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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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Lin BB, Lei HQ, Xiong HY, Fu X, Shi F, Yang XW, Yang YF, Liao GL, Feng YP, Jiang DG, Pang J. MicroRNA-regulated transcriptome analysis identifies four major subtypes with prognostic and therapeutic implications in prostate cancer. Comput Struct Biotechnol J 2021; 19:4941-4953. [PMID: 34527198 PMCID: PMC8433071 DOI: 10.1016/j.csbj.2021.08.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/17/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
MicroRNA (miRNA) deregulation plays a critical role in the heterogeneous development of prostate cancer (PCa) by tuning mRNA levels. Herein, we aimed to characterize the molecular features of PCa by clustering the miRNA-regulated transcriptome with non-negative matrix factorization. Using 478 PCa samples from The Cancer Genome Atlas, four molecular subtypes (S-I, S-II, S-III, and S-IV) were identified and validated in two merged microarray and RNAseq datasets with 656 and 252 samples, respectively. Interestingly, the four subtypes showed distinct clinical and biological features after comprehensive analyses of clinical features, multiomic profiles, immune infiltration, and drug sensitivity. S-I is basal/stem/mesenchymal-like and immune-excluded with marked transforming growth factor β, epithelial-mesenchymal transition and hypoxia signals, increased sensitivity to olaparib, and intermediate prognosis. S-II is luminal/metabolism-active and responsive to androgen deprivation therapy with frequent TMPRSS2-ERG fusion and a good prognosis. S-III is characterized by moderate proliferative and metabolic activity, sensitivity to taxane-based chemotherapy, and intermediate prognosis. S-IV is highly proliferative with moderate EMT and stemness, frequent deletions of TP53, PTEN and RB, and the poorest prognosis; it is also immune-inflamed and sensitive to anti-PD-L1 therapy. Overall, based on miRNA-regulated gene profiles, this study identified four distinct PCa subtypes that could improve risk stratification at diagnosis and provide therapeutic guidance.
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Key Words
- ADT, androgen deprivation therapy
- AR, androgen receptor
- AUC, Area under the dose-response curve
- BCR, biochemical recurrence
- CAFs, cancer-associated fibroblasts
- CCLs, cancer cell lines
- CTLA-4, cytotoxic T-lymphocyte associated protein-4
- DEmiRs, differentially expressed miRNAs
- DFS, disease-free survival
- EMT, epithelial-mesenchymal transition
- FDR, false discovery rate
- GEO, Gene Expression Omnibus
- GEP, gene expression profile
- GO, Gene Ontology
- GSEA, Gene Set Enrichment Analysis
- Heterogeneity
- ICB, immune checkpoint blockade
- IFN, interferon
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MDSCs, myeloid-derived suppressor cells
- MIRcor, miRNA-correlated
- Molecular subtypes
- NEPC, neuroendocrine prostate cancer
- NMF, non-negative matrix factorization
- NTP, Nearest template prediction
- OS, overall survival
- PCa, prostate cancer
- PD-1, programmed cell death protein-1
- PD-L1, programmed death-ligand 1
- Prostate cancer
- SCNAs, somatic copy number alterations
- SubMap, Subclass mapping
- TCGA, The Cancer Genome Atlas
- TGFβ, transforming growth factor β
- TMB, tumor mutation burden
- TNAs, tumor neoantigens
- Tregs, regulatory T cells
- k-NN, K-nearest neighbor
- mCRPC, metastatic castration-resistant prostate cancer
- miRNAs
- miRNAs, microRNAs
- ssGSEA, single-sample gene set enrichment analysis
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Affiliation(s)
- Bing-Biao Lin
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Han-Qi Lei
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Hai-Yun Xiong
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Xing Fu
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, Guangdong 518055, China
| | - Fu Shi
- Department of Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518000, China
| | - Xiang-Wei Yang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Ya-Fei Yang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Guo-Long Liao
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Yu-Peng Feng
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Dong-Gen Jiang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Jun Pang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518000, China
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Liu Q, Nie R, Li M, Li L, Zhou H, Lu H, Wang X. Identification of subtypes correlated with tumor immunity and immunotherapy in cutaneous melanoma. Comput Struct Biotechnol J 2021; 19:4472-4485. [PMID: 34471493 PMCID: PMC8379294 DOI: 10.1016/j.csbj.2021.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 02/25/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 01/15/2023] Open
Abstract
Because immune checkpoint inhibitors (ICIs) are effective for a subset of melanoma patients, identification of melanoma subtypes responsive to ICIs is crucial. We performed clustering analyses to identify immune subtypes of melanoma based on the enrichment levels of 28 immune cells using transcriptome datasets for six melanoma cohorts, including four cohorts not treated with ICIs and two cohorts treated with ICIs. We identified three immune subtypes (Im-H, Im-M, and Im-L), reproducible in these cohorts. Im-H displayed strong immune signatures, low stemness and proliferation potential, genomic stability, high immunotherapy response rate, and favorable prognosis. Im-L showed weak immune signatures, high stemness and proliferation potential, genomic instability, low immunotherapy response rate, and unfavorable prognosis. The pathways highly enriched in Im-H included immune, MAPK, apoptosis, calcium, VEGF, cell adhesion molecules, focal adhesion, gap junction, and PPAR. The pathways highly enriched in Im-L included Hippo, cell cycle, and ErbB. Copy number alterations correlated inversely with immune signatures in melanoma, while tumor mutation burden showed no significant correlation. The molecular features correlated with favorable immunotherapy response included immune-promoting signatures and pathways of PPAR, MAPK, VEGF, calcium, and glycolysis/gluconeogenesis. Our data recapture the immunological heterogeneity in melanoma and provide clinical implications for the immunotherapy of melanoma.
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Key Words
- Clustering analysis
- DMFS, distant-metastasis free survival
- DSS, disease-specific survival
- EMT, epithelial-mesenchymal transition
- FDR, false discovery rate
- GO, gene ontology
- GSEA, gene-set enrichment analysis
- HLA, human leukocyte antigen
- HRD, homologous recombination deficiency
- ICIs, immune checkpoint inhibitors
- Immune subtypes
- Immunotherapy
- MDSC, myeloid-derived suppressor cell
- Melanoma
- NK, natural killer
- OS, overall survival
- SCNAs, somatic copy number alterations
- TCGA, The Cancer Genome Atlas
- TIME, tumor immune microenvironment
- TMB, tumor mutation burden
- TME, tumor microenvironment
- Tumor immune microenvironment
- WGCNA, weighted gene co-expression network analysis
- ssGSEA, single-sample gene-set enrichment analysis
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Affiliation(s)
- Qian Liu
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Rongfang Nie
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Mengyuan Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Lin Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Haiying Zhou
- Department of Orthopedics, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Hui Lu
- Department of Orthopedics, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
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Lumish MA, Anderson MA, Rush PS, Fintelmann FJ, Duncan L, Sullivan RJ, Mooradian MJ. The metastatic dissemination of a squamous cell carcinoma arising from an epidermal cyst and subsequent failure to respond to programmed death 1 inhibition. JAAD Case Rep 2019; 5:375-8. [PMID: 31008173 DOI: 10.1016/j.jdcr.2019.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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