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Mizukoshi C, Kojima Y, Nomura S, Hayashi S, Abe K, Shimamura T. DeepKINET: a deep generative model for estimating single-cell RNA splicing and degradation rates. Genome Biol 2024; 25:229. [PMID: 39237934 PMCID: PMC11378460 DOI: 10.1186/s13059-024-03367-8] [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: 12/14/2023] [Accepted: 08/04/2024] [Indexed: 09/07/2024] Open
Abstract
Messenger RNA splicing and degradation are critical for gene expression regulation, the abnormality of which leads to diseases. Previous methods for estimating kinetic rates have limitations, assuming uniform rates across cells. DeepKINET is a deep generative model that estimates splicing and degradation rates at single-cell resolution from scRNA-seq data. DeepKINET outperforms existing methods on simulated and metabolic labeling datasets. Applied to forebrain and breast cancer data, it identifies RNA-binding proteins responsible for kinetic rate diversity. DeepKINET also analyzes the effects of splicing factor mutations on target genes in erythroid lineage cells. DeepKINET effectively reveals cellular heterogeneity in post-transcriptional regulation.
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Affiliation(s)
- Chikara Mizukoshi
- Division of Systems Biology, Graduate School of Medicine, Nagoya University, Aichi, Japan.
- Nagoya University Hospital, Aichi, Japan.
| | - Yasuhiro Kojima
- Laboratory of Computational Life Science, National Cancer Center Research Institute, Tokyo, Japan.
- Department of Computational and Systems Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Satoshi Nomura
- Division of Systems Biology, Graduate School of Medicine, Nagoya University, Aichi, Japan
| | - Shuto Hayashi
- Department of Computational and Systems Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ko Abe
- Department of Computational and Systems Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Graduate School of Medicine, Nagoya University, Aichi, Japan.
- Department of Computational and Systems Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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Tilajka Á, Kurilla A, László L, Lovrics A, Novák J, Takács T, Buday L, Vas V. Predictive value analysis of the interaction network of Tks4 scaffold protein in colon cancer. Front Mol Biosci 2024; 11:1414805. [PMID: 39234565 PMCID: PMC11371697 DOI: 10.3389/fmolb.2024.1414805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024] Open
Abstract
Background Colorectal carcinoma (CRC) has emerged as one of the most widespread cancers and was the third leading cause of cancer-related mortality in 2020. The role of the podosomal protein Tks4 in tumor formation and progression is well established, including its involvement in gastric carcinoma and hepatocellular carcinoma; however, exploration of Tks4 and its associated EMT-regulating interactome in the context of colon cancer remains largely unexplored. Methods We conducted a comprehensive bioinformatic analysis to investigate the mRNA and protein expression levels of Tks4 and its associated partner molecules (CD2AP, GRB2, WASL, SRC, CTTN, and CAPZA1) across different tumor types. We quantified the expression levels of Tks4 and its partner molecules using qPCR, utilizing a TissueScan colon cancer array. We then validated the usefulness of Tks4 and its associated molecules as biomarkers via careful statistical analyses, including Pearson's correlation analysis, principal component analysis (PCA), multiple logistic regression, confusion matrix analysis, and ROC analysis. Results Our findings indicate that the co-expression patterns of the seven examined biomarker candidates better differentiate between tumor and normal samples compared with the expression levels of the individual genes. Moreover, variable importance analysis of these seven genes revealed four core genes that yield consistent results similar to the seven genes. Thus, these four core genes from the Tks4 interactome hold promise as potential combined biomarkers for colon adenocarcinoma diagnosis and prognosis. Conclusion Our proposed biomarker set from the Tks4 interactome shows promising sensitivity and specificity, aiding in colon cancer prevention and diagnosis.
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Affiliation(s)
- Álmos Tilajka
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Anita Kurilla
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Loretta László
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Anna Lovrics
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Julianna Novák
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Takács
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - László Buday
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Virag Vas
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
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László L, Kurilla A, Tilajka Á, Pancsa R, Takács T, Novák J, Buday L, Vas V. Unveiling epithelial plasticity regulation in lung cancer: Exploring the cross-talk among Tks4 scaffold protein partners. Mol Biol Cell 2024; 35:ar111. [PMID: 38985526 PMCID: PMC11321040 DOI: 10.1091/mbc.e24-03-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
The epithelial-to-mesenchymal transition (EMT) represents a hallmark event in the evolution of lung cancer. This work aims to study a recently described EMT-regulating protein, Tks4, and to explore its potential as a prognostic biomarker in non-small cell lung cancer. In this study, we used CRISPR/Cas9 method to knockout (KO) Tks4 to study its functional roles in invadopodia formation, migration, and regulation of EMT marker expressions and we identified Tks4-interacting proteins. Tks4-KO A549 cells exhibited an EMT-like phenotype characterized by elongated morphology and increased expression of EMT markers. Furthermore, analyses of a large-scale lung cancer database and a patient-derived tissue array data revealed that the Tks4 mRNA level was decreased in more aggressive lung cancer stages. To understand the regulatory role of Tks4 in lung cancer, we performed a Tks4-interactome analysis via Tks4 immunoprecipitation-mass spectrometry on five different cell lines and identified CAPZA1 as a novel Tks4 partner protein. Thus, we propose that the absence of Tks4 leads to disruption of a connectome of multiple proteins and that the resulting undocking and likely mislocalization of signaling molecules impairs actin cytoskeleton rearrangement and activates EMT-like cell fate switches, both of which likely influence disease severity.
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Affiliation(s)
- Loretta László
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Anita Kurilla
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Álmos Tilajka
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Rita Pancsa
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Tamás Takács
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Julianna Novák
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - László Buday
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Department of Molecular Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Virag Vas
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
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Zhao X, Zhao Y, Zhang Y, Fan Q, Ke H, Chen X, Jin L, Tang H, Jiang Y, Ma J. Unraveling pathogenesis, biomarkers and potential therapeutic agents for endometriosis associated with disulfidptosis based on bioinformatics analysis, machine learning and experiment validation. J Biol Eng 2024; 18:42. [PMID: 39061076 PMCID: PMC11282767 DOI: 10.1186/s13036-024-00437-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Endometriosis (EMs) is an enigmatic disease of yet-unknown pathogenesis. Disulfidptosis, a novel identified form of programmed cell death resulting from disulfide stress, stands a chance of treating diverse ailments. However, the potential roles of disulfidptosis-related genes (DRGs) in EMs remain elusive. This study aims to thoroughly explore the key disulfidptosis genes involved in EMs, and probe novel diagnostic markers and candidate therapeutic compounds from the aspect of disulfidptosis based on bioinformatics analysis, machine learning, and animal experiments. RESULTS Enrichment analysis on key module genes and differentially expressed genes (DEGs) of eutopic and ectopic endometrial tissues in EMs suggested that EMs was closely related to disulfidptosis. And then, we obtained 20 and 16 disulfidptosis-related DEGs in eutopic and ectopic endometrial tissue, respectively. The protein-protein interaction (PPI) network revealed complex interactions between genes, and screened nine and ten hub genes in eutopic and ectopic endometrial tissue, respectively. Furthermore, immune infiltration analysis uncovered distinct differences in the immunocyte, human leukocyte antigen (HLA) gene set, and immune checkpoints in the eutopic and ectopic endometrial tissues when compared with health control. Besides, the hub genes mentioned above showed a close correlation with the immune microenvironment of EMs. Furthermore, four machine learning algorithms were applied to screen signature genes in eutopic and ectopic endometrial tissue, including the binary logistic regression (BLR), the least absolute shrinkage and selection operator (LASSO), the support vector machine-recursive feature elimination (SVM-RFE), and the extreme gradient boosting (XGBoost). Model training and hyperparameter tuning were implemented on 80% of the data using a ten-fold cross-validation method, and tested in the testing sets which determined the excellent diagnostic performance of these models by six indicators (Sensitivity, Specificity, Positive Predictive Value, Negative Predictive Value, Accuracy, and Area Under Curve). And seven eutopic signature genes (ACTB, GYS1, IQGAP1, MYH10, NUBPL, SLC7A11, TLN1) and five ectopic signature genes (CAPZB, CD2AP, MYH10, OXSM, PDLIM1) were finally identified based on machine learning. The independent validation dataset also showed high accuracy of the signature genes (IQGAP1, SLC7A11, CD2AP, MYH10, PDLIM1) in predicting EMs. Moreover, we screened 12 specific compounds for EMs based on ectopic signature genes and the pharmacological impact of tretinoin on signature genes was further verified in the ectopic lesion in the EMs murine model. CONCLUSION This study verified a close association between disulfidptosis and EMs based on bioinformatics analysis, machine learning, and animal experiments. Further investigation on the biological mechanism of disulfidptosis in EMs is anticipated to yield novel advancements for searching for potential diagnostic biomarkers and revolutionary therapeutic approaches in EMs.
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Affiliation(s)
- Xiaoxuan Zhao
- Department of Traditional Chinese Medicine (TCM) Gynecology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
- Research Institute of Women's Reproductive Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yang Zhao
- The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanyuan Zhang
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qingnan Fan
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Huanxiao Ke
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaowei Chen
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Linxi Jin
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Hongying Tang
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuepeng Jiang
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China.
| | - Jing Ma
- Department of Traditional Chinese Medicine (TCM) Gynecology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China.
- Research Institute of Women's Reproductive Health, Zhejiang Chinese Medical University, Hangzhou, China.
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Cong Y, Cai G, Ding C, Zhang H, Chen J, Luo S, Liu J. Disulfidptosis-related signature elucidates the prognostic, immunologic, and therapeutic characteristics in ovarian cancer. Front Genet 2024; 15:1378907. [PMID: 38694875 PMCID: PMC11061395 DOI: 10.3389/fgene.2024.1378907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/02/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Ovarian cancer (OC) is the deadliest malignancy in gynecology, but the mechanism of its initiation and progression is poorly elucidated. Disulfidptosis is a novel discovered type of regulatory cell death. This study aimed to develop a novel disulfidptosis-related prognostic signature (DRPS) for OC and explore the effects and potential treatment by disulfidptosis-related risk stratification. Methods The disulfidptosis-related genes were first analyzed in bulk RNA-Seq and a prognostic nomogram was developed and validated by LASSO algorithm and multivariate cox regression. Then we systematically assessed the clinicopathological and mutational characteristics, pathway enrichment analysis, immune cell infiltration, single-cell-level expression, and drug sensitivity according to DRPS. Results The DRPS was established with 6 genes (MYL6, PDLIM1, ACTN4, FLNB, SLC7A11, and CD2AP) and the corresponding prognostic nomogram was constructed based on the DRPS, FIGO stage, grade, and residual disease. Stratified by the risk score derived from DRPS, patients in high-risk group tended to have worse prognosis, lower level of disulfidptosis, activated oncogenic pathways, inhibitory tumor immune microenvironment, and higher sensitivity to specific drugs including epirubicin, stauroporine, navitoclax, and tamoxifen. Single-cell transcriptomic analysis revealed the expression level of genes in the DRPS significantly varied in different cell types between tumor and normal tissues. The protein-level expression of genes in the DRPS was validated by the immunohistochemical staining analysis. Conclusion In this study, the DRPS and corresponding prognostic nomogram for OC were developed, which was important for OC prognostic assessment, tumor microenvironment modification, drug sensitivity prediction, and exploration of potential mechanisms in tumor development.
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Affiliation(s)
- Yunyan Cong
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, China
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Guangyao Cai
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Chengcheng Ding
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Han Zhang
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Jieping Chen
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Shiwei Luo
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
| | - Jihong Liu
- Department of Gynecologic Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, China
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Liu B, Luo L, Shi Z, Ju H, Yu L, Li G, Cui J. Research Progress of Porcine Reproductive and Respiratory Syndrome Virus NSP2 Protein. Viruses 2023; 15:2310. [PMID: 38140551 PMCID: PMC10747760 DOI: 10.3390/v15122310] [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: 10/30/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is globally prevalent and seriously harms the economic efficiency of pig farming. Because of its immunosuppression and high incidence of mutant recombination, PRRSV poses a great challenge for disease prevention and control. Nonstructural protein 2 (NSP2) is the most variable functional protein in the PRRSV genome and can generate NSP2N and NSP2TF variants due to programmed ribosomal frameshifts. These variants are broad and complex in function and play key roles in numerous aspects of viral protein maturation, viral particle assembly, regulation of immunity, autophagy, apoptosis, cell cycle and cell morphology. In this paper, we review the structural composition, programmed ribosomal frameshift and biological properties of NSP2 to facilitate basic research on PRRSV and to provide theoretical support for disease prevention and control and therapeutic drug development.
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Affiliation(s)
- Benjin Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150038, China; (B.L.); (L.L.); (Z.S.)
| | - Lingzhi Luo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150038, China; (B.L.); (L.L.); (Z.S.)
| | - Ziqi Shi
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150038, China; (B.L.); (L.L.); (Z.S.)
| | - Houbin Ju
- Shanghai Animal Disease Prevention and Control Center, Shanghai 201103, China;
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China;
| | - Guoxin Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China;
| | - Jin Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150038, China; (B.L.); (L.L.); (Z.S.)
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Kurilla A, László L, Takács T, Tilajka Á, Lukács L, Novák J, Pancsa R, Buday L, Vas V. Studying the Association of TKS4 and CD2AP Scaffold Proteins and Their Implications in the Partial Epithelial-Mesenchymal Transition (EMT) Process. Int J Mol Sci 2023; 24:15136. [PMID: 37894817 PMCID: PMC10606890 DOI: 10.3390/ijms242015136] [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: 07/28/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Colon cancer is a leading cause of death worldwide. Identification of new molecular factors governing the invasiveness of colon cancer holds promise in developing screening and targeted therapeutic methods. The Tyrosine Kinase Substrate with four SH3 domains (TKS4) and the CD2-associated protein (CD2AP) have previously been linked to dynamic actin assembly related processes and cancer cell migration, although their co-instructive role during tumor formation remained unknown. Therefore, this study was designed to investigate the TKS4-CD2AP interaction and study the interdependent effect of TKS4/CD2AP on oncogenic events. We identified CD2AP as a novel TKS4 interacting partner via co-immunoprecipitation-mass spectrometry methods. The interaction was validated via Western blot (WB), immunocytochemistry (ICC) and proximity ligation assay (PLA). The binding motif of CD2AP was explored via peptide microarray. To uncover the possible cooperative effects of TKS4 and CD2AP in cell movement and in epithelial-mesenchymal transition (EMT), we performed gene silencing and overexpressing experiments. Our results showed that TKS4 and CD2AP form a scaffolding protein complex and that they can regulate migration and EMT-related pathways in HCT116 colon cancer cells. This is the first study demonstrating the TKS4-CD2AP protein-protein interaction in vitro, their co-localization in intact cells, and their potential interdependent effects on partial-EMT in colon cancer.
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Affiliation(s)
- Anita Kurilla
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Loretta László
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Tamás Takács
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Álmos Tilajka
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Laura Lukács
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Julianna Novák
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Department of Molecular Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Virág Vas
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
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Zhang Y, Dong K, Jia X, Du S, Wang D, Wang L, Qu H, Zhu S, Wang Y, Wang Z, Zhang S, Sun W, Fu S. A novel extrachromosomal circular DNA related genes signature for overall survival prediction in patients with ovarian cancer. BMC Med Genomics 2023; 16:140. [PMID: 37337170 DOI: 10.1186/s12920-023-01576-x] [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: 07/17/2022] [Accepted: 06/09/2023] [Indexed: 06/21/2023] Open
Abstract
OBJECTIVE Ovarian cancer (OV) has a high mortality rate all over the world, and extrachromosomal circular DNA (eccDNA) plays a key role in carcinogenesis. We wish to study more about the molecular structure of eccDNA in the UACC-1598-4 cell line and how its genes are associated with ovarian cancer prognosis. METHODS We sequenced and annotated the eccDNA by Circle_seq of the OV cell line UACC-1598-4. To acquire the amplified genes of OV on eccDNA, the annotated eccDNA genes were intersected with the overexpression genes of OV in TCGA. Univariate Cox regression was used to find the genes on eccDNA that were linked to OV prognosis. The least absolute shrinkage and selection operator (LASSO) and cox regression models were used to create the OV prognostic model, as well as the receiver operating characteristic curve (ROC) curve and nomogram of the prediction model. By applying the median value of the risk score, the samples were separated into high-risk and low-risk groups, and the differences in immune infiltration between the two groups were examined using ssGSEA. RESULTS EccDNA in UACC-1598-4 has a length of 0-2000 bp, and some of them include the whole genes or gene fragments. These eccDNA originated from various parts of chromosomes, especially enriched in repeatmasker, introns, and coding regions. They were annotated with 2188 genes by Circle_seq. Notably, the TCGA database revealed that a total of 198 of these eccDNA genes were overexpressed in OV (p < 0.05). They were mostly enriched in pathways associated with cell adhesion, ECM receptors, and actin cytoskeleton. Univariate Cox analysis showed 13 genes associated with OV prognosis. LASSO and Cox regression analysis were used to create a risk model based on remained 9 genes. In both the training (TCGA database) and validation (International Cancer Genome Consortium, ICGC) cohorts, a 9-gene signature could successfully discriminate high-risk individuals (all p < 0.01). Immune infiltration differed significantly between the high-risk and low-risk groups. The model's area under the ROC curve was 0.67, and a nomograph was created to assist clinician. CONCLUSION EccDNA is found in UACC-1598-4, and part of its genes linked to OV prognosis. Patients with OV may be efficiently evaluated using a prognostic model based on eccDNA genes, including SLC7A1, NTN1, ADORA1, PADI2, SULT2B1, LINC00665, CILP2, EFNA5, TOMM.
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Affiliation(s)
- Ying Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
| | - Kexian Dong
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
| | - Shuomeng Du
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
| | - Dong Wang
- Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Liqiang Wang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
| | - Han Qu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
| | - Shihao Zhu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
| | - Yang Wang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
| | - Zhao Wang
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Shuopeng Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China.
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China.
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Wei P, Dong M, Bi Y, Chen S, Huang W, Li T, Liu B, Fu X, Yang Y. Identification and validation of a signature based on macrophage cell marker genes to predict recurrent miscarriage by integrated analysis of single-cell and bulk RNA-sequencing. Front Immunol 2022; 13:1053819. [PMID: 36439123 PMCID: PMC9692009 DOI: 10.3389/fimmu.2022.1053819] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/24/2022] [Indexed: 09/12/2023] Open
Abstract
Recurrent miscarriage (RM) is a chronic, heterogeneous autoimmune disease that has serious social and personal consequences. No valid and reliable diagnostic markers or therapeutic targets for RM have been identified. Macrophages impact the innate immune system and can be used as diagnostic and prognostic markers for many diseases. We first collected 16 decidua and villi tissue samples from 5 normal patients and 3 RM patients for single-cell RNA sequencing data analysis and identified 1293 macrophage marker genes. We then screened a recurrent miscarriage cohort (GSE165004) for 186 macrophage-associated marker genes that were significantly differentially expressed between RM patients and the normal pregnancy endometrial tissues, and performed a functional enrichment analysis of differentially expressed genes. We then identified seven core genes (ACTR2, CD2AP, MBNL2, NCSTN, PUM1, RPN2, and TBC1D12) from the above differentially expressed gene group that are closely related to RM using the LASSO, Random Forest and SVM-RFE algorithms. We also used GSE26787 and our own collection of clinical specimens to further evaluate the diagnostic value of the target genes. A nomogram was constructed of the expression levels of these seven target genes to predict RM, and the ROC and calibration curves showed that our nomogram had a high diagnostic value for RM. These results suggest that ACTR2 and NCSTN may be potential targets for preventative RM treatments.
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Affiliation(s)
- Peiru Wei
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, China
- The Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, China
| | - Mingyou Dong
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Key Laboratory of Molecular Pathology (For Hepatobiliary Diseases) of Guangxi, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yin Bi
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, China
- The Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, China
| | - Saiqiong Chen
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Obstetrics and Gynecology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Weiyu Huang
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, China
- The Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, China
| | - Ting Li
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, China
- The Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, China
| | - Bo Liu
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaoqian Fu
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yihua Yang
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, China
- The Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, China
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10
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Qiao H, Yin H, Feng Y, Tang H. Pan-cancer analysis reveals the relationship between RCSD1 immune infiltration and clinical prognosis in human tumors. Front Immunol 2022; 13:1008778. [PMID: 36311703 PMCID: PMC9606721 DOI: 10.3389/fimmu.2022.1008778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background RCSD1 is a cytoskeletal regulator that has been confirmed to undergo genetic mutations in hematological tumors, but the mechanisms of RCSD1 in pan-cancer and its impact on patient prognosis have not been studied. Methods Using TCGA, GEPIA, UALCAN, Kaplan-Meier plotters, Linkedomics, String, cBioPortal, TISIDB, TCIA and TIMER database methods, we investigated the expression of RCSD1 in human tumors and its relationship to clinical prognosis, functional analysis of co-expression networks, mutation status, and immune infiltration in cancers, especially lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Results The expression of RCSD1 is low in most tumors compared with normal tissues, and its high expression is associated with good patient survival. The RCSD1 co-expression network is mainly involved in the regulation of immune response. In human cancer, RCSD1 plays an important role in the tumor microenvironment (TME) and is significantly associated with the expression of immune infiltrating cells (TIL) in lung cancer. Conclusions As a prognostic biomarker of generalized cancer, RCSD1 is associated with immune infiltration.
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Affiliation(s)
- Han Qiao
- Department of Respiratory Medicine, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Hong Yin
- Department of Thoracic Surgery, Qingdao Municipal Hospital, Qingdao, China
| | - Yan Feng
- Department of Respiratory Medicine, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Huaping Tang
- Department of Respiratory Medicine, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
- *Correspondence: Huaping Tang,
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11
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Ke J, Chen M, Ma S, Zhang L, Zhang L. Circular RNA VMA21 ameliorates lung injury in septic rat via targeting microRNA-497-5p/CD2-associated protein axis. Bioengineered 2022; 13:5453-5466. [PMID: 35172672 PMCID: PMC8973665 DOI: 10.1080/21655979.2022.2031406] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Sepsis was characterized via an acute inflammatory response to infection, often accompanying by multiple organ failure, particularly lung damage. Circular RNA (circRNA) played an important role in the pathology of a variety of diseases. However, the role of circRNA in sepsis-induced lung injury (LI) remained unknown. This study was to explore the expression and role of circVMA21 in sepsis LI and the possible molecular mechanism. The results manifested circVMA21 and CD2-associated protein (CD2AP) were down-regulated in lung tissue and lipopolysaccharide (LPS)-treated BEAS-2B, while microRNA (miR)-497-5p was up-regulated. A large number of deaths in rats after surgery of 72 h were caused via cecal ligation-perforation surgery, W/D value and Bax positive cells were increased, LI was caused, cell apoptosis, tumor necrosis factor-α, Interleukin (IL)-1β and IL-6 expression were promoted and Bcl-2 positive cells were decreased. Overexpression of circVMA21 ameliorated these phenomena. In addition, LPS-induced apoptosis and inflammation of BEAS-2B cells was improved via overexpression of circVMA21, while overexpression of miR-497-5P was opposite. Apoptosis, inflammation, and oxidative damage of BEAS-2B cells were aggravated via knockdown of circVMA21, but it was reversed by knockdown of miR-497-5p or overexpression of CD2AP. Mechanistically, CircVMA21 mediated CD2AP expression through competitive adsorption of miR-497-5p. In conclusion, this work showed circVMA21 improved LI in sepsis rats by targeting miR-497-5p/CD2AP axis, suggesting that circVMA21 may be a novel therapeutic target for sepsis-induced LI.
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Affiliation(s)
- JinFang Ke
- Department of Emergency, People's Hospital of Ningxia Hui Autonomous Region, YinChuan City, NingXia Hui Autonomous Region, China
| | - MengFei Chen
- Department of Emergency, People's Hospital of Ningxia Hui Autonomous Region, YinChuan City, NingXia Hui Autonomous Region, China
| | - ShiLan Ma
- Department of Emergency, People's Hospital of Ningxia Hui Autonomous Region, YinChuan City, NingXia Hui Autonomous Region, China
| | - Liang Zhang
- Department of Emergency, People's Hospital of Ningxia Hui Autonomous Region, YinChuan City, NingXia Hui Autonomous Region, China
| | - Ling Zhang
- Department of Emergency, People's Hospital of Ningxia Hui Autonomous Region, YinChuan City, NingXia Hui Autonomous Region, China
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12
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Chu Z, Luo Y, Ni T, Zhu M, Feng X, Liu Y, Wang H. Betulonic Acid, as One of the Active Components of the Celastrus orbiculatus Extract, Inhibits the Invasion and Metastasis of Gastric Cancer Cells by Mediating Cytoskeleton Rearrangement In Vitro. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031025. [PMID: 35164287 PMCID: PMC8840099 DOI: 10.3390/molecules27031025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 12/23/2022]
Abstract
Gastric cancer is a type of malignant tumor that seriously threatens human life and health. Invasion and metastasis present difficulties in the treatment of gastric cancer, and the remodeling of the tumor cytoskeleton plays an important role in mediating the ability of tumor cells to achieve invasion and metastasis. Previous experimental results suggest that Celastrus orbiculatus extract can regulate cytoskeletal remodeling in gastric cancer, but the active component has not been determined. Betulonic acid, as an effective component of COE, inhibits the invasion and metastasis of gastric cancer cells by regulating cytoskeletal remodeling in vitro; its specific mechanisms have been studied here. After betulonic acid was dissolved, it was diluted to various working concentrations in RPMI-1640 medium and added to AGS, HGC-27 and GES-1 cell lines. Cell viability was assessed by CCK-8 and colony formation assays. Cytoskeleton staining was used to detect changes in cytoskeleton morphology. Functional assays including wound healing assays and transwell assays were used to detect the invasion and migration of cells. The effect of betulonic acid on cell invasion and migration was clearly and precisely observed by high-content imaging technology. Western blotting was used to detect the regulation of matrix metalloproteinase-related proteins and epithelial–mesenchymal transformation-related proteins. We found that betulonic acid inhibited the migration and invasion of gastric cancer cells. Therefore, betulonic acid inhibits the invasion and metastasis of gastric cancer cells by mediating cytoskeletal remodeling and regulating epithelial mesenchymal transformation.
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Affiliation(s)
- Zewen Chu
- Department of Integrated Chinese and Western Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China; (Z.C.); (Y.L.); (T.N.); (M.Z.); (X.F.)
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Department of Integrated Chinese and Western Medicine, Yangzhou University, Yangzhou 225001, China
- Department of Integrated Chinese and Western Medicine, Yangzhou Cancer Research Institute, Yangzhou University, Yangzhou 225001, China
| | - Yuanyuan Luo
- Department of Integrated Chinese and Western Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China; (Z.C.); (Y.L.); (T.N.); (M.Z.); (X.F.)
| | - Tengyang Ni
- Department of Integrated Chinese and Western Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China; (Z.C.); (Y.L.); (T.N.); (M.Z.); (X.F.)
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Department of Integrated Chinese and Western Medicine, Yangzhou University, Yangzhou 225001, China
- Department of Integrated Chinese and Western Medicine, Yangzhou Cancer Research Institute, Yangzhou University, Yangzhou 225001, China
| | - Miao Zhu
- Department of Integrated Chinese and Western Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China; (Z.C.); (Y.L.); (T.N.); (M.Z.); (X.F.)
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Department of Integrated Chinese and Western Medicine, Yangzhou University, Yangzhou 225001, China
- Department of Integrated Chinese and Western Medicine, Yangzhou Cancer Research Institute, Yangzhou University, Yangzhou 225001, China
| | - Xinyi Feng
- Department of Integrated Chinese and Western Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China; (Z.C.); (Y.L.); (T.N.); (M.Z.); (X.F.)
| | - Yanqing Liu
- Department of Integrated Chinese and Western Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China; (Z.C.); (Y.L.); (T.N.); (M.Z.); (X.F.)
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Department of Integrated Chinese and Western Medicine, Yangzhou University, Yangzhou 225001, China
- Department of Integrated Chinese and Western Medicine, Yangzhou Cancer Research Institute, Yangzhou University, Yangzhou 225001, China
- Correspondence: (Y.L.); (H.W.)
| | - Haibo Wang
- Department of Integrated Chinese and Western Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China; (Z.C.); (Y.L.); (T.N.); (M.Z.); (X.F.)
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Department of Integrated Chinese and Western Medicine, Yangzhou University, Yangzhou 225001, China
- Department of Integrated Chinese and Western Medicine, Yangzhou Cancer Research Institute, Yangzhou University, Yangzhou 225001, China
- Correspondence: (Y.L.); (H.W.)
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13
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Lou S, Zhang J, Zhai Z, Yin X, Wang Y, Fang T, Xue Y. The landscape of alternative splicing reveals novel events associated with tumorigenesis and the immune microenvironment in gastric cancer. Aging (Albany NY) 2021; 13:4317-4334. [PMID: 33428603 PMCID: PMC7906195 DOI: 10.18632/aging.202393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022]
Abstract
Alternative splicing (AS), contributing to vast protein diversity from a rather limited number of genes in eukaryotic transcripts, has emerged as an important signature for tumor initiation and progression. However, a systematic understanding of its functional impact and relevance to gastric cancer (GC) tumorigenesis is lacking. Differentially expressed AS (DEAS) was verified among GC-associated AS events based on RNA-seq profiles from the TCGA database. Functional enrichment analysis, unsupervised clustering analysis and prognostic models were used to infer the potential roles of DEAS events and their molecular, clinical and immune features. In total, 12,225 AS events were detected from 5,199 genes, among which 314 AS events were identified as DEAS events in GC. The parental genes of the DEAS events were significantly enriched in the regulation of GC-related processes. The splicing correlation network suggested a significant relationship between DEAS events and splicing factors (SFs). Three clusters of DEAS events were identified to be different in prognosis, cancer-specific signatures and immune features between distinct clusters. Univariate and multivariate analyses regarded 3 DEAS events as independent prognostic indicators. Profiling of the AS landscape in GC elucidated the functional roles of the splicing network in GC and might serve as a novel prognostic indicator and therapeutic target.
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Affiliation(s)
- Shenghan Lou
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, 150081 Harbin, Heilongjiang Province, China
| | - Jian Zhang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150081 Harbin, Heilongjiang Province, China
| | - Zhao Zhai
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, 150081 Harbin, Heilongjiang Province, China
| | - Xin Yin
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, 150081 Harbin, Heilongjiang Province, China
| | - Yimin Wang
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, 150081 Harbin, Heilongjiang Province, China
| | - Tianyi Fang
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, 150081 Harbin, Heilongjiang Province, China
| | - Yingwei Xue
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, 150081 Harbin, Heilongjiang Province, China
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14
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Xie W, Chen C, Han Z, Huang J, Liu X, Chen H, Zhang T, Chen S, Chen C, Lu M, Shen X, Xue X. CD2AP inhibits metastasis in gastric cancer by promoting cellular adhesion and cytoskeleton assembly. Mol Carcinog 2020; 59:339-352. [PMID: 31989722 PMCID: PMC7078920 DOI: 10.1002/mc.23158] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/29/2019] [Accepted: 01/13/2020] [Indexed: 12/15/2022]
Abstract
Diffuse gastric cancer (DGC) is a lethal malignancy lacking effective systemic therapy. Among the most provocative recent results in DGC has been that the alter of the cellular cytoskeleton and intercellular adhesion. CD2‐associated protein (CD2AP) is one of the critical proteins regulating cytoskeleton assembly and intercellular adhesion. However, no study has investigated the expression and biological significance of CD2AP in gastric cancer (GC) to date. Therefore, the aim of our study was to explore if the expression of CD2AP is associated with any clinical features of GC and to elucidate the underlying mechanism. Immunohistochemistry of 620 patient tissue samples indicated that the expression of CD2AP is downregulated in DGC. Moreover, a low CD2AP level was indicative of poor patient prognosis. In vitro, forced expression of CD2AP caused a significant decrease in the migration and invasion of GC cells, whereas depletion of CD2AP had the opposite effect. Immunofluorescence analysis indicated that CD2AP promoted cellular adhesion and influenced cell cytoskeleton assembly via interaction with the F‐actin capping protein CAPZA1. Overall, the upregulation of CD2AP could attenuate GC metastasis, suggesting CD2AP as a novel biomarker for the prognosis and treatment of patients with GC.
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Affiliation(s)
- Wangkai Xie
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Microbiology and Immunology, School of Basic Medical Science, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Chao Chen
- Department of Microbiology and Immunology, School of Basic Medical Science, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China.,Department of Oncology, Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Zhejiang Chinese Medical University, Wenzhou, China
| | - Zheng Han
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Microbiology and Immunology, School of Basic Medical Science, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jingjing Huang
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xin Liu
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Microbiology and Immunology, School of Basic Medical Science, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Hongjun Chen
- Department of Microbiology and Immunology, School of Basic Medical Science, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Teming Zhang
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Microbiology and Immunology, School of Basic Medical Science, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Sian Chen
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chenbin Chen
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Microbiology and Immunology, School of Basic Medical Science, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Mingdong Lu
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xian Shen
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Department of Microbiology and Immunology, School of Basic Medical Science, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, Wenzhou Medical University, Wenzhou, China
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