Evaluation of Inflammatory Cellular Model by Advanced Bioanalytic and Artificial Intelligence Analyses of Lipids: Lipidomic Landscape of Inflammaging
Abstract
:1. Introduction
2. Materials and Methods
2.1. Chemicals
2.2. Cell Culture and Treatment
2.3. Sample Preparation
2.4. Lipid Extraction by MTBE
2.5. Mass Spectrometry for Untargeted Analysis of Lipidome
2.6. Statistical and Networking Data Analysis
2.7. AI, ML, Monte Carlo, and ROC Analyses
3. Results and Discussion
3.1. Setup of Analytical Method of Lipid Analysis
3.2. Effect of Induced Inflammation on R3/1 NF-κB Reporter Cells: Study of Lipidome of Cellular Model
3.3. Effect of Thinned Apple Polyphenols (TAPs) on Inflamed R3/1 NF-κB Reporter Cells
Ceramide Species | Inf_TAP vs. Inf | |
---|---|---|
Log2Ratio | References | |
Cer 32:1;2O| Cer(d18:1/14:0) | −1.28 | [27] |
Cer 33:1;2O| Cer(d17:1/16:0) | −1.52 | |
Cer 34:1;2O| Cer(d18:1/16:0) | −1.56 | [28,29] |
Cer 34:2;2O| Cer(d18:2/16:0) | −1.38 | |
Cer 34:2;3O| Cer(d18:2/16:0(2OH)) | −1.88 | |
Cer 35:1;2O| Cer(d18:1/17:0) | −1.22 | |
Cer 36:1;2O| Cer(d18:1/18:0) | −1.48 | [28,29] |
Cer 36:2;2O| Cer(d18:2/18:0) | −1.42 | |
Cer 37:1;2O| Cer(d18:1/19:0) | −1.46 | |
Cer 38:0;2O| Cer(d18:0/20:0) | −1.09 | |
Cer 38:1;2O| Cer(d18:1/20:0) | −1.58 | |
Cer 38:2;2O| Cer(d18:2/20:0) | −1.53 | |
Cer 39:1;2O| Cer(d17:1/22:0) | −2.26 | |
Cer 40:0;2O| Cer(d18:0/22:0) | −1.08 | |
Cer 40:1;2O| Cer(d18:1/22:0) | −1.99 | |
Cer 40:2;2O| Cer(d18:2/22:0) | −1.93 | |
Cer 41:1;2O| Cer(d18:1/23:0) | −2.33 | |
Cer 41:2;2O| Cer(d18:1/23:1) | −1.75 | |
Cer 42:1;2O| Cer(d18:0/24:1) | −1.11 | |
Cer 42:1;2O| Cer(d18:1/24:0) | −1.88 | [28,29] |
Cer 42:1;3O| Cer(d18:0/24:1(2OH)) | −0.80 | [28,29] |
Cer 42:2;2O| Cer(d18:1/24:1) | −1.66 | |
Cer 42:3;2O| Cer(d18:2/24:1) | −1.66 | |
Cer 43:2;2O| Cer(d18:1/25:1) | −1.35 |
3.4. Construction of ML Diagnostic Model for Inf vs. Wt and Inf_TAP vs. Inf
3.5. Effect of TNF-α and TAPs on Signaling Pathway Modulation by Network Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Number of Lipids | % | Number of Lipids | % | ||
---|---|---|---|---|---|
Identified Features in MS-DIAL | 469 | Identified Features in MS-DIAL | |||
PC | 94 | 20.2 | |||
PE | 96 | 20.2 | LPE | 10 | 2.0 |
SM | 47 | 10.1 | HexCer | 9 | 1.8 |
PI | 28 | 6.9 | CAR | 3 | 0.6 |
Cer | 3 | 6.3 | CE | 3 | 0.6 |
PG | 26 | 5.3 | NAE | 5 | 1.0 |
PS | 24 | 5.1 | MG | 2 | 0.4 |
DG | 18 | 4.5 | ST | 2 | 0.4 |
FA | 21 | 4.3 | SPB | 2 | 0.4 |
TG | 19 | 3.8 | LPG | 1 | 0.2 |
CL | 16 | 3.2 | LPI | 1 | 0.2 |
LPC | 10 | 2.2 | LPS | 1 | 0.2 |
Inf vs. Wt | Inf_TAP vs. Inf | |||
Canonical Pathway | p-Value | z-Score | p-Value | z-Score |
Accumulation of lipids | 4.23 × 10−3 | 1.23 | 4.23 × 10−3 | −0.54 |
Inf vs. Wt | Inf_TAP vs. Inf | |||
Lipid nomenclature | Log2Ratio | Log2Ratio | ||
FA 14:0 (myristic acid) | −5.9 × 10−1 | 4.2 × 10−1 | ||
TG 54:3|TG 18:1_18:1_18:1 (triolein) | −6.0 × 10−3 | 7.0 × 10−2 | ||
FA 16:0 (palmitic acid) | 9.0 × 10−3 | −2.7 × 10−1 | ||
FA 18:0 (stearic acid) | 1.5 × 10−2 | −2.3 × 10−1 |
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Aiello, G.; Tosi, D.; Aldini, G.; Carini, M.; D’Amato, A. Evaluation of Inflammatory Cellular Model by Advanced Bioanalytic and Artificial Intelligence Analyses of Lipids: Lipidomic Landscape of Inflammaging. Cosmetics 2024, 11, 140. https://doi.org/10.3390/cosmetics11040140
Aiello G, Tosi D, Aldini G, Carini M, D’Amato A. Evaluation of Inflammatory Cellular Model by Advanced Bioanalytic and Artificial Intelligence Analyses of Lipids: Lipidomic Landscape of Inflammaging. Cosmetics. 2024; 11(4):140. https://doi.org/10.3390/cosmetics11040140
Chicago/Turabian StyleAiello, Gilda, Davide Tosi, Giancarlo Aldini, Marina Carini, and Alfonsina D’Amato. 2024. "Evaluation of Inflammatory Cellular Model by Advanced Bioanalytic and Artificial Intelligence Analyses of Lipids: Lipidomic Landscape of Inflammaging" Cosmetics 11, no. 4: 140. https://doi.org/10.3390/cosmetics11040140