1
|
Liu HX, Feng J, Jiang JJ, Shen WJ, Zheng Y, Liu G, Gao XY. Integrated single-cell and bulk RNA sequencing revealed an epigenetic signature predicts prognosis and tumor microenvironment colorectal cancer heterogeneity. World J Gastrointest Oncol 2024; 16:3032-3054. [PMID: 39072180 PMCID: PMC11271797 DOI: 10.4251/wjgo.v16.i7.3032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) prognosis prediction is currently a major challenge. Epigenetic regulation has been widely reported for its role in cancer development. AIM To construct a robust prognostic signature, we used developed and validated across datasets. METHODS After constructing the signature, the prognostic value of the signature was evaluated in the TCGA cohort and six independent datasets (GSE17526, GSE17537, GSE33113, GSE37892, GSE39048 and GSE39582). The clinical, genomic and transcriptomic features related to the signature were identified. The correlations of the signature score with immune cell infiltration and cell-cell interactions were analyzed. The correlations between the signature score and the sensitivity to different drugs were also predicted. RESULTS In the TCGA cohort, patients in the low-risk group according to the signature score had longer survival than those in the high-risk group, and this finding was validated in the validation datasets. The signature was a prognostic factor independent of age and sex and was correlated with stage and PD-1/PD-L1 expression. Area under the receiving operating characteristic curve was 0.72. Genomic association analyses revealed that samples from high-risk patients exhibited chromosomal instability. Transcriptomic analyses revealed that the signature score was significantly associated with multiple cellular pathways. Bulk RNA-seq and single-cell sequencing data revealed that the signature reflected differences in infiltrating immune cell-tumor cell interactions, especially for macrophages. The signature also predicted the putative drug sensitivity of CRC samples. CONCLUSION The signature is a valuable biomarker for predicting CRC prognosis and reflects multiple features of CRC, especially macrophage infiltration in the microenvironment.
Collapse
Affiliation(s)
- Han-Xuan Liu
- Beijing Jinghua Anliang Technology, Beijing 102627, China
| | - Jie Feng
- Department of Clinical Laboratory, The First Medical Centre of Chinese PLA General Hospital, Beijing 100853, China
| | - Jing-Jing Jiang
- Clinical Biological Sample Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Wan-Jun Shen
- Department of Nephrology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Yu Zheng
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Gang Liu
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xiang-Yang Gao
- The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| |
Collapse
|
2
|
Song Y, Zhang Y, Wang X, Han X, Shi M, Xu L, Yu J, Zhang L, Han S. SPI1 activates TGF-β1/PI3K/Akt signaling through transcriptional upregulation of FKBP12 to support the mesenchymal phenotype of glioma stem cells. Brain Pathol 2024; 34:e13217. [PMID: 37865975 PMCID: PMC11007049 DOI: 10.1111/bpa.13217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
Glioma stem cells (GSCs) exhibit diverse molecular subtypes with the mesenchymal (MES) population representing the most malignant variant. The oncogenic potential of Salmonella pathogenicity island 1 (SPI1), an oncogenic transcription factor, has been established across various human malignancies. In this study, we explored the association between the SPI1 pathway and the MES GSC phenotype. Through comprehensive analysis of the Cancer Genome Atlas and Chinese Glioma Genome Atlas glioma databases, along with patient-derived GSC cultures, we analyzed SPI1 expression. Using genetic knockdown and overexpression techniques, we assessed the functional impact of SPI1 on GSC MES marker expression, invasion, proliferation, self-renewal, and sensitivity to radiation in vitro, as well as its influence on tumor formation in vivo. Additionally, we investigated the downstream signaling cascades activated by SPI1. Our findings revealed a positive correlation between elevated SPI1 expression and the MES phenotype, which in turn, correlated with poor survival. SPI1 enhanced GSC MES differentiation, self-renewal, and radioresistance in vitro, promoting tumorigenicity in vivo. Mechanistically, SPI1 augmented the transcriptional activity of both TGF-β1 and FKBP12 while activating the non-canonical PI3K/Akt pathway. Notably, inhibition of TGF-β1/PI3K/Akt signaling partially attenuated SPI1-induced GSC MES differentiation and its associated malignant phenotype. Collectively, our results underscore SPI1's role in activating TGF-β1/PI3K/Akt signaling through transcriptional upregulation of FKBP12, thereby supporting the aggressive MES phenotype of GSCs. Therefore, SPI1 emerges as a potential therapeutic target in glioma treatment.
Collapse
Affiliation(s)
- Yifu Song
- Department of NeurosurgeryThe First Hospital of China Medical UniversityShenyangChina
| | - Yaochuan Zhang
- Department of NeurosurgeryThe First Hospital of China Medical UniversityShenyangChina
| | - Xiaoliang Wang
- Department of NeurosurgeryThe First Hospital of China Medical UniversityShenyangChina
| | - Xiaodi Han
- Department of NeurosurgeryThe First Hospital of China Medical UniversityShenyangChina
| | - Mengwu Shi
- Department of NeurosurgeryThe First Hospital of China Medical UniversityShenyangChina
| | - Ling Xu
- Department of Medical Oncologythe First Hospital of China Medical UniversityShenyangChina
| | - Juanhan Yu
- Department of PathologyChina Medical UniversityShenyangChina
| | - Li Zhang
- Department of NeurosurgeryThe First Hospital of China Medical UniversityShenyangChina
| | - Sheng Han
- Department of NeurosurgeryThe First Hospital of China Medical UniversityShenyangChina
| |
Collapse
|
3
|
Huang J, Huang C, Huang C, Xiang Z, Ni Y, Zeng J, Cai S. Comprehensive analysis reveals the prognostic and immunogenic characteristics of DNA methylation regulators in lung adenocarcinoma. Respir Res 2024; 25:74. [PMID: 38317133 PMCID: PMC10845581 DOI: 10.1186/s12931-024-02695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
DNA methylation regulators (DMRs) play a key role in DNA methylation, thus mediating tumor occurrence, metastasis, and immunomodulation. However, the effects of DMRs on clinical outcomes and immunotherapy response remain unexplored in lung adenocarcinoma (LUAD). In this study, eight LUAD cohorts and one immunotherapeutic cohort of lung cancer were utilized. We constructed a DNA methylation regulators-related signature (DMRRS) using univariate and multivariate COX regression analysis. The DMRRS-defined low-risk group was preferentially associated with favorable prognosis, tumor-inhibiting microenvironment, more sensitivity to several targeted therapy drugs, and better immune response. Afterward, the prognostic value and predictive potential in immunotherapy response were validated. Collectively, our findings uncovered that the DMRRS was closely associated with the tumor immune microenvironment and could effectively predict the clinical outcome and immune response of LUAD patients.
Collapse
Affiliation(s)
- Jing Huang
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, 510120, China
| | - Chujian Huang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Can Huang
- Eight-year MD program, Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100087, China
| | - Zichang Xiang
- Shenzhen University Medical School, Shenzhen, 518055, Guangdong, China
| | - Yao Ni
- Shenzhen University Medical School, Shenzhen, 518055, Guangdong, China
| | - Jian Zeng
- Department of Anesthesiology, Longgang District Central Hospital of Shenzhen, Shenzhen, 518116, Guangdong, China.
| | - Songhua Cai
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China.
| |
Collapse
|
4
|
Li M, Ni QY, Yu SY. Integration of single-cell transcriptomics and epigenetic analysis reveals enhancer-controlled TIMP1 as a regulator of ferroptosis in colorectal cancer. Genes Genomics 2024; 46:121-133. [PMID: 38032469 DOI: 10.1007/s13258-023-01474-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Ferroptosis is an iron-dependent non-apoptotic programmed cell death. However, the regulatory mechanism of ferroptosis in colorectal cancer (CRC) is still unclear. OBJECTIVE The aim of this study was to investigate the role and mechanism of enhancer-controlled genes in ferroptosis in CRC. METHODS Dimensionality reduction and differentially expressed genes (DEGs) identification were conducted using Seurat algorithm based on single-cell RNA sequencing (scRNA-seq) data from the GSE200997 dataset. Ferroptosis-related pathway enrichment analysis was performed using the FerrDb V2 database. Enhancers were identified using HOMER algorithm based on H3K27ac ChIP-seq data from the GSE166254 dataset. Kaplan-Meier Plotter online tool was used to analyze prognosis and gene expression correlation. Transcription factors were predicted using the transcription factor affinity prediction web tool. The binding of enhancer to transcription factor and H3K27ac enrichment were detected by ChIP-qPCR. RSL3 was used to induce ferroptosis in CRC cells. Gene transcription was detected by qRT-PCR. Cell proliferation was detected by CCK8 assay. RESULTS Nine cell clusters including T cells, natural killer cells, macrophages, mast cells, epithelial cells, fibroblasts, goblet cells, B cells and dendritic cells were identified in CRC and normal colonic tissue samples. Compared to normal colonic tissue-derived epithelial cells, 1075 DEGs were screened in CRC tissue-derived epithelial cells. Ferroptosis-related pathway enrichment suggested that DEGs were associated with the regulation of ferroptosis. DPEP1, ETV4, CEBPG, TIMP1, DUOX2 and LCN2 were identified as the significantly upregulated genes enriched in the "ferroptosis regulator" term, and their H3K27ac signals were significantly higher in CRC tissues than in normal colonic tissues. Of these, only the expression of TIMP1 predicted a poor prognosis of CRC patients. Transcription factor SPI1 drove TIMP1 transcription by binding to its enhancer. Overexpression of TIMP1 significantly promoted the resistance to ferroptosis induced by RSL3 in CRC cells, which was partially restored by SPI1 knockdown. CONCLUSION Transcription of TIMP1 was driven by transcription factor SPI1 in combination with its enhancer, consequently promoting CRC cells against ferroptosis. The SPI1/TIMP1 axis confers ferroptosis resistance in CRC, and thus has the potential to be the molecular targets for CRC treatment.
Collapse
Affiliation(s)
- Meng Li
- Department of Gastrointestinal Surgery, Hebei Medical University Third Hospital, Shijiazhuang, Hebei, 050051, China
| | - Qian-Yang Ni
- Department of Gastrointestinal Surgery, Hebei Medical University Third Hospital, Shijiazhuang, Hebei, 050051, China
| | - Su-Yang Yu
- Department of Gastrointestinal Surgery, Hebei Medical University Third Hospital, Shijiazhuang, Hebei, 050051, China.
| |
Collapse
|
5
|
Wang Z, Liu J, Qiu X, Zhang D, Inuzuka H, Chen L, Chen H, Xie L, Kaniskan HÜ, Chen X, Jin J, Wei W. Methylated Nucleotide-Based Proteolysis-Targeting Chimera Enables Targeted Degradation of Methyl-CpG-Binding Protein 2. J Am Chem Soc 2023; 145:21871-21878. [PMID: 37774414 PMCID: PMC10979653 DOI: 10.1021/jacs.3c06023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Methyl-CpG-binding protein 2 (MeCP2), a reader of DNA methylation, has been extensively investigated for its function in neurological and neurodevelopmental disorders. Emerging evidence indicates that MeCP2 exerts an oncogenic function in cancer; however, the endeavor to develop a MeCP2-targeted therapy remains a challenge. This work attempts to address it by introducing a methylated nucleotide-based targeting chimera termed methyl-proteolysis-targeting chimera (methyl-PROTAC). The methyl-PROTAC incorporates a methylated cytosine into an oligodeoxynucleotide moiety to recruit MeCP2 for targeted degradation in a von Hippel-Lindau- and proteasome-dependent manner, thus displaying antiproliferative effects in cancer cells reliant on MeCP2 overexpression. This selective cytotoxicity endows methyl-PROTAC with the capacity to selectively eliminate cancer cells that are addicted to the overexpression of the MeCP2 oncoprotein. Furthermore, methyl-PROTAC-mediated MeCP2 degradation induces apoptosis in cancer cells. These findings underscore the therapeutic potential of methyl-PROTAC to degrade undruggable epigenetic regulatory proteins. In summary, the development of methyl-PROTAC introduces an innovative strategy by designing a modified nucleotide-based degradation approach for manipulating epigenetic factors, thereby representing a promising avenue for the advancement of PROTAC-based therapeutics.
Collapse
Affiliation(s)
- Zhen Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Xing Qiu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Dingpeng Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Li Chen
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - He Chen
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Ling Xie
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xian Chen
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| |
Collapse
|
6
|
Chen Y, Lin B, Yang S, Huang J. IRF1 suppresses colon cancer proliferation by reducing SPI1-mediated transcriptional activation of GPX4 and promoting ferroptosis. Exp Cell Res 2023; 431:113733. [PMID: 37517591 DOI: 10.1016/j.yexcr.2023.113733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Abstract
IRF1 is a tumor suppressor gene in colon cancer. This study aimed to explore the potential regulation of IRF1 on the ferroptosis of colon cancer and the mechanisms underlying its regulation of GPX4 transcription. IRF1 interacting transcription factors regulating GPX4 transcription were predicted and validated. The role of the IRF1/SPI1-GPX4 axis on the ferroptosis of colon cancer cells was explored. Results showed that IRF1 overexpression reduced GPX4 transcription, increased reactive oxygen species (ROS) and lipid ROS accumulation, and enhanced erastin-induced colon cancer cell growth in vitro and in vivo. SPI1 could directly bind to the GPX4 promoter (-414 to -409) and activate its transcription. IRF1 could bind to SPI1 and suppress its transcriptional activating effects on GPX4 expression. SPI1 overexpression reduced ROS and lipid ROS accumulation and increased colon cancer cell viability and colony formation upon erastin induction. These trends were reversed by IRF1 overexpression. In conclusion, this study revealed a novel oncogenic mechanism of SPI1 by reducing erastin-induced ferroptosis in colon cancer. IRF1 interacts with SPI1 and suppresses its transcriptional activating effect on GPX4 expression. Through this mechanism, IRF1 can enhance erastin-induced ferroptosis of colon cancer. The IRF1/SPI1-GPX4 axis might play a crucial role in modulating ferroptosis in colon cancer and might serve as a potential therapeutic target in the future.
Collapse
Affiliation(s)
- Yilin Chen
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Beian Lin
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Shiyu Yang
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Jingshan Huang
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, Fujian, China.
| |
Collapse
|
7
|
Li J, Lv J, Chen Y, Li L. Tumor suppressor circPDE4D inhibits the progression of colorectal cancer and regulates oxaliplatin chemoresistance. Gene 2023; 864:147323. [PMID: 36858188 DOI: 10.1016/j.gene.2023.147323] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/08/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023]
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide, and it frequently develops resistance to chemotherapy. It was discovered that circular RNAs, which function as microRNA sponges, are involved in the pathogenesis of many cancers. This study aimed to investigate the biological functions of a circRNA derived from phosphodiesterase 4D (circPDE4D, hsa_circ_0072568) and its potential mechanism in oxaliplatin-resistant CRC. CircPDE4D expression were validated in human CRC cell lines and tissues. CircPDE4D siRNAs (si-circPDE4D) and LV003-circPDE4D plasmid were applied to investigate the function of circPDE4D. A quantitative real-time polymerase chain reaction was used to detect the levels of circPDE4D, its predicted sponge miRNAs, and their target genes. Cell proliferation was assessed by MTS(3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) assay. Cell migration and invasion capacity were evaluated by transwell assay. Terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling was used to stain apoptotic cells. The results showed that circPDE4D expression was downregulated in CRC cells and tissues. Transfection with si-circPDE4D promoted cell proliferation, migration, and invasion, and inhibited apoptosis in DLD1 cells. Transfection with LV003-circPDE4D showed the opposite effect. Besides, circPDE4D presented higher expression in HCT116/L cells than that in HCT116 cells. Si-circPDE4D or lv003-circPDE4D transfection increased or decreased cell proliferationin in both two cells. Moreover, si-circPDE4D transfection inhibited cell apoptosis, while LV003-circPDE4D induced apoptosis in HCT116/L cells. LV003-CircPDE4D reduced hsa-miR-569 expression while increasing SPI1 expression in HCT116/L. CircPDE4D could inhibit tumorigenesis and progression of both CRC and oxaliplatin-resistant CRC, providing insight for the development of therapeutic strategies.
Collapse
Affiliation(s)
- Jiaying Li
- Department of Pharmacy, Branch of The First Affiliated Hospital of Xinjiang Medical University, Changji 831100, Xinjiang, China.
| | - Jingsen Lv
- Forevergen Biosciences Center, Guangzhou 510000, Guangdong, China
| | - Yuan Chen
- Information Section, Changji People's Hospital, Changji 831100, Xinjiang, China
| | - Li Li
- General Department of Party and government, Branch of The First Affiliated Hospital of Xinjiang Medical University, Changji 831100, Xinjiang, China.
| |
Collapse
|
8
|
Nejati-Koshki K, Roberts CT, Babaei G, Rastegar M. The Epigenetic Reader Methyl-CpG-Binding Protein 2 (MeCP2) Is an Emerging Oncogene in Cancer Biology. Cancers (Basel) 2023; 15:2683. [PMID: 37345019 DOI: 10.3390/cancers15102683] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 06/23/2023] Open
Abstract
Epigenetic mechanisms are gene regulatory processes that control gene expression and cellular identity. Epigenetic factors include the "writers", "readers", and "erasers" of epigenetic modifications such as DNA methylation. Accordingly, the nuclear protein Methyl-CpG-Binding Protein 2 (MeCP2) is a reader of DNA methylation with key roles in cellular identity and function. Research studies have linked altered DNA methylation, deregulation of MeCP2 levels, or MECP2 gene mutations to different types of human disease. Due to the high expression level of MeCP2 in the brain, many studies have focused on its role in neurological and neurodevelopmental disorders. However, it is becoming increasingly apparent that MeCP2 also participates in the tumorigenesis of different types of human cancer, with potential oncogenic properties. It is well documented that aberrant epigenetic regulation such as altered DNA methylation may lead to cancer and the process of tumorigenesis. However, direct involvement of MeCP2 with that of human cancer was not fully investigated until lately. In recent years, a multitude of research studies from independent groups have explored the molecular mechanisms involving MeCP2 in a vast array of human cancers that focus on the oncogenic characteristics of MeCP2. Here, we provide an overview of the proposed role of MeCP2 as an emerging oncogene in different types of human cancer.
Collapse
Affiliation(s)
- Kazem Nejati-Koshki
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil 85991-56189, Iran
| | - Chris-Tiann Roberts
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Ghader Babaei
- Department of Clinical Biochemistry, Faculty of Medicine, Urmia University of Medical Sciences, Urmia 57157-89400, Iran
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| |
Collapse
|
9
|
Huang G, Wu Y, Du Y, Gan H, Hao S. Methyl-CpG Binding Protein 2 as a Potential Diagnostic and Prognostic Marker Facilitates Glioma Progression Through Activation of Wnt/β-Catenin Pathway. World Neurosurg 2023; 171:e560-e571. [PMID: 36529430 DOI: 10.1016/j.wneu.2022.12.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Glioma is the primary malignant tumor in the central nervous system and has high malignancy, mortality, and recurrence rates. Because of its heterogeneity and drug resistance, the blood-brain barrier, and other factors, the treatment of glioma has mainly been surgical resection combined with traditional radiotherapy and chemotherapy. However, the therapeutic effect has not been satisfactory. Methyl-CpG binding protein 2 (MeCP2) is an epigenetic regulator that has been reported to regulate the initiation and progression of glioma. However, the underlying mechanism in glioma has remained unclear. METHODS The gene expression of MeCp2, miR-138-5p, the epithelial-mesenchymal transition, the apoptosis-related gene, and the Wnt/β-Catenin pathway-related gene and proliferation were detected by reverse transcription-quantitative polymerase chain reaction or Western blot. The cell proliferation and apoptosis of the glioma cell was assessed using the CCK-8 assay and flow cytometry assay. The relationship between miR-138-5p and MeCp2 was measured using the dual luciferase reporter assay. The effect of MeCp2 in U87 cells was examined in a xenograft tumorigenesis model in vivo. RESULTS In our study, we found that MeCP2 was upregulated in glioma tissues and cell lines and that MeCP2 knockdown repressed cell proliferation and epithelial-mesenchymal transition but boosted cell apoptosis in glioma. Furthermore, MeCP2 knockdown attenuated in vivo glioma growth in a mice model. Mechanistically, miR-138-5p hindered the expression of MeCP2 by target MeCP2 and then inactivated the Wnt/β-catenin signaling pathway. In addition, subsequent rescue assays disclosed that miR-138-5p repressed the glioma malignant phenotype and MeCP2 overexpression reversed the inhibitory effect of miR-138-5p upregulation. Consistently, overexpression of MeCP2 elevated glioma development. However, inhibition of the Wnt/β-catenin signaling pathway with XAV-939 rescued the facilitation effect by overexpressing miR-138-5p. CONCLUSIONS Our results have revealed that miR-138-5p/MeCP2/Wnt/β-catenin signaling might be a new target axis for glioma treatment strategies.
Collapse
Affiliation(s)
- Guanyou Huang
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jingyang Hospital), Guiyang, China.
| | - Yujuan Wu
- Department of Neurology, The Second People's Hospital of Guiyang (Jingyang Hospital), Guiyang, China
| | - Yonggui Du
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jingyang Hospital), Guiyang, China
| | - Hongchuan Gan
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jingyang Hospital), Guiyang, China
| | - Shuyu Hao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
10
|
Chen Y, Chang Y, Zhou J, Lv L, Ying H. Inhibiting lncRNA NEAT1 facilitates the sensitization of melanoma cells to cisplatin through modulating the miR-519c-3p-MeCP2 axis. Pathol Res Pract 2023; 243:154364. [PMID: 36841132 DOI: 10.1016/j.prp.2023.154364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/09/2023]
Abstract
Cutaneous melanoma is an aggressive human malignancy, leading to high mortality worldwide. In addition to surgery, radiotherapy and chemotherapy are routine approaches to treat melanoma at late or metastatic stage. However, a group of melanoma patients developed chemoresistance, which ultimately limited the efficiency of chemotherapy. LncRNA NEAT1 (Nuclear-enriched abundant transcript 1) is frequently overexpressed in various cancers. Currently, the precise roles and underlying mechanisms of NEAT1 in chemoresistant melanoma remain unclear. This study reports NEAT1 was significantly upregulated in melanoma tumor specimens and cell lines. Blocking NEAT1 effectively sensitized melanoma cells to cisplatin (CDDP), a frequently used first-line anticancer agent. From the established cisplatin resistant melanoma cell line (SK-MEL-5 CDDP Res), we detected significantly upregulated NEAT1 expression and downregulated miR-519c-3p expression compared with those from SK-MEL-5 parental cells. Subsequently, expression of miR-519c-3p was remarkedly attenuated in melanoma tumors and cell lines. Bioinformatics analysis, RNA pull-down assay and luciferase assay consistently demonstrated that NEAT1 sponged miR-519c-3p to downregulate its expression in melanoma cells. Moreover, we identified the methyl CpG binding protein 2 (MeCP2), which is positively associated with cisplatin resistance in melanoma, was a direct target of miR-519c-3p in melanoma cells. Restoration of MeCP2 rescued the miR-519c-3p-promoted cisplatin sensitization. Finally, we showed restoration of miR-519c-3p in NEAT1-overexpressing SK-MEL-5 CDDP Res cells successfully overrode the NEAT1-promoted cisplatin resistance in melanoma from in vitro and in vivo results. In summary, our results unveiled biological roles and molecular mechanisms of the noncoding RNA-mediated cisplatin resistance in melanoma, suggesting blocking the NEAT1-miR-519c-3p-MeCP2 axis as a therapeutic strategy against chemoresistant melanoma.
Collapse
Affiliation(s)
- Yan Chen
- Department of Dermatology, First People's Hospital of Linping District, Zhejiang Province 311100, China
| | - Yan Chang
- Department of Dermatology, First People's Hospital of Linping District, Zhejiang Province 311100, China
| | - Jianping Zhou
- Department of Dermatology, First People's Hospital of Linping District, Zhejiang Province 311100, China
| | - Linna Lv
- Department of Dermatology, First People's Hospital of Linping District, Zhejiang Province 311100, China
| | - Hangyu Ying
- Department of Dermatology, Hangzhou Hospital of Traditional Chinese Medicine, Zhejiang Province 310012, China.
| |
Collapse
|
11
|
Hauschild AC, Pastrello C, Ekaputeri G, Bethune-Waddell D, Abovsky M, Ahmed Z, Kotlyar M, Lu R, Jurisica I. MirDIP 5.2: tissue context annotation and novel microRNA curation. Nucleic Acids Res 2022; 51:D217-D225. [PMID: 36453996 PMCID: PMC9825511 DOI: 10.1093/nar/gkac1070] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/16/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
MirDIP is a well-established database that aggregates microRNA-gene human interactions from multiple databases to increase coverage, reduce bias, and improve usability by providing an integrated score proportional to the probability of the interaction occurring. In version 5.2, we removed eight outdated resources, added a new resource (miRNATIP), and ran five prediction algorithms for miRBase and mirGeneDB. In total, mirDIP 5.2 includes 46 364 047 predictions for 27 936 genes and 2734 microRNAs, making it the first database to provide interactions using data from mirGeneDB. Moreover, we curated and integrated 32 497 novel microRNAs from 14 publications to accelerate the use of these novel data. In this release, we also extend the content and functionality of mirDIP by associating contexts with microRNAs, genes, and microRNA-gene interactions. We collected and processed microRNA and gene expression data from 20 resources and acquired information on 330 tissue and disease contexts for 2657 microRNAs, 27 576 genes and 123 651 910 gene-microRNA-tissue interactions. Finally, we improved the usability of mirDIP by enabling the user to search the database using precursor IDs, and we integrated miRAnno, a network-based tool for identifying pathways linked to specific microRNAs. We also provide a mirDIP API to facilitate access to its integrated predictions. Updated mirDIP is available at https://ophid.utoronto.ca/mirDIP.
Collapse
Affiliation(s)
| | | | - Gitta Kirana Anindya Ekaputeri
- Department of Medical Informatics, University Medical Center Göttingen, Georg-August University, Göttingen, Lower Saxony 37075, Germany
| | - Dylan Bethune-Waddell
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Mark Abovsky
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Zuhaib Ahmed
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Richard Lu
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Igor Jurisica
- To whom correspondence should be addressed. Tel: +1 416 581 7437;
| |
Collapse
|
12
|
Wang Y, Zhang Y, Wang F, Li T, Song X, Shi H, Du J, Zhang H, Jing H, Han J, Tong D, Zhang J. Bioinformatics analysis of prognostic value and immunological role of MeCP2 in pan-cancer. Sci Rep 2022; 12:18518. [PMID: 36323715 PMCID: PMC9630441 DOI: 10.1038/s41598-022-21328-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022] Open
Abstract
Methyl-CpG-binding protein 2(MeCP2) is an important epigenetic regulatory factor that promotes many tumor developments, such as liver cancer, breast cancer, and colorectal cancer. So far, no pan-cancer analysis has been reported. Therefore, this study aims to explore pan-cancer's prognostic value, immune infiltration pattern, and biological function. We used bioinformatics methods to analyze the expression and prognostic significance of MeCP2, and the relationship between MeCP2 and clinicopathological parameters, genetic variation, methylation, phosphorylation, immune cell infiltration, and biological function in pan-cancer from using a public database. The results showed that expression of MeCP2 was up-regulated in 8 cancers and down-regulated in 2 cancers, which was remarkably correlated with the prognosis, pathological stage, grade and subtype of cancers. The promoter methylation level of MeCP2 DNA was decreased in bladder urothelial carcinoma (BLCA), breast invasive carcinoma (BRCA), liver hepatocellular carcinoma (LIHC), prostate adenocarcinoma (PRAD), uterine corpus endometrial carcinoma (UCEC), testicular germ cell tumors (TGCT), and stomach adenocarcinoma (STAD);decreased phosphorylation of S25, S90, S92, S241, S286, S325 and S435 was found in MeCP2, such as UCEC, lung adenocarcinoma (LUAD), ovarian serous cystadenocarcinoma (OV), colon adenocarcinoma (COAD), and kidney renal clear cell carcinoma (KIRC). Furthermore, MeCP2 expression was significantly associated with multiple immunomodulators and immune cell infiltration levels across most tumors. Therefore, our pan-cancer explored the prognostic markers and immunotherapeutic value of MeCP2 in different cancers.
Collapse
Affiliation(s)
- Yanfeng Wang
- grid.440747.40000 0001 0473 0092Department of Cell Biology and Genetics, Medical College of Yan’an University, No. 38, Guanghua Road, Yan’an, 716000 Shaanxi Province People’s Republic of China ,grid.507892.10000 0004 8519 1271Clinical Laboratory of Affiliated Hospital of Yan’an University, Yan’an, 716000 Shaanxi Province People’s Republic of China
| | - Yunqing Zhang
- grid.507892.10000 0004 8519 1271Laboratory of Obstetrics and Gynecology, Affiliated Hospital of Yan’an University, Yan’an, 716000 Shaanxi Province People’s Republic of China
| | - Fenghui Wang
- grid.440747.40000 0001 0473 0092Department of Cell Biology and Genetics, Medical College of Yan’an University, No. 38, Guanghua Road, Yan’an, 716000 Shaanxi Province People’s Republic of China
| | - Ting Li
- grid.440257.00000 0004 1758 3118Department of Anesthesiology, Northwest Women’s and Children’s Hospital, Xi’an, 710061 Shaanxi People’s Republic of China
| | - Xinqiu Song
- grid.440747.40000 0001 0473 0092Department of Cell Biology and Genetics, Medical College of Yan’an University, No. 38, Guanghua Road, Yan’an, 716000 Shaanxi Province People’s Republic of China
| | - Haiyan Shi
- grid.440747.40000 0001 0473 0092Department of Cell Biology and Genetics, Medical College of Yan’an University, No. 38, Guanghua Road, Yan’an, 716000 Shaanxi Province People’s Republic of China
| | - Juan Du
- grid.440747.40000 0001 0473 0092Department of Cell Biology and Genetics, Medical College of Yan’an University, No. 38, Guanghua Road, Yan’an, 716000 Shaanxi Province People’s Republic of China
| | - Huahua Zhang
- grid.440747.40000 0001 0473 0092Department of Cell Biology and Genetics, Medical College of Yan’an University, No. 38, Guanghua Road, Yan’an, 716000 Shaanxi Province People’s Republic of China
| | - Hongmei Jing
- grid.440747.40000 0001 0473 0092Department of Cell Biology and Genetics, Medical College of Yan’an University, No. 38, Guanghua Road, Yan’an, 716000 Shaanxi Province People’s Republic of China
| | - Jiaqi Han
- grid.440747.40000 0001 0473 0092Department of Cell Biology and Genetics, Medical College of Yan’an University, No. 38, Guanghua Road, Yan’an, 716000 Shaanxi Province People’s Republic of China
| | - Dongdong Tong
- grid.43169.390000 0001 0599 1243Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, 710061 Shaanxi People’s Republic of China
| | - Jing Zhang
- grid.440747.40000 0001 0473 0092Department of Cell Biology and Genetics, Medical College of Yan’an University, No. 38, Guanghua Road, Yan’an, 716000 Shaanxi Province People’s Republic of China
| |
Collapse
|
13
|
He Y, Lin L, Ou Y, Hu X, Xu C, Wang C. Endothelial cell-specific molecule 1 (ESM1) promoted by transcription factor SPI1 acts as an oncogene to modulate the malignant phenotype of endometrial cancer. Open Med (Wars) 2022; 17:1376-1389. [PMID: 36117773 PMCID: PMC9420884 DOI: 10.1515/med-2022-0529] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 12/02/2022] Open
Abstract
We aimed to study the function and mechanism of endothelial cell-specific molecule 1 (ESM1) in endometrial cancer (EC). The binding relationship between SPI1 and ESM1 was predicted by bioinformatics analysis and verified by the dual-luciferase reporter assay. The expressions and effects of SPI1 and ESM1 were determined using quantitative real-time PCR, immunohistochemistry, Western blot, and functional experiments. ESM1 was highly expressed in EC and was associated with the poor prognosis of patients. ESM1 silencing suppressed the viability, proliferation, invasion, and angiogenesis of EC cells, down-regulated expressions of PCNA, N-cadherin, Vimentin, VEGFR-1, VEGFR2, and EGFR, but upregulated E-cadherin level, while ESM1 overexpression did oppositely. Moreover, SPI1 bound to ESM1. Overexpressed SPI1 promoted the expression of ESM1 and induced malignant phenotype (viability, proliferation, and invasion), which were countervailed by ESM1 silencing. Collectively, ESM1 induced by SPI1 promotes the malignant phenotype of EC.
Collapse
Affiliation(s)
- Yu He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Bengbu Medical College , Bengbu City , Anhui Province, 233004 , China
| | - Lu Lin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Bengbu Medical College , Bengbu City , Anhui Province, 233004 , China
| | - Yurong Ou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Bengbu Medical College , Bengbu City , Anhui Province, 233004 , China
| | - Xiaowen Hu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Bengbu Medical College , Bengbu City , Anhui Province, 233004 , China
| | - Chi Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Bengbu Medical College , Bengbu City , Anhui Province, 233004 , China
| | - Caizhi Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Bengbu Medical College , No. 287, Changhuai Road , Bengbu City , Anhui Province, 233004 , China
| |
Collapse
|
14
|
Tian J, Yang L, Wang Z, Yan H. MIR503HG impeded ovarian cancer progression by interacting with SPI1 and preventing TMEFF1 transcription. Aging (Albany NY) 2022; 14:5390-5405. [PMID: 35771155 PMCID: PMC9320548 DOI: 10.18632/aging.204147] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/30/2022] [Indexed: 11/25/2022]
Abstract
MIR503 host gene (MIR503HG) acts as an important tumor suppressor in many human cancers, but its role and regulatory mechanism in ovarian cancer need to be further studied. In this study, lower expressed MIR503HG was observed in ovarian tumor tissues and cells than in adjacent normal tissues and normal human ovarian epithelial cells. MIR503HG overexpression impaired the proliferative, invasive and EMT properties, and facilitated cell apoptosis in ovarian cancer cells. Nuclear and cytoplasmic separation test suggested that MIR503HG was mainly expressed in the nucleus. RNA immunoprecipitation and RNA pull-down assays confirmed that MIR503HG could bind to transcription factor SPI1 (Spi-1 proto-oncogene), and dual luciferase reporter gene and Chromatin immunoprecipitation assays verified that SPI1 could bind to TMEFF1 (Transmembrane protein with EGF like and two follistatin like domains 1) promoter, suggesting that MIR503HG suppressed TMEFF1 expression by competitively binding SPI1 and blocking transcriptional activation of TMEFF1. Moreover, interference with TMEFF1 reversed the promotion effect of MIR503HG silence on the malignant behaviors of ovarian cancer cells. Moreover, MIR503HG knockdown activated the MAPK and PI3K/AKT pathways by increasing the expression of TMEFF1. In addition, overexpression of MIR503HG in vivo suppressed the tumorigenic ability in nude mice. In conclusion, MIR503HG acted as a tumor suppressor lncRNA in ovarian cancer by suppressing transcription factor SPI1-mediated transcriptional activation of TMEFF1.
Collapse
Affiliation(s)
- Jun Tian
- Department Gynecology, HuaiHe Hospital of HeNan University, Kaifeng, HeNan, China
| | - Lei Yang
- Department Gynecology, Baoji Maternal and Child Health Care Hospital, Baoji, Shaanxi, China
| | - Zhongtai Wang
- Health Management Center, Taizhou Hospital of Zhejiang Province, Taizhou, Zhejiang, China
| | - Haiya Yan
- Department Gynecology, Baoji Maternal and Child Health Care Hospital, Baoji, Shaanxi, China
| |
Collapse
|
15
|
Priya S, Burns MB, Ward T, Mars RAT, Adamowicz B, Lock EF, Kashyap PC, Knights D, Blekhman R. Identification of shared and disease-specific host gene-microbiome associations across human diseases using multi-omic integration. Nat Microbiol 2022; 7:780-795. [PMID: 35577971 PMCID: PMC9159953 DOI: 10.1038/s41564-022-01121-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/06/2022] [Indexed: 12/19/2022]
Abstract
While gut microbiome and host gene regulation independently contribute to gastrointestinal disorders, it is unclear how the two may interact to influence host pathophysiology. Here we developed a machine learning-based framework to jointly analyse paired host transcriptomic (n = 208) and gut microbiome (n = 208) profiles from colonic mucosal samples of patients with colorectal cancer, inflammatory bowel disease and irritable bowel syndrome. We identified associations between gut microbes and host genes that depict shared as well as disease-specific patterns. We found that a common set of host genes and pathways implicated in gastrointestinal inflammation, gut barrier protection and energy metabolism are associated with disease-specific gut microbes. Additionally, we also found that mucosal gut microbes that have been implicated in all three diseases, such as Streptococcus, are associated with different host pathways in each disease, suggesting that similar microbes can affect host pathophysiology in a disease-specific manner through regulation of different host genes. Our framework can be applied to other diseases for the identification of host gene-microbiome associations that may influence disease outcomes.
Collapse
Affiliation(s)
- Sambhawa Priya
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA
| | - Michael B Burns
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Tonya Ward
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Ruben A T Mars
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Beth Adamowicz
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Eric F Lock
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
16
|
Jafari H, Hussain S, Campbell MJ. Nuclear Receptor Coregulators in Hormone-Dependent Cancers. Cancers (Basel) 2022; 14:2402. [PMID: 35626007 PMCID: PMC9139824 DOI: 10.3390/cancers14102402] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 12/10/2022] Open
Abstract
Nuclear receptors (NRs) function collectively as a transcriptional signaling network that mediates gene regulatory actions to either maintain cellular homeostasis in response to hormonal, dietary and other environmental factors, or act as orphan receptors with no known ligand. NR complexes are large and interact with multiple protein partners, collectively termed coregulators. Coregulators are essential for regulating NR activity and can dictate whether a target gene is activated or repressed by a variety of mechanisms including the regulation of chromatin accessibility. Altered expression of coregulators contributes to a variety of hormone-dependent cancers including breast and prostate cancers. Therefore, understanding the mechanisms by which coregulators interact with and modulate the activity of NRs provides opportunities to develop better prognostic and diagnostic approaches, as well as novel therapeutic targets. This review aims to gather and summarize recent studies, techniques and bioinformatics methods used to identify distorted NR coregulator interactions that contribute as cancer drivers in hormone-dependent cancers.
Collapse
Affiliation(s)
- Hedieh Jafari
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA;
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Shahid Hussain
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Moray J. Campbell
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| |
Collapse
|
17
|
Shen PC, Wang YF, Chang HC, Huang WY, Lo CH, Su YF, Yang JF, Lin CS, Dai YH. Developing a novel DNA methylation risk score for survival and identification of prognostic gene mutations in endometrial cancer: a study based on TCGA data. Jpn J Clin Oncol 2022; 52:992-1000. [DOI: 10.1093/jjco/hyac077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Few studies have focused on DNA methylation in endometrial cancer. The aim of our study is identify its role in endometrial cancer prognosis.
Methods
A publicly available dataset was retrieved from The Cancer Genome Atlas. For validation of expression alteration due to methylation, RNA sequencing data were obtained from other independent cohorts. MethSurv was used to search for candidate CpG probes, which were then filtered by least absolute shrinkage and selection operator Cox regression and multivariate Cox regression analyses to identify final set of CpG probes for overall survival. A methylation-based risk model was developed and receiver operating characteristic analysis with area under curve was used for evaluation. Patients were divided into high- and low-risk groups using an optimal cut-off point. Comprehensive bioinformatic analyses were conducted to identify hub genes, key transcription factors, and enriched cancer-related pathways. Kaplan–Meier curve was used for survival analysis.
Results
A 5-CpG signature score was established. Its predictive value for 5-year overall survival was high, with area under curve of 0.828, 0.835 and 0.816 for the training, testing and entire cohorts. cg27487839 and cg12885678 had strong correlation with their gene expression, XKR6 and PTPRN2, and lower PTPRN2 expression was associated with poorer survival in both The Cancer Genome Atlas and the validation datasets. Low-risk group was associated with significantly better survival. Low-risk group harboured more mutations in hub genes and key transcription factors, and mutations in SP1 and MECP2 represented favourable outcome.
Conclusion
We developed a methylation-based prognostic stratification system for endometrial cancer. Low-risk group was associated with better survival and harboured more mutations in the key regulatory genes.
Collapse
Affiliation(s)
- Po-Chien Shen
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, Taipei
- Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Ying-Fu Wang
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, Taipei
| | - Hao-Chih Chang
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, Taipei
| | - Wen-Yen Huang
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, Taipei
| | - Cheng-Hsiang Lo
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, Taipei
| | - Yu-Fu Su
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, Taipei
| | - Jen-Fu Yang
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, Taipei
| | - Chun-Shu Lin
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, Taipei
| | - Yang-Hong Dai
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, Taipei
| |
Collapse
|
18
|
Zhang S, Zhao S, Qi Y, Li B, Wang H, Pan Z, Xue H, Jin C, Qiu W, Chen Z, Guo Q, Fan Y, Xu J, Gao Z, Wang S, Guo X, Deng L, Ni S, Xue F, Wang J, Zhao R, Li G. SPI1-induced downregulation of FTO promotes GBM progression by regulating pri-miR-10a processing in an m6A-dependent manner. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:699-717. [PMID: 35317283 PMCID: PMC8905236 DOI: 10.1016/j.omtn.2021.12.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022]
Abstract
As one of the most common post-transcriptional modifications of mRNAs and noncoding RNAs, N6-methyladenosine (m6A) modification regulates almost every aspect of RNA metabolism. Evidence indicates that dysregulation of m6A modification and associated proteins contributes to glioblastoma (GBM) progression. However, the function of fat mass and obesity-associated protein (FTO), an m6A demethylase, has not been systematically and comprehensively explored in GBM. Here, we found that decreased FTO expression in clinical specimens correlated with higher glioma grades and poorer clinical outcomes. Functionally, FTO inhibited growth and invasion in GBM cells in vitro and in vivo. Mechanistically, FTO regulated the m6A modification of primary microRNA-10a (pri-miR-10a), which could be recognized by reader HNRNPA2B1, recruiting the microRNA microprocessor complex protein DGCR8 and mediating pri-miR-10a processing. Furthermore, the transcriptional activity of FTO was inhibited by the transcription factor SPI1, which could be specifically disrupted by the SPI1 inhibitor DB2313. Treatment with this inhibitor restored endogenous FTO expression and decreased GBM tumor burden, suggesting that FTO may serve as a novel prognostic indicator and therapeutic molecular target of GBM.
Collapse
Affiliation(s)
- Shouji Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Shulin Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Yanhua Qi
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Boyan Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Huizhi Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Ziwen Pan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Hao Xue
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Chuandi Jin
- Institute for Medical Dataology of Shandong University, Jinan, People’s Republic of China
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, Shandong Province, People’s Republic of China
| | - Wei Qiu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Zihang Chen
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Qindong Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Yang Fan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Jianye Xu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Zijie Gao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Shaobo Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Xing Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Lin Deng
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Shilei Ni
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Fuzhong Xue
- Institute for Medical Dataology of Shandong University, Jinan, People’s Republic of China
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, Shandong Province, People’s Republic of China
| | - Jian Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
- Department of Biomedicine, University of Bergen, Jonas Lies Vei 91, 5009 Bergen, Norway
| | - Rongrong Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
- Corresponding author: Rongrong Zhao, Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China.
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
- Corresponding author: Gang Li, Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China.
| |
Collapse
|
19
|
Wang L, Gao Y, Tong D, Wang X, Guo C, Guo B, Yang Y, Zhao L, Zhang J, Yang J, Qin Y, Liu L, Huang C. MeCP2 drives hepatocellular carcinoma progression via enforcing HOXD3 promoter methylation and expression through the HB-EGF/EGFR pathway. Mol Oncol 2021; 15:3147-3163. [PMID: 34028973 PMCID: PMC8564637 DOI: 10.1002/1878-0261.13019] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/21/2021] [Accepted: 05/20/2021] [Indexed: 12/31/2022] Open
Abstract
Homeobox D3 (HOXD3), a member of the homeobox family, was described to regulate tumorigenesis, invasion, metastasis, and angiogenesis in various tumor types. However, the molecular mechanisms regulating HOXD3 during hepatocellular carcinoma (HCC) migration, invasion, and angiogenesis remain elusive. In this study, we demonstrated that HOXD3 expression is enhanced by the binding of methyl-CpG-binding protein 2 (MeCP2), a methyl-CpG binding protein, together with CREB1to the hypermethylated promoter of HOXD3. Inhibition of HOXD3 eliminated the tumorigenic effects of MeCP2 on HCC cells. Furthermore, HOXD3 directly targeted the promoter region of heparin-binding epidermal growth factor (HB-EGF) via the EGFR-ERK1/2 cell signaling pathway and promoted invasion, metastasis, and angiogenesis of HCC in vitro and in vivo. Additionally, elevated expression of MeCP2, CREB1, and HB-EGF in HCC correlated with a poor survival rate. Our findings reveal the function of the MeCP2/HOXD3/HB-EGF regulatory axis in HCC, rendering it an attractive candidate for the development of targeted therapeutics and as a potential biomarker in patients with HCC.
Collapse
Affiliation(s)
- Lumin Wang
- Department of Digestive Diseases in Precision Medicine Institutethe Second Affiliated Hospital of Xi'an Jiaotong UniversityChina
| | - Yi Gao
- Department of cell Biology and GeneticsSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
- Yan'an Key Laboratory of Chronic Disease Prevention and ResearchChina
| | - Dongdong Tong
- Department of cell Biology and GeneticsSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
- Key Laboratory of Environment and Genes Related to DiseasesXi'an Jiaotong University Health Science CenterChina
- Institute of Genetics and Developmental BiologyTranslational Medicine InstituteSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
| | - Xiaofei Wang
- Department of cell Biology and GeneticsSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
- Key Laboratory of Environment and Genes Related to DiseasesXi'an Jiaotong University Health Science CenterChina
- Institute of Genetics and Developmental BiologyTranslational Medicine InstituteSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
| | - Chen Guo
- Department of cell Biology and GeneticsSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
| | - Bo Guo
- Department of cell Biology and GeneticsSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
- Key Laboratory of Environment and Genes Related to DiseasesXi'an Jiaotong University Health Science CenterChina
- Institute of Genetics and Developmental BiologyTranslational Medicine InstituteSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
| | - Yang Yang
- Department of cell Biology and GeneticsSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
- Key Laboratory of Environment and Genes Related to DiseasesXi'an Jiaotong University Health Science CenterChina
- Institute of Genetics and Developmental BiologyTranslational Medicine InstituteSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
| | - Lingyu Zhao
- Department of cell Biology and GeneticsSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
- Key Laboratory of Environment and Genes Related to DiseasesXi'an Jiaotong University Health Science CenterChina
- Institute of Genetics and Developmental BiologyTranslational Medicine InstituteSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
| | - Jing Zhang
- Yan'an Key Laboratory of Chronic Disease Prevention and ResearchChina
| | - Juan Yang
- Department of cell Biology and GeneticsSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
- Key Laboratory of Environment and Genes Related to DiseasesXi'an Jiaotong University Health Science CenterChina
- Institute of Genetics and Developmental BiologyTranslational Medicine InstituteSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
| | - Yannan Qin
- Department of cell Biology and GeneticsSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
- Key Laboratory of Environment and Genes Related to DiseasesXi'an Jiaotong University Health Science CenterChina
- Institute of Genetics and Developmental BiologyTranslational Medicine InstituteSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
| | - Liying Liu
- Key Laboratory of Environment and Genes Related to DiseasesXi'an Jiaotong University Health Science CenterChina
- Institute of Genetics and Developmental BiologyTranslational Medicine InstituteSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
| | - Chen Huang
- Department of cell Biology and GeneticsSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
- Key Laboratory of Environment and Genes Related to DiseasesXi'an Jiaotong University Health Science CenterChina
- Institute of Genetics and Developmental BiologyTranslational Medicine InstituteSchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterChina
- Cardiovascular Research CenterXi'an Jiaotong University Health Science CenterChina
| |
Collapse
|
20
|
Nersisyan S, Ahlers AK, Lange T, Wicklein D, Galatenko A, Bohnenberger H, Elakad O, Conradi LC, Genduso S, Maar H, Schiecke A, Maltseva D, Raygorodskaya M, Makarova J, Schumacher U, Tonevitsky A. Low expression of CD24 is associated with poor survival in colorectal cancer. Biochimie 2021; 192:91-101. [PMID: 34637894 DOI: 10.1016/j.biochi.2021.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022]
Abstract
In this study we analyzed expression of CD24 in a cohort of colorectal cancer patients using immunohistochemistry staining of CD24. We found a significant association between absence or low expression of CD24 (10% of membranous and 55% of cytoplasmic staining) and shortened patient survival. Protein localization played a crucial role in the prognosis: membranous form was the major and prognostic one in primary tumors, while cytoplasmic expression was elevated in liver metastases compared to the primary tumors and contained prognostic information. Then, using The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) RNA-seq data, we showed that CD24 mRNA level was two-fold decreased in primary colorectal cancers compared to adjacent normal mucosa. Like the protein staining data, ten percent of patients with the lowest mRNA expression levels of CD24 in primary tumors had reduced survival compared to the ones with higher expression. To explain these findings mechanistically, shRNA-mediated CD24 knockdown was performed in HT-29 colorectal cancer cells. It resulted in the increase of cell migration in vitro, no changes in proliferation and apoptosis, and a slight decrease in cell invasion. As increased cell migration is a hallmark of metastasis formation, this finding corroborates the association of a decreased CD24 expression with poor prognosis. Differential gene expression analysis revealed upregulation of genes involved in cell migration in the group of patients with low CD24 expression, including integrin subunit α3 and α3, β3 subunits of laminin 332. Further co-expression analysis identified SPI1, STAT1 and IRF1 transcription factors as putative master-regulators in this group.
Collapse
Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia; SRC Bioclinicum, Moscow, Russia
| | - Ann-Kristin Ahlers
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias Lange
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Daniel Wicklein
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Alexei Galatenko
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia; Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | | | - Omar Elakad
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Lena-Christin Conradi
- Clinic for General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Sandra Genduso
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Hanna Maar
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Alina Schiecke
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia; SRC Bioclinicum, Moscow, Russia
| | - Maria Raygorodskaya
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia; SRC Bioclinicum, Moscow, Russia
| | - Julia Makarova
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Udo Schumacher
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia; SRC Bioclinicum, Moscow, Russia.
| |
Collapse
|
21
|
Wang S, Gan M, Chen C, Zhang Y, Kong J, Zhang H, Lai M. Methyl CpG binding protein 2 promotes colorectal cancer metastasis by regulating N 6 -methyladenosine methylation through methyltransferase-like 14. Cancer Sci 2021; 112:3243-3254. [PMID: 34097350 PMCID: PMC8353896 DOI: 10.1111/cas.15011] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/24/2022] Open
Abstract
RNA N6‐methyladenosine (m6A) is an emerging regulatory mechanism for tumor progression in several types of cancer. However, the underlying regulation mechanisms of m6A methylation in colorectal cancer (CRC) remain unknown. Although the oncogenic function of methyl CpG binding protein 2 (MeCP2) has been reported, it is still unclear whether MeCP2 could alter RNA m6A methylation state. Here, we systematically identified MeCP2 as a prometastasis gene to regulate m6A methylation in CRC. Interestingly, MeCP2 could bind to methyltransferase‐like 14 (METTL14) to coregulate tumor suppressor Kruppel‐like factor 4 (KLF4) expression through changing m6A methylation modification. Furthermore, insulin‐like growth factor 2 mRNA‐binding protein 2 recognized the unique modified m6A methylation sites to enhance KLF4 mRNA stability. Taken together, these findings highlight the novel function of MeCP2 for regulating m6A methylation and reveal the underlying molecular mechanism for the interaction between MeCP2 and METTL14, which offers a better understanding of CRC progression and metastasis.
Collapse
Affiliation(s)
- Shuo Wang
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China
| | - Meifu Gan
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China
| | - Chaoyi Chen
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Zhang
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China
| | - Jianlu Kong
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China
| | - Honghe Zhang
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China
| | - Maode Lai
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China.,Department of Pharmacology, China Pharmaceutical University, Nanjing, China
| |
Collapse
|
22
|
Mo BY, Li GS, Huang SN, Wei ZX, Su YS, Dai WB, Ruan L. Laryngeal Squamous Cell Carcinoma: Potential Molecular Mechanism and Prognostic Signature Based on Immune-Related Genes. Med Sci Monit 2020; 26:e928185. [PMID: 33361747 PMCID: PMC7772955 DOI: 10.12659/msm.928185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Immune-related genes (IRGs) are closely related to the incidence and progression of tumors, potentially indicating that IRGs play an important role in laryngeal squamous cell carcinoma (LSCC). MATERIAL AND METHODS An RNA sequencing dataset containing 123 samples was collected from The Cancer Genome Atlas. Based on immune-related differentially expressed genes (IRDEGs), a potential molecular mechanism of LSCC was explored through analysis of information in the Gene Ontology (GO) resource and the Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interactions (PPIs). A regulatory network of transcriptional regulators and IRDEGs was constructed to explore the underlying molecular mechanism of LSCC at the upstream level. Candidates from IRDEGs for signature were screened via univariate Cox analysis and using the least absolute shrinkage and selection operator (LASSO) technique. The IRDEG signature of LSCC was constructed by using a multivariate Cox proportional hazards model. RESULTS GO and KEGG analysis showed that IRDEGs may participate in the progression of LSCC through immune-related reactions. PPI analysis demonstrated that, among the IRDEGs in LSCC, the Kininogen 1; C-X-X motif chemokine ligand 10; elastase, neutrophil expressed; and LYZ genes are hub genes in the development of LSCC. At the upstream level, SPI1, SP140, signal transducer and activator of transcription 4, zinc finger E-box binding homeobox, and Ikaros family zinc finger 2 are the hub transcriptional regulators of IRDEGs. The risk score based on the IRDEG signature was able to distinguish prognosis in patients with LSCC and represents an independent prognostic risk factor for LSCC. CONCLUSIONS From the perspective of IRGs, we first constructed an IRDEG signature related to the prognosis of LSCC, which can be used as a novel marker to predict prognosis in patients with LSCC.
Collapse
Affiliation(s)
- Bin-Yu Mo
- Department of Otolaryngology, Liuzhou People's Hospital of Guangxi, Liuzhou, Guangxi, China (mainland)
| | - Guo-Sheng Li
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Su-Ning Huang
- Department of Radiotherapy, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China (mainland)
| | - Zhu-Xin Wei
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Ya-Si Su
- Department of Pathology, Liuzhou People's Hospital, Liuzhou, Guangxi, China (mainland)
| | - Wen-Bin Dai
- Department of Pathology, Liuzhou People's Hospital, Liuzhou, Guangxi, China (mainland)
| | - Lin Ruan
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| |
Collapse
|