Ribonucleic Acid Sequencing Reveals the Upregulation and Resolution of Inflammation and Extracellular Matrix Remodeling in Lidocaine-Treated Human Acute Monocytic Leukemia Cell Line THP-1
Abstract
:1. Introduction
2. Materials and Methods
2.1. THP-1 Cell Culture
2.2. Cell Viability
2.3. RNA Sequencing
2.4. Bioinformatic Analysis
2.5. Reverse Transcription Polymerase Chain Reaction
2.6. Statistical Analysis
3. Results
3.1. High Concentrations of Lidocaine Affect Macrophage Viability
3.2. Transcriptome Analysis of Lidocaine-Treated Macrophages Revealed Significant Upregulation of Tissue Remodeling Cassettes in Macrophages
3.3. Lidocaine Increases the Resolution of Inflammation-Associated Gene Expression in Macrophages
4. Discussion
5. Conclusions
6. Limitations
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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(A) The top 20 enriched GO terms of upregulated genes | |||
Category | Term | Count | p Value |
BP | signal transduction | 64 | 1.9 × 10−5 |
BP | cell adhesion | 50 | 4.3 × 10−12 |
BP | cell differentiation | 40 | 4.4 × 10−5 |
BP | proteolysis | 26 | 5.2 × 10−4 |
BP | nervous system development | 23 | 4.7 × 10−3 |
BP | protein phosphorylation | 23 | 5.9 × 10−2 |
BP | spermatogenesis | 22 | 2.1 × 10−2 |
CC | plasma membrane | 224 | 4.7 × 10−11 |
CC | integral component of membrane | 210 | 2.2 × 10−7 |
CC | extracellular region | 90 | 3.4 × 10−4 |
CC | integral component of plasma membrane | 89 | 6.9 × 10−12 |
CC | extracellular exosome | 78 | 4.0 × 10−2 |
CC | extracellular space | 71 | 3.2 × 10−2 |
CC | cell surface | 37 | 1.4 × 10−4 |
CC | apical plasma membrane | 34 | 3.7 × 10−8 |
CC | synapse | 34 | 3.3 × 10−5 |
CC | neuron projection | 29 | 2.7 × 10−6 |
CC | external side of plasma membrane | 29 | 2.7 × 10−4 |
CC | dendrite | 24 | 5.1 × 10−3 |
CC | glutamatergic synapse | 22 | 7.5 × 10−3 |
MF | identical protein binding | 61 | 7.5 × 10−2 |
MF | calcium ion binding | 47 | 1.9 × 10−6 |
MF | protein homodimerization activity | 38 | 1.0 × 10−3 |
MF | sequence-specific double-stranded DNA binding | 30 | 2.2 × 10−3 |
MF | transcription factor activity, sequence-specific DNA binding | 29 | 4.6 × 10−3 |
MF | protein serine/threonine/tyrosine kinase activity | 24 | 5.5 × 10−3 |
MF | receptor binding | 22 | 9.0 × 10−3 |
(B) The top 20 enriched GO terms of downregulated genes | |||
Category | Term | Count | p Value |
BP | signal transduction | 83 | 2.6 × 10−4 |
BP | cell adhesion | 57 | 6.1 × 10−9 |
BP | nervous system development | 50 | 2.5 × 10−10 |
BP | cell differentiation | 44 | 1.1 × 10−2 |
BP | chemical synaptic transmission | 36 | 1.6 × 10−9 |
BP | positive regulation of gene expression | 35 | 9.0 × 10−3 |
BP | cell–cell signaling | 34 | 1.4 × 10−9 |
BP | positive regulation of cell proliferation | 33 | 4.6 × 10−2 |
BP | proteolysis | 30 | 1.0 × 10−2 |
BP | inflammatory response | 30 | 1.2 × 10−2 |
BP | intracellular signal transduction | 29 | 4.2 × 10−2 |
BP | brain development | 27 | 7.2 × 10−5 |
BP | axon guidance | 26 | 7.5 × 10−7 |
BP | positive regulation of cell migration | 26 | 1.9 × 10−4 |
BP | cell surface receptor signaling pathway | 26 | 3.8 × 10−3 |
BP | homophilic cell adhesion via plasma membrane adhesion molecules | 24 | 1.9 × 10−6 |
BP | positive regulation of protein phosphorylation | 22 | 3.9 × 10−4 |
BP | extracellular matrix organization | 20 | 4.7 × 10−4 |
BP | visual perception | 20 | 2.2 × 10−3 |
CC | plasma membrane | 346 | 3.9 × 10−19 |
CC | integral component of membrane | 309 | 2.5 × 10−9 |
CC | extracellular region | 157 | 5.5 × 10−11 |
CC | extracellular space | 138 | 6.0 × 10−9 |
CC | integral component of plasma membrane | 136 | 1.0 × 10−18 |
CC | Golgi apparatus | 63 | 3.2 × 10−2 |
CC | synapse | 58 | 2.6 × 10−10 |
CC | cell surface | 53 | 1.4 × 10−5 |
CC | dendrite | 52 | 2.0 × 10−10 |
CC | glutamatergic synapse | 49 | 2.9 × 10−10 |
CC | neuronal cell body | 46 | 2.2 × 10−10 |
CC | neuron projection | 43 | 7.5 × 10−9 |
CC | axon | 41 | 3.6 × 10−8 |
CC | perinuclear region of cytoplasm | 40 | 9.8 × 10−2 |
CC | Golgi membrane | 38 | 6.2 × 10−2 |
CC | endoplasmic reticulum lumen | 36 | 1.4 × 10−7 |
CC | apical plasma membrane | 33 | 4.1 × 10−4 |
CC | extracellular matrix | 30 | 2.1 × 10−6 |
CC | external side of plasma membrane | 26 | 3.7 × 10−2 |
CC | perikaryon | 26 | 2.3 × 10−8 |
MF | calcium ion binding | 72 | 2.1 × 10−9 |
MF | receptor binding | 36 | 1.9 × 10−4 |
MF | sequence-specific double-stranded DNA binding | 36 | 3.0 × 10−2 |
MF | macromolecular complex binding | 28 | 5.9 × 10−3 |
MF | growth factor activity | 22 | 1.9 × 10−5 |
MF | cytokine activity | 22 | 1.5 × 10−4 |
MF | integrin binding | 21 | 2.8 × 10−5 |
MF | transmembrane signaling receptor activity | 21 | 3.1 × 10−4 |
MF | signaling receptor activity | 21 | 2.9 × 10−3 |
(A) The KEGG pathway enrichment analysis of upregulated genes | ||
Term | Count | p Value |
Pathways in cancer | 30 | 9.4 × 10−4 |
Neuroactive ligand–receptor interaction | 25 | 2.1 × 10−4 |
Calcium signaling pathway | 22 | 1.7 × 10−5 |
PI3K-Akt signaling pathway | 19 | 1.7 × 10−2 |
Cytokine–cytokine receptor interaction | 16 | 3.0 × 10−2 |
MAPK signaling pathway | 15 | 6.4 × 10−2 |
cGMP-PKG signaling pathway | 14 | 1.3 × 10−3 |
Hematopoietic cell lineage | 13 | 3.2 × 10−5 |
Platelet activation | 13 | 2.9 × 10−4 |
Oxytocin signaling pathway | 13 | 2.0 × 10−3 |
(B) The KEGG pathway enrichment analysis of downregulated genes | ||
Term | Count | p Value |
Neuroactive ligand–receptor interaction | 37 | 2.3 × 10−6 |
Pathways in cancer | 32 | 4.6 × 10−2 |
Cytokine–cytokine receptor interaction | 24 | 4.2 × 10−3 |
Calcium signaling pathway | 21 | 5.9 × 10−3 |
MAPK signaling pathway | 21 | 3.4 × 10−2 |
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Feng, S.-W.; Lin, W.-C.; Lee, I.-T.; Luo, S.-D.; Wang, C.-S. Ribonucleic Acid Sequencing Reveals the Upregulation and Resolution of Inflammation and Extracellular Matrix Remodeling in Lidocaine-Treated Human Acute Monocytic Leukemia Cell Line THP-1. Biomedicines 2024, 12, 509. https://doi.org/10.3390/biomedicines12030509
Feng S-W, Lin W-C, Lee I-T, Luo S-D, Wang C-S. Ribonucleic Acid Sequencing Reveals the Upregulation and Resolution of Inflammation and Extracellular Matrix Remodeling in Lidocaine-Treated Human Acute Monocytic Leukemia Cell Line THP-1. Biomedicines. 2024; 12(3):509. https://doi.org/10.3390/biomedicines12030509
Chicago/Turabian StyleFeng, Sheng-Wei, Wei-Chun Lin, I-Ta Lee, Sheng-Dean Luo, and Ching-Shuen Wang. 2024. "Ribonucleic Acid Sequencing Reveals the Upregulation and Resolution of Inflammation and Extracellular Matrix Remodeling in Lidocaine-Treated Human Acute Monocytic Leukemia Cell Line THP-1" Biomedicines 12, no. 3: 509. https://doi.org/10.3390/biomedicines12030509
APA StyleFeng, S. -W., Lin, W. -C., Lee, I. -T., Luo, S. -D., & Wang, C. -S. (2024). Ribonucleic Acid Sequencing Reveals the Upregulation and Resolution of Inflammation and Extracellular Matrix Remodeling in Lidocaine-Treated Human Acute Monocytic Leukemia Cell Line THP-1. Biomedicines, 12(3), 509. https://doi.org/10.3390/biomedicines12030509