1
|
Jha K, Kumar A, Bhatnagar K, Patra A, Bhavesh NS, Singh B, Chaudhary S. Modulation of Krüppel-like factors (KLFs) interaction with their binding partners in cancers through acetylation and phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195003. [PMID: 37992989 DOI: 10.1016/j.bbagrm.2023.195003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/05/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023]
Abstract
Post-translational modifications (PTMs) of transcription factors regulate transcriptional activity and play a key role in essentially all biological processes and generate indispensable insight towards biological function including activity state, subcellular localization, protein solubility, protein folding, substrate trafficking, and protein-protein interactions. Amino acids modified chemically via PTMs, function as molecular switches and affect the protein function and characterization and increase the proteome complexity. Krüppel-like transcription factors (KLFs) control essential cellular processes including proliferation, differentiation, migration, programmed cell death and various cancer-relevant processes. We investigated the interactions of KLF group-2 members with their binding partners to assess the role of acetylation and phosphorylation in KLFs on their binding affinity. It was observed that acetylation and phosphorylation at different positions in KLFs have a variable effect on binding with specific partners. KLF2-EP300, KLF4-SP1, KLF6-ATF3, KLF6-JUN, and KLF7-JUN show stabilization upon acetylation or phosphorylation at variable positions. On the other hand, KLF4-CBP, KLF4-EP300, KLF5-CBP, KLF5-WWP1, KLF6-SP1, and KLF7-ATF3 show stabilization or destabilization due to acetylation or phosphorylation at variable positions in KLFs. This provides a molecular explanation of the experimentally observed dual role of KLF group-2 members as a suppressor or activator of cancers in a PTM-dependent manner.
Collapse
Affiliation(s)
- Kanupriya Jha
- Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Plot Nos. 8-11, Tech Zone 2, Greater Noida, Uttar Pradesh 201310, India.
| | - Amit Kumar
- Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Plot Nos. 8-11, Tech Zone 2, Greater Noida, Uttar Pradesh 201310, India.
| | - Kartik Bhatnagar
- Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Plot Nos. 8-11, Tech Zone 2, Greater Noida, Uttar Pradesh 201310, India.
| | - Anupam Patra
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India.
| | - Neel Sarovar Bhavesh
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India.
| | - Bipin Singh
- Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Plot Nos. 8-11, Tech Zone 2, Greater Noida, Uttar Pradesh 201310, India; Centre for Life Sciences, Mahindra University, Bahadurpally, Jeedimetla, Hyderabad, Telangana 500043, India.
| | - Sarika Chaudhary
- Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Plot Nos. 8-11, Tech Zone 2, Greater Noida, Uttar Pradesh 201310, India.
| |
Collapse
|
2
|
Mollanoori H, Ghelmani Y, Hassani B, Dehghani M. Integrated whole transcriptome profiling revealed a convoluted circular RNA-based competing endogenous RNAs regulatory network in colorectal cancer. Sci Rep 2024; 14:91. [PMID: 38167453 PMCID: PMC10761719 DOI: 10.1038/s41598-023-50230-0] [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: 03/28/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024] Open
Abstract
Recently, it has been identified that circRNAs can act as miRNA sponge to regulate gene expression in various types of cancers, associating them with cancer initiation and progression. The present study aims to identify colorectal cancer-related circRNAs and the underpinning mechanisms of circRNA/miRNA/mRNA networks in the development and progress of Colorectal Cancer. Differentially expressed circRNAs, miRNAs, and mRNAs were identified in GEO microarray datasets using the Limma package of R. The analysis of differentially expressed circRNAs resulted in 23 upregulated and 31 downregulated circRNAs. CeRNAs networks were constructed by intersecting the results of predicted and experimentally validated databases, circbank and miRWalk, and by performing DEMs and DEGs analysis using Cytoscape. Next, functional enrichment analysis was performed for DEGs included in ceRNA networks. Followed by survival analysis, expression profile assessment using TCGA and GEO data, and ROC curve analysis we identified a ceRNA sub-networks that revealed the potential regulatory effect of hsa_circ_0001955 and hsa_circ_0071681 on survival-related genes, namely KLF4, MYC, CCNA2, RACGAP1, and CD44. Overall, we constructed a convoluted regulatory network and outlined its likely mechanisms of action in CRC, which may contribute to the development of more effective approaches for early diagnosis, prognosis, and treatment of CRC.
Collapse
Affiliation(s)
- Hasan Mollanoori
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Yaser Ghelmani
- Clinical Research Development Center, Shahid Sadoughi Hospital, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Bita Hassani
- Sarem Gynecology, Obstertrics and Infertility Research Center, Sarem Women's Hospital, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Mohammadreza Dehghani
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| |
Collapse
|
3
|
Guilz NC, Ahn YO, Seo S, Mace EM. Unwinding the Role of the CMG Helicase in Inborn Errors of Immunity. J Clin Immunol 2023; 43:847-861. [PMID: 36809597 PMCID: PMC10789183 DOI: 10.1007/s10875-023-01437-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/20/2023] [Indexed: 02/23/2023]
Abstract
Inborn errors of immunity (IEI) are a collection of diseases resulting from genetic causes that impact the immune system through multiple mechanisms. Natural killer cell deficiency (NKD) is one such IEI where natural killer (NK) cells are the main immune lineage affected. Though rare, the deficiency of several genes has been described as underlying causes of NKD, including MCM4, GINS1, MCM10 , and GINS4 , all of which are involved in the eukaryotic CMG helicase. The CMG helicase is made up of C DC45 – M CM – G INS and accessory proteins including MCM10. The CMG helicase plays a critical role in DNA replication by unwinding the double helix and enabling access of polymerases to single-stranded DNA, and thus helicase proteins are active in any proliferating cell. Replication stress, DNA damage, and cell cycle arrest are among the cellular phenotypes attributed to loss of function variants in CMG helicase proteins. Despite the ubiquitous function of the CMG helicase, NK cells have an apparent susceptibility to the deficiency of helicase proteins. This review will examine the role of the CMG helicase in inborn errors of immunity through the lens of NKD and further discuss why natural killer cells can be so strongly affected by helicase deficiency.
Collapse
Affiliation(s)
- Nicole C Guilz
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Yong-Oon Ahn
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Seungmae Seo
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA.
| |
Collapse
|
4
|
Lee E, Cheung J, Bialkowska AB. Krüppel-like Factors 4 and 5 in Colorectal Tumorigenesis. Cancers (Basel) 2023; 15:cancers15092430. [PMID: 37173904 PMCID: PMC10177156 DOI: 10.3390/cancers15092430] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
Krüppel-like factors (KLFs) are transcription factors regulating various biological processes such as proliferation, differentiation, migration, invasion, and homeostasis. Importantly, they participate in disease development and progression. KLFs are expressed in multiple tissues, and their role is tissue- and context-dependent. KLF4 and KLF5 are two fascinating members of this family that regulate crucial stages of cellular identity from embryogenesis through differentiation and, finally, during tumorigenesis. They maintain homeostasis of various tissues and regulate inflammation, response to injury, regeneration, and development and progression of multiple cancers such as colorectal, breast, ovarian, pancreatic, lung, and prostate, to name a few. Recent studies broaden our understanding of their function and demonstrate their opposing roles in regulating gene expression, cellular function, and tumorigenesis. This review will focus on the roles KLF4 and KLF5 play in colorectal cancer. Understanding the context-dependent functions of KLF4 and KLF5 and the mechanisms through which they exert their effects will be extremely helpful in developing targeted cancer therapy.
Collapse
Affiliation(s)
- Esther Lee
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jacky Cheung
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Agnieszka B Bialkowska
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|
5
|
Chen L, Cai Q, Yang R, Wang H, Ling H, Li T, Liu N, Wang Z, Sun J, Tao T, Shi Y, Cao Y, Wang X, Xiao D, Liu S, Tao Y. GINS4 suppresses ferroptosis by antagonizing p53 acetylation with Snail. Proc Natl Acad Sci U S A 2023; 120:e2219585120. [PMID: 37018198 PMCID: PMC10104543 DOI: 10.1073/pnas.2219585120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/23/2023] [Indexed: 04/06/2023] Open
Abstract
Ferroptosis is an iron-dependent oxidative, nonapoptotic form of regulated cell death caused by the destruction of redox homeostasis. Recent studies have uncovered complex cellular networks that regulate ferroptosis. GINS4 is a promoter of eukaryotic G1/S-cell cycle as a regulator of initiation and elongation of DNA replication, but little is known about its impact on ferroptosis. Here, we found that GINS4 was involved in the regulation of ferroptosis in lung adenocarcinoma (LUAD). CRISPR/Cas9-mediated GINS4 KO facilitated ferroptosis. Interestingly, depletion of GINS4 could effectively induce G1, G1/S, S, and G2/M cells to ferroptosis, especially for G2/M cells. Mechanistically, GINS4 suppressed p53 stability through activating Snail that antagonized the acetylation of p53, and p53 lysine residue 351 (K351 for human p53) was the key site for GINS4-suppressed p53-mediated ferroptosis. Together, our data demonstrate that GINS4 is a potential oncogene in LUAD that functions to destabilize p53 and then inhibits ferroptosis, providing a potential therapeutic target for LUAD.
Collapse
Affiliation(s)
- Ling Chen
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha Hunan410031, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Health Commission Key Laboratory of Carcinogenesis, Cancer Research Institute, Central South University, Changsha Hunan410078, China
| | - Qidong Cai
- Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha Hunan410011, China
| | - Rui Yang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha Hunan410031, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha Hunan410013, China
| | - Haiyan Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha Hunan410031, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha Hunan410013, China
| | - Huli Ling
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha Hunan410031, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha Hunan410013, China
| | - Tiansheng Li
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha Hunan410031, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha Hunan410013, China
| | - Na Liu
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Postdoctoral Research Workstation, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha Hunan410008, China
| | - Zuli Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha Hunan410031, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha Hunan410013, China
| | - Jingyue Sun
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha Hunan410031, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha Hunan410013, China
| | - Tania Tao
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Health Commission Key Laboratory of Carcinogenesis, Cancer Research Institute, Central South University, Changsha Hunan410078, China
| | - Ying Shi
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha Hunan410031, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Health Commission Key Laboratory of Carcinogenesis, Cancer Research Institute, Central South University, Changsha Hunan410078, China
| | - Ya Cao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha Hunan410031, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Health Commission Key Laboratory of Carcinogenesis, Cancer Research Institute, Central South University, Changsha Hunan410078, China
| | - Xiang Wang
- Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha Hunan410011, China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha Hunan410013, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha Hunan410008, China
| | - Yongguang Tao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha Hunan410031, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha Hunan410008, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, National Health Commission Key Laboratory of Carcinogenesis, Cancer Research Institute, Central South University, Changsha Hunan410078, China
- Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha Hunan410011, China
- Department of Pathology, School of Basic Medicine, Central South University, Changsha Hunan410013, China
| |
Collapse
|
6
|
He Z, He J, Xie K. KLF4 transcription factor in tumorigenesis. Cell Death Discov 2023; 9:118. [PMID: 37031197 PMCID: PMC10082813 DOI: 10.1038/s41420-023-01416-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
Krüppel-like transcriptional factor is important in maintaining cellular functions. Deletion of Krüppel-like transcriptional factor usually causes abnormal embryonic development and even embryonic death. KLF4 is a prominent member of this family, and embryonic deletion of KLF4 leads to alterations in skin permeability and postnatal death. In addition to its important role in embryo development, it also plays a critical role in inflammation and malignancy. It has been investigated that KLF4 has a regulatory role in a variety of cancers, including lung, breast, prostate, colorectal, pancreatic, hepatocellular, ovarian, esophageal, bladder and brain cancer. However, the role of KLF4 in tumorigenesis is complex, which may link to its unique structure with both transcriptional activation and transcriptional repression domains, and to the regulation of its upstream and downstream signaling molecules. In this review, we will summarize the structural and functional aspects of KLF4, with a focus on KLF4 as a clinical biomarker and therapeutic target in different types of tumors.
Collapse
Affiliation(s)
- Zhihong He
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, China
- The South China University of Technology Comprehensive Cancer Center, Guangdong, China
| | - Jie He
- The Second Affiliated Hospital and Guangzhou First People's Hospital, South China University of Technology School of Medicine, Guangdong, China
| | - Keping Xie
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, China.
- The South China University of Technology Comprehensive Cancer Center, Guangdong, China.
| |
Collapse
|
7
|
Sun L, Chen S, Wang T, Bi S. Hsa_circ_0008673 Promotes Breast Cancer Progression by MiR-578/GINS4 Axis. Clin Breast Cancer 2023; 23:281-290. [PMID: 36628810 DOI: 10.1016/j.clbc.2022.12.015] [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: 03/28/2022] [Revised: 11/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs) play a crucial role in breast cancer (BC) development. This study aimed to explore the new potential mechanism of hsa_circ_0008673 in BC. MATERIALS AND METHODS Hsa_circ_0008673, microRNA-578 (miR-578) and recombinant human GINS complex subunit 4 (GINS4) abundances were measured via quantitative real-time PCR or western blot. Cell proliferation, metastasis, angiogenesis and apoptosis were assessed via EdU assay, transwell assay, tube formation assay, and flow cytometry. The interactions among hsa_circ_0008673, miR-578 and GINS4 were tested via dual-luciferase reporter analysis and RNA pull-down assay. Animal studies were performed to assess the effect of hsa_circ_0008673 on BC tumor growth. RESULTS Hsa_circ_0008673 level was increased in BC tissues and cells. Hsa_circ_0008673 silencing repressed BC cell growth, metastasis and angiogenesis, as well as hampered BC tumor growth. Hsa_circ_0008673 acted as miR-578 sponge, and miR-578 targeted GINS4. Furthermore, hsa_circ_0008673 modulated GINS4 expression through sponging miR-578. Additionally, miR-578 inhibitor or GINS4 overexpression could reverse the inhibitory effect of hsa_circ_0008673 silencing on BC cell progression. CONCLUSION Hsa_circ_0008673 might promote BC progression via modulating miR-578/GINS4 pathway.
Collapse
Affiliation(s)
- Lu Sun
- Department of Breast Surgery, Taizhou Hospital of Traditional Chinese Medicine, Taizhou, China
| | - Shuai Chen
- Department of Breast Surgery, Taizhou Hospital of Traditional Chinese Medicine, Taizhou, China
| | - Taiyu Wang
- Department of Breast Surgery, Taizhou Hospital of Traditional Chinese Medicine, Taizhou, China
| | - Shisheng Bi
- Department of Breast Surgery, Taizhou Hospital of Traditional Chinese Medicine, Taizhou, China.
| |
Collapse
|
8
|
Li H, Zhou Q, Wu Z, Lu X. Identification of novel key genes associated with uterine corpus endometrial carcinoma progression and prognosis. ANNALS OF TRANSLATIONAL MEDICINE 2023; 11:100. [PMID: 36819577 PMCID: PMC9929804 DOI: 10.21037/atm-22-6461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
Background Uterine corpus endometrial carcinoma (UCEC) is a common malignant cancer type which affects the health of women worldwide. However, its molecular mechanism has not been elucidated. Methods To identify the hub modules and genes in UCEC associated with clinical phenotypes, the RNA sequencing data and clinical data of 543 UCEC samples were obtained from The Cancer Genome Atlas (TCGA) database and then subjected to weighted gene co-expression network analysis (WGCNA). To explore the potential biological function of the hub modules, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. Genes differentially expressed in UCEC were screened according to TCGA data using the "gdcDEAnalysis" package in R (The R Foundation for Statistical Computing). After intersecting with hub genes, the shared genes were used for further survival analyses. The relationship between gene expression level and clinical phenotype was analyzed in the TCGA-UCEC cohort in The University of ALabama at Birmingham CANcer data analysis Portal and the Human Protein Atlas. The microarray data set GSE17025 was also analyzed to validate the gene expression profiles. Results There were 19 coexpression modules generated by WGCNA. Among them, 2 modules with 198 hub genes were highly correlated with clinical features (especially histologic grade and clinical stage). Meanwhile, 4,003 differentially expressed genes (DEGs) were screened out, and 164 DEGs overlapped with hub genes. Survival analyses revealed that high expression of GINS4 and low expression of ESR1 showed a trend of poor prognosis. Further analyses demonstrated that both messenger RNA (mRNA) and protein expression profiles of GINS4 and ESR1 were significantly associated with UCEC development and progression in TCGA and GSE17025 cohorts. Conclusions Based on the integrated bioinformatic analyses, our data indicated that GINS4 and ESR1 might serve as potential prognostic markers and targets for UCEC therapy.
Collapse
Affiliation(s)
- Haixia Li
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China;,College of Stomatology, Hospital of Stomatology, Guangxi Key Laboratory of Nanobody Research/Guangxi Nanobody Engineering Research Center, Guangxi Medical University, Nanning, China;,Department of Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Quan Zhou
- Department of Traditional Chinese Medicine, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhangying Wu
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xiaoling Lu
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China;,College of Stomatology, Hospital of Stomatology, Guangxi Key Laboratory of Nanobody Research/Guangxi Nanobody Engineering Research Center, Guangxi Medical University, Nanning, China
| |
Collapse
|
9
|
Zhang Y, Yao C, Ju Z, Jiao D, Hu D, Qi L, Liu S, Wu X, Zhao C. Krüppel-like factors in tumors: Key regulators and therapeutic avenues. Front Oncol 2023; 13:1080720. [PMID: 36761967 PMCID: PMC9905823 DOI: 10.3389/fonc.2023.1080720] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Krüppel-like factors (KLFs) are a group of DNA-binding transcriptional regulators with multiple essential functions in various cellular processes, including proliferation, migration, inflammation, and angiogenesis. The aberrant expression of KLFs is often found in tumor tissues and is essential for tumor development. At the molecular level, KLFs regulate multiple signaling pathways and mediate crosstalk among them. Some KLFs may also be molecular switches for specific biological signals, driving their transition from tumor suppressors to promoters. At the histological level, the abnormal expression of KLFs is closely associated with tumor cell stemness, proliferation, apoptosis, and alterations in the tumor microenvironment. Notably, the role of each KLF in tumors varies according to tumor type and different stages of tumor development rather than being invariant. In this review, we focus on the advances in the molecular biology of KLFs, particularly the regulations of several classical signaling pathways by these factors, and the critical role of KLFs in tumor development. We also highlight their strong potential as molecular targets in tumor therapy and suggest potential directions for clinical translational research.
Collapse
Affiliation(s)
- Yuchen Zhang
- School of Acupuncture-moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chongjie Yao
- School of Acupuncture-moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ziyong Ju
- School of Acupuncture-moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Danli Jiao
- School of Acupuncture-moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dan Hu
- School of Acupuncture-moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Li Qi
- School of Acupuncture-moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shimin Liu
- School of Acupuncture-moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Shanghai Research Institute of Acupuncture and Meridian, Shanghai, China
| | - Xueqing Wu
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,*Correspondence: Chen Zhao, ; Xueqing Wu,
| | - Chen Zhao
- School of Acupuncture-moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, China,*Correspondence: Chen Zhao, ; Xueqing Wu,
| |
Collapse
|
10
|
Novel hypoxia-induced HIF1α-circTDRD3-positive feedback loop promotes the growth and metastasis of colorectal cancer. Oncogene 2023; 42:238-252. [PMID: 36418471 DOI: 10.1038/s41388-022-02548-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022]
Abstract
Tumor hypoxia and circular RNAs (circRNAs) are considered to play key roles in tumor progression and malignancy, respectively. Nevertheless, the biological functions and underlying mechanisms of specific circRNAs exposed to hypoxic microenvironments in colorectal cancer (CRC) remain largely elusive. Herein, a novel circRNA, circTDRD3, which is upregulated under hypoxic conditions, was identified. The expression of circTDRD3 was highly expressed in CRC tissues and positively correlated with overall survival, tumor size, lymph node invasion and clinical stage. CircTDRD3 facilitated CRC cell proliferation, migration and metastasis in vitro and in vivo. Mechanistically, circTDRD3 promoted HIF1α expression by sponging miR-1231, which facilitated CRC progression. Meanwhile, HIF1α directly combined with TDRD3 promoter to increase the expression of TDRD3 pre-mRNA. Then HIF1a-induced PTBP1 accelerated the formation of circTDRD3. Our findings reveal that circTDRD3 facilitates the proliferation and metastasis of CRC through a positive feedback loop mediated by the HIF1α/PTBP1/circTDRD3/miR-1231/HIF1α axis. Therefore, circTDRD3 may serve as a prognostic biomarker and therapeutic target for patients with CRC.
Collapse
|
11
|
Zhou Y, Yan J, Chen H, Zhou W, Yang J. MicroRNA-133a-3p Inhibits Lung Adenocarcinoma Development and Cisplatin Resistance through Targeting GINS4. Cells Tissues Organs 2022; 213:55-66. [PMID: 36273455 DOI: 10.1159/000527684] [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: 03/31/2022] [Accepted: 10/13/2022] [Indexed: 02/18/2024] Open
Abstract
GINS subunit complex 4 (GINS4) is fundamental to DNA replication and G1/S phase transition of the cell cycle in eukaryotes. Further, recent studies implied that GINS4 can mediate the progression of several tumors, but its mechanism in lung adenocarcinoma (LUAD) is not clarified. Therefore, the role of GINS4 in LUAD was explored. miR-133a-3p and GINS4 mRNA expression were tested through qRT-PCR. Protein levels of the two genes were assayed by Western blot. Their targeting relationship was predicted and verified by bioinformatics prediction and dual-luciferase analysis. The functions of miR-133a-3p and GINS4 in LUAD were evaluated by Transwell, wound healing, CCK-8, and flow cytometry assays. MTT assay and caspase-3 activity detection were utilized to measure the regulation of miR-133a-3p/GINS4 in the cisplatin sensitivity of LUAD cells. The results showed that GINS4 was highly expressed in LUAD cells (p < 0.05). miR-133a-3p, the upstream gene of GINS4 in LUAD, negatively mediated GINS4 expression. Moreover, overexpressing GINS4 enhanced the proliferative, migratory, and invasive abilities of LUAD cells and inhibited cell apoptosis and the sensitivity to cisplatin, while overexpressing miR-133a-3p caused the contrary results. However, the promoting effects of GINS4 overexpression on LUAD could be offset by miR-133a-3p overexpression. miR-133a-3p could regulate malignant behaviors and cisplatin sensitivity of LUAD cells through negatively regulating GINS4. In conclusion, our findings demonstrated that GINS4 was overexpressed in LUAD and promoted the malignant behavior of LUAD cells. Moreover, miR-133a-3p could negatively regulate GINS4, thereby suppressing the malignant progression and increasing the cisplatin sensitivity of LUAD.
Collapse
Affiliation(s)
- Yafu Zhou
- The First-Affiliated Hospital of Hunan Normal University (Department of Cardiac Thoracic Surgery, Hunan Provincial People's Hospital), Changsha, China
| | - Jianhua Yan
- The First-Affiliated Hospital of Hunan Normal University (Department of Cardiac Thoracic Surgery, Hunan Provincial People's Hospital), Changsha, China
| | - Huiguo Chen
- The First-Affiliated Hospital of Hunan Normal University (Department of Cardiac Thoracic Surgery, Hunan Provincial People's Hospital), Changsha, China
| | - Wenwu Zhou
- The First-Affiliated Hospital of Hunan Normal University (Department of Cardiac Thoracic Surgery, Hunan Provincial People's Hospital), Changsha, China
| | - Jinsong Yang
- The First-Affiliated Hospital of Hunan Normal University (Department of Cardiac Thoracic Surgery, Hunan Provincial People's Hospital), Changsha, China
| |
Collapse
|
12
|
Zhou C, Chen Z, Xiao B, Xiang C, Li A, Zhao Z, Li H. Comprehensive analysis of GINS subunits prognostic value and ceRNA network in sarcoma. Front Cell Dev Biol 2022; 10:951363. [PMID: 36092720 PMCID: PMC9462653 DOI: 10.3389/fcell.2022.951363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The GINS complex, composed of GINS1/2/3/4 subunits, is an essential structure of Cdc45-MCM-GINS (CMG) helicase and plays a vital role in establishing the DNA replication fork and chromosome replication. Meanwhile, GINS genes have been associated with the poor prognosis of various malignancies. However, the abnormal expression of GINS genes and their diagnostic and prognostic value in sarcomas (SARC) remain unclear. Methods: Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier Plotter, Cancer cell line encyclopedia (CCLE), The University of Alabama at Birmingham Cancer Data Analysis Portal (UALCAN), R studio, and Tumor Immune Estimation Resource (TIMER) were used to analyze the expression profiles, prognostic value, biological function, ceRNA, and immune infiltration associated with GINS genes in sarcomas. Results: We found that GINS1/2/3/4 genes exhibited significantly upregulated transcription levels in SARC samples compared to non-tumor tissues and exhibited high expression levels in sarcoma cell lines. In addition, SARC patients with increased expression levels of GINS1/2/3/4 showed poorer survival rates. Immune infiltration analysis showed that GINS subunits were closely associated with the infiltration of immune cells in sarcomas. Conclusion: Our research identified GINS subunits as potential diagnostic and prognostic biological targets in SARC and elucidated their underlying effects in the genesis and progression of SARC. These results may provide new opportunities and research directions for targeted sarcoma therapy.
Collapse
Affiliation(s)
- Chuqiao Zhou
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Zhuoyuan Chen
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Bo Xiao
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Cheng Xiang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Aoyu Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Ziyue Zhao
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
| | - Hui Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Orthopedic Biomedical Materials Engineering Laboratory of Hunan Province, Changsha, China
- *Correspondence: Hui Li,
| |
Collapse
|
13
|
Zhang K, Zhou J, Wu T, Tian Q, Liu T, Wang W, Zhong H, Chen Z, Xiao X, Wu G. Combined analysis of expression, prognosis and immune infiltration of GINS family genes in human sarcoma. Aging (Albany NY) 2022; 14:5895-5907. [PMID: 35896011 PMCID: PMC9365567 DOI: 10.18632/aging.204191] [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: 04/16/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Abstract
Objective: This study was undertaken to explore the expression and prognostic value of GINS family in human sarcoma, as well as the association between the expression levels of the GINS family and sarcoma immune infiltration. Results: We discovered that the mRNA expression levels of GINS1, GINS2, GINS3, and GINS4 were all higher in the majority of tumor tissues than in normal samples, of course, including sarcoma. Through the CCLE, all the four members expression were observed in high levels in sarcoma cell lines. In Gene Expression Profiling Analysis (GEPIA) and Kaplan-Meier Plotter, our results indicated that the poor overall survival (OS), disease-free survival (DFS) and relapse free survival (RFS) were tightly associated with the increased expression of GINS genes. In TIMER database, we found that highly expressed GINS was significantly correlated with the low infiltration level of CD4+ T cell and macrophage. Conclusions: The four GINS family members were all the prognostic biomarkers for the prognosis of human sarcoma and can reduce the level of immune cell infiltration in the sarcoma microenvironment. Methods: In terms of the expression levels of mRNA for GINS family members, a particular contrast in various cancers, especially human sarcoma, was conducted through ONCOMINE and GEPIA and CCLE databases. Kaplan-Meier Plotter was used to identify the prognostic value of GINS family in sarcoma. The relationship between the expression level of GINS and the infiltration of immune cells was analyzed in TIMER database.
Collapse
Affiliation(s)
- Kexin Zhang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China.,Department of Psychology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Jian Zhou
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Tong Wu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Qunyan Tian
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Hua Zhong
- Department of Orthopedics, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou 510900, Guangdong, China
| | - Ziyuan Chen
- Department of Orthopedics, The First People's Hospital of Changde City, Changde 415003, Hunan, China
| | - Xungang Xiao
- Department of Orthopedics, Chenzhou No.1 People's Hospital, Chenzhou 423000, Hunan, China
| | - Gen Wu
- Department of Orthopedics, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou 510900, Guangdong, China
| |
Collapse
|
14
|
Zhang J, Zhang J, Fu Z, Zhang Y, Luo Z, Zhang P, Xu Y, Huang C. CHREBP suppresses gastric cancer progression via the cyclin D1-Rb-E2F1 pathway. Cell Death Dis 2022; 8:300. [PMID: 35768405 PMCID: PMC9243070 DOI: 10.1038/s41420-022-01079-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 12/03/2022]
Abstract
Accumulating evidence has demonstrated that carbohydrate response element binding protein (CHREBP) has a crucial function in tumor pathology. In this study, we found CHREBP downregulation in gastric cancer (GC) tissues, and CHREBP was determined to be an independent diagnostic marker of GC. The downregulation of CHREBP promoted cell proliferation and inhibited apoptosis. Moreover, the level of cyclin D1 was significantly correlated with CHREBP expression in GC and paracancerous normal samples. In addition, CHREBP transcriptionally inhibited cyclin D1 expression in GC cells. Tumor suppressor activity of CHREBP could be affected by the upregulation of cyclin D1. In summary, CHREBP was found to be an independent diagnostic marker of GC and to influence GC growth and apoptosis via targeting the cyclin D1-Rb-E2F1 pathway.
Collapse
Affiliation(s)
- Jianming Zhang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China
| | - Jing Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China.
| | - Zhongmao Fu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China
| | - Yuan Zhang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China
| | - Zai Luo
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China
| | - Pengshan Zhang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China
| | - Yitian Xu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China
| | - Chen Huang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, 100 Haining Road, Hongkou District, Shanghai, 200080, China.
| |
Collapse
|
15
|
Jin D, Yuan L, Li F, Wang S, Mao Y. GINS4 might be a novel prognostic immune-related biomarker of not only esophageal squamous cell carcinoma and other cancers. BMC Med Genomics 2022; 15:75. [PMID: 35365175 PMCID: PMC8976371 DOI: 10.1186/s12920-022-01223-x] [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: 10/18/2021] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Immunotherapy using immune checkpoint inhibitors (ICIs), such as antibody of programmed death-1 (PD-1)/programmed death-ligand 1 (PD-L1) has showed as a promising treatment for esophageal squamous cell carcinoma (ESCC), but resistance is unavoidable. This study aimed to find more immune-related genes to promote the efficiency of immunotherapy. Materials and methods Three datasets were downloaded from Gene Expression Omnibus (GEO) database. Gene differential analysis was performed to identify differentially expressed genes (DEGs), then ceRNA network was constructed based on differentially expressed lncRNAs and mRNAs. Next, Functional enrichment analysis and protein–protein interaction (PPI) network were built to reveal the potential function of mRNAs in ceRNA network. Survival analysis and immune cell infiltration level analysis were utilized to identify prognostic immune-related genes. Finally, pan-cancer analysis was performed to show the role of immune-related genes in other cancers. Results The data of 215 samples in total were obtained from GEO database (98 normal tissues and 117 tumor tissues), and 1685 differentially expressed mRNAs (176 downregulated and 1509 upregulated) and 3 upregulated lncRNAs (MCM3AP-AS1, HCP5 and GUSBP11, all upregulated) were found. ceRNA network was constructed to reveal some special correlation. Function enrichment showed some potential functions of mRNAs in ceRNA network such as mitotic cell cycle process, negative regulation of DNA-binding transcription factor activity, ossification, VEGFA-VEGFR2 signaling pathway, epithelial to mesenchymal transition, embryonic morphogenesis and so on. PPI network showed the physical interactions between each mRNA in ceRNA network. Through survival analysis and immune cell infiltration level analysis, GINS4 was confirmed as an immune-related prognostic gene in ESCC. GSEA showed some potential functions such as negative regulation of monocyte chemotaxis, antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, positive regulation of antigen processing and presentation, dendritic cell antigen processing and presentation and so on. Finally, pan-cancer analysis revealed that GINS4 might be a novel immune-related prognostic gene in ESCC and other cancers. Conclusion Our study suggested that GINS4 was correlated with prognosis and immune cell infiltration level of ESCC and other cancers. It may deserve further investigation as a potential immune-related prognostic biomarker of ESCC and other cancers.
Collapse
Affiliation(s)
- Donghui Jin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ligong Yuan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Feng Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shuaibo Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yousheng Mao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| |
Collapse
|
16
|
Usman M, Okla MK, Asif HM, AbdElgayed G, Muccee F, Ghazanfar S, Ahmad M, Iqbal MJ, Sahar AM, Khaliq G, Shoaib R, Zaheer H, Hameed Y. A pan-cancer analysis of GINS complex subunit 4 to identify its potential role as a biomarker in multiple human cancers. Am J Cancer Res 2022; 12:986-1008. [PMID: 35411239 PMCID: PMC8984884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023] Open
Abstract
This study was initiated to explore the expression variation, clinical significance, and biological importance of the GINS complex subunit 4 (GINS4) in different human cancers as a shared biomarker via pan-cancer analysis through different platforms including UALCAN, Kaplan Meier (KM) plotter, TNMplot, GENT2, GEPIA, DriverDBv3, Human Protein Atlas (HPA), MEXPRESS, cBioportal, STRING, DAVID, MuTarge, Enrichr, TIMER, and CTD. Our findings have verified the up-regulation of GINS4 in 24 major subtypes of human cancers, and its overexpression was found to be substantially associated with poor overall survival (OS), relapse-free survival (RFs), and metastasis in ESCA, KIRC, LIHC, LUAD, and UCEC. This suggested that GINS4 plays a significant role in the development and progression of these five cancers. Furthermore, we noticed that GINS4 is also overexpressed in ESCA, KIRC, LIHC, LUAD, and UCEC patients with different clinicopathological characteristics. Enrichment analysis revealed the involvement of GINS4 associated genes in a variety of diverse GO and KEGG terms. We also explored few significant correlations between GINS4 expression and promoter methylation, genetic alterations, CNVs, other mutant genes, tumor purity, and immune cells infiltration. In conclusion, our results elucidated that GINS4 can serve as a shared diagnostic, prognostic biomarker, and a potential therapeutic target in ESCA, KIRC, LIHC, LUAD, and UCEC patients with different clinicopathological characteristics.
Collapse
Affiliation(s)
- Muhammad Usman
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
| | - Mohammad K Okla
- Department of Botany and Microbiology, College of Science, King Saud UniversityRiyadh 11451, Saudi Arabia
| | - Hafiz Muhammad Asif
- University College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, The Islamia University of BahawalpurBahawalpur 63100, Pakistan
| | - Gehad AbdElgayed
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp2020 Antwerp, Belgium
| | - Fatima Muccee
- Department of Biotechnology, Virtual University of PakistanLahore 54000, Pakistan
| | - Shakira Ghazanfar
- Functional Genomics and Bioinformatics, National Agricultural Research CentreIslamabad 45500, Pakistan
| | - Mukhtiar Ahmad
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
| | | | - Aamina Murad Sahar
- Department of Biosciences, COMSATS University IslamabadIslamabad 4400, Pakistan
| | - Ghania Khaliq
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences BahawalpurBahawalpur 63100, Pakistan
| | - Rabbia Shoaib
- Department of Chemistry, Government College University FaisalabadFaisalabad 3800, Pakistan
| | - Hira Zaheer
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
| | - Yasir Hameed
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
| |
Collapse
|
17
|
In silico recognition of a prognostic signature in basal-like breast cancer patients. PLoS One 2022; 17:e0264024. [PMID: 35167614 PMCID: PMC8846521 DOI: 10.1371/journal.pone.0264024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/31/2022] [Indexed: 01/22/2023] Open
Abstract
Background Triple-negative breast cancers (TNBCs) display poor prognosis, have a high risk of tumour recurrence, and exhibit high resistance to drug treatments. Based on their gene expression profiles, the majority of TNBCs are classified as basal-like breast cancers. Currently, there are not available widely-accepted prognostic markers to predict outcomes in basal-like subtype, so the selection of new prognostic indicators for this BC phenotype represents an unmet clinical challenge. Results Here, we attempted to address this challenging issue by exploiting a bioinformatics pipeline able to integrate transcriptomic, genomic, epigenomic, and clinical data freely accessible from public repositories. This pipeline starts from the application of the well-established network-based SWIM methodology on the transcriptomic data to unveil important (switch) genes in relation with a complex disease of interest. Then, survival and linear regression analyses are performed to associate the gene expression profiles of the switch genes with both the patients’ clinical outcome and the disease aggressiveness. This allows us to identify a prognostic gene signature that in turn is fed to the last step of the pipeline consisting of an analysis at DNA level, to investigate whether variations in the expression of identified prognostic switch genes could be related to genetic (copy number variations) or epigenetic (DNA methylation differences) alterations in their gene loci, or to the activities of transcription factors binding to their promoter regions. Finally, changes in the protein expression levels corresponding to the so far identified prognostic switch genes are evaluated by immunohistochemical staining results taking advantage of the Human Protein Atlas. Conclusion The application of the proposed pipeline on the dataset of The Cancer Genome Atlas (TCGA)-Breast Invasive Carcinoma (BRCA) patients affected by basal-like subtype led to an in silico recognition of a basal-like specific gene signature composed of 11 potential prognostic biomarkers to be further investigated.
Collapse
|
18
|
Feng H, Zeng J, Gao L, Zhou Z, Wang L. GINS Complex Subunit 2 Facilitates Gastric Adenocarcinoma Proliferation and Indicates Poor Prognosis. TOHOKU J EXP MED 2021; 255:111-121. [PMID: 34629365 DOI: 10.1620/tjem.255.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Gastric cancer is the one of the most lethal malignancies of digestive system. Identifying molecular biomarkers is invaluable in help predicting clinical outcomes and developing targeted chemotherapies. GINS complex subunit 2 (GINS2) plays an essential role in the initiation and elongation of DNA replication. Although there have been studies revealing the prognostic significance of GINS2 in breast cancer and lung cancer, its involvement and function in gastric cancer need to be elucidated. We retrospectively enrolled a cohort of gastric adenocarcinoma patients after surgical resection (n = 123). By analyzing the mRNA and protein levels of GINS2 in tissue samples, we found that GINS2 presented a higher expression in tumor tissues than in adjacent normal stomach tissues. Besides, GINS2 level was positively correlated with tumor size and gastric adenocarcinoma tumor stage, implying its potential role as a tumor promoter. Univariate and multivariate analyses identified that patients with lower GINS2 showed a better overall survival compared to those with higher GINS2 expression. In addition, cellular and xenograft experiments confirmed the role of GINS2 in facilitating tumor proliferation both in vitro and in vivo. To our knowledge, this is the initial finding on GINS2 in promoting gastric adenocarcinoma progression. In conclusion, our study revealed a pro-oncogenic role of GINS2 in gastric cancer.
Collapse
Affiliation(s)
- Hongjun Feng
- Department of Gastroenterology, Sanya Central Hospital (Hainan Third People's Hospital)
| | - Juntao Zeng
- Department of Gastroenterology, Sanya Central Hospital (Hainan Third People's Hospital)
| | - Lei Gao
- Department of Gastroenterology, Sanya Central Hospital (Hainan Third People's Hospital)
| | - Zhenzhen Zhou
- Department of Gastroenterology, Sanya Central Hospital (Hainan Third People's Hospital)
| | - Liya Wang
- Department of Gastroenterology, Sanya Central Hospital (Hainan Third People's Hospital)
| |
Collapse
|
19
|
Liu B, Liu Z, Wang Y, Lian X, Han Z, Cheng X, Zhu Y, Liu R, Zhao Y, Gao Y. Overexpression of GINS4 is associated with poor prognosis and survival in glioma patients. Mol Med 2021; 27:117. [PMID: 34556022 PMCID: PMC8461916 DOI: 10.1186/s10020-021-00378-0] [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: 06/04/2021] [Accepted: 09/11/2021] [Indexed: 12/21/2022] Open
Abstract
Background GINS4, an indispensable component of the GINS complex, is vital for a variety of cancer. However, no known empirical research has focused on exploring relationships between GINS4 and glioma. Thus, this study aims to understand and explain the role of GINS4 in glioma. Method First, we used the data in the CGGA, TCGA, GEO, GEPIA, and HPA databases to explore the expression level of GINS4 in glioma, the correlation between GINS4 expression and the clinical features of glioma, its impact on the survival of glioma patients, and verified the analysis results through RT-qPCR, IHC, and meta-analysis. Subsequently, GSEA enrichment analysis is used to find the potential molecular mechanism of GINS4 to promote the malignant process of glioma and the anti-glioma drugs that may target GINS4 screened by CMap analysis. Moreover, we further explored the influence of the GINS4 expression on the immune microenvironment of glioma patients through the TIMER database. Results Our results suggested that GINS4 was elevated in glioma, and the overexpression of GINS4 was connected with a vast number of clinical features. The next, GINS4 as an independent prognostic factor, which can result in an unfavorable prognosis of glioma. Once more, GINS4 may be participating in the oncogenesis of glioma through JAK-STAT signaling pathways, etc. 6-thioguanine, Doxazosin, and Emetine had potential value in the clinical application of drugs targeting GINS4. Finally, the expression exhibited a close relationship with some immune cells, especially Dendritic cells. Conclusion GINS4 is an independent prognostic factor that led to a poor prognosis of glioma. The present study revealed the probable underlying molecular mechanisms of GINS4 in glioma and provided a potential target for improving the prognosis of glioma. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-021-00378-0.
Collapse
Affiliation(s)
- Binfeng Liu
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan, 450003, Zhengzhou, China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital, Henan International Joint Laboratory of Intelligentized Orthopedics Innovation and Transformation, Henan Key Laboratory for Intelligent Precision Orthopedics, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Henan, 450003, Zhengzhou, China
| | - Yanbiao Wang
- Department of Orthopedics, First Affiliated Hospital of Xinxiang Medical College, Xinjiang, China
| | - Xiaoyu Lian
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan, 450003, Zhengzhou, China
| | - Zhibin Han
- Department of Neurosurgery of the First Affiliate Hospital of Harbin Medical University, Harbin, China
| | - Xingbo Cheng
- Department of Neurosurgery of the First Affiliate Hospital of Harbin Medical University, Harbin, China
| | - Yongjie Zhu
- Department of Surgery of Spine and Spinal Cord, Henan University People's Hospital, Henan Provincial People's Hospital, Henan, 450003, Zhengzhou, China
| | - Runze Liu
- Department of Surgery of Spine and Spinal Cord, Henan University People's Hospital, Henan Provincial People's Hospital, Henan, 450003, Zhengzhou, China
| | - Yaoye Zhao
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan, 450003, Zhengzhou, China
| | - Yanzheng Gao
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital, Henan International Joint Laboratory of Intelligentized Orthopedics Innovation and Transformation, Henan Key Laboratory for Intelligent Precision Orthopedics, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Henan, 450003, Zhengzhou, China.
| |
Collapse
|
20
|
Xiang F, Zhu Z, Zhang M, Wang J, Chen Z, Li X, Zhang T, Gu Q, Wu R, Kang X. 3,3'-Diindolylmethane Enhances Paclitaxel Sensitivity by Suppressing DNMT1-Mediated KLF4 Methylation in Breast Cancer. Front Oncol 2021; 11:627856. [PMID: 34150611 PMCID: PMC8209418 DOI: 10.3389/fonc.2021.627856] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/12/2021] [Indexed: 12/11/2022] Open
Abstract
Paclitaxel (PTX) is a first-line chemotherapeutic drug for the treatment of breast cancer, but drug resistance seriously limits its clinical use. The aim of the present work was to explore the effect of 3,3’-diindolylmethane (DIM) on PTX sensitivity and its possible mechanism in breast cancer. The expression of Krüppel-like factor 4 (KLF4) and DNA-methyltransferase 1 (DNMT1) in breast cancer tissues were assessed by immunohistochemistry and Western blotting. The methylation of KLF4 was evaluated by the MassARRAY platform. The lentivirus carrying KLF4 and DNMT1 gene or shRNA targeting DNMT1 were used to overexpress KLF4 or knockdown DNMT1 in MCF-7 and T47D breast cancer cells and the role of KLF4 and DNMT1 in regulation of PTX sensitivity was investigated. The effect of PTX on inhibiting the proliferation of MCF-7 and T47D cells was measured by CCK-8 assay. Flow cytometry was used to examine cell apoptosis. The expression of mRNA and protein was evaluated by qRT-PCR and Western blotting analysis, respectively. Our data showed that the expression of DNMT1 was increased, and the methylation level of CpG sites (−148 bp) in the KLF4 promoter was increased while the KLF4 expression was significantly decreased in breast cancer tissues. Overexpression of KLF4 increased the sensitivity of MCF-7 and T47D cells to PTX. DNMT1 increased the methylation of the KLF4 promoter and decrease the expression of KLF4. Knockdown of DNMT1 increased the sensitivity of MCF-7 and T47D cells to PTX. DIM enhanced the PTX sensitivity of MCF-7 and T47D cells, decreased the expression of DNMT1 and the methylation level of KLF4 promoter, thus increasing the level of KLF4. Furthermore, overexpression of DNMT1 attenuated the effect of DIM on the regulation of PTX sensitivity. Collectively, our data indicated that DNMT1-mediated hypermethylation of KLF4 promoter leads to downregulation of KLF4 in breast cancer. The level of KLF4 is correlated with the sensitivity of MCF-7 and T47D cells to PTX. DIM could enhance the antitumor efficacy of PTX on MCF-7 and T47D cells by regulating DNMT1 and KLF4.
Collapse
Affiliation(s)
- Fenfen Xiang
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhaowei Zhu
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mengzhe Zhang
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jie Wang
- General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zixi Chen
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoxiao Li
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tao Zhang
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing Gu
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rong Wu
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiangdong Kang
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| |
Collapse
|
21
|
Yang X, Chen C, Li L, Xiao T, Zou YD, Zheng D. Current research advances in microRNA-mediated regulation of Krüppel-like factor 4 in cancer: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:948. [PMID: 34350263 PMCID: PMC8263881 DOI: 10.21037/atm-21-2347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/28/2021] [Indexed: 11/06/2022]
Abstract
Objective The purpose of this study was to investigate the miRNAs and related mechanisms that regulates KLF4 in different cancers. Furthermore, we summarized the potential targets of miRNAs regulating the KLF4 pathway in cancer research. Background MiRNAs are single-stranded, endogenous non-coding small RNAs, some of which are related to human cancers. miRNAs carry out post-transcriptional gene regulation through translation inhibition and degradation of target messenger RNAs (mRNAs) via complementarily pairing with their 3' untranslated regions. KLF4 is an important transcription factor with complex involvement in cancer. Increasing evidence shows that miRNAs are dysregulated in cancer and can regulate cancer-related signaling pathways, thereby affecting tumor progression. Methods Systematic scientific literature searches were undertaken on PubMed using the following terms: "miRNAs and KLF4", "KLF4 and cancer", "miRNAs and cancer", and "miRNAs, KLF4 and cancer". Relevant papers were retrieved and further results were found by reviewing related papers and the references of the retrieved papers. We then conducted a narrative overview of the literature to summarize the results of the papers. Conclusions The role of KLF4 in cancer varies in a context-dependent manner. KLF4-regulating miRNAs in different tumors include miR-124, miR-9-5p, miR-10b, miR-18a, miR-25-3p, miR-10b, miR-92a, miR-103, miR-155, miR-135b-5p, miR-32-5p, miR-148-3p, miR-152-3p, miR-10b, miR-25, miR-3120-5p, miR-7, miR-1233-3p, miR-10b, miR-145, miR-139-5p, miR-16, miR-152, miR-375, and miR-145.
Collapse
Affiliation(s)
- Xi Yang
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, China.,Shenzhen University International Cancer Center, Department of Cell Biology and Genetics, School of Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Cheng Chen
- Shenzhen University International Cancer Center, Department of Cell Biology and Genetics, School of Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Li Li
- Shenzhen University International Cancer Center, Department of Cell Biology and Genetics, School of Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Tian Xiao
- Shenzhen University International Cancer Center, Department of Cell Biology and Genetics, School of Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yong-Dong Zou
- Shenzhen University International Cancer Center, Department of Cell Biology and Genetics, School of Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Duo Zheng
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, China.,Shenzhen University International Cancer Center, Department of Cell Biology and Genetics, School of Medicine, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| |
Collapse
|
22
|
Zhang Z, Chen P, Xie H, Cao P. Overexpression of GINS4 Is Associated With Tumor Progression and Poor Survival in Hepatocellular Carcinoma. Front Oncol 2021; 11:654185. [PMID: 33842367 PMCID: PMC8027117 DOI: 10.3389/fonc.2021.654185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
Purpose Our research was aimed to identify the expression, clinical value and biological significance of GINS complex subunit 4 (GINS4) in hepatocellular carcinoma (HCC). Materials and Methods GINS4 was initially screened through weighted gene co-expression network analysis (WGCNA). The TCGA, GEO, and TIMER databases were applied for analyzing the GINS4 mRNA expression in HCC. GINS4 protein levels were detected via immunohistochemistry (IHC). Receiver operating characteristic (ROC) curve was applied for estimating the diagnostic significance of GINS4 in HCC. Kaplan-Meier plots, Cox model, and nomogram were used to assess the prognostic performance of GINS4 in HCC. Nomogram validation was conducted through time-dependent ROC and decision curve analysis (DCA). The Wanderer, UALCAN, and DiseaseMeth databases were utilized to identify GINS4 methylation levels in HCC. Genes co-expressed with GINS4 in HCC were estimated through the TCGA, cBioPortal, and GEPIA. GO, KEGG, and GSEA unraveled the possible biological mechanisms of GINS4 in HCC. Results WGCNA confirmed that GINS4 was one of hub genes significantly associated with histological grade of HCC. Multiple databases confirmed the significant upregulation of GINS4 in HCC tissues compared with non-tumor controls. IHC analysis of 35 HCC patients demonstrated that overexpressed GINS4 positively correlated with advanced TNM stage and poor pathological differentiation. GINS4 could effectively differentiate HCC cases from healthy individuals, with an AUC of 0.865. Increased GINS4 expression predicted unsatisfactory prognosis in HCC patients, especially in age >60 years, histological grade 1, HBV infection-negative, and occurring relapse subgroup. Nomogram incorporating GINS4 level and TNM stage displayed satisfactory predictive accuracy and clinical utility in predicting HCC prognosis. Upregulated GINS4 exhibited hypomethylated levels in HCC. Functional analysis indicated that GINS4 potentially positively modulated cell cycle and PI3K/AKT/mTOR pathway. Conclusion GINS4 is overexpressed in HCC and is correlated with undesirable survival of HCC patients.
Collapse
Affiliation(s)
- Ziying Zhang
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Peng Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Hui Xie
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Peiguo Cao
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
23
|
Li T, Xu Y, Wang Y, Jiang Y. Differential expression profiles of long noncoding RNAs and mRNAs in human bone marrow mesenchymal stem cells after exposure to a high dosage of dexamethasone. Stem Cell Res Ther 2021; 12:9. [PMID: 33407832 PMCID: PMC7788840 DOI: 10.1186/s13287-020-02040-8] [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: 06/14/2020] [Accepted: 11/19/2020] [Indexed: 12/28/2022] Open
Abstract
Background Abnormalities in apoptosis, cell cycle, proliferation, and differentiation of human bone marrow mesenchymal stem cells (hBMSCs) significantly impact bone metabolism and remodeling, resulting in various skeletal disorders. Long-term exposure to a high dosage of dexamethasone (Dex) induces apoptosis and inhibits the proliferation of mesenchymal stromal cells (MSCs), which are probable primary causes of various skeletal disorders. However, to date, the exact mechanisms of action of Dex on hBMSCs have not been fully elucidated. Methods To explore the effects of Dex on apoptosis, cell cycle, proliferation, senescence, osteogenic and adipogenic differentiation of hBMSCs at the various exposure times and concentrations, Hoechst 33342/PI staining, flow cytometry, crystal violet assay, β-galactosidase (β-GAL) activity assay, alizarin red S (ARS) staining assay, and Oil Red O (ORO) staining assay were performed. A microarray assay was used to identify differentially expressed lncRNAs and mRNAs in 10− 6 mol/L Dex-treated hBMSCs, and a bioinformatics analysis was conducted to further explore the role of these differentially expressed lncRNAs and mRNAs in the coding and noncoding (CNC) network. Furthermore, the microarray results were validated using quantitative real-time PCR (qRT-PCR) analysis. Results Over the range of 10−8, 10−7, and 10−6 mol/L, Dex induced apoptosis, arrest of the cell cycle, inhibition of osteogenic differentiation, and promotion adipogenic differentiation of the hBMSCs in a dose-dependent manner. In addition, 10−6 mol/L Dex significantly induced apoptosis, suppressed proliferation, and increased the senescence of hBMSCs in a time-dependent manner. Interestingly, this time-dependent effect of Dex on the apoptosis of hBMSCs plateaued at the 7th day and decreased from the 8th day to the 10th day, while Dex treatment increased senescence of the hBMSCs on the 6th day. Furthermore, the microarray analysis identified a total of 137 differentially expressed mRNAs (90 upregulated and 47 downregulated) and 90 differentially expressed lncRNAs (61 upregulated and 29 downregulated) in hBMSCs after exposure to 10−6 mol/L Dex. The differentially expressed mRNAs and lncRNAs were associated with the regulation of cell apoptosis, proliferation, and cell cycle. Meanwhile, several signaling pathways involved in these processes, including the mTOR signaling pathway, Ras signaling pathway, HIF-1 signaling pathway, NF-kappa B signaling pathway, and TGF-beta signaling pathway, also were identified through the interaction net in the significant pathways (Path-Net) analysis. Furthermore, the CNC network further identified 78 core regulatory genes involved in the regulation of apoptosis. Additionally, qRT-PCR was used to confirm the identity of the key differentially expressed mRNAs and lncRNAs found to be closely associated with cell apoptosis to confirm the reliability of the microarray dataset. Conclusions In summary, the effect of Dex on apoptosis, cell cycle, proliferation, and osteogenic differentiation and adipogenic differentiation of the hBMSCs depended on exposure time and concentration. Continuous exposure to 10−6 mol/L of Dex for 7 days may be a suitable protocol for inducing the apoptosis of hBMSCs. Under this protocol, differentially expressed lncRNAs and mRNAs associated with apoptosis, cell cycle, and proliferation were identified, providing a new research direction for further studies. Supplementary information The online version contains supplementary material available at 10.1186/s13287-020-02040-8.
Collapse
Affiliation(s)
- Tao Li
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Yingxing Xu
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China.,Qingdao University, Qingdao, 266071, Shandong, China.,Medical Department of Qingdao University, Qingdao, 266071, Shandong, China
| | - Yingzhen Wang
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Yaping Jiang
- Department of Oral Implantology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China.
| |
Collapse
|
24
|
Recent Discoveries on the Involvement of Krüppel-Like Factor 4 in the Most Common Cancer Types. Int J Mol Sci 2020; 21:ijms21228843. [PMID: 33266506 PMCID: PMC7700188 DOI: 10.3390/ijms21228843] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/20/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023] Open
Abstract
Krüppel-like factor 4 (KLF4) is a transcription factor highly conserved in evolution. It is particularly well known for its role in inducing pluripotent stem cells. In addition, KLF4 plays many roles in cancer. The results of most studies suggest that KLF4 is a tumor suppressor. However, the functioning of KLF4 is regulated at many levels. These include regulation of transcription, alternative splicing, miRNA, post-translational modifications, subcellular localization, protein stability and interactions with other molecules. Simple experiments aimed at assaying transcript levels or protein levels fail to address this complexity and thus may deliver misleading results. Tumor subtypes are also important; for example, in prostate cancer KLF4 is highly expressed in indolent tumors where it impedes tumor progression, while it is absent from aggressive prostate tumors. KLF4 is important in regulating response to many known drugs, and it also plays a role in tumor microenvironment. More and more information is available about upstream regulators, downstream targets and signaling pathways associated with the involvement of KLF4 in cancer. Furthermore, KLF4 performs critical function in the overall regulation of tissue homeostasis, cellular integrity, and progression towards malignancy. Here we summarize and analyze the latest findings concerning this fascinating transcription factor.
Collapse
|
25
|
Bu F, Zhu X, Zhu J, Liu Z, Wu T, Luo C, Lin K, Huang J. Bioinformatics Analysis Identifies a Novel Role of GINS1 Gene in Colorectal Cancer. Cancer Manag Res 2020; 12:11677-11687. [PMID: 33235499 PMCID: PMC7680165 DOI: 10.2147/cmar.s279165] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 12/15/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most lethal malignancies and the incidence of CRC has been on the rise. Herein, we aimed to identify effective biomarkers for early diagnosis and treatment of colorectal cancer via bioinformatic tools. Methods To identify differentially expressed genes (DEGs) in CRC, we downloaded CRC gene expression data from GSE24514 and GSE110223 datasets in Gene Expression Omnibus (GEO) and employed R to analyze the data. We further performed functional enrichment analysis of the DEGs on the DAVID gene ontology analysis tool. STRING database and Cytoscape visualization tool were employed to construct a PPI (protein–protein interaction) network and establish intensive intervals in the network. Immunohistochemistry, qRT-PCR and Western blotting were performed to identify the expression level of GINS1 in CRC. In vitro and in vivo experiments were performed to assess the impact of GINS1 in the pathogenesis of CRC in terms of proliferation, migration and metastasis. Results Among the two datasets, 389 DEGs were identified and used to construct a PPI network. These genes were mainly involved in cell proliferation and cell cycle. Among them, 15 genes including GINS1 were found to be strongly associated with the PPI network. We further performed immunohistochemistry, qRT-PCR and Western blotting to identify that GINS1 expression was higher in CRC than in paired normal tissues. Moreover, in vitro and in vivo experiments demonstrated GINS1 could promote the proliferation, invasion and migration of colorectal cancer cells. Conclusions GINS1 could be considered as a potential biomarker for CRC patients.
Collapse
Affiliation(s)
- Fanqin Bu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Xiaojian Zhu
- Research Center of The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Jinfeng Zhu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Zitao Liu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Ting Wu
- Department of Infectious Diseases of Guixi Traditional Chinese Medicine Hospital, Yingtan, People's Republic of China
| | - Chen Luo
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Kang Lin
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China.,Jiangxi Medical College of Nanchang University, Nanchang, People's Republic of China
| | - Jun Huang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, People's Republic of China
| |
Collapse
|
26
|
Rong Z, Luo Z, Zhang J, Li T, Zhu Z, Yu Z, Fu Z, Qiu Z, Huang C. GINS complex subunit 4, a prognostic biomarker and reversely mediated by Krüppel-like factor 4, promotes the growth of colorectal cancer. Cancer Sci 2020; 111:1203-1217. [PMID: 32012389 PMCID: PMC7156840 DOI: 10.1111/cas.14341] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/23/2020] [Accepted: 01/25/2020] [Indexed: 12/11/2022] Open
Abstract
GINS complex subunit 4 (GINS4) is essential for DNA replication initiation and elongation in the G1 /S phase cell cycle in eukaryotes, however, its functional roles and molecular mechanisms remain unclear in many aspects. Our study was designed to investigate the clinical significance, biological function, and molecular mechanism of GINS4 in colorectal cancer (CRC). First, we confirmed that GINS4 expression was significantly overexpressed in CRC cells and tissues. The immunohistochemical results in tissue microarray from 106 CRC patients showed that a high level of GINS4 expression was positively correlated with advanced T stage, higher tumor TNM stage, and poor differentiation. The results from univariate and multivariate survival analysis models based on 106 CRC patients revealed that GINS4 might serve as an independent prognostic indicator for overall survival and disease-free survival of CRC patients. Moreover, downregulated GINS4 can inhibit growth and the cell cycle and accelerate cell apoptosis progression in vitro as well as inhibit tumorigenesis in vivo. Besides, our results also indicated that Krüppel-like factor 4 (KLF4) can negatively regulate GINS4 expression at the transcriptional level and the KLF/GINS4 pathway might play a vital role in the growth and prognosis of CRC.
Collapse
Affiliation(s)
- Zeyin Rong
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zai Luo
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jianming Zhang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Tengfei Li
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhonglin Zhu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhilong Yu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhongmao Fu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhengjun Qiu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chen Huang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| |
Collapse
|