| Literature DB >> 34605330 |
Shuo Wang1, Jiang Chen1, Hongyu Li1, Xingshun Qi1, Xu Liu1, Xiaozhong Guo1.
Abstract
Background: Pancreatic cancer (PC) has a poor prognosis and is prone to liver metastasis. The KAI1/CD82 gene inhibits PC metastasis. This study aimed to explore differential metabolites and enrich the pathways in serum samples between PC and liver metastasis nude mouse models stably expressing KAI1/CD82.Entities:
Keywords: KAI1/CD82; biomarker; metabolomics; nude mouse models; pancreatic cancer
Mesh:
Substances:
Year: 2021 PMID: 34605330 PMCID: PMC8493323 DOI: 10.1177/15330338211045204
Source DB: PubMed Journal: Technol Cancer Res Treat ISSN: 1533-0338
Figure 1.Lentivirus packaging and nude mouse xenograft models. (a) Polymerase chain reaction (PCR) identification results of KAI1/CD82 PLV-EF1α-positive bacterial solution. (b) Efficiency of PANC1 cell lentivirus infection. (c and d) Western blot of KAI1/CD82 protein expression. (e) Three PC tissues of nude mouse models. (f) Three liver metastasis tissues of nude mouse models.
Figure 2.Flow chart of metabolomic analysis.
Figure 3.Principal component analysis (PCA) was performed on the samples (including the quality control samples) in order to preliminarily understand the total metabolic differences between the samples of each group and the degree of variation between the samples within the group. (a) PCA 2D results of grouped metabolites. (b) PCA 3D results of grouped metabolites. (c) Explainable variation in the first 5 principal components of PCA. PCA showed a distinct clustering between groups.
Figure 4.OPLS-DA score plot. (a) OPLS-DA score plot. The abscissa is the difference between groups. The ordinate represents the score value of orthogonal components, and the ordinate direction shows the difference within the group. (b) OPLS-DA model validation. The prediction parameters of the evaluation model include R2X, R2Y, and Q2. R2X and R2Y, respectively, represent the interpretation rate of the established model to the X and Y matrix, and Q2 represents the prediction ability of the model. The closer these 3 indicators are to 1, the more stable and reliable the model will be.
Figure 5.(a) VIP value plot. VIP values of the differentially expressed metabolites. (b) Bar chart. The difference multiple changes of the quantitative information of metabolites in each group were compared according to the grouping of specific samples.
Differential Metabolite Screening Results Based on UPLC-MS/MS Platform.
| Formula | Compounds | Class | VIP | Log2FC | Type |
|---|---|---|---|---|---|
| C26H45NO7S | Taurocholic acid | Bile acids | 1.35 | 1.18 | Up |
| C24H40O4 | Hododeoxycholic acid | Bile acids | 1.02 | 1.88 | Up |
| C24H40O4 | Chenodeoxycholic Acid | Bile acids | 2.06 | 1.54 | Up |
| C10H14N5O8P | Guanosine Monophosphate | Nucleotide and its metabolomics | 2.40 | 1.41 | Up |
| C20H32O5 | Prostaglandin E2 | Hormones and hormone related compunds | 2.02 | 1.28 | Up |
| C23H38O4 | 23-deoxydeoxycholic acid | Bile acids | 1.64 | 2.15 | Up |
| C15H28O2 | cis-1-Pentadecenoic Acid (C15: 1) | FA | 2.39 | 2.08 | Up |
| C2H5NO2 | Glycine | Amino acid and its metabolomics | 1.72 | 1.38 | Up |
| C24H40O5 | Beta-murine | Bile acids | 1.71 | 1.30 | Up |
| C27H44O | Vitamin D3 | CoEnzyme and vitamins | 2.50 | −1.23 | Down |
| C10H12N4O5 | Hypoxanthine-9-β-D-Arabinofuranoside | Nucleotide and its metabolomics | 1.30 | −5.41 | Down |
| C18H32O3 | 12,13-EpOME [(±)12 (13) epoxy-9Z-octadecenoic acid] | Oxidized lipids | 1.13 | −1.14 | Down |
| C18H32O3 | 9,10-EpOME [(±)9,10-epoxy-12Z-octadecenoic acid] | Oxidized lipids | 1.13 | −1.14 | Down |
| C10H12N4O5 | Inosine | Nucleotide and its metabolomics | 1.30 | −5.41 | Down |
| C6H12O3 | (S)-Leucic acid | Organic acid and its derivatives | 1.08 | −1.44 | Down |
| C4H9NO2S | D-Homocysteine | Amino acid and its metabolomics | 2.27 | −1.20 | Down |
| C5H5N5O | 2-Hydroxy-6-Aminopurine | Nucleotide and its metabolomics | 1.96 | −1.12 | Down |
| C7H8N2O | 6-Methylnicotinamide | Heterocyclic compounds | 1.36 | −5.28 | Down |
Abbreviations: Class, substance class; Log2FC, the logarithm of fold change is taken as the base of 2; Type, up/down regulated type of metabolite; VIP, projection of variable importance.
Figure 6.(a) OPLS-DA S-plot. The red points indicate that the VIP value of these metabolites ≥1; the green points indicate that the VIP value of these metabolites ≤1. The upper right corner or lower left corner metabolites have more significant difference. (b) Volcano plot. Each point in the map represents a metabolite, and the abscisic coordinate represents the logarithm of the quantitative difference multiples of a metabolite in the 2 samples. (c) Violin plot. Violin plot is a combination of boxplot and density map and is mainly used to display the data distribution and its probability density. (d) Z-score plot. The different metabolites in different samples were normalized by calculating the Z-value. The distribution of each differential metabolite between different groups can be distinguished visually. (e). Heatmap clustering. The clustering tree on the left of the figure represents differential metabolites, and the scale represents the expression amount obtained after standardized processing.
KEGG Differential Enrichment Statistics.
| KEGG pathway | Com all | Com |
| Uni compounds |
|---|---|---|---|---|
| Primary bile acid biosynthesis | 729 | 6 | 2.56 × 10−5 | Taurocholic acid; Glycine; Chenodeoxycholic Acid |
| Purine metabolism | 729 | 12 | 2.72 × 10−4 | Inosine; Glycine; Guanosine Monophosphate |
| Rheumatoid arthritis | 729 | 3 | 4.04 × 10−4 | Vitamin D3; Prostaglandin E2 |
| Antifolate resistance | 729 | 3 | 4.04 × 10−4 | D-Homocysteine; Guanosine Monophosphate |
| Bile secretion | 729 | 34 | .006 | Chenodeoxycholic Acid; Prostaglandin E2; Taurocholic acid |
| NOD-like receptor signaling pathway | 729 | 1 | .012 | D-Homocysteine |
| Neuroactive ligand-receptor interaction | 729 | 20 | .023 | Prostaglandin E2; Glycine |
| Phototransduction | 729 | 2 | .024 | Guanosine Monophosphate |
| Olfactory transduction | 729 | 2 | .024 | Guanosine Monophosphate |
| Human cytomegalovirus infection | 729 | 2 | .024 | Prostaglandin E2 |
| cGMP-PKG signaling pathway | 729 | 3 | .037 | Guanosine Monophosphate |
| Phosphonate and phosphinate metabolism | 729 | 3 | .037 | Glycine |
| Human papillomavirus infection | 729 | 3 | .036 | Prostaglandin E2 |
| Thiamine metabolism | 729 | 4 | .049 | Glycine |
| African trypanosomiasis | 729 | 4 | .049 | Prostaglandin E2 |
| C-type lectin receptor signaling pathway | 729 | 4 | .049 | Prostaglandin E2 |
Abbreviations: Com, the number of metabolites detected that belong to the pathway; Com all, the number of metabolites noted by KEGG in all measured metabolites; P, P value of hypergeometric distribution; Uni compounds, metabolites that are significantly different and annotated by KEGG.
Figure 7.Enrichment analysis. (a) Statistics of KEGG enrichment. (b) Statistics of HMDB enrichment. Rich factor is the ratio between the number of differentially expressed metabolites in the corresponding pathway and the total number of metabolites detected and annotated in the pathway. The size of the points in the figure represents the number of significantly different metabolites enriched to the corresponding pathways.
Figure 8.Kyoto encyclopedia of genes and genomes (KEGG) annotation of bile secretion.
Figure 9.Kyoto encyclopedia of genes and genomes (KEGG) annotation of primary bile acid biosynthesis.
Figure 10.Kyoto encyclopedia of genes and genomes (KEGG) annotation of purine metabolism.
HMDB Differential Enrichment Statistics.
| SMPDB pathway | N |
|
| Uni compounds |
|---|---|---|---|---|
| Bile acid biosynthesis | 219 | 9 | .002 | Taurocholic acid; chenodeoxycholic acid; glycine |
| Congenital bile acid synthesis defect type III | 219 | 9 | .002 | Taurocholic acid; chenodeoxycholic acid; glycine |
| Congenital bile acid synthesis defect type II | 219 | 9 | .002 | Taurocholic acid; chenodeoxycholic acid; glycine |
| Cerebrotendinous xanthomatosis (CTX) | 219 | 9 | .002 | Taurocholic acid; chenodeoxycholic acid; glycine |
| Zellweger syndrome | 219 | 9 | .002 | Taurocholic acid; chenodeoxycholic acid; glycine |
| 27-Hydroxylase deficiency | 219 | 9 | .002 | Taurocholic acid; chenodeoxycholic acid; glycine |
| Familial hypercholanemia (FHCA) | 219 | 9 | .002 | Taurocholic acid; chenodeoxycholic acid; glycine |
| Xanthine dehydrogenase deficiency (Xanthinuria) | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| AICA-ribosiduria | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| Xanthinuria type I | 219 | 14 | .010 | Guanosine Monophosphate; Inosine; glycine |
| Adenosine deaminase deficiency | 219 | 14 | .010 | Guanosine Monophosphate; Inosine; glycine |
| Adenylosuccinate lyase deficiency | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| Gout or Kelley-Seegmiller syndrome | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| Molybdenum cofactor deficiency | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| Purine nucleoside phosphorylase deficiency | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| Lesch-Nyhan syndrome (LNS) | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| Myoadenylate deaminase deficiency | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| Mitochondrial DNA depletion syndrome | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| Adenine phosphoribosyltransferase deficiency | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| Purine metabolism | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| Xanthinuria type II | 219 | 14 | .010 | Guanosine monophosphate; inosine; glycine |
| Thioguanine action pathway | 219 | 16 | .014 | Guanosine monophosphate; Inosine; glycine |
| Mercaptopurine action pathway | 219 | 16 | .014 | Guanosine monophosphate; inosine; glycine |
| Azathioprine action pathway | 219 | 16 | .014 | Guanosine monophosphate; inosine; glycine |
| tRNA charging: glycine | 219 | 1 | .037 | glycine |
| Sarcosine oncometabolite pathway | 219 | 10 | .045 | D-homocysteine; glycine |
Abbreviations: M, the number of metabolites belonging to this pathway in the detected metabolites; N, the number of metabolites annotated by SMPDB primary pathway in all the metabolites measured; P, P value of hypergeometric distribution; Uni compounds, metabolites that are significantly different and annotated by SMPDB.
Human Diseases Associated with Differential Metabolites.
| Compound name | KEGG diseases | HMDB diseases |
|---|---|---|
| Taurocholic acid | – | Hepatocellular carcinoma | Cirrhosis | Colorectal cancer | Crohn's disease | Ulcerative colitis | Metastatic melanoma | Biliary atresia |
| Chenodeoxycholic acid | – | Cystic fibrosis | Biliary atresia | Cirrhosis | Hepatocellular carcinoma | Primary biliary cirrhosis |
| Glycine | – | D-Glyceric acidemia | Refractory localization-related epilepsy | Juvenile myoclonic epilepsy | Alzheimer's disease | D-Glyceric acidura | Early preeclampsia | Pregnancy | Late-onset preeclampsia | 3-Methyl-crotonyl-glycinuria | Sarcosinemia | N-acetylglutamate synthetase deficiency | Histidinemia | Obesity | Neu-Laxova Syndrome 1 | Hyperglycinemia, lactic acidosis, and seizures | Pyridoxamine 5-prime-phosphate oxidase deficiency | Lipoyltransferase 1 Deficiency | Phosphoserine Aminotransferase Deficiency | Phosphoserine Phosphatase Deficiency | Leukemia | Schizophrenia | Nonketotic Hyperglycinemia | 3-Phosphoglycerate dehydrogenase deficiency | Epilepsy, early-onset, vitamin B6-dependent | Irritable bowel syndrome | Ulcerative colitis | Colorectal cancer | Autism | Crohn's disease | Diverticular disease | Gout | Perillyl alcohol administration for cancer treatment | Pancreatic cancer | Periodontal disease | Frontotemporal dementia | Lewy body disease | Lung Cancer | Carbamoyl Phosphate Synthetase Deficiency | Iminoglycinuria | Autosomal dominant polycystic kidney disease | Argininosuccinic aciduria | Propionic acidemia | Tyrosinemia I | Phenylketonuria | Maple syrup urine disease | Eosinophilic esophagitis | Glucoglycinuria |
| Prostaglandin E2 | – | Amyotrophic lateral sclerosis | Hydrocephalus | Meningitis |
| Vitamin D3 | Hypercalcemia infantile | Anephric patients | Cerebrotendinous xanthomatosis |
| Guanosine monophosphate | – | – |
| Inosine | – | Critical illnesses | Canavan disease | Kidney disease | Purine nucleoside phosphorylase deficiency | Thymidine treatment | Septic shock | Xanthinuria type 1 | Degenerative disc disease | Irritable bowel syndrome | Colorectal cancer | Crohn's disease | Ulcerative colitis | Gout | Coronary artery disease | Attachment loss | Periodontal Probing Depth | Tooth Decay | Eosinophilic esophagitis |