1
|
Wang M, Yan X, Dong Y, Li X, Gao B. From driver genes to gene families: A computational analysis of oncogenic mutations and ubiquitination anomalies in hepatocellular carcinoma. Comput Biol Chem 2024; 112:108119. [PMID: 38852361 DOI: 10.1016/j.compbiolchem.2024.108119] [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: 03/19/2024] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Hepatocellular carcinoma (HCC) is a widespread primary liver cancer with a high fatality rate. Despite several genes with oncogenic effects in HCC have been identified, many remain undiscovered. In this study, we conducted a comprehensive computational analysis to explore the involvement of genes within the same families as known driver genes in HCC. Specifically, we expanded the concept beyond single-gene mutations to encompass gene families sharing homologous structures, integrating various omics data to comprehensively understand gene abnormalities in cancer. Our analysis identified 74 domains with an enriched mutation burden, 404 domain mutation hotspots, and 233 dysregulated driver genes. We observed that specific low-frequency somatic mutations may contribute to HCC occurrence, potentially overlooked by single-gene algorithms. Furthermore, we systematically analyzed how abnormalities in the ubiquitinated proteasome system (UPS) impact HCC, finding that abnormal genes in E3, E2, DUB families, and Degron genes often result in HCC by affecting the stability of oncogenic or tumor suppressor proteins. In conclusion, expanding the exploration of driver genes to include gene families with homologous structures emerges as a promising strategy for uncovering additional oncogenic alterations in HCC.
Collapse
Affiliation(s)
- Meng Wang
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Xinyue Yan
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Yanan Dong
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Xiaoqin Li
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China.
| | - Bin Gao
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| |
Collapse
|
2
|
Wang Z, Zheng Z, Wang B, Zhan C, Yuan X, Lin X, Xin Q, Zhong Z, Qiu X. Characterization of a G2M checkpoint-related gene model and subtypes associated with immunotherapy response for clear cell renal cell carcinoma. Heliyon 2024; 10:e29289. [PMID: 38617927 PMCID: PMC11015143 DOI: 10.1016/j.heliyon.2024.e29289] [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: 02/06/2024] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/16/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) presents challenges in early diagnosis and effective treatment. In this study, we aimed to establish a prognostic model based on G2M checkpoint-related genes and identify associated clusters in ccRCC through clinical bioinformatic analysis and experimental validation. Utilizing a single-cell RNA dataset (GSE159115) and bulk-sequencing data from The Cancer Genome Atlas (TCGA) database, we analyzed the G2M checkpoint pathway in ccRCC. Differential expression analysis identified 45 genes associated with the G2M checkpoint, leading to the construction of a predictive model with four key genes (E2F2, GTSE1, RAD54L, and UBE2C). The model demonstrated reliable predictive ability for 1-, 3-, and 5-year overall survival, with AUC values of 0.794, 0.790, and 0.794, respectively. Patients in the high-risk group exhibited a worse prognosis, accompanied by significant differences in immune cell infiltration, immune function, TIDE and IPS scores, and drug sensitivities. Two clusters of ccRCC were identified using the "ConsensusClusterPlus" package, cluster 1 exhibited a worse survival rate and was resistant to chemotherapeutic drugs of Axitinib, Erlotinib, Pazopanib, Sunitinib, and Temsirolimus, but not Sorafenib. Targeted experiments on RAD54L, a gene involved in DNA repair processes, revealed its crucial role in inhibiting proliferation, invasion, and migration in 786-O cells. In conclusion, our study offers valuable insights into the molecular mechanisms underlying ccRCC, identifying potential prognostic genes and molecular subtypes associated with the G2M checkpoint. These findings hold promise for guiding personalized treatment strategies in the management of ccRCC.
Collapse
Affiliation(s)
- Zhenwei Wang
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Zongtai Zheng
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Bangqi Wang
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Changxin Zhan
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
- The Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, 510317, China
| | - Xuefeng Yuan
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoqi Lin
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Qifan Xin
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Zhihui Zhong
- Center of Stem Cell and Regenerative Medicine, Gaozhou People's Hospital, Gaozhou, 525200, Guangdong, China
| | - Xiaofu Qiu
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
- The Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, 510317, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| |
Collapse
|
3
|
Ong KH, Lai HY, Sun DP, Chen TJ, Huang SKH, Tian YF, Chou CL, Shiue YL, Chan TC, Li CF, Kuo YH. Ubiquitin-conjugating enzyme E2C (UBE2C) is a prognostic indicator for cholangiocarcinoma. Eur J Med Res 2023; 28:593. [PMID: 38102624 PMCID: PMC10724938 DOI: 10.1186/s40001-023-01575-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/07/2023] [Indexed: 12/17/2023] Open
Abstract
Cholangiocarcinoma is the most common malignant bile duct tumor in Southeast Asia. The special location of cholangiocarcinoma leads to it being difficult to diagnose. Currently, the progress in clinical prognosis outcomes remains abysmal owing to the lack of definitive diagnostic criteria. Therefore, uncovering the potential markers for cholangiocarcinoma is a pressing issue. Ubiquitin-conjugating enzyme E2 C (UBE2C) is a critical ubiquitination enzyme; it is involved in the tumorigenesis of various malignancies and affects the patient's prognosis. However, there is currently no relevant literature to indicate whether UBE2C is related to the clinical survival outcome of cholangiocarcinoma patients. In this report, we mined the published cholangiocarcinoma transcriptome data set (GSE26566), compared it with the ubiquitination-associated gene (GO:0016567), and identified that UBE2C was highly expressed in cholangiocarcinoma tumor tissue. Moreover, high expression of UBE2C was markedly correlated with surgical margin, primary tumor, histological variants, and histological grade. More specifically, high expression of UBE2C was negatively associated with overall survival, disease-specific survival, local recurrence-free survival, and metastasis-free survival in patients with cholangiocarcinoma. Our findings demonstrate that UBE2C may provide a potential therapeutic marker and prognostic factor for cholangiocarcinoma patients.
Collapse
Affiliation(s)
- Khaa Hoo Ong
- Division of Gastroenterology & General Surgery, Department of Surgery, Chi Mei Medical Center, Tainan, 710, Taiwan
- Department of Medical Technology, Chung Hwa University of Medical Technology, Tainan, 717, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
| | - Hong-Yue Lai
- Department of Pharmacology, School of Medicine, China Medical University, Taichung, 404333, Taiwan
| | - Ding-Ping Sun
- Division of Gastroenterology & General Surgery, Department of Surgery, Chi Mei Medical Center, Tainan, 710, Taiwan
| | - Tzu-Ju Chen
- Department of Medical Technology, Chung Hwa University of Medical Technology, Tainan, 717, Taiwan
- Department of Clinical Pathology, Chi Mei Medical Center, Tainan, 710, Taiwan
| | - Steven Kuan-Hua Huang
- Division of Urology, Department of Surgery, Chi Mei Medical Center, Tainan, 710, Taiwan
- Department of Medical Science Industries, College of Health Sciences, Chang Jung Christian University, Tainan, 711, Taiwan
| | - Yu-Feng Tian
- Division of Colon and Rectal Surgery, Department of Surgery, Chi Mei Medical Center, Tainan, 710, Taiwan
| | - Chia-Lin Chou
- Department of Medical Technology, Chung Hwa University of Medical Technology, Tainan, 717, Taiwan
- Division of Colon and Rectal Surgery, Department of Surgery, Chi Mei Medical Center, Tainan, 710, Taiwan
| | - Yow-Ling Shiue
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
- Institute of Precision Medicine, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
| | - Ti-Chun Chan
- Department of Medical Research, Chi Mei Medical Center, Tainan, 710, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan
| | - Chien-Feng Li
- Institute of Precision Medicine, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
- Department of Medical Research, Chi Mei Medical Center, Tainan, 710, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan
- Trans-Omic Laboratory for Precision Medicine, Chi Mei Medical Center, Tainan, 710, Taiwan
| | - Yu-Hsuan Kuo
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan.
- Division of Hematology and Oncology, Department of Internal Medicine, Chi-Mei Medical Center, Tainan, 71004, Taiwan.
- College of Pharmacy and Science, Chia Nan University, Tainan, 71710, Taiwan.
| |
Collapse
|
4
|
Zhou H, Zeng C, Liu J, Luo H, Huang W. F-Box Protein 43, Stabilized by N6-Methyladenosine Methylation, Enhances Hepatocellular Carcinoma Cell Growth and Invasion via Promoting p53 Degradation in a Ubiquitin Conjugating Enzyme E2 C-Dependent Manner. Cancers (Basel) 2023; 15:cancers15030957. [PMID: 36765911 PMCID: PMC9913344 DOI: 10.3390/cancers15030957] [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: 12/22/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The roles of F-box protein 43 (FBXO43) in carcinogenesis have been rarely revealed. The present study investigates the expression, function, and underlying mechanism of FBXO43 in hepatocellular carcinoma (HCC). Firstly, the expression and clinical significance of FBXO43 in HCC were investigated bioinformatically and experimentally using online omics data and local tissue samples. The role of N6-methyladenosine modification (m6A) of mRNA in regulating FBXO43 expression and the effects of m6A/FBXO43 axis alteration on cell proliferation and invasion were investigated further. Moreover, the underlying mechanism of the oncogenic FBXO43 was also explored. The results demonstrated that FBXO43 was significantly upregulated in HCC and was positively correlated with advanced progression and poor prognosis in patients. METTL3 and IGF2BP2 expressions were positively correlated with FBXO43 expression and served as the writer and reader of FBXO43 m6A, respectively, which stabilized and upregulated FBXO43 mRNA in HCC. FBXO43 silencing significantly reduced cell proliferation and invasion, and ectopic expression of FBXO43 could significantly restore the inhibitory effects caused by METTL3 and IGF2BP2 depletion in HCC cells. Mechanistically, FBXO43 depletion reduced the expression of UBE2C, a p53 ubiquitin-conjugating enzyme, suppressed proteasomal degradation of p53, and thus inhibited cell proliferation and invasion in HCC. In summary, the present study revealed that METTL3/IGF2BP2 mediated m6A contributed to the upregulation of FBXO43 that promoted the malignant progression of HCC by stimulating p53 degradation in a UBE2C-dependent manner, highlighting the promising application of FBXO43 as a target in HCC treatment.
Collapse
Affiliation(s)
- Huijun Zhou
- Department of Gastroenterology and Urology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410083, China
| | - Chong Zeng
- Department of Medicine, The Seventh Affiliated Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Jie Liu
- Department of Pathology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Haijun Luo
- Department of Pathology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Wei Huang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410083, China
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha 410083, China
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410083, China
- Correspondence: ; Tel.: +86-18773187433
| |
Collapse
|
5
|
Thankam FG, La V, Agrawal DK. Single-cell genomics illustrates heterogeneous phenotypes of myocardial fibroblasts under ischemic insults. Biochem Cell Biol 2023; 101:12-51. [PMID: 36458696 DOI: 10.1139/bcb-2022-0229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myocardial regenerative strategies are promising where the choice of ideal cell population is crucial for successful translational applications. Herein, we explored the regenerative/repair responses of infarct zone cardiac fibroblast(s) (CF) by unveiling their phenotype heterogeneity at single-cell resolution. CF were isolated from the infarct zone of Yucatan miniswine that suffered myocardial infarction, cultured under simulated ischemic and reperfusion, and grouped into control, ischemia, and ischemia/reperfusion. The single-cell RNA sequencing analysis revealed 19 unique cell clusters suggesting distinct subpopulations. The status of gene expression (log2 fold change (log2 FC) > 2 and log2 FC < -2) was used to define the characteristics of each cluster unveiling with diverse features, including the pro-survival/cardioprotective (Clusters 1, 3, 5, 9, and 18), vasculoprotective (Clusters 2 and 5), anti-inflammatory (Clusters 4 and 17), proliferative (Clusters 4 and 5), nonproliferative (Clusters 6, 8, 11, 16, 17, and 18), proinflammatory (Cluster 6), profibrotic/pathologic (Clusters 8 and 19), antihypertrophic (Clusters 8 and 10), extracellular matrix restorative (Clusters 9 and 12), angiogenic (Cluster 16), and normal (Clusters 7 and 15) phenotypes. Further understanding of these unique phenotypes of CF will provide significant translational opportunities for myocardial regeneration and cardiac management.
Collapse
Affiliation(s)
- Finosh G Thankam
- Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Vy La
- Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Devendra K Agrawal
- Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA
| |
Collapse
|
6
|
Li Q, Zhang W. Progress in Anticancer Drug Development Targeting Ubiquitination-Related Factors. Int J Mol Sci 2022; 23:ijms232315104. [PMID: 36499442 PMCID: PMC9737479 DOI: 10.3390/ijms232315104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022] Open
Abstract
Ubiquitination is extensively involved in critical signaling pathways through monitoring protein stability, subcellular localization, and activity. Dysregulation of this process results in severe diseases including malignant cancers. To develop drugs targeting ubiquitination-related factors is a hotspot in research to realize better therapy of human diseases. Ubiquitination comprises three successive reactions mediated by Ub-activating enzyme E1, Ub-conjugating enzyme E2, and Ub ligase E3. As expected, multiple ubiquitination enzymes have been highlighted as targets for anticancer drug development due to their dominant effect on tumorigenesis and cancer progression. In this review, we discuss recent progresses in anticancer drug development targeting enzymatic machinery components.
Collapse
|
7
|
You D, Guo J, Zhang Y, Guo L, Lu X, Huang X, Sun S, Li H. The heterogeneity of mammalian utricular cells over the course of development. Clin Transl Med 2022; 12:e1052. [PMID: 36178017 PMCID: PMC9523683 DOI: 10.1002/ctm2.1052] [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: 03/21/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The inner ear organ is a delicate tissue consisting of hair cells (HCs) and supporting cells (SCs).The mammalian inner ear HCs are terminally differentiated cells that cannot spontaneously regenerate in adults. Epithelial non-hair cells (ENHCs) in the utricle include HC progenitors and SCs, and the progenitors share similar characteristics with SCs in the neonatal inner ear. METHODS We applied single-cell sequencing to whole mouse utricles from the neonatal period to adulthood, including samples from postnatal day (P)2, P7 and P30 mice. Furthermore, using transgenic mice and immunostaining, we traced the source of new HC generation. RESULTS We identified several sensory epithelial cell clusters and further found that new HCs arose mainly through differentiation from Sox9+ progenitor cells and that only a few cells were produced by mitotic proliferation in both neonatal and adult mouse utricles. In addition, we identified the proliferative cells using the marker UbcH10 and demonstrated that in adulthood the mitotically generated HCs were primarily found in the extrastriola. Moreover, we observed that not only Type II, but also Type I HCs could be regenerated by either mitotic cell proliferation or progenitor cell differentiation. CONCLUSIONS Overall, our findings expand our understanding of ENHC cell fate and the characteristics of the vestibular organs in mammals over the course of development.
Collapse
Affiliation(s)
- Dan You
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghaiChina,Department of Otorhinolaryngology‐Head and Neck SurgeryZhongshan HospitalFudan UniversityShanghaiChina
| | - Jin Guo
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghaiChina
| | - Yunzhong Zhang
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghaiChina
| | - Luo Guo
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghaiChina
| | - Xiaoling Lu
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghaiChina
| | - Xinsheng Huang
- Department of Otorhinolaryngology‐Head and Neck SurgeryZhongshan HospitalFudan UniversityShanghaiChina
| | - Shan Sun
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghaiChina
| | - Huawei Li
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghaiChina,Institutes of Biomedical SciencesFudan UniversityShanghaiChina,NHC Key Laboratory of Hearing Medicine, Fudan UniversityShanghaiChina,The Institutes of Brain Science and the Collaborative Innovation Center for Brain ScienceFudan UniversityShanghaiChina
| |
Collapse
|
8
|
Identification of Human Cell Cycle Phase Markers Based on Single-Cell RNA-Seq Data by Using Machine Learning Methods. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2516653. [PMID: 36004205 PMCID: PMC9393965 DOI: 10.1155/2022/2516653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 12/17/2022]
Abstract
The cell cycle is composed of a series of ordered, highly regulated processes through which a cell grows and duplicates its genome and eventually divides into two daughter cells. According to the complex changes in cell structure and biosynthesis, the cell cycle is divided into four phases: gap 1 (G1), DNA synthesis (S), gap 2 (G2), and mitosis (M). Determining which cell cycle phases a cell is in is critical to the research of cancer development and pharmacy for targeting cell cycle. However, current detection methods have the following problems: (1) they are complicated and time consuming to perform, and (2) they cannot detect the cell cycle on a large scale. Rapid developments in single-cell technology have made dissecting cells on a large scale possible with unprecedented resolution. In the present research, we construct efficient classifiers and identify essential gene biomarkers based on single-cell RNA sequencing data through Boruta and three feature ranking algorithms (e.g., mRMR, MCFS, and SHAP by LightGBM) by utilizing four advanced classification algorithms. Meanwhile, we mine a series of classification rules that can distinguish different cell cycle phases. Collectively, we have provided a novel method for determining the cell cycle and identified new potential cell cycle-related genes, thereby contributing to the understanding of the processes that regulate the cell cycle.
Collapse
|
9
|
Dong Y, Xiong Y, Zhou D, Yao M, Wang X, Bi W, Zhang J. TRIM56 Reduces Radiosensitization of Human Glioblastoma by Regulating FOXM1-Mediated DNA Repair. Mol Neurobiol 2022; 59:5312-5325. [PMID: 35696011 DOI: 10.1007/s12035-022-02898-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/21/2022] [Indexed: 12/01/2022]
Abstract
Recurrent glioblastoma is characterized by resistance to radiotherapy or chemotherapy. In this study, we investigated the role of TRIM56 in radiosensitization and its potential underlying molecular mechanism. TRIM56 expression levels were measured in glioblastoma tissues and cell lines by immunohistochemical staining, western blot, and qRT-PCR. MTT assay, colony formation assay, and TUNEL assay were used to investigate the effect of TRIM56 on cell viability, cell proliferation, and cell apoptosis. Co-immunoprecipitation was used to clarify the interaction between TRIM56 and FOXM1. Finally, tumor xenograft experiments were performed to analyze the effect of TRIM56 on tumor growth in vivo. The expression of TRIM56 was significantly increased in glioblastoma tissues and cell lines and its expression was associated with poor prognosis of patients with glioblastoma. Moreover, TRIM56 reduced the radiosensitivity of glioblastoma cells and promoted DNA repairment. Mechanistically, TRIM56 promoted FOXM1 protein level, enhanced the stability of FOXM1 by de-ubiquitination, and promoted DNA damage repair through FOXM1 in glioblastoma cells. TRIM56 could reduce the radiosensitivity of glioblastoma in vivo. TRIM56 may suppress the radiosensitization of human glioblastoma by regulating FOXM1-mediated DNA repair. Targeting the TRIM56 may be an effective method to reverse radiotherapy-resistant in glioblastoma recurrent.
Collapse
Affiliation(s)
- Yun Dong
- School of Pharmacy and Food Sciences, Zhuhai College of Science and Technology, Zhuhai, 519040, Guangdong Province, China.,School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Nanshan District, No.1066, Xueyuan Road, Shenzhen City, 518055, Guangdong Province, China
| | - Yiping Xiong
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Nanshan District, No.1066, Xueyuan Road, Shenzhen City, 518055, Guangdong Province, China
| | - Duanyang Zhou
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Nanshan District, No.1066, Xueyuan Road, Shenzhen City, 518055, Guangdong Province, China
| | - Min Yao
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Nanshan District, No.1066, Xueyuan Road, Shenzhen City, 518055, Guangdong Province, China
| | - Xiao Wang
- Department of Pharmacy, Shenzhen People's Hospital, Shenzhen City, 815020, Guangdong Province, China
| | - Wenchuan Bi
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Nanshan District, No.1066, Xueyuan Road, Shenzhen City, 518055, Guangdong Province, China.
| | - Jian Zhang
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Nanshan District, No.1066, Xueyuan Road, Shenzhen City, 518055, Guangdong Province, China.
| |
Collapse
|
10
|
Luo L, Santos A, Konganti K, Hillhouse A, Lambertz IU, Zheng Y, Gunaratna RT, Threadgill DW, Fuchs-Young RS. Overexpression of IGF-1 During Early Development Expands the Number of Mammary Stem Cells and Primes them for Transformation. Stem Cells 2022; 40:273-289. [DOI: 10.1093/stmcls/sxab018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Indexed: 11/13/2022]
Abstract
Abstract
Insulin-like growth factor I (IGF-1) has been implicated in breast cancer due to its mitogenic and anti-apoptotic effects. Despite substantial research on the role of IGF-1 in tumor progression, the relationship of IGF-1 to tissue stem cells, particularly in mammary tissue, and the resulting tumor susceptibility has not been elucidated. Previous studies with the BK5.IGF-1 transgenic (Tg) mouse model reveals that IGF-1 does not act as a classical, post-carcinogen tumor promoter in the mammary gland. Pre-pubertal Tg mammary glands display increased numbers and enlarged sizes of terminal end buds, a niche for mammary stem cells (MaSCs). Here we show that MaSCs from both wild type (WT) and Tg mice expressed IGF-1R and that overexpression of Tg IGF-1 increased numbers of MaSCs by undergoing symmetric division, resulting in an expansion of the MaSC and luminal progenitor (LP) compartments in pre-pubertal female mice. This expansion was maintained post-pubertally and validated by mammosphere assays in vitro and transplantation assays in vivo. The addition of recombinant IGF-1 promoted, and IGF-1R downstream inhibitors decreased mammosphere formation. Single-cell transcriptomic profiles generated from two related platforms reveal that IGF-1 stimulated quiescent MaSCs to enter the cell cycle and increased their expression of genes involved in proliferation, plasticity, tumorigenesis, invasion, and metastasis. This study identifies a novel, pro-tumorigenic mechanism, where IGF-1 increases the number of transformation-susceptible carcinogen targets during the early stages of mammary tissue development, and “primes” their gene expression profiles for transformation.
Collapse
Affiliation(s)
- Linjie Luo
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andres Santos
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
- Department of Anatomic Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Kranti Konganti
- Texas A&M Institute for Genome Sciences & Society, Texas A&M University, College Station, TX, USA
| | - Andrew Hillhouse
- Texas A&M Institute for Genome Sciences & Society, Texas A&M University, College Station, TX, USA
| | - Isabel U Lambertz
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Yuanning Zheng
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Ramesh T Gunaratna
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David W Threadgill
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
- Texas A&M Institute for Genome Sciences & Society, Texas A&M University, College Station, TX, USA
| | - Robin S Fuchs-Young
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
| |
Collapse
|
11
|
Wu SQ, Huang SH, Lin QW, Tang YX, Huang L, Xu YG, Wang SP. FDI-6 and olaparib synergistically inhibit the growth of pancreatic cancer by repressing BUB1, BRCA1 and CDC25A signaling pathways. Pharmacol Res 2022; 175:106040. [PMID: 34954029 DOI: 10.1016/j.phrs.2021.106040] [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: 10/29/2021] [Revised: 12/14/2021] [Accepted: 12/19/2021] [Indexed: 11/28/2022]
Abstract
Inducing homologous recombination (HR) deficiency is a promising strategy to broaden the indication of PARP1/2 inhibitors in pancreatic cancer treatment. In addition to inhibition kinases, repression of the transcriptional function of FOXM1 has been reported to inhibit HR-mediated DNA repair. We found that FOXM1 inhibitor FDI-6 and PARP1/2 inhibitor Olaparib synergistically inhibited the malignant growth of pancreatic cancer cells in vitro and in vivo. The results of bioinformatic analysis and mechanistic study showed that FOXM1 directly interacted with PARP1. Olaparib induced the feedback overexpression of PARP1/2, FOXM1, CDC25A, CCND1, CDK1, CCNA2, CCNB1, CDC25B, BRCA1/2 and Rad51 to promote the acceleration of cell mitosis and recovery of DNA repair, which caused the generation of adaptive resistance. FDI-6 reversed Olaparib-induced adaptive resistance and inhibited cell cycle progression and DNA damage repair by repressing the expression of FOXM1, PARP1/2, BUB1, CDC25A, BRCA1 and other genes-involved in cell cycle control and DNA damage repair. We believe that targeting FOXM1 and PARP1/2 is a promising combination therapy for pancreatic cancer without HR deficiency.
Collapse
Affiliation(s)
- Shi-Qi Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Shi-Hui Huang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Qian-Wen Lin
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Yi-Xuan Tang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Huang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Yun-Gen Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 211198 Nanjing, China.
| | - Shu-Ping Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
| |
Collapse
|
12
|
Poloznikov A, Nikulin S, Bolotina L, Kachmazov A, Raigorodskaya M, Kudryavtseva A, Bakhtogarimov I, Rodin S, Gaisina I, Topchiy M, Asachenko A, Novosad V, Tonevitsky A, Alekseev B. 9-ING-41, a Small Molecule Inhibitor of GSK-3β, Potentiates the Effects of Chemotherapy on Colorectal Cancer Cells. Front Pharmacol 2021; 12:777114. [PMID: 34955846 PMCID: PMC8696016 DOI: 10.3389/fphar.2021.777114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common and lethal types of cancer. Although researchers have made significant efforts to study the mechanisms underlying CRC drug resistance, our knowledge of this disease is still limited, and novel therapies are in high demand. It is urgent to find new targeted therapy considering limited chemotherapy options. KRAS mutations are the most frequent molecular alterations in CRC. However, there are no approved K-Ras targeted therapies for these tumors yet. GSK-3β is demonstrated to be a critically important kinase for the survival and proliferation of K-Ras–dependent pancreatic cancer cells. In this study, we tested combinations of standard-of-care therapy and 9-ING-41, a small molecule inhibitor of GSK-3β, in CRC cell lines and patient-derived tumor organoid models of CRC. We demonstrate that 9-ING-41 inhibits the growth of CRC cells via a distinct from chemotherapy mechanism of action. Although molecular biomarkers of 9-ING-41 efficacy are yet to be identified, the addition of 9-ING-41 to the standard-of-care drugs 5-FU and oxaliplatin could significantly enhance growth inhibition in certain CRC cells. The results of the transcriptomic analysis support our findings of cell cycle arrest and DNA repair deficiency in 9-ING-41–treated CRC cells. Notably, we find substantial similarity in the changes of the transcriptomic profile after inhibition of GSK-3β and suppression of STK33, another critically important kinase for K-Ras–dependent cells, which could be an interesting point for future research. Overall, the results of this study provide a rationale for the further investigation of GSK-3 inhibitors in combination with standard-of-care treatment of CRC.
Collapse
Affiliation(s)
- Andrey Poloznikov
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | - Sergey Nikulin
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Larisa Bolotina
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | - Andrei Kachmazov
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | | | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ildar Bakhtogarimov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Rodin
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Irina Gaisina
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, IL, United States
| | - Maxim Topchiy
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Asachenko
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - Victor Novosad
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,Scientific Research Centre Bioclinicum, Moscow, Russia.,Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Boris Alekseev
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| |
Collapse
|
13
|
Zarei Ghobadi M, Mozhgani SH, Erfani Y. Identification of dysregulated pathways underlying HTLV-1-associated myelopathy/tropical spastic paraparesis through co-expression network analysis. J Neurovirol 2021; 27:820-830. [PMID: 33405203 DOI: 10.1007/s13365-020-00919-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/29/2020] [Accepted: 10/08/2020] [Indexed: 12/13/2022]
Abstract
Human T cell lymphotropic virus-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a pathogen-caused disease which is associated with the progressive neurological disorder. HAM/TSP affects the expression level of several proteins and dysregulates some biological pathways. To identify the interaction patterns among expressed genes in HAM/TSP patients, weighted gene co-expression network analysis (WGCNA) was applied. Three microarray datasets regarding HAM/TSP were merged, and the co-expression network was constructed among genes. A total of 38 modules were identified. Three preserved modules in HAM/TSP in comparison to the healthy subjects which also had the most connected proteins and enriched in the biological pathways were selected. These modules were enriched in pathways related to immune systems, cell cycle, viral infection, and neuronal systems. Moreover, the involvement of novel immunological-related proteins including C1QB, GBP5, PSME1, SERPING1, and UBE2C; neurological-related proteins including TUBA4A, TUBB8, and TP63; and also proteins including TRPC6, PRKG2, OPRD1, PRKACA, and TUBB4A involved in the cGMP-PKG signaling pathway, thyroid hormone synthesis, and recruitment of mitotic centrosome proteins and complexes were found. Therefore, tracing these proteins and the identified modules can shed light on the pathogenesis mechanism of HAM/TSP and help to find potential therapeutic targets. However, further experimental validation should be performed to confirm the proposed functional players.
Collapse
Affiliation(s)
- Mohadeseh Zarei Ghobadi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sayed-Hamidreza Mozhgani
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Yousef Erfani
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
14
|
Jeong JH, Ryu JH, Lee HJ. In Vitro Inhibition of Piper nigrum and Piperine on Growth, Migration, and Invasion of PANC-1 Human Pancreatic Cancer Cells. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211057694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Several dietary and medicinal herbs have been shown to be effective in the treatment and prevention of cancer. Although Piper nigrum has been shown to have anti-cancer activities against various cancer cells, its anti-pancreatic cancer properties have not been reported. In the present study, P. nigrum extract (PNE) inhibited proliferation of PANC-1 human pancreatic cancer cells. Flow cytometry showed G0/G1 arrest caused by PNE in PANC-1 cells. In addition, Western blot analysis showed that PNE suppressed the protein levels of cell cycle regulators such as cyclin B1, cyclin D1, survivin, and Forkhead box M1 (FoxM1). These findings suggested that the inhibitory activity of PNE against the growth of PANC-1 cells was correlated with cell cycle arrest and repression of cell cycle regulators. Wound healing and trans-well assays showed that PNE suppressed migration and invasion of PANC-1 cells. Piperine, a major alkaloid of Piper nigrum, was identified as the main component of PNE by HPLC analysis. Piperine also attenuated the cell growth, migration, and invasion of PANC-1 cells, suggesting its contribution to the anti-pancreatic cancer effects of PNE. These results demonstrate that PNE and its major constituent, piperine, have anti-pancreatic cancer properties such as growth-inhibition, anti-migration, and anti-invasion of cancer cells.
Collapse
Affiliation(s)
- Ji Hye Jeong
- College of Pharmacy, Sookmyung Women's University, Yongsan-gu, Seoul, Korea
| | - Jae-Ha Ryu
- College of Pharmacy, Sookmyung Women's University, Yongsan-gu, Seoul, Korea
| | - Hwa Jin Lee
- School of Industrial Bio-Pharmaceutical Science, Semyung University, Jecheon, Korea
| |
Collapse
|
15
|
Li R, Pang XF, Huang ZG, Yang LH, Peng ZG, Ma J, He RQ. Overexpression of UBE2C in esophageal squamous cell carcinoma tissues and molecular analysis. BMC Cancer 2021; 21:996. [PMID: 34488675 PMCID: PMC8422647 DOI: 10.1186/s12885-021-08634-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/26/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Esophageal cancer is a common malignant tumor and its 5-year survival rate is much lower than 30% due to its invasiveness and pronounced metastasis ability, as well as the difficulty in early diagnosis. This study aimed to elucidate the molecular mechanism of ubiquitin conjugating enzyme E2 C (UBE2C) in esophageal squamous cell carcinoma (ESCC). METHODS In this study, we conducted a comprehensive evaluation of the UBE2C expression in ESCC by collecting the protein and mRNA expression data (including in-house RNA-seq, in-hosue immunohistochemistry, TCGA-GTEx RNA-seq and tissue microarray) to calculate a combined standardized mean difference (SMD) and summary receiver operating characteristic curve (sROC). Kaplan-Meier (K-M) method was used for survival analysis. We also explored the mechanism of UBE2C in ESCC by combing the differentially expressed genes (DEGs) of ESCC, related-genes of UBE2C in ESCC and the putative miRNAs and lncRNAs which may regulate UBE2C. RESULTS UBE2C protein and mRNA were highly expressed in ESCC tissues (including 772 ESCC tissue samples and 1837 non-cancerous tissue control samples). The pooled SMD of UBE2C expression values was 1.98 (95% CI: 1.51-2.45, p < 0.001), and the the area under the curve (AUC) of the sROC was 0.93 (95% CI: 0.90-0.95). The results of survival analysis suggested that UBE2C is likely to play different roles in different stages of the ESCC. Pathway anaylsis showed that UBE2C mainly influenced the biological function of esophageal cancer by synergistic effects with CDK1, PTTG1 and SKP2. We also constructed a potential UBE2C-related ceRNA network for ESCC (HCP5/has-miR-139-5p/UBE2C). CONCLUSION UBE2C mRNA and protein level were highly expressed in ESCC and UBE2C was likely to play different roles in different stages of the ESCC.
Collapse
Affiliation(s)
- Rong Li
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xing-Feng Pang
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Li-Hua Yang
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhi-Gang Peng
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jie Ma
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Rong-Quan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.
| |
Collapse
|
16
|
Novel FOXM1 inhibitor identified via gene network analysis induces autophagic FOXM1 degradation to overcome chemoresistance of human cancer cells. Cell Death Dis 2021; 12:704. [PMID: 34262016 PMCID: PMC8280155 DOI: 10.1038/s41419-021-03978-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022]
Abstract
FOXM1 transcription factor is an oncogene and a master regulator of chemoresistance in multiple cancers. Pharmacological inhibition of FOXM1 is a promising approach but has proven to be challenging. We performed a network-centric transcriptomic analysis to identify a novel compound STL427944 that selectively suppresses FOXM1 by inducing the relocalization of nuclear FOXM1 protein to the cytoplasm and promoting its subsequent degradation by autophagosomes. Human cancer cells treated with STL427944 exhibit increased sensitivity to cytotoxic effects of conventional chemotherapeutic treatments (platinum-based agents, 5-fluorouracil, and taxanes). RNA-seq analysis of STL427944-induced gene expression changes revealed prominent suppression of gene signatures characteristic for FOXM1 and its downstream targets but no significant changes in other important regulatory pathways, thereby suggesting high selectivity of STL427944 toward the FOXM1 pathway. Collectively, the novel autophagy-dependent mode of FOXM1 suppression by STL427944 validates a unique pathway to overcome tumor chemoresistance and improve the efficacy of treatment with conventional cancer drugs.
Collapse
|
17
|
Du X, Song H, Shen N, Hua R, Yang G. The Molecular Basis of Ubiquitin-Conjugating Enzymes (E2s) as a Potential Target for Cancer Therapy. Int J Mol Sci 2021; 22:ijms22073440. [PMID: 33810518 PMCID: PMC8037234 DOI: 10.3390/ijms22073440] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 01/06/2023] Open
Abstract
Ubiquitin-conjugating enzymes (E2s) are one of the three enzymes required by the ubiquitin-proteasome pathway to connect activated ubiquitin to target proteins via ubiquitin ligases. E2s determine the connection type of the ubiquitin chains, and different types of ubiquitin chains regulate the stability and activity of substrate proteins. Thus, E2s participate in the regulation of a variety of biological processes. In recent years, the importance of E2s in human health and diseases has been particularly emphasized. Studies have shown that E2s are dysregulated in variety of cancers, thus it might be a potential therapeutic target. However, the molecular basis of E2s as a therapeutic target has not been described systematically. We reviewed this issue from the perspective of the special position and role of E2s in the ubiquitin-proteasome pathway, the structure of E2s and biological processes they are involved in. In addition, the inhibitors and microRNAs targeting E2s are also summarized. This article not only provides a direction for the development of effective drugs but also lays a foundation for further study on this enzyme in the future.
Collapse
|
18
|
Current Status and Future Perspectives of Androgen Receptor Inhibition Therapy for Prostate Cancer: A Comprehensive Review. Biomolecules 2021; 11:biom11040492. [PMID: 33805919 PMCID: PMC8064397 DOI: 10.3390/biom11040492] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
The androgen receptor (AR) is one of the main components in the development and progression of prostate cancer (PCa), and treatment strategies are mostly directed toward manipulation of the AR pathway. In the metastatic setting, androgen deprivation therapy (ADT) is the foundation of treatment in patients with hormone-sensitive prostate cancer (HSPC). However, treatment response is short-lived, and the majority of patients ultimately progress to castration-resistant prostate cancer (CRPC). Surmountable data from clinical trials have shown that the maintenance of AR signaling in the castration environment is accountable for disease progression. Study results indicate multiple factors and survival pathways involved in PCa. Based on these findings, the alternative molecular pathways involved in PCa progression can be manipulated to improve current regimens and develop novel treatment modalities in the management of CRPC. In this review, the interaction between AR signaling and other molecular pathways involved in tumor pathogenesis and its clinical implications in metastasis and advanced disease will be discussed, along with a thorough overview of current and ongoing novel treatments for AR signaling inhibition.
Collapse
|
19
|
Xu T, Chen L, Lim YT, Zhao H, Chen H, Chen MW, Huan T, Huang Y, Sobota RM, Fang M. System Biology-Guided Chemical Proteomics to Discover Protein Targets of Monoethylhexyl Phthalate in Regulating Cell Cycle. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1842-1851. [PMID: 33459556 DOI: 10.1021/acs.est.0c05832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chemical proteomics methods have been used as effective tools to identify novel protein targets for small molecules. These methods have great potential to be applied as environmental toxicants to figure out their mode of action. However, these assays usually generate dozens of possible targets, making it challenging to validate the most important one. In this study, we have integrated the cellular thermal shift assay (CETSA), quantitative proteomics, metabolomics, computer-assisted docking, and target validation methods to uncover the protein targets of monoethylhexyl phthalate (MEHP). Using the mass spectrometry implementation of CETSA (MS-CETSA), we have identified 74 possible protein targets of MEHP. The Gene Ontology (GO) enrichment integration was further conducted for the target proteins, the cellular dysregulated proteins, and the metabolites, showing that cell cycle dysregulation could be one primary change due to the MEHP-induced toxicity. Flow cytometry analysis confirmed that hepatocytes were arrested at the G1 stage due to the treatment with MEHP. Subsequently, the potential protein targets were ranked by their binding energy calculated from the computer-assisted docking with MEHP. In summary, we have demonstrated the development of interactomics workflow to simplify the redundant information from multiomics data and identified novel cell cycle regulatory protein targets (CPEB4, ANAPC5, and SPOUT1) for MEHP.
Collapse
Affiliation(s)
- Tengfei Xu
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, 637141 Singapore
| | - Liyan Chen
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673 Singapore
| | - Yan Ting Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673 Singapore
| | - Haoduo Zhao
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
| | - Hongjin Chen
- Department of Pathology in the School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211112, P. R. China
| | - Ming Wei Chen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Yichao Huang
- School of Environment, Jinan University, Guangzhou, Guangdong 511443, P. R. China
| | - Radoslaw Mikolaj Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673 Singapore
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, 637141 Singapore
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 639798 Singapore
| |
Collapse
|
20
|
Aurilio G, Cimadamore A, Mazzucchelli R, Lopez-Beltran A, Verri E, Scarpelli M, Massari F, Cheng L, Santoni M, Montironi R. Androgen Receptor Signaling Pathway in Prostate Cancer: From Genetics to Clinical Applications. Cells 2020; 9:E2653. [PMID: 33321757 PMCID: PMC7763510 DOI: 10.3390/cells9122653] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 01/10/2023] Open
Abstract
Around 80-90% of prostate cancer (PCa) cases are dependent on androgens at initial diagnosis; hence, androgen ablation therapy directed toward a reduction in serum androgens and the inhibition of androgen receptor (AR) is generally the first therapy adopted. However, the patient's response to androgen ablation therapy is variable, and 20-30% of PCa cases become castration resistant (CRPCa). Several mechanisms can guide treatment resistance to anti-AR molecules. In this regard, AR-dependent and -independent resistance mechanisms can be distinguished within the AR pathway. In this article, we investigate the multitude of AR signaling aspects, encompassing the biological structure of AR, current AR-targeted therapies, mechanisms driving resistance to AR, and AR crosstalk with other pathways, in an attempt to provide a comprehensive review for the PCa research community. We also summarize the new anti-AR drugs approved in non-metastatic castration-resistant PCa, in the castration-sensitive setting, and combination therapies with other drugs.
Collapse
Affiliation(s)
- Gaetano Aurilio
- Medical Oncology Division of Urogenital and Head and Neck Tumours, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (G.A.); (E.V.)
| | - Alessia Cimadamore
- Section of Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy; (A.C.); (R.M.); (M.S.)
| | - Roberta Mazzucchelli
- Section of Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy; (A.C.); (R.M.); (M.S.)
| | | | - Elena Verri
- Medical Oncology Division of Urogenital and Head and Neck Tumours, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (G.A.); (E.V.)
| | - Marina Scarpelli
- Section of Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy; (A.C.); (R.M.); (M.S.)
| | - Francesco Massari
- Division of Oncology, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy;
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Matteo Santoni
- Oncology Unit, Macerata Hospital, 62100 Macerata, Italy;
| | - Rodolfo Montironi
- Section of Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy; (A.C.); (R.M.); (M.S.)
| |
Collapse
|
21
|
VanGenderen C, Harkness TAA, Arnason TG. The role of Anaphase Promoting Complex activation, inhibition and substrates in cancer development and progression. Aging (Albany NY) 2020; 12:15818-15855. [PMID: 32805721 PMCID: PMC7467358 DOI: 10.18632/aging.103792] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023]
Abstract
The Anaphase Promoting Complex (APC), a multi-subunit ubiquitin ligase, facilitates mitotic and G1 progression, and is now recognized to play a role in maintaining genomic stability. Many APC substrates have been observed overexpressed in multiple cancer types, such as CDC20, the Aurora A and B kinases, and Forkhead box M1 (FOXM1), suggesting APC activity is important for cell health. We performed BioGRID analyses of the APC coactivators CDC20 and CDH1, which revealed that at least 69 proteins serve as APC substrates, with 60 of them identified as playing a role in tumor promotion and 9 involved in tumor suppression. While these substrates and their association with malignancies have been studied in isolation, the possibility exists that generalized APC dysfunction could result in the inappropriate stabilization of multiple APC targets, thereby changing tumor behavior and treatment responsiveness. It is also possible that the APC itself plays a crucial role in tumorigenesis through its regulation of mitotic progression. In this review the connections between APC activity and dysregulation will be discussed with regards to cell cycle dysfunction and chromosome instability in cancer, along with the individual roles that the accumulation of various APC substrates may play in cancer progression.
Collapse
Affiliation(s)
- Cordell VanGenderen
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Troy Anthony Alan Harkness
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Terra Gayle Arnason
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.,Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| |
Collapse
|
22
|
Yu-jing T, Wen-jing T, Biao T. Integrated Analysis of Hub Genes and Pathways In Esophageal Carcinoma Based on NCBI's Gene Expression Omnibus (GEO) Database: A Bioinformatics Analysis. Med Sci Monit 2020; 26:e923934. [PMID: 32756534 PMCID: PMC7431388 DOI: 10.12659/msm.923934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Esophageal carcinoma (ESCA) is a health challenge with poor prognosis and limited treatment options. Our aim is to screen for hub genes and pathways associated with ESCA pathology as diagnostic or therapeutic targets. MATERIAL AND METHODS We downloaded 2 ESCA-related datasets from the Gene Expression Omnibus (GEO) database. Subsequently, differentially expressed genes (DEGs) of ESCA were determined by statistical analysis. Both Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using online analytic tools. Network analysis was employed to construct a protein-protein interaction (PPI) network and to filter hub genes. We evaluated the expression level and impact of hub genes on survival of ESCA patients using the OncoLoc webserver. RESULTS A total of 210 DEGs were identified. The GO analysis showed that the DEGs were enriched in cell division. The KEGG pathway analysis showed DEGs that were enriched in cell cycle regulation, known cancer pathways, the PI3K-Akt signaling pathway, and the cGMP-PKG signaling pathway. The top 10 hub genes were markedly upregulated in ESCA tissue compared with normal esophageal tissue. Moreover, the expression level of the hub genes was different at different pathological stages of ESCA. Further prognostic analysis identified that the top 10 hub genes were related to late survival of ESCA patients, while exhibiting few associations with early survival time. CONCLUSIONS The signaling pathways involving the DEGs probably represent the pathological mechanism underlying ESCA. The hub genes were associated with survival of ESCA patients, and as such have the potential to serve as diagnostic indicators and therapeutic targets.
Collapse
|
23
|
Epigenetic Alterations in Oesophageal Cancer: Expression and Role of the Involved Enzymes. Int J Mol Sci 2020; 21:ijms21103522. [PMID: 32429269 PMCID: PMC7278932 DOI: 10.3390/ijms21103522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/25/2022] Open
Abstract
Oesophageal cancer is a life-threatening disease, accounting for high mortality rates. The poor prognosis of this malignancy is mostly due to late diagnosis and lack of effective therapies for advanced disease. Epigenetic alterations may constitute novel and attractive therapeutic targets, owing to their ubiquity in cancer and their reversible nature. Herein, we offer an overview of the most important studies which compared differences in expression of enzymes that mediate epigenetic alterations between oesophageal cancer and normal mucosa, as well as in vitro data addressing the role of these genes/proteins in oesophageal cancer. Furthermore, The Cancer Genome Atlas database was interrogated for the correlation between expression of these epigenetic markers and standard clinicopathological features. We concluded that most epigenetic players studied thus far are overexpressed in tumours compared to normal tissue. Furthermore, functional assays suggest an oncogenic role for most of those enzymes, supporting their potential as therapeutic targets in oesophageal cancer.
Collapse
|
24
|
HMGA1-pseudogene7 transgenic mice develop B cell lymphomas. Sci Rep 2020; 10:7057. [PMID: 32341372 PMCID: PMC7184748 DOI: 10.1038/s41598-020-62974-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 03/22/2020] [Indexed: 01/07/2023] Open
Abstract
We have recently identified and characterized two pseudogenes (HMGA1P6 and HMGA1P7) of the HMGA1 gene, which has a critical role in malignant cell transformation and cancer progression. HMGA1P6 and HMGAP17 act as microRNA decoy for HMGA1 and other cancer-related genes upregulating their protein levels. We have previously shown that they are upregulated in several human carcinomas, and their expression positively correlates with a poor prognosis and an advanced cancer stage. To evaluate in vivo oncogenic activity of HMGA1 pseudogenes, we have generated a HMGA1P7 transgenic mouse line overexpressing this pseudogene. By a mean age of 12 months, about 50% of the transgenic mice developed splenomegaly and accumulation of lymphoid cells in several body compartments. For these mice FACS and immunohistochemical analyses suggested the diagnosis of B-cell lymphoma that was further supported by clonality analyses and RNA expression profile of the pathological tissues of the HMGA1P7 transgenic tissues. Therefore, these results clearly demonstrate the oncogenic activity of HMGA1 pseudogenes in vivo.
Collapse
|
25
|
Abstract
Introduction: FOXM1 is one of the most frequently overexpressed proteins in human solid cancers. Here, we discuss novel direct targets of FOXM1 as well as new pathways involving FOXM1, through which this protein exerts its oncogenic activity.Areas covered: We give a detailed review of FOXM1 transcriptional targets involved in 16 different types of human cancer as published in the literature in the last 5 years. We also discuss a novel positive feedback loop between FOXM1 and AKT - both well-established master regulators of cancer.Expert opinion: Despite the discovery of several FOXM1 inhibitors over the years (by our team and others), their therapeutic use is limited by their adverse off-target effects.Newly-discovered proteins regulated by FOXM1 present a promising alternative approach to target its pro-cancer activity. In addition, targeting regulating proteins that take part in the positive feedback loop between FOXM1/AKT has the double advantage of suppressing both, and can lead to developing novel anti-cancer drugs.
Collapse
Affiliation(s)
- Soheila Borhani
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Andrei L Gartel
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| |
Collapse
|
26
|
Kim YJ, Lee G, Han J, Song K, Choi JS, Choi YL, Shin YK. UBE2C Overexpression Aggravates Patient Outcome by Promoting Estrogen-Dependent/Independent Cell Proliferation in Early Hormone Receptor-Positive and HER2-Negative Breast Cancer. Front Oncol 2020; 9:1574. [PMID: 32039034 PMCID: PMC6989552 DOI: 10.3389/fonc.2019.01574] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/30/2019] [Indexed: 12/17/2022] Open
Abstract
We previously showed that UBE2C mRNA expression is significantly associated with poor prognosis only in patients with hormone receptor (HR)+/human epidermal growth factor receptor 2 (HER2)– breast cancer. In this study, we further reanalyzed the correlation between UBE2C mRNA expression and clinical outcomes in patients with HR+/HER2– breast cancer, and we investigated the molecular mechanism underlying the role of UBE2C modulation in disease progression in this subgroup of patients. Univariate and multivariate analyses showed that high UBE2C expression was associated with significantly shorter survival of breast cancer patients with pN0 and pN1 tumors but not pN2/N3 tumors (P < 0.05). In vitro functional experiments in HR+/HER2– breast cancer cells showed that UBE2C expression is a tumorigenic factor, and that estrogen upregulated UBE2C mRNA and protein by directly binding to the UBE2C promoter region. UBE2C knockdown inhibited cell proliferation by affecting cell cycle progression, and UBE2C overexpression was associated with estrogen-independent growth. UBE2C depletion markedly increased the cytotoxicity of tamoxifen by inducing apoptosis. The present findings suggest that UBE2C overexpression is correlated with relapse and promotes estrogen-dependent/independent proliferation in early HR+/HER2– breast cancer.
Collapse
Affiliation(s)
- Yu-Jin Kim
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Gyunghwa Lee
- Laboratory of Molecular Pathology and Cancer Genomics, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, South Korea
| | | | - Kyoung Song
- The Center for Companion Diagnostics, LOGONE Bio Convergence Research Foundation, Seoul, South Korea
| | - Joon-Seok Choi
- College of Pharmacy, Daegu Catholic University, Gyeongsan-si, South Korea
| | - Yoon-La Choi
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.,Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, South Korea
| | - Young Kee Shin
- Laboratory of Molecular Pathology and Cancer Genomics, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, South Korea.,The Center for Anti-cancer Companion Diagnostics, BioMAX/N-Bio, Seoul National University, Seoul, South Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| |
Collapse
|
27
|
Wu S, Zhang Y, Li Y, Wei H, Guo Z, Wang S, Zhang L, Bao Z. Identification and expression profiles of Fox transcription factors in the Yesso scallop (Patinopecten yessoensis). Gene 2020; 733:144387. [PMID: 31972308 DOI: 10.1016/j.gene.2020.144387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 02/07/2023]
Abstract
The forkhead box (Fox) gene family is a family of transcription factors that play important roles in a variety of biological processes in vertebrates, including early development and cell proliferation and differentiation. However, at present, studies on the mollusk Fox family are relatively lacking. In the present study, the Fox gene family of the Yesso scallop (Patinopecten yessoensis) was systematically identified. In addition, the expression profiles of the Fox gene family in early development and adult tissues were analyzed. The results showed that there were 26 Fox genes in P. yessoensis. Of the 26 genes, 24 belonged to 20 subfamilies. The Fox genes belonging to the I, Q1, R and S subfamilies were absent in P. yessoensis. The other 2 genes formed 2 independent clades with the Fox genes of other mollusks and protostomes. They might be new members of the Fox family and were named FoxY and FoxZ. P. yessoensis contained a FoxC-FoxL1 gene cluster similar in structure to that of Branchiostoma floridae, suggesting that the cluster might already exist in the ancestors of bilaterally symmetrical animals. The gene expression analysis of Fox showed that most of the genes were continuously expressed in multiple stages of early development, suggesting that Fox genes might be widely involved in the regulation of embryo and larval development of P. yessoensis. Nine Fox genes were specifically expressed in certain tissues, such as the nerve ganglia, foot, ovary, testis, and gills. For the 9 genes that were differentially expressed between the testis and ovary, their expression levels were analyzed during the 4 developmental stages of gonads. The results showed that FoxL2, FoxE and FoxY were highly expressed in the ovary during all developmental stages, while FoxZ was highly expressed in the testis during all developmental stages. The results suggested that these genes might play an important role in sex maintenance or gametogenesis. The present study could provide a reference for evolutionary and functional studies of the Fox family in metazoans.
Collapse
Affiliation(s)
- Shaoxuan Wu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yang Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yajuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Huilan Wei
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Zhenyi Guo
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, Shandong, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, Shandong, China.
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, Shandong, China
| |
Collapse
|
28
|
Jin Z, Zhao X, Cui L, Xu X, Zhao Y, Younai F, Messadi D, Hu S. UBE2C promotes the progression of head and neck squamous cell carcinoma. Biochem Biophys Res Commun 2019; 523:389-397. [PMID: 31870550 DOI: 10.1016/j.bbrc.2019.12.064] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022]
Abstract
The development of head and neck squamous cell carcinoma (HNSCC) is a complex pathological process and many cellular and molecular events may occur. The ubiquitin conjugating enzyme E2 (UBE2C) was found to play an oncogenic role in several human cancers. However, its functional role in HNSCC tumorigenesis remains unknown. In this study, UBE2C gene expression in HNSCC was first evaluated using the data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The connection between UBE2C gene expression and patients' survival rates of HNSCC and other human cancers was also investigated. Liquid chromatography with tandem mass spectrometry was used to identify differentially expressed proteins, including UBE2C, between UMSCC1 oral cancer cells and normal human oral keratinocytes (NHOKs). Immunohistochemistry (IHC) was used to verify the differential expression of UBE2C protein between HNSCC and adjacent control tissues. Cell cycle analysis, MTT, colony formation, Transwell migration, and Matrigel invasion assays were used to study the effect of UBE2C downregulation on the malignant phenotypes of HNSCC cells. The bioinformatic analysis of the proteins interacting with UBE2C in HNSCC cells was also performed. Based on the data obtained from the cancer databases and our in vitro studies, we found that UBE2C was overexpressed in HNSCC and patients with high UBE2C expression suffered a remarkably worse overall survival rate than those with low UBE2C expression, and a similar observation was found in a number of other human cancers. UBE2C was also found to be overexpressed in HNSCC cells versus normal human oral keratinocytes and inhibition of UBE2C expression significantly suppressed the malignant phenotypes of HNSCC cells in vitro. The bioinformatic analysis indicated that UBE2C may be involved in head and neck tumorigenesis through the mediation of important pathways such as ubiquitin mediated proteolysis, proteasome, and cell cycle. In conclusion, our results suggest that UBE2C is consistently upregulated in many human solid tumors. It promotes HNSCC progression and may serve as a potential prognostic biomarker in HNSCC. Future studies are warranted to unveil the underlying molecular pathways of UBE2C in HNSCC.
Collapse
Affiliation(s)
- Zhenning Jin
- UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Xinyuan Zhao
- Stomatological Hospital, Southern Medical University, Guangzhou, 510280, China
| | - Li Cui
- UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Xiangdong Xu
- UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Yutian Zhao
- UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Fariba Younai
- UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Diana Messadi
- UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Shen Hu
- UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA.
| |
Collapse
|
29
|
Lv S, Xu X, Wu Z. Identification of key candidate genes and pathways in endometrial cancer: Evidence from bioinformatics analysis. Oncol Lett 2019; 18:6679-6689. [PMID: 31807178 PMCID: PMC6876294 DOI: 10.3892/ol.2019.11040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/24/2019] [Indexed: 01/03/2023] Open
Abstract
Endometrial cancer (EC) is the fourth most common cancer in women worldwide. Although researchers are exploring the biological processes of tumorigenesis and development of EC, the gene interactions and biological pathways of EC are not accurately verified. In the present study, bioinformatics methods were used to screen for key candidate genes and pathways that were associated with EC and to reveal the possible mechanisms at molecular level. Microarray datasets (GSE63678, GSE17025 and GSE3013) from the Gene Expression Omnibus database were downloaded and 118 differentially expressed genes (DEGs) were selected using a Venn diagram. Functional enrichment analyses were performed on the DEGs. A protein-protein interaction network was constructed, including the module analysis. A total of 11 hub genes were identified from the DEGs, and functional enrichment analyses were performed to clarify their possible biological processes. A total of 118 DEGs were selected from three mRNA datasets. Functional enrichment demonstrated 27 downregulated genes that were primarily involved in the positive regulation of transcription from RNA polymerase II promoter, protein binding and the nucleus. A total of 91 upregulated DEGs were mainly associated with cell division, protein binding and the nucleus. Pathway analysis indicated that the downregulated DEGs were mainly enriched in pathways associated with cancer, and the upregulated DEGs were mainly enriched in the cell cycle. The 11 hub genes were primarily enriched in the cell cycle, oocyte meiosis, progesterone-mediated oocyte maturation, the p53 signaling pathway and viral carcinogenesis. The integrated analysis showed that cyclin B1, ubiquitin conjugating enzyme E2 C and cell division cycle 20 may participate in the tumorigenesis, development and invasion of EC. In conclusion, the hub genes and pathways identified in the present study contributed to the understanding of carcinogenesis and progression of EC at the mechanistic and molecular-biological level. As candidate targets for the diagnosis and treatment of EC, these genes deserve further investigation.
Collapse
Affiliation(s)
- Sha Lv
- Department of Gynecology and Obstetrics, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550001, P.R. China
| | - Xiaoxiao Xu
- Department of Gynecology and Obstetrics, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550001, P.R. China
| | - Zhangying Wu
- Department of Gynecology and Obstetrics, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550001, P.R. China
| |
Collapse
|
30
|
Ahmed F. Integrated Network Analysis Reveals FOXM1 and MYBL2 as Key Regulators of Cell Proliferation in Non-small Cell Lung Cancer. Front Oncol 2019; 9:1011. [PMID: 31681566 PMCID: PMC6804573 DOI: 10.3389/fonc.2019.01011] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/20/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Loss of control on cell division is an important factor for the development of non-small cell lung cancer (NSCLC), however, its molecular mechanism and gene regulatory network are not clearly understood. This study utilized the systems bioinformatics approach to reveal the “driver-network” involve in tumorigenic processes in NSCLC. Methods: A meta-analysis of gene expression data of NSCLC was integrated with protein-protein interaction (PPI) data to construct an NSCLC network. MCODE and iRegulone were used to identify the local clusters and its upstream transcription regulators involve in NSCLC. Pair-wise gene expression correlation was performed using GEPIA. The survival analysis was performed by the Kaplan-Meier plot. Results: This study identified a local “driver-network” with highest MCODE score having 26 up-regulated genes involved in the process of cell proliferation in NSCLC. Interestingly, the “driver-network” is under the regulation of TFs FOXM1 and MYBL2 as well as miRNAs. Furthermore, the overexpression of member genes in “driver-network” and the TFs are associated with poor overall survival (OS) in NSCLC patients. Conclusion: This study identified a local “driver-network” and its upstream regulators responsible for the cell proliferation in NSCLC, which could be promising biomarkers and therapeutic targets for NSCLC treatment.
Collapse
Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, University of Jeddah, Jeddah, Saudi Arabia.,University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
| |
Collapse
|
31
|
A Comprehensive Bioinformatics Analysis of UBE2C in Cancers. Int J Mol Sci 2019; 20:ijms20092228. [PMID: 31067633 PMCID: PMC6539744 DOI: 10.3390/ijms20092228] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/24/2019] [Accepted: 05/03/2019] [Indexed: 12/22/2022] Open
Abstract
Ubiquitination is one of the main post-translational modification of proteins. It plays key roles in a broad range of cellular functions, including protein degradation, protein interactions, and subcellular location. In the ubiquitination system, different proteins are involved and their dysregulation can lead to various human diseases, including cancers. By using data available from the Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases, we here show that the ubiquitin conjugating enzyme, E2C (UBE2C), is overexpressed in all 27 cancers we investigated. UBE2C expression is significantly higher in late-stage tumors, which might indicate its involvement in tumor progression and invasion. This study also revealed that patients with higher UBE2C levels showed a shorter overall survival (OS) time and worse OS prognosis. Moreover, our data show that UBE2C higher-expression leads to worse disease-free survival prognosis (DFS), indicating that UBE2C overexpression correlates with poor clinical outcomes. We also identified genes with positive correlations with UBE2C in several cancers. We found a number of poorly studied genes (family with sequence similarity 72-member D, FAM72D; meiotic nuclear divisions 1, MND1; mitochondrial fission regulator 2, MTFR2; and POC1 centriolar protein A, POC1A) whose expression correlates with UBE2C. These genes might be considered as new targets for cancers therapies since they showed overexpression in several cancers and correlate with worse OS prognosis.
Collapse
|
32
|
UBE2C functions as a potential oncogene by enhancing cell proliferation, migration, invasion, and drug resistance in hepatocellular carcinoma cells. Biosci Rep 2019; 39:BSR20182384. [PMID: 30914455 PMCID: PMC6470407 DOI: 10.1042/bsr20182384] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/12/2019] [Accepted: 03/21/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related mortality worldwide. Recently, ubiquitin-conjugating enzyme E2C (UBE2C) has been reported to be overexpressed in human cancers and act as a potential oncogene. However, little is known about the functional roles of UBE2C in HCC progression. In the present study, analysis of UBE2C mRNA expression in The Cancer Genome Atlas (TCGA) dataset reveals that significantly higher UBE2C mRNA levels was found in HCC tissues and associated with higher HCC grade. Elevated UBE2C mRNA levels in HCC indicated worsened survival probabilities. Through performing loss-of-function assays, we demonstrated that knockdown of UBE2C expression obviously suppressed proliferation, migration, and invasion of HCC cells in vitro Moreover, HCC cells with UBE2C knockdown showed higher sensitivity for the treatment of chemotherapeutic drug, including adriamycin (ADR) and 5-fluorouracil (5-FU). Silencing of UBE2C also increased the sensitivity of HCC cells to sorafenib, an approved treatment for patients with advanced-stage HCC. Our findings strongly suggest that UBE2C emerges as a marker for prognosis in HCC, and blocking UBE2C may be a novel strategy for HCC therapies.
Collapse
|
33
|
Hotfilder M, Mallela N, Seggewiß J, Dirksen U, Korsching E. Defining a Characteristic Gene Expression Set Responsible for Cancer Stem Cell-Like Features in a Sub-Population of Ewing Sarcoma Cells CADO-ES1. Int J Mol Sci 2018; 19:ijms19123908. [PMID: 30563222 PMCID: PMC6321634 DOI: 10.3390/ijms19123908] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/26/2018] [Accepted: 12/04/2018] [Indexed: 12/20/2022] Open
Abstract
One of the still open questions in Ewing sarcoma, a rare bone tumor with weak therapeutic options, is to identify the tumor-driving cell (sub) population and to understand the specifics in the biological network of these cells. This basic scientific insight might foster the development of more specific therapeutic target patterns. The experimental approach is based on a side population (SP) of Ewing cells, based on the model cell line CADO-ES1. The SP is established by flow cytometry and defined by the idea that tumor stem-like cells can be identified by the time-course in clearing a given artificial dye. The SP was characterized by a higher colony forming activity, by a higher differentiation potential, by higher resistance to cytotoxic drugs, and by morphology. Several SP and non-SP cell fractions and bone marrow-derived mesenchymal stem cell reference were analyzed by short read sequencing of the full transcriptome. The double-differential analysis leads to an altered expression structure of SP cells centered around the AP-1 and APC/c complex. The SP cells share only a limited proportion of the full mesenchymal stem cell stemness set of genes. This is in line with the expectation that tumor stem-like cells share only a limited subset of stemness features which are relevant for tumor survival.
Collapse
Affiliation(s)
- Marc Hotfilder
- Department of Pediatric Hematology and Oncology, University Hospital Münster, 48149 Münster, Germany.
| | - Nikhil Mallela
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, 48149 Münster, Germany.
| | - Jochen Seggewiß
- Institute of Human Genetics, Faculty of Medicine, University of Münster, 48149 Münster, Germany.
| | - Uta Dirksen
- University Hospital Essen, Pediatrics III, Hematology and Oncology, West German Cancer Centre, 45147 Essen, Germany.
| | - Eberhard Korsching
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, 48149 Münster, Germany.
| |
Collapse
|
34
|
Zhang J, Liu X, Yu G, Liu L, Wang J, Chen X, Bian Y, Ji Y, Zhou X, Chen Y, Ji J, Xiang Z, Guo L, Fang J, Sun Y, Cao H, Zhu Z, Yu Y. UBE2C Is a Potential Biomarker of Intestinal-Type Gastric Cancer With Chromosomal Instability. Front Pharmacol 2018; 9:847. [PMID: 30116193 PMCID: PMC6082955 DOI: 10.3389/fphar.2018.00847] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/13/2018] [Indexed: 12/28/2022] Open
Abstract
This study explored potential biomarkers associated with Lauren classification of gastric cancer. We screened microarray datasets on gastric cancer with information of Lauren classification in gene expression omnibus (GEO) database, and compared differentially expressing genes between intestinal-type or diffuse-type gastric cancer. Four sets of microarray data (GSE2669, GSE2680, GDS3438, and GDS4007) were enrolled into analysis. By differential gene analysis, UBE2C, CDH1, CENPF, ERO1L, SCD, SOX9, CKS1B, SPP1, MMP11, and ANLN were identified as the top genes related to intestinal-type gastric cancer, and MGP, FXYD1, FAT4, SIPA1L2, MUC5AC, MMP15, RAB23, FBLN1, ANXA10, and ADH1B were genes related to diffuse-type gastric cancer. We comprehensively validated the biological functions of the intestinal-type gastric cancer related gene UBE2C and evaluated its clinical significance on 1,868 cases of gastric cancer tissues from multiple medical centers of Shanghai, China. The gain of copy number on 20q was found in 4 out of 5 intestinal-type cancer cell lines, and no similar copy number variation (CNV) was found in any diffuse-type cancer cell line. Interfering UBE2C expression inhibited cell proliferation, migration and invasion in vitro, and tumorigenesis in vivo. Knockdown of UBE2C resulted in G2/M blockage in intestinal-type gastric cancer cells. Overexpression of UBE2C activated ERK signal pathway and promoted cancer cell proliferation. U0126, an inhibitor of ERK signaling pathway reversed the oncogenic phenotypes caused by UBE2C. Moreover, overexpression of UBE2C was identified in human intestinal-type gastric cancer. Overexpression of UBE2C protein predicted poor clinical outcome. Taken together, we characterized a group of Lauren classification-associated biomarkers, and clarified biological functions of UBE2C, an intestinal-type gastric cancer associated gene. Overexpression of UBE2C resulted in chromosomal instability that disturbed cell cycle and led to poor prognosis of intestinal-type gastric cancer.
Collapse
Affiliation(s)
- Jun Zhang
- Department of Surgery, Ruijin Hospital, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyu Liu
- Department of Surgery, Ruijin Hospital, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guanzhen Yu
- Changzheng Hospital, Affiliated to Second Military Medical University, Shanghai, China.,Department of Oncology, Longhua Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lei Liu
- Department of Surgery, Ruijin Hospital, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiejun Wang
- Changzheng Hospital, Affiliated to Second Military Medical University, Shanghai, China
| | - Xiaoyu Chen
- Renji Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhai Bian
- Renji Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuan Ji
- Zhongshan Hospital, Affiliated to Fudan University, School of Medicine, Shanghai, China
| | - Xiaoyan Zhou
- Cancer Hospital, Affiliated to Fudan University School of Medicine, Shanghai, China
| | - Yinan Chen
- Department of Surgery, Ruijin Hospital, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Ji
- Department of Surgery, Ruijin Hospital, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen Xiang
- Department of Surgery, Ruijin Hospital, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Guo
- Department of Surgery, Ruijin Hospital, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingyuan Fang
- Renji Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yihong Sun
- Zhongshan Hospital, Affiliated to Fudan University, School of Medicine, Shanghai, China
| | - Hui Cao
- Renji Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenggang Zhu
- Department of Surgery, Ruijin Hospital, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingyan Yu
- Department of Surgery, Ruijin Hospital, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|