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Li H, Cui J, Hu C, Li H, Luo X, Hao Y. Identification and Analysis of ZIC-Related Genes in Cerebellum of Autism Spectrum Disorders. Neuropsychiatr Dis Treat 2024; 20:325-339. [PMID: 38410689 PMCID: PMC10895985 DOI: 10.2147/ndt.s444138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/09/2024] [Indexed: 02/28/2024] Open
Abstract
Objective Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with significant genetic heterogeneity. The ZIC gene family can regulate neurodevelopment, especially in the cerebellum, and has been implicated in ASD-like behaviors in mice. We performed bioinformatic analysis to identify the ZIC gene family in the ASD cerebellum. Methods We explored the roles of ZIC family genes in ASD by investigating (i) the association of ZIC genes with ASD risk genes from the Simons Foundation Autism Research Initiative (SFARI) database and ZIC genes in the brain regions of the Human Protein Atlas (HPA) database; (ii) co-expressed gene networks of genes positively and negatively correlated with ZIC1, ZIC2, and ZIC3, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and receiver operating characteristic (ROC) curve analysis of genes in these networks; and (iii) the relationship between ZIC1, ZIC2, ZIC3, and their related genes with cerebellar immune cells and stromal cells in ASD patients. Results (i) ZIC1, ZIC2, and ZIC3 were associated with neurodevelopmental disorders and risk genes related to ASD in the human cerebellum and (ii) ZIC1, ZIC2, and ZIC3 were highly expressed in the cerebellum, which may play a pathogenic role by affecting neuronal development and the cerebellar internal environment in patients with ASD, including immune cells, astrocytes, and endothelial cells. (iii) OLFM3, SLC27A4, GRB2, TMED1, NR2F1, and STRBP are closely related to ZIC1, ZIC2, and ZIC3 in ASD cerebellum and have good diagnostic accuracy. (iv) ASD mice in the maternal immune activation model demonstrated that Zic3 and Nr2f1 levels were decreased in the immune-activated cerebellum. Conclusion Our study supports the role of ZIC1, ZIC2, and ZIC3 in ASD pathogenesis and provides potential targets for early and accurate prediction of ASD.
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Affiliation(s)
- Heli Li
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Jinru Cui
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Cong Hu
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Hao Li
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Xiaoping Luo
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Yan Hao
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
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2
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Gao J, Liu L, Wu Z, Gan H. Zic family member 3 attenuates oxidative stress-induced vascular smooth muscle cell apoptosis in patients with chronic kidney disease. Tissue Cell 2024; 86:102286. [PMID: 38091851 DOI: 10.1016/j.tice.2023.102286] [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: 06/29/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 01/21/2024]
Abstract
Neointimal hyperplasia is reportedly essential for arteriovenous fistulas (AVF) in patients undergoing hemodialysis. Oxidative stress is vital in the progression of uremic venous intimal hyperplasia. Studies have suggested that zinc ions obstruct vascular calcification in patients with chronic kidney disease (CKD). Recent studies have shown that the zinc finger protein, Zic family member 3 (ZIC3), is crucial for the earliest cardiovascular progenitors. ZIC3 mutations are associated with congenital heart disease. However, the mechanism of action of ZIC3 in vascular intimal hyperplasia in CKD remains unelucidated. Venous specimens were collected during primary AVF surgery and traumatic amputation, and serum samples were collected from patients with CKD and healthy controls. Mouse vascular smooth muscle cells (VSMCs) were treated with hydrogen peroxide (H2O2) to clarify the role of ZIC3 in CKD. ZIC3 expression was reduced in the veins of patients with uremia and the serum of those with CKD. Zic3 and Bcl2 levels were significantly decreased in mouse VSMCs treated with H2O2·H2O2 inhibited mouse VSMC activity, upregulated Bax, and cleaved caspase 3 expression. Following Zic3 overexpression, Bcl2 expression level and cell viability were elevated, whereas Bax and cleaved caspase 3 expression levels were downregulated. In contrast, Zic3 knockdown yielded the opposite results. Therefore, ZIC3 could be a new therapeutic target in venous neointimal hyperplasia of CKD.
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Affiliation(s)
- Jianya Gao
- Department of Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Nephrology, Chongqing University Three Gorges Hospital, Chongqing 404100, China
| | - Lei Liu
- Department of Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Nephrology, Chongqing University Three Gorges Hospital, Chongqing 404100, China
| | - Zecheng Wu
- Department of Nephrology, Chongqing University Three Gorges Hospital, Chongqing 404100, China
| | - Hua Gan
- Department of Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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3
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Minto M, Sotelo-Fonseca JE, Ramesh V, West AE. Genome binding properties of Zic transcription factors underlie their changing functions during neuronal maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574185. [PMID: 38260638 PMCID: PMC10802290 DOI: 10.1101/2024.01.04.574185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background The Zic family of transcription factors (TFs) promote both proliferation and maturation of cerebellar granule neurons (CGNs), raising the question of how a single, constitutively expressed TF family can support distinct developmental processes. Here we use an integrative experimental and bioinformatic approach to discover the regulatory relationship between Zic TF binding and changing programs of gene transcription during CGN differentiation. Results We first established a bioinformatic pipeline to integrate Zic ChIP-seq data from the developing mouse cerebellum with other genomic datasets from the same tissue. In newborn CGNs, Zic TF binding predominates at active enhancers that are co-bound by developmentally-regulated TFs including Atoh1, whereas in mature CGNs, Zic TF binding consolidates toward promoters where it co-localizes with activity-regulated TFs. We then performed CUT&RUN-seq in differentiating CGNs to define both the time course of developmental shifts in Zic TF binding and their relationship to gene expression. Mapping Zic TF binding sites to genes using chromatin looping, we identified the set of Zic target genes that have altered expression in RNA-seq from Zic1 or Zic2 knockdown CGNs. Conclusion Our data show that Zic TFs are required for both induction and repression of distinct, developmentally regulated target genes through a mechanism that is largely independent of changes in Zic TF binding. We suggest that the differential collaboration of Zic TFs with other TF families underlies the shift in their biological functions across CGN development.
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Affiliation(s)
- Melyssa Minto
- Duke University, Program in Computational Biology and Bioinformatics, Durham, NC 27710
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC 27709
| | | | | | - Anne E. West
- Duke University, Department of Neurobiology, Durham, NC 27710
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4
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Gu H, Duan Z. Silencing of circDPP4 suppresses cell progression of human prostate cancer and enhances docetaxel cytotoxicity through regulating miR-564/ZIC2 axis. J Gene Med 2021; 24:e3403. [PMID: 34904327 DOI: 10.1002/jgm.3403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Circular RNA derived from dipeptidyl peptidase 4 (circDPP4; ID: hsa_circ_0056881) is one top increased circRNA in prostate cancer (PC), and docetaxel (DTX)-based chemotherapy is the primary therapeutic choice for PC. However, its repertoire in PC development and chemoresistance remains to be documented. METHODS Expression of circDPP4, microRNA (miR)-564 and zinc finger of the cerebellum 2 (ZIC2) was detected by real-time quantitative PCR and western blotting; the direct interaction was validated by RNA pull-down assay, dual-luciferase reporter assay and RNA immunoprecipitation. Cell progression was measured by cell counting kit-8, colony formation assay, flow cytometry, Transwell assay, xenograft experiment, and immunohistochemistry. DTX cytotoxicity was confirmed by MTT cell viability assay. RESULTS Expression of circDPP4 is upregulated in PC tumors from 60 patients and PC cell lines, and higher circDPP4 might predict poor overall survival. Decreasing circDPP4 suppresses cell proliferation, colony formation, migration/invasion, and 50% inhibitory concentration of DTX in PC cells, and promotes apoptosis rate. Both overexpressing miR-564 and inhibiting ZIC2 could imitate those effects, while inhibiting miR-564 and restoring ZIC2 could separately counteract that. Mechanistically, circDPP4 functions as miR-564 sponge and regulates the expression of ZIC2, a target gene for miR-564. Tumor growth is retarded by silencing circDPP4, accompanied with elevated miR-564 and attenuated Ki-67 and ZIC2. CONCLUSION Blocking circDPP4 antagonizes cell progression of PC and contributes to in vitro DTX cytotoxicity via regulating miR-564/ZIC2 axis, at least. This study suggests circDPP4 as a potential biomarker and target for PC.
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Affiliation(s)
- Hao Gu
- Department of Urinary Surgery, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, China
| | - Zhongqi Duan
- Department of Urinary Surgery, Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, China
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5
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Wang J, Huang Y, Huang L, Shi K, Wang J, Zhu C, Li L, Zhang L, Feng G, Liu L, Song Y. Novel biomarkers of intervertebral disc cells and evidence of stem cells in the intervertebral disc. Osteoarthritis Cartilage 2021; 29:389-401. [PMID: 33338640 DOI: 10.1016/j.joca.2020.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 10/23/2020] [Accepted: 12/09/2020] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Rat intervertebral disc (IVD) is one of the most commonly used and cost-effective alternative models for human IVD. Many IVD related clinical studies need to be pre-tested on rat IVDs. However, studies on the heterogeneous cell clusters of the rat IVD are inadequate, and a further understanding of the marker genes and cell phenotypes of healthy mature IVD cells is essential. METHODS In this study, we used the 10X Genomics technology to analyze the single-cell transcriptome of purified wild-type rat IVDs. RESULTS We identified potentially new gene markers of IVDs via single-cell sequencing. Based on the unsupervised cluster analysis of 13,578 single-cell transcripts, 3 known IVD cell types were identified. We provided a complete single-cell gene expression map of the IVD. Immunohistochemical and immunofluorescence images of rat disc sections confirmed the new marker genes of all cell types. One group of heterologous cell groups expressed multi-functional stem cell (MSC)-specific genes, indicating the stem cell potential of IVD cells. CONCLUSION We provided the phenotype and marker genes of IVD cells at the single-cell level, reconfirmed existing data, and proposed new marker genes, including MSC marker genes. By identifying more accurate target cells and genes, our results pave the way for further study of the response of individual disc cells to disease states and provide the basis for future disc regeneration therapies.
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Affiliation(s)
- J Wang
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Y Huang
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - L Huang
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - K Shi
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - J Wang
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - C Zhu
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - L Li
- Department of Science and Technology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - L Zhang
- Analytical and Testing Center, State Key Laboratory of Oral Diseases, School of Materials Science and Engineering, Sichuan University, Chengdu, 610065, China.
| | - G Feng
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - L Liu
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Y Song
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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6
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Szenajch J, Szabelska-Beręsewicz A, Świercz A, Zyprych-Walczak J, Siatkowski I, Góralski M, Synowiec A, Handschuh L. Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells. Int J Mol Sci 2020; 21:E9218. [PMID: 33287223 PMCID: PMC7730278 DOI: 10.3390/ijms21239218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
Resistance to anti-cancer drugs is the main challenge in oncology. In pre-clinical studies, established cancer cell lines are primary tools in deciphering molecular mechanisms of this phenomenon. In this study, we proposed a new, transcriptome-focused approach, utilizing a model of isogenic cancer cell lines with gradually changing resistance. We analyzed trends in gene expression in the aim to find out a scaffold of resistance development process. The ovarian cancer cell line A2780 was treated with stepwise increased concentrations of paclitaxel (PTX) to generate a series of drug resistant sublines. To monitor transcriptome changes we submitted them to mRNA-sequencing, followed by the identification of differentially expressed genes (DEGs), principal component analysis (PCA), and hierarchical clustering. Functional interactions of proteins, encoded by DEGs, were analyzed by building protein-protein interaction (PPI) networks. We obtained human ovarian cancer cell lines with gradually developed resistance to PTX and collateral sensitivity to cisplatin (CDDP) (inverse resistance). In their transcriptomes, we identified two groups of DEGs: (1) With fluctuations in expression in the course of resistance acquiring; and (2) with a consistently changed expression at each stage of resistance development, constituting a scaffold of the process. In the scaffold PPI network, the cell cycle regulator-polo-like kinase 2 (PLK2); proteins belonging to the tumor necrosis factor (TNF) ligand and receptor family, as well as to the ephrin receptor family were found, and moreover, proteins linked to osteo- and chondrogenesis and the nervous system development. Our cellular model of drug resistance allowed for keeping track of trends in gene expression and studying this phenomenon as a process of evolution, reflected by global transcriptome remodeling. This approach enabled us to explore novel candidate genes and surmise that abrogation of the osteomimic phenotype in ovarian cancer cells might occur during the development of inverse resistance between PTX and CDDP.
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Affiliation(s)
- Jolanta Szenajch
- Laboratory for Molecular Oncology and Innovative Therapies, Military Institute of Medicine, 04-141 Warsaw, Poland;
| | - Alicja Szabelska-Beręsewicz
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-637 Poznań, Poland; (A.S.-B.); (J.Z.-W.); (I.S.)
| | - Aleksandra Świercz
- Laboratory of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Science, 61-704 Poznań, Poland; (A.Ś.); (M.G.); (L.H.)
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznań, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-637 Poznań, Poland; (A.S.-B.); (J.Z.-W.); (I.S.)
| | - Idzi Siatkowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-637 Poznań, Poland; (A.S.-B.); (J.Z.-W.); (I.S.)
| | - Michał Góralski
- Laboratory of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Science, 61-704 Poznań, Poland; (A.Ś.); (M.G.); (L.H.)
| | - Agnieszka Synowiec
- Laboratory for Molecular Oncology and Innovative Therapies, Military Institute of Medicine, 04-141 Warsaw, Poland;
| | - Luiza Handschuh
- Laboratory of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Science, 61-704 Poznań, Poland; (A.Ś.); (M.G.); (L.H.)
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7
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Liu X, Wu P, Su R, Xue Y, Yang C, Wang D, Ruan X, Zheng J, Yang Y, Li Z, Liu Y. IGF2BP2 stabilized FBXL19-AS1 regulates the blood-tumour barrier permeability by negatively regulating ZNF765 by STAU1-mediated mRNA decay. RNA Biol 2020; 17:1777-1788. [PMID: 32713259 DOI: 10.1080/15476286.2020.1795583] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Blood-tumour barrier (BTB) has been known to significantly attenuate the efficacy of chemotherapy for glioma. In this report, we identified that insulin-like grown factor 2 mRNA-binding protein 2 (IGF2BP2) was over-expressed in glioma microvessel and glioma endothelial cells (GECs). Knockdown of IGF2BP2 decreased the expression of lncRNA FBXL19-AS1 and tight junction-related proteins, thereby promoting BTB permeability. FBXL19-AS1 was over-expressed and more enriched in the cytoplasm of GECs. In addition, FBXL19-AS1 could bind to 3'-UTR of ZNF765 mRNA and down-regulate ZNF765 mRNA expression through STAU1-mediated mRNA decay (SMD). The low expression of ZNF765 was discovered in GECs and verified to increase BTB permeability by inhibiting the promoter activities of tight junction-related proteins. Meanwhile, ZNF765 also inhibited the transcriptional activity of IGF2BP2, thereby forming a feedback loop in regulating the BTB permeability. Single or combined application of silenced IGF2BP2 and FBXL19-AS1 improved the delivery and antitumor efficiency of doxorubicin (DOX). In general, our study revealed the regulation mechanism of IGF2BP2/FBXL19-AS1/ZNF765 axis on BTB permeability, which may provide valuable insight into treatment strategy for glioma.
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Affiliation(s)
- Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
| | - Peiqi Wu
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
| | - Rui Su
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
| | - Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
| | - Xuelei Ruan
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
| | - Yang Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
| | - Zhen Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
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8
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Yang J, Song K, Guo W, Zheng H, Fu Y, You T, Wang K, Qi L, Zhao W, Guo Z. A Qualitative Transcriptional Signature for Predicting Prognosis and Response to Bevacizumab in Metastatic Colorectal Cancer. Mol Cancer Ther 2020; 19:1497-1505. [PMID: 32371582 DOI: 10.1158/1535-7163.mct-19-0864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/17/2019] [Accepted: 05/01/2020] [Indexed: 11/16/2022]
Abstract
Bevacizumab is the molecular-targeted agent used for the antiangiogenic therapy of metastatic colorectal cancer. But some patients are resistant to bevacizumab, it needs an effective biomarker to predict the prognosis and responses of metastatic colorectal cancer (mCRC) to bevacizumab therapy. In this work, we developed a qualitative transcriptional signature to individually predict the response of bevacizumab in patients with mCRC. First, using mCRC samples treated with bevacizumab, we detected differentially expressed genes between response and nonresponse groups. Then, the gene pairs, consisting of at least one differentially expressed gene, with stable relative expression orderings in the response samples but reversal stable relative expression orderings in the nonresponse samples were identified, denoted as pairs-bevacizumab. Similarly, we screened the gene pairs significantly associated with primary tumor locations, donated as pairs-LR. Among the overlapped gene pairs between the pairs-bevacizumab and pairs-LR, we adopted a feature selection process to extract gene pairs that reached the highest F-score for predicting bevacizumab response status in mCRC as the final gene pair signature (GPS), denoted as 64-GPS. In two independent datasets, the predicted response group showed significantly better overall survival than the nonresponse group (P = 6.00e-4 in GSE72970; P = 0.04 in TCGA). Genomic analyses showed that the predicted response group was characterized by frequent copy number alternations, whereas the nonresponse group was characterized by hypermutation. In conclusion, 64-GPS was an objective and robust predictive signature for patients with mCRC treated with bevacizumab, which could effectively assist in the decision of clinical therapy.
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Affiliation(s)
- Jing Yang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kai Song
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenbing Guo
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hailong Zheng
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yelin Fu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Tianyi You
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kai Wang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lishuang Qi
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenyuan Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
| | - Zheng Guo
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou, China
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9
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Liu ZH, Chen ML, Zhang Q, Zhang Y, An X, Luo YL, Liu XM, Liu SX, Liu Q, Yang T, Liu YM, Liu BL, Zhou AJ, Li MZ, Liu YJ, Liu ZX, Zhong Q. ZIC2 is downregulated and represses tumor growth via the regulation of STAT3 in breast cancer. Int J Cancer 2020; 147:505-518. [PMID: 32064600 DOI: 10.1002/ijc.32922] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 01/15/2023]
Abstract
Although early detection and systemic therapies have improved the diagnosis and clinical cure rate of breast cancer, breast cancer remains the most frequently occurring malignant cancer in women due to a lack of sufficiently effective treatments. Thus, to develop potential targeted therapies and thus benefit more patients, it is helpful to understand how cancer cells work. ZIC family members have been shown to play important roles in neural development and carcinogenesis. In our study, we found that ZIC2 is downregulated in breast cancer tissues at both the mRNA and protein levels. Low expression of ZIC2 was correlated with poor outcome in breast cancer patients and serves as an independent prognostic marker. Furthermore, overexpression of ZIC2 repressed, whereas knockdown of ZIC2 promoted, cell proliferation and colony formation ability in vitro and tumor growth in vivo. Using ChIP-seq and RNA-seq analysis, we screened and identified STAT3 as a potential target for ZIC2. ZIC2 bound to the STAT3 promoter and repressed the promoter activities of STAT3. ZIC2 knockdown induced the expression of STAT3, increasing the level of phosphorylated STAT3. These results suggest that ZIC2 regulates the transcription of STAT3 by directly binding to the STAT3 promoter. Additionally, interfering STAT3 with siRNAs or inhibitors abrogated the oncogenic effects induced by decreased ZIC2. Taken together, our results indicate that ZIC2 serves as a useful prognostic marker in breast cancer and acts as a tumor suppressor by regulating STAT3, implying that STAT3 inhibitors might provide an alternative treatment option for breast cancer patients with ZIC2 downregulation.
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Affiliation(s)
- Zhi-Hua Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China.,Department of Pathology, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Mei-Ling Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Qi Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China.,Department of Ultrasound, The Fifth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yu Zhang
- Department of Pathology, SYSUCC, Guangzhou, China
| | - Xin An
- Department of Medical Oncology, SYSUCC, Guangzhou, China
| | - Yi-Ling Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Xue-Min Liu
- Section 3 of Internal Medicine, Guangzhou Medical University Affiliated Cancer Hospital, Guangzhou, Guangdong, China
| | - Shang-Xin Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Qian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Ting Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Yan-Min Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Bin-Liu Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Ai-Jun Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Man-Zhi Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Yu-Jie Liu
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
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