number of CRC patients. High mRNA expression of CBX3 was significantly associated with better OS and FP. We also found that none of the eight CBXs family genes had a mutation rate of less than 5% in gastric cancer, and the highest mutation rate was in CBX3 (14%). Conclusions These results suggest that CBX3/4/5/6/7/8 could be a prognostic biomarker in gastric cancer patients.
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Affiliation(s)
- Kang Lin
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jinfeng Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Cegui Hu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fanqin Bu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chen Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaojian Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhengming Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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18
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Ma T, Ma N, Chen JL, Tang FX, Zong Z, Yu ZM, Chen S, Zhou TC. Expression and prognostic value of Chromobox family members in gastric cancer. J Gastrointest Oncol 2020; 11:983-998. [PMID: 33209492 DOI: 10.21037/jgo-20-223] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background The Chromobox (CBX) protein family, which is a crucial part of the epigenetic regulatory complex, plays an important role in the occurrence and development of cancer; however, the function and prognostic value of CBX family members in gastric cancer is not clear. Methods we investigated the relationship between CBX members and gastric cancer using a range of tools and databases: Oncomine, Kaplan-Meier plotter, cBioPortal, ULCAN, Metascape, and GEPIA. Results The results showed that, relative to normal gastric tissue, mRNA expression levels of CBX1-6 were significantly higher in gastric cancer tissue, whereas the level of CBX7 was significantly lower. Furthermore, overexpression of CBX3-6 and underexpression of CBX7 mRNAs was significantly related to the poor prognosis and survival of gastric cancer patients, making these CBX family members useful biomarkers. Finally, overexpression of CBX1 mRNA was significantly related to the poor prognosis of gastric cancer patients treated with adjuvant 5-fluorouracil-based chemotherapy. Conclusions The members of the CBX family can be used as prognosis and survival biomarkers for gastric cancer and CBX1 may be a biomarker for choosing the chemotherapy regimen of gastric cancer patients.
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Affiliation(s)
- Tao Ma
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Ning Ma
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Jia-Lin Chen
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Fu-Xin Tang
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Zhen Zong
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhuo-Min Yu
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Shuang Chen
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
| | - Tai-Cheng Zhou
- Department of Gastrointestinal Surgery and Hernia Center, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, China
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Wu Y, Liu Y. miR-758-3p Inhibits Proliferation, Migration, and Invasion of Clear Cell Renal Cell Carcinoma and Predicts Favorable Prognosis. Cancer Manag Res 2020; 12:9285-9295. [PMID: 33061618 PMCID: PMC7535938 DOI: 10.2147/cmar.s261882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/07/2020] [Indexed: 12/18/2022] Open
Abstract
Background Although miR-758-3p has been reported to be associated with multiple cancers, including hepatocellular carcinoma, bladder cancer, gastric cancer and papillary thyroid cancer, its role in clear cell renal cell carcinoma (ccRCC) remains unclear. Methods The expression levels of miR-758-3p in ccRCC tissues and cell lines were examined using qRT-PCR. Survival analysis was performed using Kaplan–Meier, while the prognostic significance of miR-758-3p was evaluated by Cox regression analysis. The effects of miR-758-3p on cell proliferation, migration and invasion were analyzed with CCK-8, crystal violet and transwell assays. Luciferase reporter assays were performed to determine the effect of miR-758-3p on MDM2. Western blot was applied to measure the expression of MDM2. Results The expression levels of miR-758-3p were down-regulated in human ccRCC tissues and cell lines. Moreover, the expression of miR-758-3p was closely associated with histological grade, TNM stage and vascular invasion. High expression of miR-758-3p was found to be capable of predicting favorable clinical prognosis in ccRCC patients. Additionally, whilst the proliferation, migration and invasion of ccRCC cells were inhibited upon overexpression of miR-758-3p, the effects were reversed upon miR-758-3p knockdown. Moreover, miR-758-3p was a modulator of MDM2 in ccRCC. Conclusion This study demonstrated that miR-758-3p is a potential prognostic biomarker for ccRCC patients. Data from this study showed that miR-758-3p exhibits different biological functions that inhibit the progression of ccRCC cells, hence it can be a potential therapeutic target candidate for treating ccRCC.
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Affiliation(s)
- Yao Wu
- Endoscopy Center, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121000, People's Republic of China
| | - Yan Liu
- Department of Urology Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121000, People's Republic of China
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Bioinformatics Analysis of Key Genes and circRNA-miRNA-mRNA Regulatory Network in Gastric Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2862701. [PMID: 32908877 PMCID: PMC7463386 DOI: 10.1155/2020/2862701] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
Abstract
Gastric cancer (GC) is one of the most common malignancies in the world, with morbidity and mortality ranking second among all cancers. Accumulating evidences indicate that circular RNAs (circRNAs) are closely correlated with tumorigenesis. However, the mechanisms of circRNAs still remain unclear. This study is aimed at determining hub genes and circRNAs and analyzing their potential biological functions in GC. Expression profiles of mRNAs and circRNAs were downloaded from the Gene Expression Omnibus (GEO) data sets of GC and paracancer tissues. Differentially expressed genes (DEGs) and differentially expressed circRNAs (DE-circRNAs) were identified. The target miRNAs of DE-circRNAs and the bidirectional interaction between target miRNAs and DEGs were predicted. Functional analysis was performed, and the protein-protein interaction (PPI) network and the circRNA-miRNA-mRNA network were established. A total of 456 DEGs and 2 DE-circRNAs were identified with 3 mRNA expression profiles and 2 circRNA expression profiles. GO analysis indicated that DEGs were mainly enriched in extracellular matrix and cell adhesion, and KEGG confirmed that DEGs were mainly associated with focal adhesion, the PI3K-Akt signaling pathway, extracellular matrix- (ECM)- receptor interaction, and gastric acid secretion. 15 hub DEGs (BGN, COL1A1, COL1A2, FBN1, FN1, SPARC, SPP1, TIMP1, UBE2C, CCNB1, CD44, CXCL8, COL3A1, COL5A2, and THBS1) were identified from the PPI network. Furthermore, the survival analysis indicate that GC patients with a high expression of the following 9 hub DEGs, namely, BGN, COL1A1, COL1A2, FBN1, FN1, SPARC, SPP1, TIMP1, and UBE2C, had significantly worse overall survival. The circRNA-miRNA-mRNA network was constructed based on 1 circRNA, 15 miRNAs, and 45 DEGs. In addition, the 45 DEGs included 5 hub DEGs. These results suggested that hub DEGs and circRNAs could be implicated in the pathogenesis and development of GC. Our findings provide novel evidence on the circRNA-miRNA-mRNA network and lay the foundation for future research of circRNAs in GC.
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Zhao M, Di X, Jin X, Tian C, Cong S, Liu J, Wang K. Identification of Biomarkers for Sarcoidosis and Tuberculosis of the Lung Using Systematic and Integrated Analysis. Med Sci Monit 2020; 26:e925438. [PMID: 32701935 PMCID: PMC7397754 DOI: 10.12659/msm.925438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Sarcoidosis (SARC) is a multisystem inflammatory disease of unknown etiology and pulmonary tuberculosis (PTB) is caused by Mycobacterium tuberculosis. Both of these diseases affect lungs and lymph nodes and share similar clinical manifestations. However, the underlying mechanisms for the similarities and differences in genetic characteristics of SARC and PTB remain unclear. Material/Methods Three datasets (GSE16538, GSE20050, and GSE19314) were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in SARC and PTB were identified using GEO2R online analyzer and Venn diagram software. Functional enrichment analysis was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) and R packages. Two protein–protein interaction (PPI) networks were constructed using Search Tool for the Retrieval of Interacting Genes database, and module analysis was performed using Cytoscape. Hub genes were identified using area under the receiver operating characteristic curve analysis. Results We identified 228 DEGs, including 56 common SARC-PTB DEGs (enriched in interferon-gamma-mediated signaling, response to gamma radiation, and immune response) and 172 SARC-only DEGs (enriched in immune response, cellular calcium ion homeostasis, and dendritic cell chemotaxis). Potential biomarkers for SARC included CBX5, BCL11B, and GPR18. Conclusions We identified potential biomarkers that can be used as candidates for diagnosis and/or treatment of patients with SARC.
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Affiliation(s)
- Min Zhao
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Xin Di
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Xin Jin
- Department of Oncology and Hematology, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Chang Tian
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Shan Cong
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Jiaying Liu
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Ke Wang
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China (mainland)
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Zhang X, Xu J, Zhang H, Sun J, Li N, Huang X. MicroRNA-758 acts as a tumor inhibitor in colorectal cancer through targeting PAX6 and regulating PI3K/AKT pathway. Oncol Lett 2020; 19:3923-3930. [PMID: 32391100 PMCID: PMC7204622 DOI: 10.3892/ol.2020.11516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/06/2020] [Indexed: 12/24/2022] Open
Abstract
Recently, a number of microRNAs (miRNAs) have been reported to play different roles in human cancers, including colorectal cancer (CRC). However, the specific role of miR-758 has not been clarified in CRC. Therefore, the aim of the present study was to explore the role of miR-758 in CRC. RT-qPCR and western blot analysis were used to quantify the expression of miR-758 and genes. The function of miR-758 in CRC was investigated using Transwell, CCK-8 and luciferase reporter assays. According to the results, the downregulation of miR-758 expression was associated with aggressive behavior and poor prognosis in CRC patients. miR-758 was shown to restrain the cell viability and metastasis in CRC. In addition, it was confirmed that miR-758 directly targets PAX6 and inhibits CRC progression through targeting PAX6. The results also revealed that miR-758 blocked EMT and PI3K/AKT pathway in CRC. In conclusion, miR-758 acts as a tumor suppressor in CRC by downregulating PAX6.
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Affiliation(s)
- Xinli Zhang
- Medical Records Management Office, Qingdao West Coast New Area Central Hospital, Qingdao, Shandong 266555, P.R. China
| | - Jumei Xu
- Department of Hepatobiliary Gastrointestinal Surgery, The People's Hospital of Zhangqiu Area, Jinan, Shandong 250200, P.R. China
| | - Hongchang Zhang
- Department of Infectious Diseases, The People's Hospital of Zhangqiu Area, Jinan, Shandong 250200, P.R. China
| | - Jilan Sun
- Sterilization Supply Room, The People's Hospital of Zhangqiu Area, Jinan, Shandong 250200, P.R. China
| | - Na Li
- Department of Radiology, The People's Hospital of Zhangqiu Area, Jinan, Shandong 250200, P.R. China
| | - Xianyu Huang
- Radiotherapy Center, Qingdao Central Hospital, Qingdao University, Qingdao, Shandong 266042, P.R. China
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Liu XY, Guo JW, Kou JQ, Sun YL, Zheng XJ. Repair mechanism of astrocytes and non-astrocytes in spinal cord injury. World J Clin Cases 2020; 8:854-863. [PMID: 32190622 PMCID: PMC7062612 DOI: 10.12998/wjcc.v8.i5.854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/30/2019] [Accepted: 02/09/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Spinal cord injury (SCI) is a destructive disease that incurs huge personal and social costs, and there is no effective treatment. Although the pathogenesis and treatment mechanism of SCI has always been a strong scientific focus, the pathogenesis of SCI is still under investigation.
AIM To determine the key genes based on the modularization of in-depth analysis, in order to identify the repair mechanism of astrocytes and non-astrocytes in SCI.
METHODS Firstly, the differences between injured and non-injured spinal cord of astrocyte (HA), injured and non-injured spinal cord of non-astrocyte (FLOW), injured spinal cord of non-injured astrocyte (HA) and non-injured spinal cord of non-astrocyte (FLOW), and non-injured spinal cord of astrocyte (HA) and non-astrocyte (FLOW) were analyzed. The total number of differentially expressed genes was obtained by merging the four groups of differential results. Secondly, the genes were co-expressed and clustered. Then, the enrichment of GO function and KEGG pathway of module genes was analyzed. Finally, non-coding RNA, transcription factors and drugs that regulate module genes were predicted using hypergeometric tests.
RESULTS In summary, we obtained 19 expression modules involving 5216 differentially expressed genes. Among them, miR-494, XIST and other genes were differentially expressed in SCI patients, and played an active regulatory role in dysfunction module, and these genes were recognized as the driving genes of SCI. Enrichment results showed that module genes were significantly involved in the biological processes of inflammation, oxidation and apoptosis. Signal pathways such as NF-kappa B/A20, AMPK and MAPK were significantly regulated. In addition, non-coding RNA pivot (including miR-136-5p and let-7d-5p, etc.) and transcription factor pivot (including NFKB1, MYC, etc.) were identified as significant regulatory dysfunction modules.
CONCLUSION Overall, this study uncovered a co-expression network of key genes involved in astrocyte and non-astrocyte regulation in SCI. These findings helped to reveal the core dysfunction modules, potential regulatory factors and driving genes of the disease, and to improve our understanding of its pathogenesis.
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Affiliation(s)
- Xiang-Yun Liu
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong Province, China
| | - Jian-Wei Guo
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong Province, China
| | - Jian-Qiang Kou
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong Province, China
| | - Yuan-Liang Sun
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong Province, China
| | - Xiu-Jun Zheng
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong Province, China
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