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Zhong Y, Cao H, Li W, Deng J, Li D, Deng J. An analysis of the prognostic role of reactive oxygen species-associated genes in breast cancer. ENVIRONMENTAL TOXICOLOGY 2024; 39:3055-3148. [PMID: 38319140 DOI: 10.1002/tox.24128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/11/2023] [Accepted: 12/25/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND This study aimed to type breast cancer in relation to reactive oxygen species (ROS), clinical indicators, single nucleotide variant (SNV) mutations, functional differences, immune infiltration, and predictive responses to immunotherapy or chemotherapy, and constructing a prognostic model. METHODS We used uniCox analysis, ConsensusClusterPlus, and the proportion of ambiguous clustering (PAC) to analyze The Cancer Genome Atlas (TCGA) data to determine optimal groupings and obtain differentially expressed ROS-related genes. Clinical indicators were then combined with the classification results and the Chi-square test was used to assess differences. We further examined SNV mutations, and functional differences using gene set enrichment analysis (GSEA) analysis, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, immune cell infiltration, and response to immunotherapy and chemotherapy. A prognostic model for breast cancer was constructed using these differentially expressed genes, immunotherapy or chemotherapy responses, and survival curves. RT-qPCR was used to detect the differences in the expression of LCE3D, CA1, PIRT and SMR3A in breast cancer cell lines and normal breast epithelial cell line. RESULTS We identified two distinct tumor types with significant differences in ROS-related gene expression, clinical indicators, SNV mutations, functional pathways, and immune infiltration. The response to specific chemotherapy drugs and immunotherapy treatments also documented significant differences. The prognostic model constructed with 16 genes linked to survival could efficiently divide patients into high- and low-risk groups. The high-risk group showed a poorer prognosis, higher tumor purity, distinct immune microenvironment, and lower immunotherapy response. RT-qPCR results showed that LCE3D, CA1, PIRT and SMR3A are highly expressed in breast cancer. CONCLUSION Our methodical examination presented an enhanced insight into the molecular and immunological heterogeneity of breast cancer. It can contribute to the understanding of prognosis and offer valuable insights for personalized treatment strategies. Further, the prognostic model can potentially serve as a powerful tool for risk stratification and therapeutic decision-making in clinical settings.
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Affiliation(s)
- Yangyan Zhong
- The Second Affiliated Hospital, Department of Breast and Thyroid Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Clinical Research Center for Breast and Thyroid Disease Prevention and Control in Hunan Province, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Hong Cao
- The Second Affiliated Hospital, Department of Breast and Thyroid Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Clinical Research Center for Breast and Thyroid Disease Prevention and Control in Hunan Province, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wei Li
- The Second Affiliated Hospital, Department of Breast and Thyroid Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Clinical Research Center for Breast and Thyroid Disease Prevention and Control in Hunan Province, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jian Deng
- The Second Affiliated Hospital, Department of Breast and Thyroid Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Clinical Research Center for Breast and Thyroid Disease Prevention and Control in Hunan Province, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Dan Li
- The Second Affiliated Hospital, Department of Breast and Thyroid Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Clinical Research Center for Breast and Thyroid Disease Prevention and Control in Hunan Province, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Junjie Deng
- The Second Affiliated Hospital, Department of Breast and Thyroid Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Clinical Research Center for Breast and Thyroid Disease Prevention and Control in Hunan Province, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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Li D, Ding J, Bar-joseph Z. UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation. J Comput Biol 2022; 29:1229-1232. [PMID: 36036832 PMCID: PMC9700341 DOI: 10.1089/cmb.2022.0251] [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] [Indexed: 11/12/2022] Open
Abstract
UNIFAN is an unsupervised cell type annotation tool for single-cell RNA sequencing data (scRNA-seq). Given single-cell expression data as input, UNIFAN outputs cell clusters as well as annotations for each cluster. The clustering process utilizes information on pathways and biological processes and these are also used to annotate the resulting clusters. In this software article, we focus on how to install UNIFAN and on the main steps involved in using UNIFAN for cell type annotations.
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Affiliation(s)
- Dongshunyi Li
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Jun Ding
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, Canada
| | - Ziv Bar-joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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