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Qin L, Li B, Wang S, Tang Y, Fahira A, Kou Y, Li T, Hu Z, Huang Z. Construction of an immune-related prognostic signature and lncRNA-miRNA-mRNA ceRNA network in acute myeloid leukemia. J Leukoc Biol 2024; 116:146-165. [PMID: 38393298 DOI: 10.1093/jleuko/qiae041] [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: 08/17/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
The progression of acute myeloid leukemia (AML) is influenced by the immune microenvironment in the bone marrow and dysregulated intracellular competing endogenous RNA (ceRNA) networks. Our study utilized data from UCSC Xena, The Cancer Genome Atlas Program, the Gene Expression Omnibus, and the Immunology Database and Analysis Portal. Using Cox regression analysis, we identified an immune-related prognostic signature. Genomic analysis of prognostic messenger RNA (mRNA) was conducted through Gene Set Cancer Analysis (GSCA), and a prognostic ceRNA network was constructed using the Encyclopedia of RNA Interactomes. Correlations between signature mRNAs and immune cell infiltration, checkpoints, and drug sensitivity were assessed using R software, gene expression profiling interactive analysis (GEPIA), and CellMiner, respectively. Adhering to the ceRNA hypothesis, we established a potential long noncoding RNA (lncRNA)/microRNA (miRNA)/mRNA regulatory axis. Our findings pinpointed 9 immune-related prognostic mRNAs (KIR2DL1, CSRP1, APOBEC3G, CKLF, PLXNC1, PNOC, ANGPT1, IL1R2, and IL3RA). GSCA analysis revealed the impact of copy number variations and methylation on AML. The ceRNA network comprised 14 prognostic differentially expressed lncRNAs (DE-lncRNAs), 6 prognostic DE-miRNAs, and 3 prognostic immune-related DE-mRNAs. Correlation analyses linked these mRNAs' expression to 22 immune cell types and 6 immune checkpoints, with potential sensitivity to 27 antitumor drugs. Finally, we identified a potential LINC00963/hsa-miR-431-5p/CSRP1 axis. This study offers innovative insights for AML diagnosis and treatment through a novel immune-related signature and ceRNA axis. Identified novel biomarkers, including 2 mRNAs (CKLF, PNOC), 1 miRNA (hsa-miR-323a-3p), and 10 lncRNAs (SNHG25, LINC01857, AL390728.6, AC127024.5, Z83843.1, AP002884.1, AC007038.1, AC112512, AC020659.1, AC005921.3) present promising candidates as potential targets for precision medicine, contributing to the ongoing advancements in the field.
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Affiliation(s)
- Ling Qin
- Department of Hematology, The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, No. 24 Jinghua Road, Jianxi District, Luoyang 471003, China
| | - Boya Li
- Department of Hematology, The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, No. 24 Jinghua Road, Jianxi District, Luoyang 471003, China
| | - Shijie Wang
- Department of Hematology, The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, No. 24 Jinghua Road, Jianxi District, Luoyang 471003, China
| | - Yulai Tang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory of Computer-Aided Drug Design of Dongguan City, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, No. 1 Xincheng Road, Songshan Lake District, Dongguan 523808, Guangdong, China
| | - Aamir Fahira
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory of Computer-Aided Drug Design of Dongguan City, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, No. 1 Xincheng Road, Songshan Lake District, Dongguan 523808, Guangdong, China
| | - Yanqi Kou
- Department of Hematology, The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, No. 24 Jinghua Road, Jianxi District, Luoyang 471003, China
| | - Tong Li
- Department of Hematology, The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, No. 24 Jinghua Road, Jianxi District, Luoyang 471003, China
| | - Zhigang Hu
- School of Medical Technology and Engineering, Henan University of Science and Technology, No.263 Kaiyuan Avenue, Luolong District, Luoyang 471000, China
| | - Zunnan Huang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory of Computer-Aided Drug Design of Dongguan City, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, No. 1 Xincheng Road, Songshan Lake District, Dongguan 523808, Guangdong, China
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Jeong S, Kim YG, Kim S, Kim K. Enhanced anticancer efficacy of primed natural killer cells via coacervate-mediated exogenous interleukin-15 delivery. Biomater Sci 2022; 10:5968-5979. [PMID: 36048163 DOI: 10.1039/d2bm00876a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Effective exogenous delivery of interleukin (IL)-15 to natural killer (NK) cells with subsequent anticancer efficacy could be a promising immune cell-based cancer immunotherapy. For the protection of encapsulated cargo IL-15 while maintaining its bioactivity under physiological conditions, we utilized a coacervate (Coa) consisting of a cationic methoxy polyethylene glycol-poly(ethylene arginyl aspartate diglyceride) (mPEG-PEAD) polymer, anionic counterpart heparin, and cargo IL-15. mPEGylation into the backbone cation effectively preserved the colloidal stability of Coa in harsh environments and enhanced the protection of cargo IL-15 than normal Coa without mPEGylation. Proliferation and anticancer efficacy of primed NK cells through co-culture with multiple cancer cell lines were enhanced in the mPEG-Coa group due to the maintained bioactivity of cargo IL-15 during the ex vivo expansion of NK cells. These facilitated functions of NK cells were also supported by the increased expression of mRNAs related to anticancer effects of NK cells, including cytotoxic granules, death ligands, anti-apoptotic proteins, and activation receptors. In summary, our Coa-mediated exogenous IL-15 delivery could be an effective ex vivo priming technique for NK cells with sustained immune activation that can effectively facilitate its usage for cancer immunotherapy.
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Affiliation(s)
- Sehwan Jeong
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, Republic of Korea.
| | - Young Guk Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, Republic of Korea.
| | - Sungjun Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, Republic of Korea.
| | - Kyobum Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, Republic of Korea.
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Balla B, Tripon F, Banescu C. From Descriptive to Functional Genomics of Leukemias Focusing on Genome Engineering Techniques. Int J Mol Sci 2021; 22:10065. [PMID: 34576226 PMCID: PMC8470190 DOI: 10.3390/ijms221810065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 12/17/2022] Open
Abstract
Genome engineering makes the precise manipulation of DNA sequences possible in a cell. Therefore, it is essential for understanding gene function. Meganucleases were the start of genome engineering, and it continued with the discovery of Zinc finger nucleases (ZFNs), followed by Transcription activator-like effector nucleases (TALENs). They can generate double-strand breaks at a desired target site in the genome, and therefore can be used to knock in mutations or knock out genes in the same way. Years later, genome engineering was transformed by the discovery of clustered regularly interspaced short palindromic repeats (CRISPR). Implementation of CRISPR systems involves recognition guided by RNA and the precise cleaving of DNA molecules. This property proves its utility in epigenetics and genome engineering. CRISPR has been and is being continuously successfully used to model mutations in leukemic cell lines and control gene expression. Furthermore, it is used to identify targets and discover drugs for immune therapies. The descriptive and functional genomics of leukemias is discussed in this study, with an emphasis on genome engineering methods. The CRISPR/Cas9 system's challenges, viewpoints, limits, and solutions are also explored.
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Affiliation(s)
- Beata Balla
- Genetics Department, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureș, Strada Gheorghe Marinescu 38, 540139 Târgu Mureș, Romania; (B.B.); (C.B.)
- Center for Advanced Medical and Pharmaceutical Research, Genetics Laboratory, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureș, Strada Gheorghe Marinescu 38, 540139 Târgu Mureș, Romania
| | - Florin Tripon
- Genetics Department, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureș, Strada Gheorghe Marinescu 38, 540139 Târgu Mureș, Romania; (B.B.); (C.B.)
- Center for Advanced Medical and Pharmaceutical Research, Genetics Laboratory, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureș, Strada Gheorghe Marinescu 38, 540139 Târgu Mureș, Romania
| | - Claudia Banescu
- Genetics Department, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureș, Strada Gheorghe Marinescu 38, 540139 Târgu Mureș, Romania; (B.B.); (C.B.)
- Center for Advanced Medical and Pharmaceutical Research, Genetics Laboratory, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureș, Strada Gheorghe Marinescu 38, 540139 Târgu Mureș, Romania
- Clinical and Emergency County Hospital of Târgu Mureș, Strada Gheorghe Marinescu 50, 540136 Târgu Mureș, Romania
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