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Mares-Quiñones MD, Galán-Vásquez E, Pérez-Rueda E, Pérez-Ishiwara DG, Medel-Flores MO, Gómez-García MDC. Identification of modules and key genes associated with breast cancer subtypes through network analysis. Sci Rep 2024; 14:12350. [PMID: 38811600 PMCID: PMC11137066 DOI: 10.1038/s41598-024-61908-4] [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] [Received: 07/13/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Breast cancer is the most common malignancy in women around the world. Intratumor and intertumoral heterogeneity persist in mammary tumors. Therefore, the identification of biomarkers is essential for the treatment of this malignancy. This study analyzed 28,143 genes expressed in 49 breast cancer cell lines using a Weighted Gene Co-expression Network Analysis to determine specific target proteins for Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes. Sixty-five modules were identified, of which five were characterized as having a high correlation with breast cancer subtypes. Genes overexpressed in the tumor were found to participate in the following mechanisms: regulation of the apoptotic process, transcriptional regulation, angiogenesis, signaling, and cellular survival. In particular, we identified the following genes, considered as hubs: IFIT3, an inhibitor of viral and cellular processes; ETS1, a transcription factor involved in cell death and tumorigenesis; ENSG00000259723 lncRNA, expressed in cancers; AL033519.3, a hypothetical gene; and TMEM86A, important for regulating keratinocyte membrane properties, considered as a key in Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes, respectively. The modules and genes identified in this work can be used to identify possible biomarkers or therapeutic targets in different breast cancer subtypes.
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Affiliation(s)
- María Daniela Mares-Quiñones
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Mexico
| | - D Guillermo Pérez-Ishiwara
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Olivia Medel-Flores
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Del Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico.
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Kaur P, Ring A, Porras TB, Zhou G, Lu J, Kang I, Lang JE. Integrated Proteogenomic Analysis Reveals Distinct Potentially Actionable Therapeutic Vulnerabilities in Triple-Negative Breast Cancer Subtypes. Cancers (Basel) 2024; 16:516. [PMID: 38339267 PMCID: PMC10854633 DOI: 10.3390/cancers16030516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is characterized by an aggressive clinical presentation and a paucity of clinically actionable genomic alterations. Here, we utilized the Cancer Genome Atlas (TCGA) to explore the proteogenomic landscape of TNBC subtypes to see whether genomic alterations can be inferred from proteomic data. We found only 4% of the protein level changes are explained by mutations, while 21% of the protein and 35% of the transcriptomics changes were determined by copy number alterations (CNAs). We found tighter coupling between proteome and genome in some genes that are predicted to be the targets of drug inhibitors, including CDKs, PI3K, tyrosine kinase (TKI), and mTOR. The validation of our proteogenomic workflow using mass spectrometry Clinical Proteomic Tumor Analysis Consortium (MS-CPTAC) data also demonstrated the highest correlation between protein-RNA-CNA. The integrated proteogenomic approach helps to prioritize potentially actionable targets and may enable the acceleration of personalized cancer treatment.
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Affiliation(s)
- Pushpinder Kaur
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Alexander Ring
- Department of Medical Oncology and Hematology, University Hospital Zürich, 8091 Zurich, Switzerland
| | - Tania B. Porras
- Cancer and Blood Disease Institute, Children Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA
| | - Guang Zhou
- Division of Breast Services, Department of General Surgery, Digestive Disease and Surgery Institute, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Janice Lu
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Medical Oncology, Department of Medicine, University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Irene Kang
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Medical Oncology, Department of Medicine, University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Julie E. Lang
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Breast Services, Department of General Surgery, Digestive Disease and Surgery Institute, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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