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Yang Q, Yang G, Wu Y, Zhang L, Song Z, Yang D. Bioinformatics analysis and validation of genes related to paclitaxel's anti-breast cancer effect through immunogenic cell death. Heliyon 2024; 10:e28409. [PMID: 38560098 PMCID: PMC10979210 DOI: 10.1016/j.heliyon.2024.e28409] [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: 09/28/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Research indicated that Paclitaxel (PTX) can induce immunogenic cell death (ICD) through immunogenic modulation. However, the combination of PTX and ICD has not been extensively studied in breast cancer (BRCA). The TCGA-BRCA and GSE20685 datasets were enrolled in this study. Samples from the TCGA-BRCA dataset were consistently clustered based on selected immunogenic cell death-related genes (ICD-RGs). Next, candidate genes were obtained by overlapping differentially expressed genes (DEGs) between BRCA and normal groups, intersecting genes common to DEGs between cluster1 and cluster2 and hub module genes, and target genes of PTX from five databases. The univariate Cox algorithm and the least absolute shrinkage and selection operator (LASSO) were performed to obtain biomarkers and build a risk model. Following observing the immune microenvironment in differential risk subgroups, single-gene gene set enrichment analysis (GSEA) was carried out in all biomarkers. Finally, the expression of biomarkers was analyzed. Enrichment analysis showed that 626 intersecting genes were linked with inflammatory response. Further five biomarkers (CHI3L1, IL18, PAPLN, SH2D2A, and UBE2L6) were identified and a risk model was built. The model's performance was validated using GSE20685 dataset. Furthermore, the biomarkers were enriched with adaptive immune response. Lastly, the experimental results indicated that the alterations in IL18, SH2D2A, and CHI3L1 expression after treatment matched those in the public database. In this study, Five PTX-ICD-related biomarkers (CHI3L1, IL18, PAPLN, SH2D2A, and UBE2L6) were identified to aid in predicting BRCA treatment outcomes.
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Affiliation(s)
- Qianmei Yang
- School of Pharmaceutical Science & Yunnan Provincial Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, 650500, PR China
- Yunnan College of Modern Biomedical Industry, Kunming, Yunnan, 650500, PR China
| | - Guimei Yang
- School of Pharmaceutical Science & Yunnan Provincial Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, 650500, PR China
- Yunnan College of Modern Biomedical Industry, Kunming, Yunnan, 650500, PR China
| | - Yi Wu
- Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming, Yunnan, 650500, PR China
| | - Lun Zhang
- School of Pharmaceutical Science & Yunnan Provincial Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, 650500, PR China
| | - Zhuoyang Song
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China
| | - Dan Yang
- School of Pharmaceutical Science & Yunnan Provincial Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, 650500, PR China
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Borowicz P, Chan H, Hauge A, Spurkland A. Adaptor proteins: Flexible and dynamic modulators of immune cell signalling. Scand J Immunol 2020; 92:e12951. [DOI: 10.1111/sji.12951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Paweł Borowicz
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Hanna Chan
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Anette Hauge
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Anne Spurkland
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
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Borowicz P, Chan H, Medina D, Gumpelmair S, Kjelstrup H, Spurkland A. A simple and efficient workflow for generation of knock‐in mutations in Jurkat T cells using CRISPR/Cas9. Scand J Immunol 2020; 91:e12862. [DOI: 10.1111/sji.12862] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/15/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Paweł Borowicz
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Hanna Chan
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Daniel Medina
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Simon Gumpelmair
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Hanna Kjelstrup
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Anne Spurkland
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
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Belotte J, Fletcher NM, Saed MG, Abusamaan MS, Dyson G, Diamond MP, Saed GM. A Single Nucleotide Polymorphism in Catalase Is Strongly Associated with Ovarian Cancer Survival. PLoS One 2015; 10:e0135739. [PMID: 26301412 PMCID: PMC4547699 DOI: 10.1371/journal.pone.0135739] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/25/2015] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer is the deadliest of all gynecologic cancers. Recent evidence demonstrates an association between enzymatic activity altering single nucleotide polymorphisms (SNP) with human cancer susceptibility. We sought to evaluate the association of SNPs in key oxidant and antioxidant enzymes with increased risk and survival in epithelial ovarian cancer. Individuals (n = 143) recruited were divided into controls, (n = 94): healthy volunteers, (n = 18), high-risk BRCA1/2 negative (n = 53), high-risk BRCA1/2 positive (n = 23) and ovarian cancer cases (n = 49). DNA was subjected to TaqMan SNP genotype analysis for selected oxidant and antioxidant enzymes. Of the seven selected SNP studied, no association with ovarian cancer risk (Pearson Chi-square) was found. However, a catalase SNP was identified as a predictor of ovarian cancer survival by the Cox regression model. The presence of this SNP was associated with a higher likelihood of death (hazard ratio (HR) of 3.68 (95% confidence interval (CI): 1.149–11.836)) for ovarian cancer patients. Kaplan-Meier survival analysis demonstrated a significant median overall survival difference (108 versus 60 months, p<0.05) for those without the catalase SNP as compared to those with the SNP. Additionally, age at diagnosis greater than the median was found to be a significant predictor of death (HR of 2.78 (95% CI: 1.022–7.578)). This study indicates a strong association with the catalase SNP and survival of ovarian cancer patients, and thus may serve as a prognosticator.
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Affiliation(s)
- Jimmy Belotte
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Nicole M. Fletcher
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Mohammed G. Saed
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Mohammed S. Abusamaan
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Gregory Dyson
- Karmanos Cancer Institute, Detroit, MI, United States of America
| | - Michael P. Diamond
- Department of Obstetrics and Gynecology, Georgia Regents University, Augusta, GA, United States of America
| | - Ghassan M. Saed
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI, United States of America
- * E-mail:
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