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Wang W, Zhang J, Wang Y, Xu Y, Zhang S. Identifies microtubule-binding protein CSPP1 as a novel cancer biomarker associated with ferroptosis and tumor microenvironment. Comput Struct Biotechnol J 2022; 20:3322-3335. [PMID: 35832625 PMCID: PMC9253833 DOI: 10.1016/j.csbj.2022.06.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 12/02/2022] Open
Abstract
Centrosome and spindle pole-associated protein (CSPP1) is a centrosome and microtubule-binding protein that plays a role in cell cycle-dependent cytoskeleton organization and cilia formation. Previous studies have suggested that CSPP1 plays a role in tumorigenesis; however, no pan-cancer analysis has been performed. This study systematically investigates the expression of CSPP1 and its potential clinical outcomes associated with diagnosis, prognosis, and therapy. CSPP1 is widely present in tissues and cells and its aberrant expression serves as a diagnostic biomarker for cancer. CSPP1 dysregulation is driven by multi-dimensional mechanisms involving genetic alterations, DNA methylation, and miRNAs. Phosphorylation of CSPP1 at specific sites may play a role in tumorigenesis. In addition, CSPP1 correlates with clinical features and outcomes in multiple cancers. Take brain low-grade gliomas (LGG) with a poor prognosis as an example, functional enrichment analysis implies that CSPP1 may play a role in ferroptosis and tumor microenvironment (TME), including regulating epithelial-mesenchymal transition, stromal response, and immune response. Further analysis confirms that CSPP1 dysregulates ferroptosis in LGG and other cancers, making it possible for ferroptosis-based drugs to be used in the treatment of these cancers. Importantly, CSPP1-associated tumors are infiltrated in different TMEs, rendering immune checkpoint blockade therapy beneficial for these cancer patients. Our study is the first to demonstrate that CSPP1 is a potential diagnostic and prognostic biomarker associated with ferroptosis and TME, providing a new target for drug therapy and immunotherapy in specific cancers.
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Key Words
- ACC, adrenocortical carcinoma
- BP, biological pathways
- BRCA, breast invasive carcinoma
- Biomarker
- C-index, concordance index
- CAF, cancer-associated fibroblasts
- CC, cellular component
- CESC, cervical squamous cell carcinoma and endocervical adenocarcinoma
- CHOL, cholangiocarcinoma
- CNA, copy number alteration
- COAD, colon adenocarcinoma
- CPTAC, Clinical Proteomic Tumor Analysis Consortium
- CSPP1
- CSPP1, centrosome and spindle pole-associated protein
- CTL, cytotoxic T lymphocyte
- DEGs, differentially expressed genes
- DLBC, diffuse large B-cell lymphoma
- DSS, disease-specific survival
- EMT, epithelial-mesenchymal transition
- ENCORI, Encyclopedia of RNA Interactomes
- ESCA, esophageal carcinoma
- FAG, ferroptosis-associated gene
- FDG, ferroptosis-driver gene
- FSG, ferroptosis-suppressor gene
- Ferroptosis
- GBM, glioblastoma multiforme
- GO, Gene Ontology
- GSEA, Gene Set Enrichment Analysis
- GSVA, gene set variation analysis
- GTEx, Genotype-Tissue Expression
- HNSC, head and neck squamous cell carcinoma
- ICB, immune checkpoint blockade
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- KICH, kidney chromophobe
- KIRC, renal clear cell carcinoma
- KM, Kaplan-Meier
- LAML, acute myeloid leukemia
- LGG, low-grade gliomas
- LIHC, liver hepatocellular carcinoma
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- MF, molecular functions
- MHC, major histocompatibility complex
- MSI, microsatellite instability
- OS, overall survival
- OV, ovarian serous cystadenocarcinoma
- PAAD, pancreatic adenocarcinoma
- PFI, progression-free interval
- PFS, progression-free survival
- PRAD, prostate cancer
- Pan-cancer
- READ, rectum adenocarcinoma
- ROC, receiver operating characteristics
- SKCM, skin cutaneous melanoma
- TCGA, The Cancer Genome Atlas
- TGCT, testicular germ cell tumors, STAD, stomach adenocarcinoma
- THCA, thyroid cancer
- THYM, thymoma
- TIDE, Tumor Immune Dysfunction and Exclusion
- TIMER, Tumor Immune Estimation Resource
- TISIDB, Tumor-Immune System Interactions DataBase
- TMB, tumor mutation burden
- TME, tumor microenvironment
- Tumor microenvironment
- UCEC, endometrial cancer uterine corpus endometrial carcinoma
- UCS, uterine carcinosarcoma
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Affiliation(s)
- Wenwen Wang
- Translational Medicine Research Center, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Cancer Center, Zhejiang University, Hangzhou, China
| | - Jingjing Zhang
- Translational Medicine Research Center, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Cancer Center, Zhejiang University, Hangzhou, China
| | - Yuqing Wang
- Translational Medicine Research Center, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Cancer Center, Zhejiang University, Hangzhou, China
| | - Yasi Xu
- Translational Medicine Research Center, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Cancer Center, Zhejiang University, Hangzhou, China
| | - Shirong Zhang
- Translational Medicine Research Center, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Cancer Center, Zhejiang University, Hangzhou, China
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Johnson K, Leary PJ, Govaere O, Barter MJ, Charlton SH, Cockell SJ, Tiniakos D, Zatorska M, Bedossa P, Brosnan MJ, Cobbold JF, Ekstedt M, Aithal GP, Clément K, Schattenberg JM, Boursier J, Ratziu V, Bugianesi E, Anstee QM, Daly AK. Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: Diagnostic and mechanistic relevance. JHEP Rep 2022; 4:100409. [PMID: 35072021 PMCID: PMC8762473 DOI: 10.1016/j.jhepr.2021.100409] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/08/2021] [Accepted: 11/09/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND & AIMS Serum microRNA (miRNA) levels are known to change in non-alcoholic fatty liver disease (NAFLD) and may serve as useful biomarkers. This study aimed to profile miRNAs comprehensively at all NAFLD stages. METHODS We profiled 2,083 serum miRNAs in a discovery cohort (183 cases with NAFLD representing the complete NAFLD spectrum and 10 population controls). miRNA libraries generated by HTG EdgeSeq were sequenced by Illumina NextSeq. Selected serum miRNAs were profiled in 372 additional cases with NAFLD and 15 population controls by quantitative reverse transcriptase PCR. RESULTS Levels of 275 miRNAs differed between cases and population controls. Fewer differences were seen within individual NAFLD stages, but miR-193a-5p consistently showed increased levels in all comparisons. Relative to NAFL/non-alcoholic steatohepatitis (NASH) with mild fibrosis (stage 0/1), 3 miRNAs (miR-193a-5p, miR-378d, and miR378d) were increased in cases with NASH and clinically significant fibrosis (stages 2-4), 7 (miR193a-5p, miR-378d, miR-378e, miR-320b, miR-320c, miR-320d, and miR-320e) increased in cases with NAFLD activity score (NAS) 5-8 compared with lower NAS, and 3 (miR-193a-5p, miR-378d, and miR-378e) increased but 1 (miR-19b-3p) decreased in steatosis, activity, and fibrosis (SAF) activity score 2-4 compared with lower SAF activity. The significant findings for miR-193a-5p were replicated in the additional cohort with NAFLD. Studies in Hep G2 cells showed that following palmitic acid treatment, miR-193a-5p expression decreased significantly. Gene targets for miR-193a-5p were investigated in liver RNAseq data for a case subgroup (n = 80); liver GPX8 levels correlated positively with serum miR-193a-5p. CONCLUSIONS Serum miR-193a-5p levels correlate strongly with NAFLD activity grade and fibrosis stage. MiR-193a-5p may have a role in the hepatic response to oxidative stress and is a potential clinically tractable circulating biomarker for progressive NAFLD. LAY SUMMARY MicroRNAs (miRNAs) are small pieces of nucleic acid that may turn expression of genes on or off. These molecules can be detected in the blood circulation, and their levels in blood may change in liver disease including non-alcoholic fatty liver disease (NAFLD). To see if we could detect specific miRNA associated with advanced stages of NAFLD, we carried out miRNA sequencing in a group of 183 patients with NAFLD of varying severity together with 10 population controls. We found that a number of miRNAs showed changes, mainly increases, in serum levels but that 1 particular miRNA miR-193a-5p consistently increased. We confirmed this increase in a second group of cases with NAFLD. Measuring this miRNA in a blood sample may be a useful way to determine whether a patient has advanced NAFLD without an invasive liver biopsy.
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Key Words
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- AUROC, area under the receiver operating characteristic
- Biomarker
- CPM, counts per million
- Ct, cycle threshold
- ER, endoplasmic reticulum
- FC, fold change
- FIB-4, fibrosis-4
- FLIP, fatty liver inhibition of progression
- GTEx, Genotype-Tissue Expression
- MicroRNA
- NAFL, non-alcoholic fatty liver
- NAFLD, non-alcoholic fatty liver disease
- NAS, NAFLD activity score
- NASH, non-alcoholic steatohepatitis
- Non-alcoholic fatty liver disease
- PCA, principal component analysis
- SAF, steatosis–activity–fibrosis
- Sequencing
- TGF-β, transforming growth factor-beta
- cDNA, complementary DNA
- logFC, log2 fold change
- miRNA, microRNA
- qPCR, quantitative PCR
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Affiliation(s)
- Katherine Johnson
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Peter J. Leary
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Olivier Govaere
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew J. Barter
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Sarah H. Charlton
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Simon J. Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Dina Tiniakos
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Michalina Zatorska
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Pierre Bedossa
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M. Julia Brosnan
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA
| | - Jeremy F. Cobbold
- Oxford Liver Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Mattias Ekstedt
- Division of Diagnostics and Specialist Medicine, Department of Health, Medicine, and Caring Sciences, Linköping University, Linköping, Sweden
| | - Guruprasad P. Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Karine Clément
- Institute of Cardiometabolism and Nutrition, Pitié Salpêtrière Hospital, Paris, France
- Assistance Publique – Hopitaux de Paris, Paris, France
| | - Jörn M. Schattenberg
- Metabolic Liver Research Program, I. Department of Medicine, University Medical Center of Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Jerome Boursier
- Hepatology Department, Angers University Hospital, Angers, France
| | - Vlad Ratziu
- Institute of Cardiometabolism and Nutrition, Pitié Salpêtrière Hospital, Paris, France
- Assistance Publique – Hopitaux de Paris, Paris, France
| | - Elisabetta Bugianesi
- Division of Gastroenterology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Quentin M. Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - Ann K. Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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Ahmetaj-Shala B, Vaja R, Atanur SS, George PM, Kirkby NS, Mitchell JA. Cardiorenal Tissues Express SARS-CoV-2 Entry Genes and Basigin (BSG/CD147) Increases With Age in Endothelial Cells. JACC Basic Transl Sci 2020; 5:1111-1123. [PMID: 33073064 PMCID: PMC7546186 DOI: 10.1016/j.jacbts.2020.09.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
Vascular and cardiovascular inflammation and thrombosis occur in patients with severe coronavirus disease-2019 (COVID-19). Advancing age is the most significant risk factor for severe COVID-19. Using transcriptomic databases, the authors found that: 1) cardiovascular tissues and endothelial cells express putative genes for severe acute respiratory syndrome coronavirus-2 infection, including angiotensin-converting enzyme 2 (ACE2) and basigin (BSG); 2) severe acute respiratory syndrome coronavirus-2 receptor pathways ACE2/transmembrane serine protease 2 and BSG/peptidylprolyl isomerase B(A) polarize to lung/epithelium and vessel/endothelium, respectively; 3) expression of host genes is relatively stable with age; and 4) notable exceptions are ACE2, which decreases with age in some tissues, and BSG, which increases with age in endothelial cells, suggesting that BSG expression in the vasculature may explain the heightened risk for severe disease with age.
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Key Words
- ACE2, angiotensin converting enzyme 2
- ADAM17, ADAM metallopeptidase domain 17
- BSG, basigin
- COVID-19
- COVID-19, coronavirus disease-2019
- CTSB, cathepsin B
- CTSL, cathepsin L
- GTEx, Genotype-Tissue Expression
- PBMC, peripheral blood mononuclear cells
- PPIA, peptidylprolyl isomerase A
- PPIB, peptidylprolyl isomerase B
- SARS-CoV-2, severe acute respiratory syndrome-coronavirus-2
- TMPRSS2, transmembrane serine protease 2
- age
- cardiovascular
- endothelial cells
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Affiliation(s)
- Blerina Ahmetaj-Shala
- Cardiorespiratory Interface, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Ricky Vaja
- Cardiorespiratory Interface, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Santosh S. Atanur
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
- Institute of Translational Medicine and Therapeutics, Data Science Group, National Institute for Health Research, Biomedical Research Centre, Imperial College London, London, United Kingdom
| | - Peter M. George
- Cardiorespiratory Interface, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Interstitial Lung Disease Unit, National Heart and Lung Institute, Imperial College London, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Nicholas S. Kirkby
- Cardiorespiratory Interface, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jane A. Mitchell
- Cardiorespiratory Interface, National Heart and Lung Institute, Imperial College London, London, United Kingdom
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