The Nutritional Gene Expression Regulation Potential of a Lysolecithin-Based Product
Abstract
1. Introduction
2. Materials and Methods
2.1. Lysolecithin Characterization
2.2. Experimental Design
2.3. Toxicity Screening
Evaluation of the Effects of Lysolecithins on Intestinal Cell Viability
2.4. Studying the Effects of Lysolecithins on Intestinal Gene Expression and Metabolite Transport/Production
2.5. RNA Sequencing
2.5.1. Total RNA Extraction
2.5.2. Library Preparation and Sequencing
2.5.3. Total RNA Sample QC
- (1)
- NanoDrop (ThermoFisher Scientific, Waltham, MA, USA): tests RNA purity (OD260/OD280);
- (2)
- Agarose gel electrophoresis: tests RNA degradation and potential contamination;
- (3)
- Agilent 2100 (Agilent Technologies, Digem, Belgium): checks RNA integrity.
2.5.4. Data Quality Control
2.5.5. Readsmapping to the Reference Genome
2.5.6. Quantification of Gene Expression Level
2.5.7. Differential Expression Analysis
2.5.8. Enrichment Analysis of Differentially Expressed Genes
2.6. Untargeted Metabolomics
2.6.1. Sample Preparation
2.6.2. Instrumental Analysis (UPLC-MS)
2.6.3. Data Processing and Quality Control
2.6.4. Statistical and Multivariate Analysis
2.6.5. Metabolite Identification and Annotation
3. Results
3.1. Lysolecithin Characterization
3.2. The Toxicity Screening of Lysolecithins for Intestinal Cells
3.3. The Effect of Lysolecithins on Intestinal Cell Viability
3.4. The Effects of Lysolecithins on Intestinal Gene Expression
3.5. Cluster Analysis
3.6. Correlation Network of Metabolites
3.7. Cluster Analysis
3.8. Correlation Network of Metabolites
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
LPL | Lysophospholipids |
FA | Fatty acid |
Caco-2 | Colorectal adenocarcinoma-2 cells |
LPC | Lysophosphatidylcholine |
LPE | Lysophosphatidylethanolamine |
LPI | Lysophosphatidylinositol |
LPA | Lysophosphatidic acid |
TEER | Transepithelial electrical resistance |
RNA-Seq | Ribonucleic acid sequencing |
NCBI | National Center for Biotechnology Information |
GEO | Gene Expression Omnibus |
cAMP | Cyclic adenosine monophosphate |
GO | Gene Ontology |
RSD | Relative standard deviation |
LC-MS | Liquid chromatography–mass spectrometry |
PCA | Principal component analysis |
FC | Fold-change |
HCA | Hierarchical clustering analysis |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
AA | Amino acid |
Thr | Threonine |
Phe | Phenylalanine |
Ile | Isoleucine |
His | Histidine |
Arg | Arginine |
Tyr | Tyrosine |
Glu | Glutamic acid |
Pro | Proline |
Gly | Glycine |
Ala | Alanine |
GC | Gas chromatography |
HPLC | High-performance liquid chromatography |
DMEM | Dulbecco’s minimum essential medium |
FBS | Fetal bovine serum |
PBS | Phosphate-buffered saline |
MTT | 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide |
DMSO | Dimethyl sulfoxide |
NAD(P)H | Nicotinamide adenine dinucleotide phosphate |
dNTP | Deoxynucleotide triphosphate |
PCR | Polymerase chain reaction |
FKPM | Fragments per kilobase of transcript sequence per million base pairs sequenced |
DEG | Differentially expressed gene |
UPLC | Ultra-performance liquid chromatography |
MS | Mass spectrometry |
ESI-MS | Electrospray ionization–mass spectrometry |
PLS-DA | Partial least squares discriminant analysis |
OPLS-DA | Orthogonal partial least squares discriminant analysis |
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Phospholipid Profile of the Lysolecithin (%) | Fatty Acid Chains on Lysophospholipids (%) | ||
---|---|---|---|
Phosphatidylglycerols | 0.72 | 14:0 | 0.07 |
Phosphatidylethanolamines | 8.84 | 15:0 | <0.05 |
Phosphatidylinositols | 7.23 | 16:0 | 15.57 |
Phosphatidylserins | <1 | 16:1 | 0.14 |
Lipid A phospholipids | 1.67 | 17:0 | 0.14 |
Phosphatidylcholines | 12.06 | 17:1 | 0.05 |
Sphingomyelins | <0.4 | 18:0 | 4.22 |
Lysophosphatidylcholines | 5.08 | 18:1 trans | <0.05 |
Lysophosphatidylethanolamines | 3.75 | 18:1 | 15.52 |
Lysophosphatidylinositols | 2.19 | 18:2 trans | 0.09 |
Total | 41.54 | 18:2 (n − 6) | 56.15 |
18:3 trans | <0.05 | ||
18:3 (n − 3) | 6.93 | ||
20:0 | 0.24 | ||
20:1 | 0.15 | ||
20:2 (n − 6) | <0.05 | ||
22:0 | 0.40 | ||
22:1 | <0.05 | ||
24:0 | 0.22 | ||
24:1 | <0.05 | ||
Content (g/100 g) | 68.52 | ||
Saturated fatty acids (%) | 20.87 | ||
Monounsaturated fatty acids (%) | 15.86 | ||
Polyunsaturated fatty acids (%) | 63.08 | ||
Of which (n − 6) (%) | 56.15 | ||
Of which (n − 3) (%) | 6.93 |
Gene_ID | log2FoldChange | padj | Gene_Name | Gene_Description |
---|---|---|---|---|
ENSG00000004799 | −4.70 | 0.0000 | PDK4 | pyruvate dehydrogenase kinase 4 [Source: HGNC Symbol; Acc:HGNC:8812] |
ENSG00000143333 | −3.30 | 0.0004 | RGS16 | regulator of G protein signaling 16 [Source: HGNC Symbol;Acc:HGNC:9997] |
ENSG00000060566 | −2.46 | 0.0000 | CREB3L3 | cAMP responsive element binding protein 3 like 3 [Source: HGNC Symbol; Acc:HGNC: 18855] |
ENSG00000279357 | −2.42 | 0.0049 | AC007224.2 | TEC |
ENSG00000199047 | −2.41 | 0.0001 | MIR378A | microRNA 378a [Source: HGNC Symbol;Acc:HGNC:31871] |
ENSG00000147872 | −2.28 | 0.0000 | PLIN2 | perilipin 2 [Source: HGNC Symbol;Acc:HGNC:248] |
ENSG00000259771 | −2.19 | 0.0016 | AC092756.1 | novel transcript, sense intronic to MYO1E |
ENSG00000268635 | −2.07 | 0.0355 | AP003680.1 | novel transcript, antisense to PAK1 |
ENSG00000103044 | −2.04 | 0.0000 | HAS3 | hyaluronan synthase 3 [Source: HGNC Symbol; Acc:HGNC:4820] |
ENSG00000168505 | −1.97 | 0.0003 | GBX2 | gastrulation brain homeobox 2 [Source: HGNC Symbol; Acc:HGNC:4186] |
Gene_ID | log2FoldChange | padj | Gene_Name | Gene_Description |
---|---|---|---|---|
ENSG00000136546 | 2.94 | 0.0009 | SCN7A | sodium voltage-gated channel alpha subunit 7 [Source:HGNC Symbol;Acc:HGNC:10594] |
ENSG00000109743 | 2.82 | 0.0108 | BST1 | bone marrow stromal cell antigen 1 [Source:HGNC Symbol;Acc:HGNC:1118] |
ENSG00000167910 | 2.73 | 0.0005 | CYP7A1 | cytochrome P450 family 7 subfamily A member 1 [Source:HGNC Symbol;Acc:HGNC:2651] |
ENSG00000256651 | 2.71 | 0.0000 | AC006518.1 | taste receptor, type 2 pseudogene |
ENSG00000081148 | 2.54 | 0.0206 | IMPG2 | interphotoreceptor matrix proteoglycan 2 [Source:HGNC Symbol;Acc:HGNC:18362] |
ENSG00000154263 | 2.51 | 0.0026 | ABCA10 | ATP binding cassette subfamily A member 10 [Source:HGNC Symbol;Acc:HGNC:30] |
ENSG00000235079 | 2.47 | 0.0117 | ZRANB2-AS1 | ZRANB2 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:43594] |
ENSG00000198939 | 2.39 | 0.0011 | ZFP2 | ZFP2 zinc finger protein [Source:HGNC Symbol;Acc:HGNC:26138] |
ENSG00000136531 | 2.32 | 0.0235 | SCN2A | sodium voltage-gated channel alpha subunit 2 [Source:HGNC Symbol;Acc:HGNC:10588] |
ENSG00000168542 | 2.27 | 0.0318 | COL3A1 | collagen type III alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2201] |
HMDB_ID | Compound_Name | Chemical Formula | FC (Lysolecithin/Control) | Log2(FC) | t-Test |
---|---|---|---|---|---|
HMDB0000792 | Sebacic acid | C10H18O4 | 19.31 | 4.27 | 0.0001 |
HMDB0249582 | Candoxatrilat | C20H33NO7 | 16.90 | 4.08 | 0.0002 |
HMDB0004704 | 9,10-DHOME | C18H34O4 | 16.17 | 4.02 | 0.0002 |
HMDB0000672 | Hexadecanedioic acid | C16H30O4 | 15.05 | 3.91 | 0.0002 |
HMDB0004708 | 9,12,13-TriHOME | C18H34O5 | 14.64 | 3.87 | 0 |
HMDB0302703 | Eremanthin | C15H18O2 | 13.83 | 3.79 | 0.0001 |
HMDB0303565 | Eucannabinolide | C22H28O8 | 13.81 | 3.79 | 0.0016 |
HMDB0000560 | Goshuyic acid | C14H24O2 | 12.26 | 3.62 | 0 |
HMDB0062363 | 6-Hydroxy-3-oxotetradecenoic acid | C14H24O4 | 11.48 | 3.52 | 0 |
HMDB0006236 | Phenylacetaldehyde | C8H8O | 10.78 | 3.43 | 0.0001 |
HMDB0034673 | Calamendiol | C15H26O2 | 9.07 | 3.18 | 0.0001 |
HMDB0004706 | 8-Hydroperoxylinoleic acid | C18H32O4 | 8.68 | 3.12 | 0.0002 |
HMDB0010387 | LysoPC(18:3) | C26H48NO7P | 8.08 | 3.01 | 0.0242 |
HMDB0040668 | Blumenol C glucoside | C19H32O7 | 7.30 | 2.87 | 0.0002 |
HMDB0114758 | LysoPA(20:2) | C23H43O7P | 7.24 | 2.86 | 0.049 |
HMDB0036143 | Monomenthyl succinate | C14H24O4 | 5.66 | 2.50 | 0.0001 |
HMDB0002259 | Heptadecanoic acid | C17H34O2 | 5.44 | 2.44 | 0.0003 |
HMDB0030982 | 6-Ketomyristic acid | C14H26O3 | 4.77 | 2.25 | 0.0003 |
HMDB0038731 | 4,7-Megastigmadien-9-ol | C13H22O | 4.67 | 2.22 | 0.0001 |
HMDB0010725 | 3-Hydroxydecanoic acid | C10H20O3 | 4.05 | 2.02 | 0 |
HMDB0004667 | 13-HODE | C18H32O3 | 3.71 | 1.89 | 0.0027 |
HMDB0061914 | 8-Hydroxyoctanoate | C8H16O3 | 3.58 | 1.84 | 0 |
HMDB0031127 | 5-Hexyltetrahydro-2-furanoctanoic acid | C18H34O3 | 3.33 | 1.73 | 0.0004 |
HMDB0036199 | 2-Methoxy-4-(4-methyl-1,3-dioxolan-2-yl)phenol | C11H14O4 | 3.31 | 1.73 | 0.0008 |
HMDB0000784 | Azelaic acid | C9H16O4 | 3.08 | 1.62 | 0.0008 |
HMDB0035338 | Sterebin B | C20H32O5 | 2.33 | 1.22 | 0.0015 |
HMDB0029610 | Ascladiol | C7H8O4 | 2.02 | 1.01 | 0.0112 |
HMDB_ID | Compound_Name | Chemical Formula | FC (Contol/Lysolecithin) | Log2(FC) | t-Test |
---|---|---|---|---|---|
HMDB0059972 | 4-Hydroxy-5-(3′,4′-dihydroxyphenyl)-valeric acid-O-methyl-O-glucuronide | C18H26O12 | 17.96 | 4.51 | 0.0025 |
HMDB0060491 | Mycophenolic acid O-acyl-glucuronide | C23H28O12 | 17.31 | 4.36 | 0.0001 |
HMDB0260340 | Cytidine-5′-diphosphocholine | C14H26N4O11P2 | 15.80 | 4.32 | 0.0033 |
HMDB0038866 | Quercetagetin 3′-methylether 7-glucoside | C22H22O13 | 10.17 | 3.82 | 0.0000 |
HMDB0258916 | Tetramethylchromanol glucoside | C20H30O7 | 9.86 | 3.49 | 0.0000 |
HMDB0252642 | Gardenoside | C17H24O11 | 7.49 | 3.42 | 0.0000 |
HMDB0038809 | Luteolin 4′-glucoside 7-galacturonide | C27H28O17 | 4.18 | 2.18 | 0.0002 |
HMDB_ID | Compound_Name | Chemical Formula | FC(LEX/Control) | Log2(FC) | t-Test |
---|---|---|---|---|---|
HMDB0094680 | Octaethylene glycol | C16H34O9 | 6.23 | 2.64 | 0.0005 |
HMDB0244865 | 1-Benzazepine | C10H9N | 3.70 | 1.89 | 0.0006 |
HMDB0006547 | Stearidonic acid | C18H28O2 | 2.95 | 1.56 | 0.0019 |
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Van Hoeck, V.; Spaepen, R.; Forier, B. The Nutritional Gene Expression Regulation Potential of a Lysolecithin-Based Product. Curr. Issues Mol. Biol. 2025, 47, 548. https://doi.org/10.3390/cimb47070548
Van Hoeck V, Spaepen R, Forier B. The Nutritional Gene Expression Regulation Potential of a Lysolecithin-Based Product. Current Issues in Molecular Biology. 2025; 47(7):548. https://doi.org/10.3390/cimb47070548
Chicago/Turabian StyleVan Hoeck, Veerle, Riet Spaepen, and Bart Forier. 2025. "The Nutritional Gene Expression Regulation Potential of a Lysolecithin-Based Product" Current Issues in Molecular Biology 47, no. 7: 548. https://doi.org/10.3390/cimb47070548
APA StyleVan Hoeck, V., Spaepen, R., & Forier, B. (2025). The Nutritional Gene Expression Regulation Potential of a Lysolecithin-Based Product. Current Issues in Molecular Biology, 47(7), 548. https://doi.org/10.3390/cimb47070548