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Mo B, Luo B, Wu Y. Pan-analysis reveals CACYBP to be a novel prognostic and predictive marker for multiple cancers. Am J Transl Res 2024; 16:12-26. [PMID: 38322570 PMCID: PMC10839390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/26/2023] [Indexed: 02/08/2024]
Abstract
OBJECTIVES Cancer has emerged as a global issue in terms of public health care and treatment. The significance of calcyclin binding protein (CACYBP) in various neoplasms suggests that it may serve as a novel biomarker for numerous types of human tumors. METHODS Our research investigated the differences in CACYBP expression between cancer tissues and normal tissues using a total of 18,787 samples from multiple centers. To explore the prognostic factor of CACYBP in cancers, we utilized Cox regression analysis and Kaplan-Meier curves. We also conducted Spearman's rank correlation analyses to determine the associations of CACYBP expression with the immune microenvironment, etc. Additionally, we applied gene set enrichment analysis to explore the underlying mechanisms of CACYBP in cancers. A partial validation of CacyBP expression in cancer tissues was performed through lung adenocarcinoma samples using Western blotting and paired t-test. RESULTS Compared to normal tissues, CACYBP exhibited high expression levels in 14 cancer types, including breast invasive carcinoma, and low expression levels in six cancers, including glioblastoma multiforme (P < 0.05). CACYBP expression was found to be significantly associated with the prognosis of 13 cancers, including adrenocortical carcinoma (P < 0.05). CACYBP demonstrated a robust ability to distinguish 15 cancers, including cholangiocarcinoma, from their control samples (area under the curve > 0.8). Furthermore, CACYBP expression was correlated with tumor mutational burden, microsatellite instability, and immune infiltration levels, indicating its potential as an exciting target for cancer treatment. CACYBP may exert its effects on several signaling pathways, including cytokine-cytokine receptor interaction, in various cancers. Compared with paired adjacent specimens, the expression level of CacyBP protein was up-regulated in lung adenocarcinoma specimens (P < 0.05), partially validating the increased expression of CACYBP in cancers. CONCLUSIONS CACYBP has the potential to serve as a novel prognostic and predictive marker for multiple human cancers.
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Affiliation(s)
- Baosen Mo
- Department of Cardiothoracic Surgery, The 923 Hospital of Joint Logistics Support Force of Chinese People’s Liberation ArmyNanning, Guangxi Zhuang Autonomous Region, China
| | - Bijun Luo
- Department of Anesthesiology, The Region Maternal and Child Health Hospital of Guangxi Zhuang AutonomousNanning, Guangxi Zhuang Autonomous Region, China
| | - Yuesong Wu
- Department of Cardiothoracic Surgery, The 923 Hospital of Joint Logistics Support Force of Chinese People’s Liberation ArmyNanning, Guangxi Zhuang Autonomous Region, China
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Barreiro K, Lay AC, Leparc G, Tran VDT, Rosler M, Dayalan L, Burdet F, Ibberson M, Coward RJM, Huber TB, Krämer BK, Delic D, Holthofer H. An in vitro approach to understand contribution of kidney cells to human urinary extracellular vesicles. J Extracell Vesicles 2023; 12:e12304. [PMID: 36785873 PMCID: PMC9925963 DOI: 10.1002/jev2.12304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/26/2022] [Accepted: 01/05/2023] [Indexed: 02/15/2023] Open
Abstract
Extracellular vesicles (EV) are membranous particles secreted by all cells and found in body fluids. Established EV contents include a variety of RNA species, proteins, lipids and metabolites that are considered to reflect the physiological status of their parental cells. However, to date, little is known about cell-type enriched EV cargo in complex EV mixtures, especially in urine. To test whether EV secretion from distinct human kidney cells in culture differ and can recapitulate findings in normal urine, we comprehensively analysed EV components, (particularly miRNAs, long RNAs and protein) from conditionally immortalised human kidney cell lines (podocyte, glomerular endothelial, mesangial and proximal tubular cells) and compared to EV secreted in human urine. EV from cell culture media derived from immortalised kidney cells were isolated by hydrostatic filtration dialysis (HFD) and characterised by electron microscopy (EM), nanoparticle tracking analysis (NTA) and Western blotting (WB). RNA was isolated from EV and subjected to miRNA and RNA sequencing and proteins were profiled by tandem mass tag proteomics. Representative sets of EV miRNAs, RNAs and proteins were detected in each cell type and compared to human urinary EV isolates (uEV), EV cargo database, kidney biopsy bulk RNA sequencing and proteomics, and single-cell transcriptomics. This revealed that a high proportion of the in vitro EV signatures were also found in in vivo datasets. Thus, highlighting the robustness of our in vitro model and showing that this approach enables the dissection of cell type specific EV cargo in biofluids and the potential identification of cell-type specific EV biomarkers of kidney disease.
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Affiliation(s)
- Karina Barreiro
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiHelsinkiFinland
| | - Abigail C. Lay
- Bristol RenalBristol Medical SchoolFaculty of Health SciencesUniversity of BristolBristolUK
| | - German Leparc
- Boehringer Ingelheim Pharma GmbH & Co. KG BiberachBiberachGermany
| | - Van Du T. Tran
- Vital‐IT GroupSIB Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Marcel Rosler
- Boehringer Ingelheim Pharma GmbH & Co. KG BiberachBiberachGermany
| | - Lusyan Dayalan
- Bristol RenalBristol Medical SchoolFaculty of Health SciencesUniversity of BristolBristolUK
| | - Frederic Burdet
- Vital‐IT GroupSIB Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Mark Ibberson
- Vital‐IT GroupSIB Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Richard J. M. Coward
- Bristol RenalBristol Medical SchoolFaculty of Health SciencesUniversity of BristolBristolUK
| | - Tobias B. Huber
- III Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Bernhard K. Krämer
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology/Pneumology)University Medical Centre MannheimUniversity of HeidelbergMannheimGermany
| | - Denis Delic
- Boehringer Ingelheim Pharma GmbH & Co. KG BiberachBiberachGermany
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology/Pneumology)University Medical Centre MannheimUniversity of HeidelbergMannheimGermany
| | - Harry Holthofer
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiHelsinkiFinland
- III Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
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Li Q, Liu Z, Ma L, Yin W, Zhang K. CACYBP knockdown inhibits progression of prostate cancer via p53. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04497-x. [PMID: 36576589 PMCID: PMC10356884 DOI: 10.1007/s00432-022-04497-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/24/2022] [Indexed: 12/29/2022]
Abstract
PURPOSE Prostate cancer (PC) is one of the most common malignant tumors of genitourinary system in men. CACYCLIN binding protein (CACYBP) is involved in the progression of a variety of cancers. The aim of this study was to explore the expression and functional role of CACYBP in PC. METHODS The expression of CACYBP in PC was evaluated by immunohistochemical (IHC) staining and qRT-PCR. Subsequently, we established lentivirus-mediated CACYBP knockdown in PC cell lines. The biological roles of CACYBP on proliferation, apoptosis, cycle distribution, migration and tumor formation of PC were investigated by Celigo cell counting assay, flow cytometry, transwell assay, wound-healing assay and mice xenograft models, respectively. RESULTS CACYBP was highly expressed in PC and was positively correlated with the pathological grade of PC patients. Knockdown of CACYBP inhibited proliferation, enhanced apoptosis, arrested cell cycle in G2 and suppressed migration of PC cell lines in vitro. In addition, CACYBP knockdown weakened the tumor growth of PC in vivo. Moreover, addition of p53 inhibitor could effectively alleviate the inhibitory effect of CACYBP knockdown on cell activity. CONCLUSION This study revealed that knockdown of CACYBP inhibited the proliferation, migration and tumorigenicity of PC, which may serve as a potential therapeutic target for the treatment of PC.
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Affiliation(s)
- Qiang Li
- Department of Urological Surgery, First Affiliated Hospital School of Medicine, Shihezi University, Shihezi, 832008, Xinjiang, China
| | - Zhili Liu
- Department of Urological Surgery, First Affiliated Hospital School of Medicine, Shihezi University, Shihezi, 832008, Xinjiang, China
| | - Luping Ma
- Department of Urological Surgery, First Affiliated Hospital School of Medicine, Shihezi University, Shihezi, 832008, Xinjiang, China
| | - Weiqi Yin
- Department of Urological Surgery, Ningbo First Hospital, Ningbo, 315010, Zhejiang, China
| | - Kan Zhang
- Department of Urological Surgery, Ningbo First Hospital, Ningbo, 315010, Zhejiang, China.
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Zhou J, Li F, Yang Y. Protective effects of calcyclin-binding protein against pulmonary vascular remodeling in flow-associated pulmonary arterial hypertension. Respir Res 2022; 23:223. [PMID: 36042446 PMCID: PMC9429705 DOI: 10.1186/s12931-022-02137-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 08/04/2022] [Indexed: 11/15/2022] Open
Abstract
Background Pulmonary arterial hypertension associated with congenital heart disease (CHD-PAH) is recognized as a cancer-like disease with a proliferative and pro-migratory phenotype in pulmonary artery smooth muscle cells (PASMCs). Calcyclin-binding protein/Siah-1-interacting protein (CacyBP/SIP) has been implicated in the progression of various cancers; however, it has not been previously studied in the context of CHD-PAH. Here, we aimed to examine the function of CacyBP/SIP in CHD-PAH and explore its potential as a novel regulatory target for the disease. Methods The expression of CacyBP/SIP in PASMCs was evaluated both in the pulmonary arterioles of patients with CHD-PAH and in high-flow-induced PAH rats. The effects of CacyBP/SIP on pulmonary vascular remodeling and PASMC phenotypic switch, proliferation, and migration were investigated. LY294002 (MedChemExpress, NJ, USA) was used to block the phosphoinositide 3-kinase/protein kinase B (PI3K/AKT) pathway to explore changes in PASMC dysfunction induced by low CacyBP/SIP levels. Hemodynamics and pulmonary arterial remodeling were further explored in rats after short-interfering RNA-mediated decrease of CacyBP/SIP expression. Results CacyBP/SIP expression was markedly reduced both in the remodeled pulmonary arterioles of patients with CHD-PAH and in high-flow-induced PAH rats. Low CacyBP/SIP expression promoted hPASMC phenotypic switch, proliferation, and migration via PI3K/AKT pathway activation. Our results indicated that CacyBP/SIP protected against pulmonary vascular remodeling through amelioration of hPASMC dysfunction in CHD-PAH. Moreover, after inhibition of CacyBP/SIP expression in vivo, we observed increased right ventricular hypertrophy index, poor hemodynamics, and severe vascular remodeling. Conclusions CacyBP/SIP regulates hPASMC dysfunction, and its increased expression may ameliorate progression of CHD-PAH. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02137-z.
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Affiliation(s)
- Jingjing Zhou
- Echocardiography Medical Center, Maternal-Fetal Medicine Center in Fetal Heart Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - FuRong Li
- Department of Laboratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Yicheng Yang
- Center of Pulmonary Vascular Disease, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, North Lishi Road, Xicheng, No. 167, Beijing, 100037, China.
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5
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Xie Y, Fu R, Xiao Z, Li G. A Risk Model Based on Immune-Related Genes Predicts Prognosis and Characterizes the Immune Landscape in Esophageal Cancer. Pathol Oncol Res 2022; 28:1610030. [PMID: 35356506 PMCID: PMC8958959 DOI: 10.3389/pore.2022.1610030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/14/2022] [Indexed: 12/24/2022]
Abstract
Aberrant immune gene expression has been shown to have close correlations with the occurrence and progression of esophageal cancer (EC). We aimed to generate a prognostic signature based on immune-related genes (IRGs) capable of predicting prognosis, immune checkpoint gene (ICG) expressions, and half-inhibitory concentration (IC50) for chemotherapy agents for EC patients. Transcriptome, clinical, and mutation data on tumorous and paratumorous tissues from EC patients were collected from The Cancer Genome Atlas (TCGA) database. Then, we performed differential analysis to identify IRGs differentially expressed in EC. Their biofunctions and related pathways were explored using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. These gene expression profiling data were merged with survival information and subjected to univariate Cox regression to select prognostic genes, which were then included in a Lasso-Cox model for signature generation (risk score calculation). Patients were divided into the high- and low-risk groups using the median risk score as a cutoff. The accuracy of the signature in overall survival prediction was assessed, so were its performances in predicting ICG expressions and IC50 for chemotherapy and targeted therapy agents and immune cell landscape characterization. Fifteen prognostic IRGs were identified, seven of which were optimal for risk score calculation. As expected, high-risk patients had worse overall survival than low-risk individuals. Significant differences were found in tumor staging, immune cell infiltration degree, frequency of tumor mutations, tumor mutation burden (TMB), and immune checkpoint gene expressions between high- vs. low-risk patients. Further, high-risk patients exhibited high predicted IC50 for paclitaxel, cisplatin, doxorubicin, and erlotinib compared to low-risk patients. The seven-IRG-based signature can independently and accurately predict overall survival and tumor progression, characterize the tumor immune microenvironment (TIME) and estimate ICG expressions and IC50 for antitumor therapies. It shows the potential of guiding personalized treatment for EC patients.
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Affiliation(s)
- Yan Xie
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Ruimin Fu
- College of Health Management, Henan Finance University, Zhengzhou, China
| | - Zheng Xiao
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Gang Li
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
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Weighted correlation network analysis revealed novel long non-coding RNAs for colorectal cancer. Sci Rep 2022; 12:2990. [PMID: 35194111 PMCID: PMC8863977 DOI: 10.1038/s41598-022-06934-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/07/2022] [Indexed: 12/25/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers worldwide, which after breast, lung and, prostate cancers, is the fourth prevalent cancer in the United States. Long non-coding RNAs (lncRNAs) have an essential role in the pathogenesis of CRC. Therefore, bioinformatics studies on lncRNAs and their target genes have potential importance as novel biomarkers. In the current study, publicly available microarray gene expression data of colorectal cancer (GSE106582) was analyzed with the Limma, Geoquery, Biobase package. Afterward, identified differentially expressed lncRNAs and their target genes were inserted into Weighted correlation network analysis (WGCNA) to obtain modules and hub genes. A total of nine differentially expressed lncRNAs (LINC01018, ITCH-IT, ITPK1-AS1, FOXP1-IT1, FAM238B, PAXIP1-AS1, ATP2B1-AS1, MIR29B2CHG, and SNHG32) were identified using microarray data analysis. The WGCNA has identified several hub genes for black (LMOD3, CDKN2AIPNL, EXO5, ZNF69, BMS1P5, METTL21A, IL17RD, MIGA1, CEP19, FKBP14), blue (CLCA1, GUCA2A, UGT2B17, DSC2, CA1, AQP8, ITLN1, BEST4, KLF4, IQCF6) and turquoise (PAFAH1B1, LMNB1, CACYBP, GLO1, PUM3, POC1A, ASF1B, SDCCAG3, ASNS, PDCD2L) modules. The findings of the current study will help to improve our understanding of CRC. Moreover, the hub genes that we have identified could be considered as possible prognostic/diagnostic biomarkers. This study led to the determination of nine lncRNAs with no previous association with CRC development.
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7
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Wang N, Wang Y, Wang H, Luo N, Yang W, Zhao Z. Knockout of Calcyclin Binding Protein Impedes the Growth of Breast Cancer Cells by Regulating Cell Apoptosis and β-Catenin Signaling. DNA Cell Biol 2021; 40:1317-1324. [PMID: 34591648 DOI: 10.1089/dna.2021.0315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Breast invasive carcinoma (BRCA) is becoming the most common malignant disease worldwide, and there is intense interest in identifying diagnostic biomarkers that can be targeted for treatment of BRCA. Recent evidence has shown that calcyclin binding protein (CacyBP) can function as either a tumor promoter or suppressor during carcinogenesis. Data in The Cancer Genome Atlas (TCGA) database show that CacyBP is overexpressed in human BRCA tissues, and high levels of CacyBP are associated with shorter overall survival. Immunohistochemical staining has shown that CacyBP levels are high in cancer tissue samples and associated with a higher likelihood of disease progression. We, therefore, conducted a knockout assay to determine the role of CacyBP in the development of BRCA. Knockout of CacyBP significantly inhibited MCF7 cell proliferation and colony formation. Apoptosis was higher in CacyBP knockout cells compared with control cells. Microarray analysis showed that the CacyBP knockout caused dysregulation of numerous genes closely related to β-catenin signaling, whereas quantitative reverse-transcription PCR and immunoblotting showed that it to be inactivated. In summary, we conclude that when overexpressed, CacyBP acts as a potential oncogene for BRCA by regulating β-catenin signaling.
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Affiliation(s)
- Ningju Wang
- The Second Department of Medicine Oncology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Yan Wang
- The First Department of Medicine Oncology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Huifeng Wang
- The First Department of Medicine Oncology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Na Luo
- The Second Department of Medicine Oncology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Wenjing Yang
- The Second Department of Medicine Oncology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Zhijun Zhao
- Clinical Laboratory Center, General Hospital of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, General Hospital of Ningxia Medical University, Yinchuan, China
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Zhou X, Dou Q, Fan G, Zhang Q, Sanderford M, Kaya A, Johnson J, Karlsson EK, Tian X, Mikhalchenko A, Kumar S, Seluanov A, Zhang ZD, Gorbunova V, Liu X, Gladyshev VN. Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity. Cell Rep 2021; 32:107949. [PMID: 32726638 DOI: 10.1016/j.celrep.2020.107949] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 02/20/2020] [Accepted: 07/02/2020] [Indexed: 11/29/2022] Open
Abstract
Long-lived rodents have become an attractive model for the studies on aging. To understand evolutionary paths to long life, we prepare chromosome-level genome assemblies of the two longest-lived rodents, Canadian beaver (Castor canadensis) and naked mole rat (NMR, Heterocephalus glaber), which were scaffolded with in vitro proximity ligation and chromosome conformation capture data and complemented with long-read sequencing. Our comparative genomic analyses reveal that amino acid substitutions at "disease-causing" sites are widespread in the rodent genomes and that identical substitutions in long-lived rodents are associated with common adaptive phenotypes, e.g., enhanced resistance to DNA damage and cellular stress. By employing a newly developed substitution model and likelihood ratio test, we find that energy and fatty acid metabolism pathways are enriched for signals of positive selection in both long-lived rodents. Thus, the high-quality genome resource of long-lived rodents can assist in the discovery of genetic factors that control longevity and adaptive evolution.
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Affiliation(s)
- Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA
| | - Qianhui Dou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Quanwei Zhang
- Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Maxwell Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Alaattin Kaya
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA; Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
| | - Jeremy Johnson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA
| | - Elinor K Karlsson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA; University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Xiao Tian
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Medicine, University of Rochester, Rochester, NY 14627, USA
| | - Aleksei Mikhalchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Medicine, University of Rochester, Rochester, NY 14627, USA
| | | | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Medicine, University of Rochester, Rochester, NY 14627, USA
| | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA.
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Zhang Z, Chen C, Fang Y, Li S, Wang X, Sun L, Zhou G, Ye J. Development of a prognostic signature for esophageal cancer based on nine immune related genes. BMC Cancer 2021; 21:113. [PMID: 33541291 PMCID: PMC7860013 DOI: 10.1186/s12885-021-07813-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/17/2021] [Indexed: 12/11/2022] Open
Abstract
Background Function of the immune system is correlated with the prognosis of the tumor. The effect of immune microenvironment on esophageal cancer (EC) development has not been fully investigated. Methods This study aimed to explore a prognostic model based on immune-related genes (IRGs) for EC. We obtained the RNA-seq dataset and clinical information of EC from the Cancer Genome Atlas (TCGA). Results We identified 247 upregulated IRGs and 56 downregulated IRGs. Pathway analysis revealed that the most differentially expressed IRGs were enriched in Cytokine-cytokine receptor interaction. We further screened 13 survival-related IRGs and constructed regulatory networks involving related transcription factors (TFs). Finally, a prognostic model was constructed with 9 IRGs (HSPA6, S100A12, CACYBP, NOS2, DKK1, OSM, STC2, NGPTL3 and NR2F2) by multivariate Cox regression analysis. The patients were classified into two subgroups with different outcomes. When adjusted with clinical factors, this model was verified as an independent predictor, which performed accurately in prognostic prediction. Next, M0 and M2 macrophages and activated mast cells were significantly enriched in high-risk group, while CD8 T cells and regulatory T cells (Tregs) were significantly enriched in low-risk group. Conclusions Prognosis related IRGs were identified and a prognostic signature for esophageal cancer based on nine IRGs was developed. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-07813-9.
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Affiliation(s)
- Zhi Zhang
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, 42 Bai Zi Ting Road, Nanjing, 210000, Jiangsu, China
| | - Cheng Chen
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, 42 Bai Zi Ting Road, Nanjing, 210000, Jiangsu, China
| | - Ying Fang
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, 42 Bai Zi Ting Road, Nanjing, 210000, Jiangsu, China
| | - Sheng Li
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, 42 Bai Zi Ting Road, Nanjing, 210000, Jiangsu, China
| | - Xiaohua Wang
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, 42 Bai Zi Ting Road, Nanjing, 210000, Jiangsu, China
| | - Lei Sun
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, 42 Bai Zi Ting Road, Nanjing, 210000, Jiangsu, China
| | - Guoren Zhou
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, 42 Bai Zi Ting Road, Nanjing, 210000, Jiangsu, China.
| | - Jinjun Ye
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, 42 Bai Zi Ting Road, Nanjing, 210000, Jiangsu, China.
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10
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Zhao M, Zhang RZ, Qi DW, Chen HY, Zhang GC. CacyBP/SIP promotes tumor progression by regulating apoptosis and arresting the cell cycle in osteosarcoma. Exp Ther Med 2020; 20:1397-1404. [PMID: 32742374 PMCID: PMC7388306 DOI: 10.3892/etm.2020.8843] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/21/2020] [Indexed: 12/30/2022] Open
Abstract
Osteosarcoma (OS) is the most common primary malignant bone tumor in pediatric and adolescent patients. The calcyclin-binding protein/Siah-1-interacting protein (CacyBP/SIP) performs an essential function in cell proliferation and apoptosis. The present study investigated the effect of CacyBP/SIP in OS cell proliferation and apoptosis. CacyBP/SIP mRNA expression levels were evaluated in four OS cell lines by quantitative PCR. CacyBP/SIP expression was downregulated in Saos-2 cells using a lentivirus transfection system and the transfection efficiency was analyzed. The effects of CacyBP/SIP downregulation on Saos-2 cell proliferation and colony-formation ability were evaluated by MTT and colony-formation assays. The effect of CacyBP/SIP knockdown on Saos-2 cell cycle and apoptosis was analyzed by flow cytometry cell sorting. The Cancer Genome Atlas (TCGA) data was analyzed for validation. Human OS cell lines Saos-2, MG-63, HOS and U20S expressed CacyBP/SIP mRNA. CacyBP/SIP knockdown significantly inhibited cell proliferation and colony-formation ability. G1/S phase arrest was induced by CacyBP/SIP downregulation, which also resulted in the downregulation of CDK and cyclins and the upregulation of p21. In addition, CacyBP/SIP downregulation induced Saos-2 cell apoptosis mediated by Bax and Bcl-2. High expression of CacyBP/SIP was significantly associated with poor prognosis in TCGA sarcoma database. Thus, CacyBP/SIP performs important functions in the proliferation and apoptosis of human OS cells.
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Affiliation(s)
- Ming Zhao
- Department of Musculoskeletal Tumors, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Run-Zi Zhang
- Department of Musculoskeletal Tumors, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Dian-Wen Qi
- Department of Musculoskeletal Tumors, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Hong-Yi Chen
- Department of Musculoskeletal Tumors, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Guo-Chuan Zhang
- Department of Musculoskeletal Tumors, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
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Bi J, Huang Y, Liu Y. Effect of NOP2 knockdown on colon cancer cell proliferation, migration, and invasion. Transl Cancer Res 2019; 8:2274-2283. [PMID: 35116980 PMCID: PMC8799236 DOI: 10.21037/tcr.2019.09.46] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 09/18/2019] [Indexed: 12/23/2022]
Abstract
Background Proliferation-associated nucleolar protein p120 (NOP2) has been proven to be a promising tumor cell maker, but it has not been specifically studied in colon cancer. This study aims to investigate the role and action mechanism of NOP2 in colon cancer. Methods Fluorescence quantitative PCR and western blot assays were used to evaluate the expression of NOP2. NOP2 siRNA was transfected into HCT116, LOVO, and CCK-8 cells, and transwell assays were performed to evaluate the cell proliferation, migration, and invasion. Transcriptome sequencing of both the NOP2 knockdown and negative control (NC) groups was performed. Results NOP2 expression is significantly upregulated in colon cancer tissues and cells compared with that in the healthy controls. The proliferation, migration, and invasion of the colon cancer cells were significantly suppressed in the NOP2 knockdown group compared with those in the NC group (P<0.05). Transcriptome sequencing showed that ASMTL and C6orf52 were significantly downregulated, while MUC19, TXK, APOBEC2, and RBM44 were upregulated in both of the two NOP2 silenced colon cancer cells relative to those in the control. Gene Ontology (GO) analysis showed that NOP2 knockdown mainly induced differential expression of the genes involved in positive regulation of T cell-mediated cytotoxicity and thiamine metabolism. Kyoto Encyclopedia of Genes and Genomes analysis showed that the gene pathways most significantly affected by NOP2 knockdown were Cytokine-cytokine receptor interaction, Type I diabetes mellitus, Taste transduction, and Systemic lupus erythematosus. Conclusions NOP2 promotes proliferation, migration, and invasion of colon cancer cells, and the underlying mechanisms may be related to TXK tyrosine kinase.
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Affiliation(s)
- Jinling Bi
- Department of Oncology, the Second Affiliated Hospital of Soochow University, Suzhou 215004, China.,Department of Oncology, the Second People's Hospital of Hefei, Hefei 230011, China
| | - Yong Huang
- Department of Oncology, the Second People's Hospital of Hefei, Hefei 230011, China
| | - Yulong Liu
- Department of Oncology, the Second Affiliated Hospital of Soochow University, Suzhou 215004, China
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Xuan C, Gao Y, Jin M, Xu S, Wang L, Wang Y, Han R, Shi K, Chen X, An Q. Bioinformatic analysis of Cacybp-associated proteins using human glioma databases. IUBMB Life 2019; 71:827-834. [PMID: 30762928 DOI: 10.1002/iub.1999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022]
Abstract
The ubiquitin-proteasome system is the primary cellular pathway for protein degradation, mediating 80% of intracellular protein degradation. Because of the widespread presence of ubiquitin-modified protein substrates, ubiquitination can regulate a variety of cellular activities including cell proliferation, apoptosis, autophagy, endocytosis, DNA damage repair, and immune responses. With the continuous generation of genomics data in recent years it has become particularly important to analyze these data effectively and reasonably. Cacybp forms a complex with the E3 ubiquitinated ligase Siah1 to participate in ubiquitination. We analyzed Cacybp-associated genes using the Gene Expression Omnibus (GEO) and CGGA (Chinese Glioma Genome Atlas) databases and identified 121 differentially expressed genes (DEGs), of which 46 were downregulated and 75 were upregulated. The biological processes, molecular functions, and protein-protein interaction (PPI) network of differential genes were analyzed by Cytoscape software and STRING software. We found no difference in Cacybp expression among different grades of gliomas and there was no significant association between the expression level of Cacybp and the prognosis of patients with glioma in LGG and GBM. © 2019 IUBMB Life, 1-8, 2019.
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Affiliation(s)
- Chengmin Xuan
- Department of Hematology, Xuzhou Children's Hospital of Xuzhou Medical University, Xuzhou, Jiangsu
| | - Yong Gao
- Department of Orthopaedics, Xuzhou Children's Hospital of Xuzhou Medical University, Xuzhou, Jiangsu
| | - Mingwei Jin
- Department of Hematology, Xuzhou Children's Hospital of Xuzhou Medical University, Xuzhou, Jiangsu
| | - Shumei Xu
- Department of Hematology, Xuzhou Children's Hospital of Xuzhou Medical University, Xuzhou, Jiangsu
| | - Lei Wang
- Department of Hematology, Xuzhou Children's Hospital of Xuzhou Medical University, Xuzhou, Jiangsu
| | - Yuan Wang
- Department of Hematology, Xuzhou Children's Hospital of Xuzhou Medical University, Xuzhou, Jiangsu
| | - Rui Han
- Department of Hematology, Xuzhou Children's Hospital of Xuzhou Medical University, Xuzhou, Jiangsu
| | - Kunpeng Shi
- Department of Hematology, Xuzhou Children's Hospital of Xuzhou Medical University, Xuzhou, Jiangsu
| | - Xincheng Chen
- Department of Neurosurgery, Xinyi People's Hospital, Xinyi, Jiangsu, People's Republic of China
| | - Qi An
- Department of Hematology, Xuzhou Children's Hospital of Xuzhou Medical University, Xuzhou, Jiangsu
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13
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Feng S, Zhou Q, Yang B, Li Q, Liu A, Zhao Y, Qiu C, Ge J, Zhai H. The effect of S100A6 on nuclear translocation of CacyBP/SIP in colon cancer cells. PLoS One 2018. [PMID: 29534068 PMCID: PMC5849316 DOI: 10.1371/journal.pone.0192208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Calcyclin Binding Protein/(Siah-1 interacting protein) (CacyBP/SIP) acts as an oncogene in colorectal cancer. The nuclear accumulation of CacyBP/SIP has been linked to the proliferation of cancer cells. It has been reported that intracellular Ca2+ induces the nuclear translocation of CacyBP/SIP. However, the molecular mechanism of CacyBP/SIP nuclear translocation has yet to be elucidated. The purpose of this study was to test whether the Ca2+-dependent binding partner S100 protein is involved in CacyBP/SIP nuclear translocation in colon cancer SW480 cells. METHODS The subcellular localization of endogenous CacyBP/SIP was observed following the stimulation of ionomycin or BAPTA/AM by immunofluorescence staining in SW480 cells. S100A6 small interfering RNAs (siRNA) were transfected into SW480 cells. Immunoprecipitation assays detected whether S100 protein is relevant to the nuclear translocation of CacyBP/SIP in response to changes in [Ca2+]i. RESULTS We observed that endogenous CacyBP/SIP is translocated from the cytosol to the nucleus following the elevation of [Ca2+]i by ionomycin in SW480 cells. Co-immunoprecipitation experiments showed that the interaction between S100A6 and CacyBP/SIP was increased simultaneously with elevated Ca2+. Knockdown of S100A6 abolished the Ca2+ effect on the subcellular translocation of CacyBP/SIP. CONCLUSION Thus, we demonstrated that S100A6 is required for the Ca2+-dependent nuclear translocation of CacyBP/SIP in colon cancer SW480 cells.
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Affiliation(s)
- Shanshan Feng
- Surgery Laboratory, General Hospital of Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China
| | - Qiaozhi Zhou
- Department of Gastroenterology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing, China
| | - Bo Yang
- Department of Gastroenterology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing, China
| | - Qianqian Li
- Department of Gastroenterology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing, China
| | - Aiqin Liu
- Department of Gastroenterology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yingying Zhao
- Department of Gastroenterology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing, China
| | - Changqing Qiu
- Department of Gastroenterology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing, China
| | - Jun Ge
- Department of Gastroenterology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing, China
| | - Huihong Zhai
- Department of Gastroenterology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing, China
- Beijing Key Laboratory for Precancerous Lesion of Digestive Diseases, Beijing, China
- National Clinical Research Center for Digestive Diseases, Beijing, China
- * E-mail:
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Zhang X, Cha IH, Kim KY. Highly preserved consensus gene modules in human papilloma virus 16 positive cervical cancer and head and neck cancers. Oncotarget 2017; 8:114031-114040. [PMID: 29371966 PMCID: PMC5768383 DOI: 10.18632/oncotarget.23116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/15/2017] [Indexed: 11/25/2022] Open
Abstract
In this study, we investigated the consensus gene modules in head and neck cancer (HNC) and cervical cancer (CC). We used a publicly available gene expression dataset, GSE6791, which included 42 HNC, 14 normal head and neck, 20 CC and 8 normal cervical tissue samples. To exclude bias because of different human papilloma virus (HPV) types, we analyzed HPV16-positive samples only. We identified 3824 genes common to HNC and CC samples. Among these, 977 genes showed high connectivity and were used to construct consensus modules. We demonstrated eight consensus gene modules for HNC and CC using the dissimilarity measure and average linkage hierarchical clustering methods. These consensus modules included genes with significant biological functions, including ATP binding and extracellular exosome. Eigengen network analysis revealed the consensus modules were highly preserved with high connectivity. These findings demonstrate that HPV16-positive head and neck and cervical cancers share highly preserved consensus gene modules with common potentially therapeutic targets.
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Affiliation(s)
- Xianglan Zhang
- Department of Pathology, Yanbian University Medical College, Yanji City, Jilin Province, China.,Oral Cancer Research Institute, College of Dentistry, Yonsei University, Seoul, Korea
| | - In-Ho Cha
- Oral Cancer Research Institute, College of Dentistry, Yonsei University, Seoul, Korea.,Department of Oral and Maxillofacial Surgery, College of Dentistry, Yonsei University, Seoul, Korea
| | - Ki-Yeol Kim
- Dental Education Research Center, BK21 PLUS Project, College of Dentistry, Yonsei University, Seoul, Korea
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Kądziołka B, Dębski KJ, Bieganowski P, Leśniak W, Filipek A. Transcriptional regulation of CacyBP/SIP gene and the influence of increased CacyBP/SIP level on gene expression pattern in colorectal cancer HCT116 cells. IUBMB Life 2017; 70:50-59. [PMID: 29197151 DOI: 10.1002/iub.1698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/13/2017] [Indexed: 11/09/2022]
Abstract
The CacyBP/SIP protein is expressed at a particularly high level in brain, spleen, and various tumors. In this work, we have studied transcriptional regulation of the CacyBP/SIP gene and the influence of increased CacyBP/SIP level on gene expression in colorectal cancer HCT116 cells. We have shown that E2F1, EGR1, and CREB transcription factors bind to the CacyBP/SIP gene promoter and stimulate transcription of CacyBP/SIP gene. The role of CREB was further confirmed by the observation that forskolin, a strong activator of CREB phosphorylation/activity, increased CacyBP/SIP gene promoter activity. Moreover, we have shown that CREB dominant negative mutants, CREB133 and KCREB, inhibits CacyBP/SIP promoter activity. To check the biological significance of increased CacyBP/SIP expression/level we have applied RNA microarray analysis and have found that upregulation of CacyBP/SIP entails changes in mRNA level of many genes involved, among others, in immune processes. © 2017 IUBMB Life, 70(1):50-59, 2018.
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Affiliation(s)
- Beata Kądziołka
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Konrad J Dębski
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Bieganowski
- Department of Experimental Pharmacology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Wiesława Leśniak
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Filipek
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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