1
|
Cai H, Chen L, Yang S, Jiang R, Guo Y, He M, Luo Y, Hong G, Li H, Song K. Personalized differential expression analysis in triple-negative breast cancer. Brief Funct Genomics 2024; 23:495-506. [PMID: 38197537 DOI: 10.1093/bfgp/elad057] [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: 01/30/2023] [Revised: 11/16/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024] Open
Abstract
Identification of individual-level differentially expressed genes (DEGs) is a pre-step for the analysis of disease-specific biological mechanisms and precision medicine. Previous algorithms cannot balance accuracy and sufficient statistical power. Herein, RankCompV2, designed for identifying population-level DEGs based on relative expression orderings, was adjusted to identify individual-level DEGs. Furthermore, an optimized version of individual-level RankCompV2, named as RankCompV2.1, was designed based on the assumption that the rank positions of genes and relative rank differences of gene pairs would influence the identification of individual-level DEGs. In comparison to other individualized analysis algorithms, RankCompV2.1 performed better on statistical power, computational efficiency, and acquired coequal accuracy in both simulation and real paired cancer-normal data from ten cancer types. Besides, single sample GSEA and Gene Set Variation Analysis analysis showed that pathways enriched with up-regulated and down-regulated genes presented higher and lower enrichment scores, respectively. Furthermore, we identified 16 genes that were universally deregulated in 966 triple-negative breast cancer (TNBC) samples and interacted with Food and Drug Administration (FDA)-approved drugs or antineoplastic agents, indicating notable therapeutic targets for TNBC. In addition, we also identified genes with highly variable deregulation status and used these genes to cluster TNBC samples into three subgroups with different prognoses. The subgroup with the poorest outcome was characterized by down-regulated immune-regulated pathways, signal transduction pathways, and apoptosis-related pathways. Protein-protein interaction network analysis revealed that OAS family genes may be promising drug targets to activate tumor immunity in this subgroup. In conclusion, RankCompV2.1 is capable of identifying individual-level DEGs with high accuracy and statistical power, analyzing mechanisms of carcinogenesis and exploring therapeutic strategy.
Collapse
Affiliation(s)
- Hao Cai
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Liangbo Chen
- School of Information Engineering, Jiangxi University of Science and Technology, Ganzhou, China
| | - Shuxin Yang
- School of Information Engineering, Jiangxi University of Science and Technology, Ganzhou, China
| | - Ronghong Jiang
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - You Guo
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Ming He
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Yun Luo
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Guini Hong
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Hongdong Li
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Kai Song
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| |
Collapse
|
2
|
Serrano-López EM, Coronado-Parra T, Marín-Vicente C, Szallasi Z, Gómez-Abellán V, López-Andreo MJ, Gragera M, Gómez-Fernández JC, López-Nicolás R, Corbalán-García S. Deciphering the Role and Signaling Pathways of PKCα in Luminal A Breast Cancer Cells. Int J Mol Sci 2022; 23:ijms232214023. [PMID: 36430510 PMCID: PMC9696894 DOI: 10.3390/ijms232214023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/11/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Protein kinase C (PKC) comprises a family of highly related serine/threonine protein kinases involved in multiple signaling pathways, which control cell proliferation, survival, and differentiation. The role of PKCα in cancer has been studied for many years. However, it has been impossible to establish whether PKCα acts as an oncogene or a tumor suppressor. Here, we analyzed the importance of PKCα in cellular processes such as proliferation, migration, or apoptosis by inhibiting its gene expression in a luminal A breast cancer cell line (MCF-7). Differential expression analysis and phospho-kinase arrays of PKCα-KD vs. PKCα-WT MCF-7 cells identified an essential set of proteins and oncogenic kinases of the JAK/STAT and PI3K/AKT pathways that were down-regulated, whereas IGF1R, ERK1/2, and p53 were up-regulated. In addition, unexpected genes related to the interferon pathway appeared down-regulated, while PLC, ERBB4, or PDGFA displayed up-regulated. The integration of this information clearly showed us the usefulness of inhibiting a multifunctional kinase-like PKCα in the first step to control the tumor phenotype. Then allowing us to design a possible selection of specific inhibitors for the unexpected up-regulated pathways to further provide a second step of treatment to inhibit the proliferation and migration of MCF-7 cells. The results of this study suggest that PKCα plays an oncogenic role in this type of breast cancer model. In addition, it reveals the signaling mode of PKCα at both gene expression and kinase activation. In this way, a wide range of proteins can implement a new strategy to fine-tune the control of crucial functions in these cells and pave the way for designing targeted cancer therapies.
Collapse
Affiliation(s)
- Emilio M. Serrano-López
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria IMIB-Arrixaca, El Palmar, 30120 Murcia, Spain
| | - Teresa Coronado-Parra
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), 30100 Murcia, Spain
- Microscopy Core Unit, Área Científica y Técnica de Investigación, Universidad de Murcia, 30100 Murcia, Spain
| | - Consuelo Marín-Vicente
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), 30100 Murcia, Spain
- Cardiovascular Proteomics and Developmental Biology Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Zoltan Szallasi
- Computational Health Informatics Program, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Bioinformatics, Semmelweis University, H-1092 Budapest, Hungary
| | - Victoria Gómez-Abellán
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), 30100 Murcia, Spain
- Department of Cellular Biology and Histology, Biology School, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), 30100 Murcia, Spain
| | - María José López-Andreo
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), 30100 Murcia, Spain
- Molecular Biology Unit, Área Científica y Técnica de Investigación, Universidad de Murcia, 30100 Murcia, Spain
| | - Marcos Gragera
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), 30100 Murcia, Spain
- Centro Nacional Biotecnología, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Juan C. Gómez-Fernández
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria IMIB-Arrixaca, El Palmar, 30120 Murcia, Spain
| | - Rubén López-Nicolás
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria IMIB-Arrixaca, El Palmar, 30120 Murcia, Spain
- Department of Bromatology and Nutrition, Veterinary School, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), 30100 Murcia, Spain
- Correspondence: (R.L.-N.); (S.C.-G.)
| | - Senena Corbalán-García
- Department of Biochemistry and Molecular Biology A, Veterinary School, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria IMIB-Arrixaca, El Palmar, 30120 Murcia, Spain
- Correspondence: (R.L.-N.); (S.C.-G.)
| |
Collapse
|
3
|
Gao LJ, Li JL, Yang RR, He ZM, Yan M, Cao X, Cao JM. Biological Characterization and Clinical Value of OAS Gene Family in Pancreatic Cancer. Front Oncol 2022; 12:884334. [PMID: 35719943 PMCID: PMC9205247 DOI: 10.3389/fonc.2022.884334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/25/2022] [Indexed: 12/20/2022] Open
Abstract
Background OAS gene family plays an important role in antiviral process, but its role in pancreatic cancer has not yet been studied. Methods We analyzed the expression, prognostic value and biological function of the OAS gene family in human pancreatic cancer through comprehensive bioinformatic analysis and cellular level validation. Results OAS family was highly expressed in pancreatic cancer, and this high expression significantly affected the clinical stage and prognosis of the tumor. OAS gene family was closely related to the immune infiltration of pancreatic cancer, especially neutrophils and dendritic cells, and many immune-related factors and pathways are enriched in the tumor, such as type I interferon signaling pathway and NOD-like receptor signaling pathway. Conclusion Taken together, high expression of OAS family is closely related to poor prognosis of pancreatic cancer. OAS gene family may serve as the biomarker and even therapeutic target of pancreatic cancer.
Collapse
Affiliation(s)
- Li-Juan Gao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China.,Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Jia-Lei Li
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China.,Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Rui-Rui Yang
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China.,Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Zhong-Mei He
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China.,Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Min Yan
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China.,Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Xia Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China.,Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Ji-Min Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China.,Department of Physiology, Shanxi Medical University, Taiyuan, China
| |
Collapse
|
4
|
Huang YZ, Zheng YX, Zhou Y, Xu F, Cui YZ, Chen XY, Wang ZY, Yan BX, Zheng M, Man XY. OAS1, OAS2, and OAS3 Contribute to Epidermal Keratinocyte Proliferation by Regulating Cell Cycle and Augment Type I Interferon-Induced JAK1-STAT1 Phosphorylation in Psoriasis. J Invest Dermatol 2022; 142:2635-2645.e9. [PMID: 35305973 DOI: 10.1016/j.jid.2022.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 11/30/2022]
Abstract
Psoriasis is a systemic immune-mediated inflammatory disease characterized by hyperproliferation and abnormal differentiation of epidermal keratinocytes. Recent studies have identified IL-17 and IL-23 as key drivers of psoriasis pathogenesis, but the underlying molecular mechanisms remain unclear. The 2'-5'-oligoadenylate synthetases, namely, OAS1, OAS2, OAS3, and OASL, are a family of interferon-induced enzymes with multiple antiviral activities, but their role in psoriasis is unknown. Here, we identified overexpression of OAS1, OAS2, and OAS3 in human lesional psoriatic skin and serum and found that their expression was downregulated by biologics. Moreover, OASs were highly expressed in epidermal keratinocytes, epidermal dendritic cells, epidermal CD3+ T cells, dermal antigen-presenting cells, and dermal T cells from the psoriatic epidermis and dermis, as determined by flow cytometry. Additionally, OASs were upregulated by poly(I:C), poly(dA:dT), and type I IFNs but downregulated by JAK inhibitors in normal human epidermal keratinocytes. Furthermore, silencing of OASs inhibited the phosphorylation of JAK1 and STAT1. Knockdown of OASs suppressed keratinocyte proliferation by inhibiting cell cycle progression. Thus, OASs may be therapeutic biomarkers in psoriasis.
Collapse
Affiliation(s)
- Yan-Zhou Huang
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu-Xin Zheng
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuan Zhou
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Fan Xu
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying-Zhe Cui
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xue-Yan Chen
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhao-Yuan Wang
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bing-Xi Yan
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Min Zheng
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Yong Man
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| |
Collapse
|