Differential Transcriptomic Profiles Following Stimulation with Lipopolysaccharide in Intestinal Organoids from Dogs with Inflammatory Bowel Disease and Intestinal Mast Cell Tumor
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethical Animal Use
2.2. Crypt Cell Isolation and Enrichment for Enteroid and Colonoid Culture
2.3. LPS Stimulation of Canine Enteroids and Colonoids
2.4. RNA Extraction and Affymetrix Canine Genome 2.0 Array Microarray Processing
2.5. Assessment of Proliferation
2.6. Analysis of Microarray Data
- Sample 2 vs. Sample 1
- Sample 4 vs. Sample 3
- Sample 6 vs. Sample 5
- Sample 5 vs. Sample 3
- Sample 3 vs. Sample 1
- Sample 6 vs. Sample 4
- Sample 4 vs. Sample 2
2.7. BLAST Search and KEGG Pathway Analyses
3. Results
3.1. LPS Stimulates Higher Intestinal Epithelial Cell Proliferation
3.2. Microarray Analysis Reveals Differential Expression of Genes Stimulated by LPS in IBD Intestinal Organoids and Tumor Enteroids
3.3. Gene Expression Profiles and Pathway Enrichment Analysis
3.3.1. The LPS Treated Tumor Enteroids vs. the Control Tumor Enteroids
3.3.2. The LPS Treated IBD Enteroids vs. the Control IBD Enteroids
3.3.3. The LPS Treated IBD Colonoids vs. the Control IBD Colonoids
3.3.4. The Control IBD Colonoids vs. the Control IBD Enteroids
3.3.5. The Control IBD Enteroids vs. the Control Tumor Enteroids
3.3.6. The LPS Treated IBD Colonoids vs. the LPS Treated IBD Enteroids
3.3.7. The LPS Treated IBD Enteroids vs. the LPS Treated Tumor Enteroids
3.4. Genes Showing Similar Expression Patterns between IBD Enteroids and Colonoids Following LPS Stimulation
3.5. Genes Upregulated in IBD Enteroids and Downregulated in IBD Colonoids (and Vice Versa) Following LPS Stimulation
3.6. KEGG Pathway Analyses
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Complete Chelating Solution (CCS) | ||
Composition | Concentration | Supplier |
Na2HPO4-2H2O | 0.996 mg/mL | Sigma |
KH2PO4 | 1.08 mg/mL | Sigma |
NaCl | 5.6 mg/mL | Fisher Chemical |
KCl | 0.12 mg/mL | Fisher Chemical |
Sucrose | 15 mg/mL | Fisher Chemical |
D-Sorbitol | 10 mg/mL | Fisher Chemical |
Dithiothreitol (DTT) | 520 μM | Promega |
Pen Strep | Penicillin: 196 units/mL; Streptomycin: 196 μg/mL | Gibco |
Incomplete Media without an ISC Growth Factor (IMGF-) | ||
Composition | Concentration | Supplier |
Advanced DMEM/F12 | Base Media | Gibco |
FBS | 8% | Corning |
GlutaMAX™ Supplement (200 mM L-alanyl-L-glutamine dipeptide in 0.85% NaCl) | 2 mM | Gibco |
HEPES | 10 mM | VWR Life Science |
Primocin | 100 µg/mL | InvivoGen |
Complete Media with ISC Growth Factors (CMGF+) | ||
Composition | Concentration | Supplier |
Advanced DMEM/F12 | Base Media | Gibco |
FBS | 8% | Corning |
GlutaMAX™ Supplement (200 mM L-alanyl-L-glutamine dipeptide in 0.85% NaCl) | 2 mM | Gibco |
HEPES | 10 mM | VWR Life Science |
Primocin | 100 µg/mL | InvivoGen |
B27 Supplement | 1x | Gibco |
N2 Supplement | 1x | Gibco |
N-Acetyl-L-cysteine | 1 mM | Sigma |
Murine EGF | 50 ng/mL | PeproTech |
Murine Noggin | 100 ng/mL | PeproTech |
Human R-Spondin-1 | 500 ng/mL | PeproTech |
Murine Wnt-3a | 100 ng/mL | PeproTech |
[Leu15]-Gastrin I human | 10 nM | Sigma |
Nicotinamide | 10 mM | Sigma |
TGF beta 1 Recombinant Protein | 500 nM | ProSci |
SB202190 (P38 inhibitor) | 10 µM | Sigma |
TMS (trimethoprim sulfate) | 10 µg/mL | Sigma |
* ROCK inhibitor (Y-27632) | 10 µM | EMD Millipore Corp. |
* Aminopyrimidine CHIR99021 (GSK3β inhibitor) | 2.5 µM | Reprocell |
Description of the Sample | Sample Designation |
---|---|
Control enteroids from the MC tumor environment (9 biological replicates (wells) pooled together) | Sample-1 |
LPS treated enteroids from the MC tumor environment (9 biological replicates (wells) pooled together) | Sample-2 |
Control enteroids from IBD dogs (9 biological replicates (wells) pooled together) | Sample-3 |
LPS treated enteroids from IBD dogs (9 biological replicates (wells) pooled together) | Sample-4 |
Control colonoids from IBD dogs (9 biological replicates (wells) pooled together) | Sample-5 |
LPS treated colonoids from IBD dogs (9 biological replicates (wells) pooled together) | Sample-6 |
Serial No | Group Comparison | Total Number of Differentially Expressed Genes | Upregulated Genes (%) | Downregulated Genes (%) |
---|---|---|---|---|
1 (2–1) | LPS treated tumor enteroids vs. Control tumor enteroids | 677 | 56 | 44 |
2 (4–3) | LPS treated IBD enteroids vs. Control IBD enteroids | 639 | 49 | 51 |
3 (6–5) | LPS treated IBD colonoids vs. Control IBD colonoids | 684 | 48 | 52 |
4 (5–3) | Control IBD colonoids vs. Control IBD enteroids | 411 | 44 | 56 |
5 (3–1) | Control IBD enteroids vs. Control tumor enteroids | 376 | 49 | 51 |
6 (6–4) | LPS treated IBD colonoids vs. LPS treated IBD enteroids | 421 | 39 | 61 |
7 (4–2) | LPS treated IBD enteroids vs. LPS treated tumor enteroids | 314 | 51 | 49 |
Details for Top Upregulated and Downregulated DEGs | ||
Gene Description | Gene Symbol | Probe Set ID |
KH domain-containing, RNA-binding, signal transduction-associated protein 3 | KHDRBS3 | CfaAffx.2644.1.S1_at |
Flap endonuclease GEN homolog 1 | GEN1 | CfaAffx.6562.1.S1_at |
Krev interaction trapped protein 1 | KRIT1 | CfaAffx.3865.1.S1_s_at |
Centromere protein F | CENPF | CfaAffx.19540.1.S1_at |
Ciliogenesis and planar polarity effector complex subunit 1 | CPLANE1 | Cfa.1768.1.A1_at |
Tyrosine-protein kinase STYK1 | STYK1 | CfaAffx.20747.1.S1_s_at |
Quinone oxidoreductase-like protein 2/Crystallin Zeta Like 2 | LOC610994 | Cfa.3282.1.S1_s_at |
G patch domain-containing protein 4 isoform X1 | Gpatch4 | CfaAffx.25660.1.S1_at |
High affinity cationic amino acid transporter 1 | SLC7A1 (CAT-1) | CfaAffx.10937.1.S1_at |
Cation-transporting ATPase 13A2 | ATP13A2 | CfaAffx.24286.1.S1_at |
Testis expressed 45 | TEX45 | CfaAffx.27913.1.S1_at |
Gene Ontology (GO) Analysis of 11 DEGs (Annotated for Biological Process) | ||
GO-Terms | Number of Genes | Genes |
Cellular metabolic process and regulation, organic substance metabolic process, nitrogen compound metabolic process (18%) | 5 | CENPF, GEN1, STYK1, KHDRBS3, ATP13A2 |
Regulation of metabolic process (11%) | 3 | CENPF, KHDRBS3, ATP13A2 |
Establishment of localization (11%) | 3 | CENPF, ATP13A2, SLC7A1/CAT-1 |
Macromolecule localization, cellular localization (7%) | 2 | CENPF, ATP13A2 |
Regulation of molecular function, cellular homeostasis, regulation of biological quality (7%) | 2 | KRIT1, ATP13A2 |
Biosynthetic process, cell cycle process, negative regulation of cellular process, chromosome segregation (7%) | 2 | CENPF, GEN1 |
Positive regulation of cellular process, cellular response to stimulus, cellular component organization or biogenesis, response to stress (7%) | 2 | GEN1, ATP13A2 |
Anatomical structure development, regulation of developmental process, multicellular organism development (7%) | 2 | CENPF, KRIT1 |
Transmembrane transport (7%) | 2 | ATP13A2, SLC7A1/CAT-1 |
Positive regulation of transport, export from cell, response to chemical, regulation of localization, catabolic process, process utilizing autophagic mechanism, positive regulation of metabolic process, positive regulation of establishment of protein localization, vesicle-mediated transport (4%) | 1 | ATP13A2 |
Negative regulation of metabolic process (4%) | 1 | CENPF |
Cell cycle checkpoint, microtubule-based process (4%) | 1 | GEN1 |
Anatomical structure formation involved in morphogenesis, Negative regulation of developmental process, regulation of multicellular organismal process, establishment or maintenance of cell polarity, negative regulation of multicellular organismal process, anatomical structure morphogenesis (4%) | 1 | KRIT1 |
Oxidation-reduction process (4%) | 1 | LOC610994 |
Gene Ontology (GO) Analysis of 11 DEGs (Annotated for Molecular Function) | ||
GO-Terms | Number of Genes | Genes |
Identical protein binding (14%) | 3 | CENPF, GEN1, KHDRBS3 |
Nucleic acid binding (14%) | 3 | Gpatch4, GEN1, KHDRBS3 |
Nucleoside phosphate binding, anion binding, ribonucleotide binding (10%) | 2 | STYK1, ATP13A2 |
Protein dimerization activity (10%) | 2 | CENPF, GEN1 |
Cation binding (10%) | 2 | GEN1, ATP13A2 |
Nucleotide binding (10%) | 2 | STYK1, ATP13A2 |
Inorganic molecular entity transmembrane transporter activity (5%) | 1 | SLC7A1 (CAT-1) |
Protein kinase activity, transferase activity, transferring phosphorus-containing groups (5%) | 1 | STYK1 |
Transcription factor binding, protein C-terminus binding, dynein complex binding, cytoskeletal protein binding (5%) | 1 | CENPF |
Phospholipid binding, hydrolase activity, acting on acid anhydrides (5%) | 1 | ATP13A2 |
Hydrolase activity, acting on ester bonds, deoxyribonuclease activity (5%) | 1 | GEN1 |
Protein domain specific binding (5%) | 1 | KHDRBS3 |
Ion transmembrane transporter activity (5%) | 1 | SLC7A1 (CAT-1) |
Gene Ontology (GO) Analysis of 11 DEGs (Annotated for Cellular Component) | ||
GO-Terms | Number of Genes | Genes |
Intracellular organelle (17%) | 5 | CENPF, GEN1, KRIT1, KHDRBS3, ATP13A2 |
Intracellular non-membrane-bounded organelle (10%) | 3 | CENPF, GEN1, KRIT1 |
Membrane-bounded organelle (10%) | 3 | CENPF, KHDRBS3, ATP13A2 |
Integral component of membrane (10%) | 3 | STYK1, ATP13A2, SLC7A1 (CAT-1) |
Non-membrane-bounded organelle (10%) | 3 | CENPF, GEN1, KRIT1 |
Intracellular organelle lumen (7%) | 2 | CENPF, KHDRBS3 |
Centrosome (7%) | 2 | CENPF, GEN1 |
Plasma membrane bounded cell projection (7%) | 2 | CENPF, ATP13A2 |
Organelle lumen (7%) | 2 | CENPF, KHDRBS3 |
Plasma membrane (7%) | 2 | STYK1, SLC7A1 (CAT-1) |
Intrinsic component of organelle membrane, endosome, organelle membrane, intracellular vesicle, vacuole, neuronal cell body, cytoplasmic vesicle, transport vesicle (3%) | 1 | ATP13A2 |
Cilium, ciliary basal body, cytoplasmic region, organelle envelope, kinetochore, chromosome, centromeric region, nuclear envelope (3%) | 1 | CENPF |
Details for Top Upregulated and Downregulated DEGs | ||
Gene Description | Gene Symbol | Probe Set ID |
DENN domain containing 5B | DENND5B | Cfa.19506.1.S1_at |
Serine/threonine/tyrosine-interacting-like protein 1 | STYXL1 | Cfa.17400.1.S1_s_at |
Regenerating islet-derived protein 3-gamma-like | REG3G | Cfa.1742.1.S1_at |
Protein S100-A16 | S100A16 | Cfa.18759.2.S1_at |
Protein FAM122B | FAM122B | CfaAffx.28830.1.S1_s_at |
Centrosomal protein of 70 kda | CEP70 | Cfa.20146.1.S1_s_at |
Beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase | MGAT3 | Cfa.9863.1.A1_at |
Mucin 1 | MUC1 | CfaAffx.26061.1.S1_at |
Gene Ontology (GO) Analysis of DEGs (Annotated for Biological Process) | ||
GO-Terms | Genes | |
Organonitrogen compound metabolic process (25%) | STYXL1 | |
Microtubule cytoskeleton organization, Regulation of microtubule-based process (25%) | CEP70 | |
Cellular component biogenesis/organization and regulation (25%) | CEP70 | |
Phosphorus/cellular macromolecule/protein metabolic process (25%) | STYXL1 | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Molecular Function) | ||
GO-Terms | Genes | |
Phosphoprotein phosphatase activity (25%) | STYXL1 | |
Identical protein binding, cytoskeletal protein binding (25%) | CEP70 | |
Hydrolase activity, acting on ester bonds (25%) | STYXL1 | |
Cation binding (25%) | S100A16 | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Cellular Component) | ||
GO-Terms | Genes | |
Intracellular organelle (29%) | MUC1, CEP70 | |
Non-membrane-bounded organelle (14%) | CEP70 | |
Intracellular non-membrane-bounded organelle (14%) | CEP70 | |
Centrosome (14%) | CEP70 | |
Membrane/intrinsic component of membrane, cytoplasm (14%) | MUC1 | |
Cell periphery/apical part of cell (14%) | MUC1 |
Details for Upregulated and Downregulated DEGs | ||
Gene Description | Gene Symbol | Probe Set ID |
Collagenase 3 | MMP13 | CfaAffx.23153.1.S1_at |
Dual oxidase maturation factor 2 | DUOXA2 | CfaAffx.21162.1.S1_at |
Ceruloplasmin | CP | CfaAffx.13209.1.S1_s_at |
UMP-CMP kinase 2, mitochondrial | CMPK2 | Cfa.19154.1.S1_a_at |
Thrombospondin-4 | THBS4 | CfaAffx.14209.1.S1_s_at |
Interleukin-8 | CXCL8 | Cfa.3510.1.S1_s_at |
abl Interactor 2 | ABI2 | Cfa.1679.1.A1_at |
Ubiquitin-conjugating enzyme E2 E3 | UBE2E3 | CfaAffx.805.1.S1_s_at |
Echinoderm microtubule-associated protein-like 2 | EML2 | Cfa.9105.1.A1_s_at |
Extracellular sulfatase Sulf-2-like | SULF2 | Cfa.6393.1.A1_at |
Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 | ENPP6 | Cfa.6996.1.A1_at |
Gene Ontology (GO) Analysis of DEGs (Annotated for Biological Process) | ||
GO-Terms | Genes | |
Primary metabolic process, organic substance/nitrogen compound metabolic process (14%) | CMPK2, ENPP6, MMP13 | |
Cellular metabolic process (9%) | CMPK2, MMP13 | |
Establishment of localization (9%) | DUOXA2, CP | |
Catabolic process (9%) | ENPP6, MMP13 | |
Biosynthetic process, small molecule metabolic process (5%) | CMPK2 | |
Regulation of biological quality, cellular homeostasis, oxidation-reduction process (5%) | CP | |
Taxis (5%) | CXCL8 | |
Movement of cell or subcellular component, cell motility (5%) | CXCL8 | |
Localization of cell, cell activation (5%) | CXCL8 | |
Cell communication, signal transduction, response to chemical/external stimulus, cellular response to stimulus, immune response (5%) | CXCL8 | |
Leukocyte activation/migration (5%) | CXCL8 | |
Regulation of cellular process, response to stress (5%) | CXCL8 | |
Macromolecule localization (5%) | DUOXA2 | |
Developmental growth, ossification, collagen metabolic process (5%) | MMP13 | |
Cellular component organization or biogenesis (5%) | MMP13 | |
Multicellular organism development, anatomical structure development/morphogenesis/organ growth, biomineral tissue development (5%) | MMP13 | |
Cell adhesion (5%) | THBS4 | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Molecular Function) | ||
GO-Terms | Genes | |
Metal ion binding (19%) | THBS4, CP, MMP13 | |
Phosphotransferase activity, phosphate group as acceptor (6%) | CMPK2 | |
Purine ribonucleoside triphosphate binding (6%) | UBE2E3 | |
Metallopeptidase activity (6%) | MMP13 | |
G protein-coupled receptor binding (6%) | CXCL8 | |
Endopeptidase activity (6%) | MMP13 | |
Receptor ligand activity (6%) | CXCL8 | |
Cytokine receptor binding (6%) | CXCL8 | |
Purine nucleotide binding (6%) | UBE2E3 | |
Phosphoric ester hydrolase activity (6%) | ENPP6 | |
Purine ribonucleotide binding (6%) | UBE2E3 | |
Sulfuric ester hydrolase activity (6%) | SULF2 | |
Kinase activity (6%) | CMPK2 | |
Oxidoreductase activity, oxidizing metal ions, oxygen as acceptor (6%) | CP | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Cellular Component) | ||
GO-Terms | Genes | |
Extracellular region (28%) | CXCL8, THBS4, ENPP6, CP, MMP13 | |
Membrane (17%) | EML2, DUOXA2, ENPP6 | |
Extracellular space (11%) | CXCL8, CP | |
Intrinsic component of membrane (11%) | EML2, DUOXA2 | |
Cytoplasm (6%) | DUOXA2 | |
Intracellular anatomical structure (6%) | DUOXA2 | |
Organelle, organelle subcompartment (6%) | DUOXA2 | |
Cell periphery (6%) | ENPP6 | |
Extracellular matrix (6%) | MMP13 | |
Endomembrane system (6%) | DUOXA2 |
Details about DEGs in Control IBD Colonoids vs. Control IBD Enteroids | ||
Gene Description | Gene Symbol | Probe Set ID |
Sulfotransferase family 1C member 3 | SULT1C3 | CfaAffx.4011.1.S1_at |
Osteopontin | SPP1 | Cfa.9240.1.S1_at |
Carbonic anhydrase 1 | CA1 | Cfa.6413.1.A1_at/CfaAffx.13785.1.S1_at |
Protein S100-A16 | S100A16 | Cfa.18759.2.S1_at |
Phospholipase C epsilon 1 | PLCE1 | Cfa.12506.3.S1_at |
Cell adhesion molecule 1 | CADM1 | Cfa.11274.1.A1_at/Cfa.10739.1.A1_s_at |
Mucin-1 | MUC1 | CfaAffx.26061.1.S1_at/Cfa.7074.1.A1_at |
WAP four-disulfide core domain protein 2 | WFDC2 | CfaAffx.15227.1.S1_s_at |
beta-Secretase 2 | BACE2 | Cfa.20396.1.S1_at |
Glioma pathogenesis-related protein 1 | GLIPR1 | Cfa.5134.1.A1_s_at |
ENSCAFT00000022799 XM_014110988.1 PREDICTED: Canis lupus familiaris fibronectin 1 | FN1 | CfaAffx.22155.1.S1_s_at |
RNA-binding motif, single-stranded-interacting protein 1 isoform X3 | RBMS1 | Cfa.5781.1.A1_s_at |
WAP four-disulfide core domain protein 2 | WFDC2 | Cfa.3780.1.S1_at |
Peripheral myelin protein 22 | PMP22 | CfaAffx.27421.1.S1_at |
Interferon alpha-inducible protein 6 | IFI6 | Cfa.20456.1.S1_s_at |
KH domain-containing, RNA-binding, signal transduction-associated protein 3 | KHDRBS3 | Cfa.334.1.A1_s_at |
Protein FAM3B | FAM3B | Cfa.12168.1.A1_s_at |
Transmembrane and immunoglobulin domain-containing protein 1 | TMIGD1 | CfaAffx.29036.1.S1_at |
Bile acid-CoA:amino acid N-acyltransferase-like | BAAT | CfaAffx.4748.1.S1_at |
Annexin A13 | ANXA13 | Cfa.3796.1.A1_s_at |
Aminopeptidase N | ANPEP | Cfa.3774.1.A1_s_at, Cfa.20798.1.S1_at |
Apolipoprotein A-IV | APOA4 | Cfa.6294.1.A1_at |
Gene Ontology (GO) Analysis of DEGs (Annotated for Biological Process) | ||
GO-Terms | Genes | |
Cellular metabolic process (7%) | CA1, ANPEP, PLCE1, BAAT, APOA4, WFDC2 | |
Regulation of cellular process (6%) | ANXA13, ANPEP, TMIGD1, APOA4, WFDC2 | |
Primary metabolic process, organic substance/nitrogen compound metabolic process (6%) | ANPEP, BAAT, APOA4, BACE2, WFDC2 | |
Regulation of biological quality (5%) | FAM3B, ANPEP, TMIGD1, APOA4 | |
Negative regulation of cellular process (4%) | ANXA13, TMIGD1, WFDC2 | |
Small molecule metabolic process (4%) | CA1, BAAT, APOA4 | |
Establishment of localization, macromolecule localization (4%) | ANXA13, FAM3B, APOA4 | |
Cell communication (4%) | FAM3B, ANPEP, PLCE1 | |
Regulation of localization (4%) | ANXA13, TMIGD1, APOA4 | |
Cell death, apoptotic process (4%) | TMIGD1, PMP22, CADM1 | |
Anatomical structure development/morphogenesis (4%) | ANPEP, PMP22 | |
Response to stress, regulation of metabolic process/molecular function/hydrolase activity (2%) | APOA4, WFDC2 | |
System process, catabolic process (2%) | ANPEP, APOA4 | |
Signal transduction, cellular response to stimulus (2%) | ANPEP, PLCE1 | |
Multicellular organism development, cellular developmental process, anatomical structure formation involved in morphogenesis (2%) | ANPEP, PMP22 | |
Positive regulation of cellular process (2%) | ANXA13, APOA4 | |
Cellular component organization or biogenesis (2%) | APOA4, PMP22 | |
Biosynthetic process (2%) | BAAT, APOA4 | |
Cell adhesion (2%) | SPP1, CADM1 | |
Biological process involved in symbiotic interaction (1%) | ANPEP | |
Positive/negative regulation of transport, vesicle-mediated transport (1%) | ANXA13 | |
Cellular localization, positive/negative regulation of establishment of protein localization (1%) | ANXA13 | |
Plasma lipoprotein particle organization, regulation of plasma lipoprotein particle levels (1%) | APOA4 | |
Response to chemical, digestion, regulation of multicellular organismal process (1%) | APOA4 | |
Positive regulation of metabolic process/catalytic activity (1%) | APOA4 | |
Cell–cell signaling, export from cell (1%) | FAM3B | |
Ensheathment of neurons (1%) | PMP22 | |
Ossification (1%) | SPP1 | |
Cell population proliferation (1%) | TMIGD1 | |
Regulation of locomotion, cell motility (1%) | TMIGD1 | |
Localization of cell, movement of cell or subcellular component (1%) | TMIGD1 | |
Response to external stimulus/biotic stimulus/other organism (1%) | WFDC2 | |
Immune response (1%) | WFDC2 | |
Negative regulation of metabolic process/catalytic activity (1%) | WFDC2 | |
Calcium-mediated signaling, positive regulation of cytosolic calcium ion concentration, epidermal growth factor receptor signaling pathway, Ras protein signal transduction, regulation of Ras protein signal transduction/G protein-coupled receptor signaling pathway, inositol phosphate-mediated signaling, phosphatidylinositol-mediated signaling, phospholipase C-activating G protein-coupled receptor signaling pathway (1%) | PLCE1 | |
Lipid catabolic process, diacylglycerol biosynthetic process (1%) | PLCE1 | |
Regulation of protein kinase activity, positive regulation of lamellipodium assembly/MAPK cascade (1%) | PLCE1 | |
Regulation of cell growth, cytoskeleton organization (1%) | PLCE1 | |
Heart development, glomerulus development, regulation of smooth muscle contraction (1%) | PLCE1 | |
Liver/brain development, spermatogenesis (1%) | CADM1 | |
Cell differentiation/recognition (1%) | CADM1 | |
Detection of stimulus (1%) | CADM1 | |
Homophilic cell adhesion/heterophilic cell–cell adhesion via plasma membrane cell adhesion molecules (1%) | CADM1 | |
Immune system process, positive regulation of cytokine production/natural killer cell mediated cytotoxicity (1%) | CADM1 | |
Susceptibility to natural killer cell mediated cytotoxicity (1%) | CADM1 | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Molecular Function) | ||
GO-Terms | Genes | |
Metal ion binding (21%) | ANXA13, CA1, ANPEP, ANPEP, CA1 | |
RNA binding (8%) | RBMS1, KHDRBS3 | |
Metallopeptidase activity (4%) | ANPEP | |
Peptidase inhibitor activity, endopeptidase regulator activity (4%) | WFDC2 | |
Exopeptidase activity (4%) | ANPEP | |
Transferase activity, transferring acyl groups other than amino-acyl groups (4%) | BAAT | |
Aspartic-type peptidase activity, endopeptidase activity (4%) | BACE2 | |
Calcium-dependent phospholipid binding, phosphatidylglycerol binding (4%) | ANXA13 | |
Sterol binding (4%) | APOA4 | |
Thiolester hydrolase activity (4%) | BAAT | |
SH3 Domain binding (4%) | KHDRBS3 | |
Sulfotransferase activity (4%) | SULT1C3 | |
Hydrolase/carboxylic ester hydrolase activity (4%) | CA1 | |
Enzyme binding, metal ion binding (4%) | PLCE1 | |
Phosphatidylinositol phospholipase C activity, small GTPase binding, guanyl-nucleotide exchange factor activity (4%) | PLCE1 | |
Cholesterol binding (4%) | APOA4 | |
Phosphatidylcholine-sterol O-acyltransferase activator activity (4%) | APOA4 | |
Signaling receptor binding (4%) | CADM1 | |
Cell adhesion molecule binding, PDZ domain binding, protein homodimerization activity (4%) | CADM1 | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Cellular Component) | ||
GO-Terms | Genes | |
Intracellular anatomical structure (14%) | ANXA13, MUC1, CA1, ANPEP, PLCE1, BAAT, TMIGD1, BACE2, KHDRBS3 | |
Membrane, cell membrane (14%) | ANXA13, MUC1, ANPEP, PLCE1, TMIGD1, GLIPR1, BACE2, PMP22, CADM1, IFI6 | |
Cytoplasm and cytosol (12%) | ANXA13, CA1, MUC1, ANPEP, PLCE1, BAAT, TMIGD1, BACE2 | |
Intrinsic component of membrane (12%) | MUC1, ANPEP, TMIGD1, GLIPR1, CADM1, BACE2, PMP22, IFI6 | |
Extracellular region (11%) | FAM3B, ANPEP, PLCE1, SPP1, APOA4, GLIPR1, WFDC2 | |
Organelle (11%) | ANXA13, MUC1, ANPEP, PLCE1, BAAT, BACE2, KHDRBS3 | |
Cell periphery (9%) | ANXA13, MUC1, ANPEP, TMIGD1, BACE2, PMP22 | |
Extracellular space (8%) | ANPEP, PLCE1, GLIPR1, APOA4, WFDC2 | |
Endomembrane system (5%) | ANXA13, PLCE1, BACE2 | |
Apical part of cell (3%) | ANXA13, MUC1 | |
Golgi apparatus membrane, lamellipodium (2%) | PLCE1 | |
Basolateral plasma membrane, cell–cell junction, neuron projection, postsynaptic density (2%) | CADM1 |
Details about DEGs in Control IBD Enteroids vs. Control Tumor Enteroids | ||
Gene Description | Gene Symbol | Probe Set ID |
Sulfotransferase family 1C member 3 | SULT1C3 | CfaAffx.4011.1.S1_at |
Osteopontin | SPP1 | Cfa.9240.1.S1_at |
Carbonic anhydrase 1 | CA1 | CfaAffx.13785.1.S1_at/Cfa.6413.1.A1_at |
Mucin-1 | MUC1 | CfaAffx.26061.1.S1_at/Cfa.7074.1.A1_at |
Phospholipase C epsilon 1 | PLCE1 | Cfa.12506.3.S1_at |
Protein S100-A16 | S100A16 | Cfa.18759.1.S1_s_at/Cfa.18759.2.S1_at |
Beta-site APP-cleaving enzyme 2 (memapsin 1) (beta-secretase 2) | BACE2 | Cfa.20396.1.S1_at |
Cell adhesion molecule 1 | CADM1 | Cfa.11274.1.A1_at/Cfa.10739.1.A1_s_at |
WAP four-disulfide core domain protein 2 | WFDC2 (CE4) | CfaAffx.15227.1.S1_s_at/Cfa.3780.1.S1_at |
RNA-binding motif, single-stranded-interacting protein 1 | RBMS1 | Cfa.5781.1.A1_s_at |
ENSCAFT00000022799 XM_014110988.1 PREDICTED: Canis lupus familiaris fibronectin 1 (FN1) | FN1 | CfaAffx.22155.1.S1_s_at |
Double-headed protease inhibitor, submandibular gland | LOC111092171 | Cfa.12226.1.A1_at |
Serine protease 23 | PRSS23 | Cfa.17835.1.S1_s_at |
Peripheral myelin protein 22 | PMP22 | CfaAffx.27421.1.S1_at |
Neutral and basic amino acid transport protein rbat | SLC3A1 | Cfa.3561.1.S1_at |
Bile acid-CoA:amino acid N-acyltransferase-like | BAAT | CfaAffx.4748.1.S1_at |
Aminopeptidase N | ANPEP | Cfa.20798.1.S1_at/Cfa.3774.1.A1_s_at |
Apolipoprotein A-IV | APOA4 | Cfa.6294.1.A1_at |
Annexin A13 | ANXA13 | Cfa.3796.1.A1_s_at |
Gene Ontology (GO) Analysis of DEGs (Annotated for Biological Process) | ||
GO-Terms | Genes | |
Primary metabolic process, organic substance metabolic process (10%) | PRSS23, anpep, BAAT, SLC3A1, LOC111092171, APOA4, BACE2, WFDC2 (CE4) | |
Nitrogen compound metabolic process (9%) | PRSS23, ANPEP, BAAT, LOC111092171, APOA4, BACE2, WFDC2 (CE4) | |
Cellular metabolic process (9%) | CA1, ANPEP, BAAT, LOC111092171, APOA4, BACE2, WFDC2 (CE4) | |
Regulation of cellular process (9%) | ANXA13, ANPEP, PLCE1, CADM1, LOC111092171, APOA4, WFDC2 (CE4) | |
Small molecule metabolic process (5%) | CA1, BAAT, APOA4, BACE2 | |
Regulation of metabolic process (4%) | LOC111092171, APOA4, WFDC2 (CE4) | |
Negative regulation of cellular process (4%) | ANXA13, LOC111092171, WFDC2 (CE4) | |
Regulation of molecular function, hydrolase activity (4%) | LOC111092171, APOA4, WFDC2 (CE4) | |
Cell communication, signal transduction, cellular response to stimulus (4%) | ANPEP, PLCE1, CADM1 | |
Biosynthetic process (4%) | BAAT, APOA4, BACE2 | |
Negative regulation of metabolic process (2%) | LOC111092171, WFDC2 (CE4) | |
Negative regulation of catalytic activity (2%) | LOC111092171, WFDC2 (CE4) | |
Response to stress (2%) | APOA4, WFDC2 (CE4) | |
Positive regulation of cellular process, regulation and establishment of localization/macromolecule localization (2%) | ANXA13, APOA4 | |
Cellular component organization or biogenesis (2%) | APOA4, PMP22 | |
System process, catabolic process, regulation of biological quality (2%) | ANPEP, APOA4 | |
Response to chemical (2%) | S100A16, APOA4 | |
Multicellular organism development, cellular developmental process, anatomical structure development/morphogenesis (2%) | ANPEP, PMP22 | |
Cell death, apoptotic process (2%) | PMP22, CADM1 | |
Cell adhesion (2%) | SPP1, CADM1 | |
Immune response, response to biotic stimulus/other organism/external stimulus (1%) | WFDC2 (CE4) | |
Heart development, glomerulus development, regulation of smooth muscle contraction, Regulation of signaling, cell growth, cytoskeleton organization (1%) | PLCE1 | |
Lipid catabolic process, diacylglycerol biosynthetic process (1%) | PLCE1 | |
Ensheathment of neurons (1%) | PMP22 | |
Biological process involved in symbiotic interaction (1%) | ANPEP | |
Ossification (1%) | SPP1 | |
Cellular localization, positive/negative regulation of establishment of protein localization (1%) | ANXA13 | |
Positive/negative regulation of transport, vesicle-mediated transport (1%) | ANXA13 | |
Regulation of multicellular organismal process, digestion (1%) | APOA4 | |
Plasma lipoprotein particle organization, regulation of plasma lipoprotein particle levels, positive regulation of metabolic process/catalytic activity (1%) | APOA4 | |
Immune system process, positive regulation of cytokine production/natural killer cell mediated cytotoxicity, detection of stimulus (1%) | CADM1 | |
Liver/brain development, spermatogenesis, cell differentiation/recognition (1%) | CADM1 | |
Response to calcium ion (1%) | S100A16 | |
Amyloid-beta metabolic process, glucose homeostasis, membrane protein ectodomain proteolysis, negative regulation of amyloid precursor protein biosynthetic process, peptide hormone processing (1%) | BACE2 | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Molecular Function) | ||
GO-Terms | Genes | |
Ion binding (18%) | ANXA13, CA1, ANPEP, S100A16, APOA4 | |
Hydrolase activity (14%) | CA1, PRSS23, ANPEP, BAAT | |
Enzyme regulator activity (11%) | LOC111092171, APOA4, WFDC2 (CE4) | |
Catalytic activity, acting on a protein (7%) | PRSS23, ANPEP | |
Organic cyclic compound binding (7%) | RBMS1, APOA4 | |
Transferase activity (7%) | BAAT, SULT1C3 | |
Lipid binding (7%) | ANXA13, APOA4 | |
Lyase activity (4%) | CA1 | |
Enzyme binding, metal ion binding (4%) | PLCE1 | |
Phosphatidylinositol phospholipase C activity, small GTPase binding, guanyl-nucleotide exchange factor activity (4%) | PLCE1 | |
Signaling receptor binding (4%) | CADM1 | |
Cell adhesion molecule binding, PDZ domain binding, protein homodimerization activity (4%) | CADM1 | |
Calcium ion/calcium-dependent protein binding, protein homodimerization activity (4%) | S100A16 | |
RNA binding (4%) | S100A16 | |
Aspartic-type endopeptidase activity (4%) | BACE2 | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Cellular Component) | ||
GO-Terms | Genes | |
Intracellular anatomical structure (14%) | ANXA13, MUC1, CA1, PRSS23, ANPEP, BAAT, PLCE1, S100A16, CADM1, BACE2 | |
Cytoplasm (13%) | ANXA13, CA1, MUC1, ANPEP, BAAT, PLCE1, S100A16, CADM1, BACE2 | |
Membrane/plasma membrane (13%) | ANXA13, MUC1, PRSS23, ANPEP, S100A16, SLC3A1, PMP22, CADM1, BACE2 | |
Organelle (11%) | ANXA13, MUC1, PRSS23, ANPEP, BAAT, PLCE1, S100A16, BACE2 | |
Extracellular region (10%) | ANPEP, PLCE1, S100A16, LOC111092171, SPP1, APOA4, WFDC2 (CE4) | |
Intrinsic component of membrane (10%) | MUC1, PRSS23, ANPEP, SLC3A1, CADM1, PMP22, BACE2 | |
Extracellular space (7%) | ANPEP, PLCE1, S100A16, APOA4, WFDC2 (CE4) | |
Cell periphery (7%) | ANXA13, MUC1, ANPEP, S100A16, PMP22 | |
Apical part of cell (3%) | ANXA13, MUC1 | |
Cytosol (3%) | BAAT, S100A16 | |
Membrane-enclosed lumen (3%) | ANXA13, S100A16 | |
Endomembrane system (3%) | ANXA13, PLCE1 | |
Golgi apparatus membrane, lamellipodium (1%) | PLCE1 | |
Basolateral plasma membrane, cell–cell junction, neuron projection, postsynaptic density (1%) | CADM1 | |
Nucleus, nucleolus (1%) | S100A16 | |
Endoplasmic reticulum, Golgi apparatus, endosome (1%) | BACE2 |
Details about DEGs in LPS Treated IBD Colonoids vs. LPS Treated IBD Enteroids | ||
Probe Set ID | Gene Description | Gene Symbol |
CfaAffx.13785.1.S1_at/Cfa.6413.1.A1_at | Carbonic anhydrase 1 | CA1 |
CfaAffx.31015.1.S1_at | Chloride channel accessory 1 | CLCA1 |
CfaAffx.4011.1.S1_at | Sulfotransferase 1C1 | SULT1C1 |
Cfa.7074.1.A1_at/CfaAffx.26061.1.S1_at | Mucin-1 | MUC1 |
Cfa.16455.1.S1_at | C-X-C motif chemokine 13 | CXCL13 |
Cfa.15827.1.S1_s_at | Fucosyltransferase 5 (alpha (1,3) fucosyltransferase) | FUT5 (fut356) |
Cfa.4456.1.S1_at | proSAAS | PCSK1N |
Cfa.18759.2.S1_at | Protein S100-A16 | S100A16 |
CfaAffx.8210.1.S1_at | ENSCAFT00000007801 XM_022408371.1 PREDICTED: Canis lupus familiaris olfactomedin 4 (OLFM4), mRNA | OLFM4 |
Cfa.5989.1.A1_s_at | Alpha-1-antitrypsin-like | SERPINA1 |
CfaAffx.3936.1.S1_at | HEPACAM family member 2 | HEPACAM2 |
CfaAffx.15227.1.S1_s_at | WAP four-disulfide core domain protein 2 | WFDC2 (CE4) |
Cfa.21325.1.S1_s_at | Epithelial membrane protein 2 | EMP2 |
Cfa.12271.1.A1_at | Ras-related protein Rap-2a-like | LOC480441 |
CfaAffx.9034.1.S1_s_at | ENSCAFT00000008689 XM_022406088.1 PREDICTED Canis lupus familiaris Fc fragment of IgG binding protein FCGBP mRNA | FCGBP |
Cfa.496.1.A1_s_at | Collagen alpha-2(V) chain | COL5A2 |
CfaAffx.14168.1.S1_s_at | Annexin A10 | ANXA10 |
Cfa.11104.1.S1_at | Phytanoyl-CoA hydroxylase-like | LOC478000 |
Cfa.18640.1.S1_at | Long-chain-fatty-acid-CoA ligase 5 | ACSL5 |
Cfa.10909.1.A1_at | 39S ribosomal protein S30, mitochondrial | MRPS30 |
CfaAffx.4748.1.S1_at | Bile acid-CoA:amino acid N-acyltransferase-like | BAAT |
Cfa.6996.1.A1_at | Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 | ENPP6 |
Cfa.6294.1.A1_at | Apolipoprotein A-IV | APOA4 |
Gene Ontology (GO) Analysis of DEGs (Annotated for Biological Process) | ||
GO-Terms | Genes | |
Cellular metabolic process (7%) | PCSK1N, CA1, BAAT, FUT5 (fut356), APOA4, ACSL5, WFDC2 (CE4), EMP2 | |
Organic substance/nitrogen compound metabolic process (7%) | PCSK1N, BAAT, FUT5 (fut356), ENPP6, APOA4, ACSL5, WFDC2 (CE4), EMP2 | |
Regulation of cellular process (7%) | PCSK1N, CLCA1, LOC480441, CXCL13, APOA4, ACSL5, WFDC2 (CE4), EMP2 | |
Primary metabolic process (7%) | PCSK1N, BAAT, ENPP6, FUT5 (fut356), APOA4, ACSL5, WFDC2 (CE4), EMP2 | |
Regulation of molecular function (5%) | PCSK1N, CLCA1, LOC480441, APOA4, WFDC2 (CE4), EMP2 | |
Positive regulation of cellular process (4%) | CLCA1, CXCL13, APOA4, ACSL5, EMP2 | |
Small molecule metabolic process (3%) | CA1, BAAT, APOA4, ACSL5 | |
Regulation of metabolic process (3%) | PCSK1N, APOA4, WFDC2 (CE4), EMP2 | |
Signal transduction, cell communication, cellular response to stimulus (3%) | CLCA1, LOC480441, CXCL13, EMP2 | |
Response to stress (3%) | CLCA1, CXCL13, APOA4, WFDC2 (CE4) | |
Biosynthetic process (3%) | BAAT, FUT5 (fut356), APOA4, ACSL5 | |
Regulation of hydrolase activity (3%) | PCSK1N, CLCA1, APOA4, WFDC2 (CE4) | |
Regulation of localization (3%) | CXCL13, APOA4, ACSL5, EMP2 | |
Immune response (3%) | CXCL13, WFDC2 (CE4), EMP2 | |
Macromolecule localization and establishment (3%) | APOA4, ACSL5, EMP2 | |
Regulation of biological quality/multicellular organismal process (3%) | CXCL13, APOA4, EMP2 | |
Negative regulation of cellular process (3%) | PCSK1N, CXCL13, WFDC2 (CE4) | |
Response to other organism/external stimulus/biotic stimulus (3%) | CLCA1, CXCL13, WFDC2 (CE4) | |
Positive regulation of catalytic activity (2%) | APOA4, EMP2 | |
Movement of cell or subcellular component, cell motility, localization of cell, positive regulation of response to stimulus (2%) | CXCL13, EMP2 | |
Response to chemical (2%) | CXCL13, APOA4 | |
Negative regulation of catalytic activity (2%) | PCSK1N, WFDC2 (CE4) | |
Taxis, leukocyte migration (2%) | CLCA1, CXCL13 | |
Regulation of signaling (2%) | CLCA1, EMP2 | |
System process, cellular component organization or biogenesis, positive regulation of metabolic process (2%) | APOA4, EMP2 | |
Catabolic process (2%) | ENPP6, APOA4 | |
Regulation of locomotion, tissue migration (2%) | CXCL13, EMP2 | |
Negative regulation of metabolic process (2%) | PCSK1N, WFDC2 (CE4) | |
Positive regulation of signaling (1%) | EMP2 | |
Transmembrane transport, positive regulation of transport/lipid localization (1%) | ACSL5 | |
Digestion, plasma lipoprotein particle organization, regulation of plasma lipoprotein particle levels (1%) | APOA4 | |
Cell–cell signaling, cellular homeostasis, response to endogenous stimulus, positive regulation of immune system process/locomotion, negative regulation of locomotion/multicellular organismal process/response to stimulus (1%) | CXCL13 | |
Cell population proliferation, actin filament-based process, cell adhesion, cell death/cell killing, multi-multicellular organism process/development, anatomical structure formation involved in morphogenesis, cellular developmental process, cellular localization, vesicle-mediated transport, embryo implantation, multi-organism reproductive process, immune effector process, regulation of developmental process/transferase activity (1%) | EMP2 | |
Protein glycosylation (1%) | FUT5 (fut356) | |
Calcium ion transport, cellular response to hypoxia, chloride transport, ion transmembrane transport (1%) | CLCA1 | |
Actin cytoskeleton reorganization, cellular response to xenobiotic stimulus, Rap protein signal transduction, regulation of dendrite morphogenesis, JNK cascade (1%) | LOC480441 | |
Establishment of protein localization, protein localization to plasma membrane, microvillus assembly, negative regulation of cell migration (1%) | LOC480441 | |
Positive regulation of protein phosphorylation/autophosphorylation (1%) | LOC480441 | |
Methyl-branched fatty acid/2-oxoglutarate/isoprenoid metabolic process, 2-oxobutyrate catabolic process (1%) | LOC478000 | |
Oxidation-reduction process, fatty acid alpha-oxidation (1%) | LOC478000 | |
Cell division, centrosome cycle (1%) | HEPACAM2 | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Molecular Function) | ||
GO-Terms | Genes | |
Cation binding (17%) | CA1, ANXA10, S100A16, COL5A2, APOA4 | |
Hydrolase activity, acting on ester bonds (10%) | CA1, BAAT, ENPP6 | |
Signaling receptor binding (7%) | CXCL13, EMP2 | |
Enzyme inhibitor activity (7%) | PCSK1N, WFDC2 (CE4) | |
Phospholipid binding (7%) | ANXA10, APOA4 | |
Peptidase regulator activity (7%) | PCSK1N, WFDC2 (CE4) | |
Hydrolase activity, acting on acid anhydrides, ligase activity, forming carbon-sulfur bonds (3%) | ACSL5 | |
Phosphatidylcholine binding, enzyme activator activity, alcohol binding, steroid binding (3%) | APOA4 | |
Transferase activity, transferring acyl groups (3%) | BAAT | |
Carbon-oxygen lyase activity (3%) | CA1 | |
Glycosaminoglycan binding, heparin binding, growth factor binding (3%) | CXCL13 | |
Enzyme binding, cell adhesion molecule binding, integrin binding (3%) | EMP2 | |
Transferase activity, transferring glycosyl groups, fucosyltransferase activity (3%) | FUT5 (fut356) | |
Transferase activity, transferring sulfur-containing groups (3%) | SULT1C3 | |
Intracellular calcium activated chloride channel activity, metal ion binding, metalloendopeptidase activity (3%) | CLCA1 | |
Signaling receptor activator activity (3%) | CXCL13 | |
GDP/GTP binding, G protein activity, GTPase activity, magnesium ion binding (3%) | LOC480441 | |
Protein/L-ascorbic acid/carboxylic acid/ferrous iron binding (3%) | LOC478000 | |
Phytanoyl-CoA dioxygenase activity (3%) | LOC478000 | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Cellular Component) | ||
GO-Terms | Genes | |
Intracellular organelle (14%) | MUC1, BAAT, FUT5 (fut356), ACSL5, EMP2, HEPACAM2 | |
Integral component of membrane (14%) | MUC1, FUT5 (fut356), HEPACAM2, ACSL5, EMP2 | |
Membrane-bounded organelle (14%) | MUC1, BAAT, FUT5 (fut356), ACSL5, EMP2, HEPACAM2 | |
Plasma membrane (14%) | MUC1, ENPP6, ACSL5, EMP2, CLCA1, LOC480441 | |
Plasma membrane region, apical plasma membrane (5%) | MUC1, EMP2 | |
Organelle membrane, Golgi apparatus subcompartment (5%) | FUT5 (fut356), EMP2 | |
Mitochondrion (5%) | ACSL5, LOC478000 | |
Plasma lipoprotein particle (3%) | APOA4 | |
Intracellular non-membrane-bounded organelle, intracellular organelle lumen/Endoplasmic reticulum (3%) | ACSL5 | |
Lipoprotein particle (3%) | APOA4 | |
Membrane microdomain, intracellular vesicle/cytoplasmic vesicle (3%) | EMP2 | |
Microbody (3%) | BAAT | |
Integral component of plasma membrane (3%) | CLCA1 | |
Extracellular space, microvillus, zymogen granule membrane (3%) | CLCA1 | |
Golgi cisterna membrane (3%) | FUT5 (fut356) | |
Cytosol, recycling endosome membrane, midbody (3%) | LOC480441 | |
Peroxisome, 9 + 0 non-motile cilium (3%) | LOC478000 | |
Cytoskeleton, centrosome, mitotic spindle, Golgi membrane, Nucleus, nucleoplasm, midbody (3%) | HEPACAM2 |
Details about DEGs in LPS Treated IBD Enteroids vs. LPS Treated Tumor Enteroids | ||
Probe Set ID | Gene Description | Gene Symbol |
CfaAffx.13785.1.S1_at/Cfa.6413.1.A1_at | Carbonic anhydrase 1 | CA1 |
CfaAffx.31015.1.S1_at | Chloride channel accessory 1 | CLCA1 |
CfaAffx.4011.1.S1_at | Sulfotransferase family 1C member 3 | SULT1C3 |
Cfa.7074.1.A1_at | Mucin-1 | MUC1 |
Cfa.16455.1.S1_at | C-X-C motif chemokine 13 | CXCL13 |
Cfa.15827.1.S1_s_at | Fucosyltransferase 5 (alpha (1,3) fucosyltransferase) | FUT5 (fut356) |
Cfa.4456.1.S1_at | proSAAS | PCSK1N |
Cfa.496.1.A1_s_at | Collagen alpha-2(V) chain | COL5A2 |
CfaAffx.15227.1.S1_s_at/Cfa.3780.1.S1_at | WAP four-disulfide core domain protein 2 | WFDC2 (CE4) |
CfaAffx.14168.1.S1_s_at | Annexin A10 | ANXA10 |
CfaAffx.3936.1.S1_at | HEPACAM family member 2 isoform X1 | HEPACAM2 |
Cfa.5989.1.A1_s_at | Alpha-1-antitrypsin-like | SERPINA1 |
CfaAffx.16198.1.S1_s_at | Trefoil factor 1 | TFF1 |
CfaAffx.9034.1.S1_s_at | ENSCAFT00000008689 XM_022406088.1 PREDICTED: Canis lupus familiaris Fc fragment of IgG binding protein (FCGBP) | FCGBP |
Cfa.12271.1.A1_at | Ras-related protein Rap-2a-like | LOC480441 |
Cfa.21325.1.S1_s_at | Epithelial membrane protein 2 | EMP2 |
CfaAffx.8210.1.S1_at | ENSCAFT00000007801 XM_022408371.1 PREDICTED: Canis lupus familiaris olfactomedin 4 (OLFM4) | OLFM4 |
Cfa.10909.1.A1_at | 39S Ribosomal protein S30, mitochondrial | MRPS30 |
Cfa.15806.1.S1_at | C-C motif chemokine 25 | CCL25 |
Cfa.18640.1.S1_at | Long-chain-fatty-acid--CoA ligase 5 | ACSL5 |
CfaAffx.4748.1.S1_at | Bile acid-CoA:amino acid N-acyltransferase-like | BAAT |
Cfa.6996.1.A1_at | Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 | ENPP6 |
Cfa.6294.1.A1_at | Apolipoprotein A-IV | APOA4 |
Gene Ontology (GO) Analysis of DEGs (Annotated for Biological Process) | ||
GO-Terms | Genes | |
Regulation of cellular process (7%) | PCSK1N, CCL25, CLCA1, LOC480441, CXCL13, TFF1, APOA4, ACSL5, WFDC2 (CE4), EMP2 | |
Cellular metabolic process (6%) | PCSK1N, CA1, BAAT, FUT5 (fut356), APOA4, ACSL5, WFDC2 (CE4), EMP2 | |
Primary metabolic process, organic substance/nitrogen compound metabolic process (6%) | PCSK1N, BAAT, FUT5 (fut356), ENPP6, ACSL5, APOA4, WFDC2 (CE4), EMP2 | |
Regulation of molecular function (5%) | PCSK1N, CCL25, CLCA1, LOC480441, APOA4, WFDC2 (CE4), EMP2 | |
Cell communication, signal transduction, cellular response to stimulus (4%) | CCL25, CLCA1, LOC480441, CXCL13, TFF1, EMP2 | |
Positive regulation of cellular process (4%) | CCL25, CLCA1, CXCL13, APOA4, ACSL5, EMP2 | |
Response to stress (3%) | CCL25, CLCA1, CXCL13, APOA4, WFDC2 (CE4) | |
Regulation of hydrolase activity (3%) | PCSK1N, CCL25, CLCA1, APOA4, WFDC2 (CE4) | |
Immune response (3%) | CCL25, CXCL13, WFDC2 (CE4), EMP2 | |
Regulation of metabolic process (3%) | PCSK1N, APOA4, WFDC2 (CE4), EMP2 | |
Small molecule metabolic process (3%) | CA1, BAAT, APOA4, ACSL5 | |
Response to biotic stimulus/external stimulus/other organism (3%) | CCL25, CLCA1, CXCL13, WFDC2 (CE4) | |
Regulation of biological quality (3%) | CXCL13, TFF1, APOA4, EMP2 | |
Cell motility, movement of cell or subcellular component, positive regulation of response to stimulus, localization of cell (3%) | CCL25, CLCA1, CXCL13, EMP2 | |
Biosynthetic process (3%) | BAAT, FUT5 (fut356), APOA4, ACSL5 | |
Response to chemical (3%) | CCL25, CLCA1, CXCL13, APOA4 | |
Regulation of localization (3%) | CXCL13, APOA4, ACSL5, EMP2 | |
Negative regulation of cellular process (2%) | PCSK1N, CXCL13, WFDC2 (CE4) | |
Positive regulation of catalytic activity (2%) | CCL25, APOA4, EMP2 | |
Negative regulation of catalytic activity (2%) | PCSK1N, LOC480441, WFDC2 (CE4) | |
Macromolecule localization (2%) | APOA4, ACSL5, EMP2 | |
Leukocyte migration, taxis (2%) | CCL25, CLCA1, CXCL13 | |
Regulation of signaling (2%) | CCL25, CLCA1, EMP2 | |
Establishment of localization (2%) | APOA4, ACSL5, EMP2 | |
Regulation of multicellular organismal process (2%) | CXCL13, APOA4, EMP2 | |
System process (2%) | TFF1, APOA4, EMP2 | |
Positive regulation of signaling (2%) | CCL25, CLCA1, EMP2 | |
Negative regulation of metabolic process (1%) | PCSK1N, WFDC2 (CE4) | |
Cellular component organization or biogenesis (1%) | APOA4, EMP2 | |
Catabolic process (1%) | ENPP6, APOA4 | |
Tissue migration (1%) | CXCL13, EMP2 | |
Digestion (1%) | TFF1, APOA4 | |
Positive regulation of metabolic process (1%) | APOA4, EMP2 | |
Regulation of locomotion (1%) | CXCL13, EMP2 | |
Transmembrane transport, positive regulation of transport/lipid localization (1%) | ACSL5 | |
Regulation of plasma lipoprotein particle levels/organization (1%) | APOA4 | |
Cell–cell signaling, negative regulation of response to stimulus/multicellular organismal process, regulation of immune system process, pos. regulation of immune system process, response to endogenous stimulus, cellular homeostasis, pos./neg. regul. of locomotion (1%) | CXCL13 | |
Multi-multicellular organism process, multicellular organism development, cellular developmental process and regulation, anatomical structure development/formation involved in morphogenesis, cellular localization, cell population proliferation, actin filament-based process, immune effector process, multi-organism reproductive process, cell adhesion, regulation of transferase activity, cell death/cell killing, embryo implantation, vesicle-mediated transport (1%) | EMP2 | |
Glycosylation (1%) | FUT5 (fut356) | |
Multicellular organismal homeostasis (1%) | TFF1 | |
Calcium ion transport, cellular response to hypoxia, chloride transport, ion transmembrane transport (1%) | CLCA1 | |
Actin cytoskeleton reorganization, cellular response to xenobiotic stimulus, Rap protein signal transduction, regulation of dendrite morphogenesis, JNK cascade (1%) | LOC480441 | |
Establishment of protein localization, protein localization to plasma membrane, microvillus assembly, negative regulation of cell migration (1%) | LOC480441 | |
Positive regulation of protein phosphorylation/autophosphorylation (1%) | LOC480441 | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Molecular Function) | ||
GO-Terms | Genes | |
Receptor ligand activity (14%) | CCL25, CXCL13, TFF1 | |
Metal ion binding (14%) | CA1, ANXA10, COL5A2 | |
Cytokine receptor binding, G protein-coupled receptor binding (9%) | CCL25, CXCL13 | |
Peptidase inhibitor activity, endopeptidase regulator activity (9%) | PCSK1N, WFDC2 (CE4) | |
Hydro-lyase activity, carboxylic ester hydrolase activity (5%) | CA1 | |
Acid-thiol ligase activity, hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, CoA-ligase activity (5%) | ACSL5 | |
Calcium-dependent phospholipid binding (5%) | ANXA10 | |
Phosphatidylcholine-sterol O-acyltransferase activator activity, sterol binding, cholesterol binding (5%) | APOA4 | |
Thiolester hydrolase activity, transferase activity, transferring acyl groups other than amino-acyl groups (5%) | BAAT | |
Fibroblast growth factor binding (5%) | CXCL13 | |
Kinase binding (5%) | EMP2 | |
Phosphoric ester hydrolase activity (5%) | ENPP6 | |
Transferase activity, transferring hexosyl/glycosyl groups (5%) | FUT5 (fut356) | |
Sulfotransferase activity (5%) | SULT1C3 | |
Intracellular calcium activated chloride channel activity, metal ion binding, metalloendopeptidase activity (5%) | CLCA1 | |
GDP/GTP binding, G protein activity, GTPase activity, magnesium ion binding (5%) | LOC480441 | |
Gene Ontology (GO) Analysis of DEGs (Annotated for Cellular Component) | ||
GO-Terms | Genes | |
Plasma membrane (23%) | MUC1, ENPP6, CLCA1, ACSL5, EMP2, LOC480441 | |
Intracellular organelle, membrane-bounded organelle (15%) | BAAT, FUT5 (fut356), ACSL5, EMP2 | |
Integral component of membrane (15%) | FUT5 (fut356), HEPACAM2, ACSL5, EMP2 | |
Organelle membrane, Golgi apparatus subcompartment (8%) | FUT5 (fut356), EMP2 | |
Apical plasma membrane (8%) | MUC1, EMP2 | |
Endoplasmic reticulum, intracellular organelle lumen, mitochondrion, intracellular non-membrane-bounded organelle (4%) | ACSL5 | |
Plasma lipoprotein particle (4%) | APOA4 | |
Microbody (4%) | BAAT | |
Intracellular vesicle, membrane microdomain, cytoplasmic vesicle (4%) | EMP2 | |
Integral component of plasma membrane (4%) | CLCA1 | |
Extracellular space, microvillus, zymogen granule membrane (4%) | CLCA1 | |
Golgi cisterna membrane (4%) | FUT5 (fut356) | |
Cytosol, recycling endosome membrane, midbody (4%) | LOC480441 |
Details about 25 DEGs Exhibiting Same Trend of Expression between IBD Enteroids and Colonoids Following LPS Stimulation | ||||
---|---|---|---|---|
Probe Set ID | Gene Description | Gene Symbol | LPS Treated vs. Control IBD Colonoids (Contrast 3) (log2 M) | LPS Treated vs. Control IBD Enteroids (Contrast 2) (log2 M) |
CfaAffx.16440.1.S1_at | 2′-5′-Oligoadenylate synthase-like protein | OASL | 0.851 | 0.770 |
CfaAffx.2163.1.S1_at | Antigen peptide transporter 2 | TAP2 | 0.649 | 0.619 |
CfaAffx.16198.1.S1_s_at | Trefoil factor 1 | TFF1 | 0.924 | 0.599 |
Cfa.12501.1.A1_at/CfaAffx.19068.1.S1_at/ CfaAffx.19068.1.S1_s_at | Insulin-like growth factor-binding protein 1 | IGFBP1 | 0.453 | 0.397 |
CfaAffx.29762.1.S1_at | NADPH oxidase organizer 1 | NOXO1 | 0.556 | 0.417 |
CfaAffx.15121.1.S1_at | Interferon-induced protein with tetratricopeptide repeats 1 | IFIT1 | 0.855 | 0.407 |
CfaAffx.21951.1.S1_s_at | Eukaryotic translation elongation factor 1 alpha 1 | EEF1A1 | 0.285 | 0.332 |
Cfa.21191.2.S1_a_at | 2′-5′-Oligoadenylate synthase 1 | OAS1 | 1.028 | 0.284 |
Cfa.10757.1.S1_at | Ubiquitin-like protein ISG15 | ISG15 | 0.953 | 0.284 |
Cfa.2878.1.A1_s_at | Ceruloplasmin | CP | 0.965 | 0.271 |
CfaAffx.14226.1.S1_s_at | DExD/H-box helicase 60 | DDX60 | 0.515 | 0.267 |
CfaAffx.17868.1.S1_at | Glutathione peroxidase 1 | GPX1 | 0.343 | 0.213 |
CfaAffx.18742.1.S1_at | Eukaryotic translation initiation factor 3 subunit A | EIF3A | 0.306 | 0.185 |
Cfa.20996.1.S1_at | MHC class I DLA-12 | DLA-12 | 0.348 | 0.118 |
Cfa.15976.1.S1_at | ATP synthase F1 subunit epsilon | ATP5F1E | −0.282 | −0.085 |
CfaAffx.23922.1.S1_x_at | 40S ribosomal protein S24 | RPS24 | −0.641 | −0.155 |
Cfa.5563.1.A1_s_at | Protein disulfide isomerase family A member 6 | PDIA6 | −0.332 | −0.180 |
Cfa.3039.1.A1_at | ATPase Na+/K+ transporting subunit alpha 1 | ATP1A1 | −0.158 | −0.189 |
Cfa.9039.1.A1_at | Fos proto-oncogene, AP-1 transcription factor subunit | FOS | −0.427 | −0.190 |
Cfa.1408.1.S1_at | Reticulon 4 | RTN4 | −0.226 | −0.303 |
Cfa.12512.1.A1_at | Ecm29 proteasome adaptor and scaffold | ECPAS | −0.196 | −0.387 |
Cfa.31.1.S1_s_at | Acidic nuclear phosphoprotein 32 family member A | ANP32A | −0.428 | −0.396 |
Cfa.15462.1.A1_at | Metallothionein-1 | LOC100686073 | −0.522 | −0.489 |
Cfa.7907.2.A1_a_at | Uncharacterized LOC611209 | LOC611209 | −0.530 | −0.645 |
CfaAffx.11648.1.S1_at | Chromodomain helicase DNA binding protein 7 | CHD7 | −0.870 | −0.834 |
Gene Ontology (GO) Analysis of DEGs (Annotated for Biological Process) | ||||
GO-Terms | Genes | |||
Response to external biotic stimulus, defense response to other organism/virus, viral process, innate immune response, negative regulation of viral genome replication (6%) | OAS1, OASL, IFIT1, ISG15 | |||
Homeostatic process (6%) | CP, TFF1, IFIT1, ISG15 | |||
Macromolecule metabolic process (6%) | OASL, EEF1A1, RPS24, ISG15 | |||
Cellular nitrogen compound metabolic process (6%) | OAS1, OASL, EEF1A1, RPS24 | |||
Organonitrogen compound metabolic process (6%) | OAS1, EEF1A1, RPS24, ISG15 | |||
Transport (6%) | TAP2, CP, ATP1A1, IFIT1 | |||
Regulation of viral process (6%) | OAS1, OASL, IFIT1, ISG15 | |||
Cellular macromolecule/protein metabolic process (4%) | EEF1A1, RPS24, ISG15 | |||
Cellular/organic substance biosynthetic process (4%) | OAS1, EEF1A1, RPS24 | |||
Response to organic substance (3%) | IFIT1, ISG15 | |||
Regulation of cellular/primary/macromolecule/nitrogen compound metabolic process (3%) | OASL, ISG15 | |||
Cellular aromatic/organic cyclic/nucleobase-containing/heterocycle compound metabolic process (3%) | OAS1, OASL | |||
Cell surface receptor signaling pathway (3%) | IGFBP1, ISG15 | |||
Cellular response to chemical stimulus (3%) | IFIT1, GPX1 | |||
Regulation of transport, ion transmembrane transport (1%) | ATP1A1 | |||
Cellular chemical homeostasis (1%) | CP | |||
Negative regulation of ERK1 and ERK2 cascade, formation of cytoplasmic translation initiation complex, IRES-dependent viral translational initiation, translational initiation, translation reinitiation, viral translational termination–reinitiation (1%) | EIF3A | |||
Response to toxic substance/oxidative stress, cellular oxidant detoxification (1%) | GPX1 | |||
Response to nitrogen compound, establishment of protein localization (1%) | IFIT1 | |||
Positive regulation of viral genome replication (1%) | IFIT1 | |||
Multi-organism transport, protein localization, biological process involved in interaction with host (1%) | IFIT1 | |||
Negative regulation of molecular function/protein binding/hydrolase activity (1%) | IFIT1 | |||
Regulation of ATPase activity/immune effector process (1%) | IFIT1 | |||
Regulation of response to biotic stimulus/stress/external stimulus (1%) | IFIT1 | |||
Regulation of cell communication/signal transduction (1%) | IGFBP1 | |||
Response to bacterium (1%) | ISG15 | |||
Cellular/organic substance catabolic process, negative regulation of cellular/macromolecule/nitrogen compound metabolic process (1%) | ISG15 | |||
Interferon-gamma/Interleukin-10 production, regulation of cytokine production (1%) | ISG15 | |||
Animal organ/system/tissue development, erythrocyte homeostasis, hemopoiesis, hematopoietic or lymphoid organ development, regulation of multicellular organismal/biomineral tissue development (1%) | ISG15 | |||
Bone mineralization, positive regulation of cell differentiation, ossification, biomineral tissue development (1%) | ISG15 | |||
Reactive oxygen species metabolic process (1%) | NOXO1 | |||
Positive regulation of molecular function (1%) | NOXO1 | |||
Cellular component organization (1%) | NOXO1 | |||
Organophosphate/phosphorus/nucleobase-containing small molecule metabolic process (1%) | OAS1 | |||
Regulation of nuclease activity (1%) | OASL | |||
Adaptive immune response, antigen processing and presentation of endogenous/peptide antigen (1%) | TAP2 | |||
Tissue homeostasis, digestive system process (1%) | TFF1 | |||
Immune response, antigen processing and presentation (1%) | DLA-12 | |||
Cellular zinc ion homeostasis, cellular response to cadmium ion/chromate/copper ion/zinc ion, detoxification of copper ion (1%) | LOC100686073 | |||
Negative regulation of growth/neuron apoptotic process, nitric oxide mediated signal transduction (1%) | LOC100686073 | |||
Gene Ontology (GO) Analysis of DEGs (Annotated for Molecular Function) | ||||
GO-Terms | Genes | |||
Nucleic acid binding (16%) | OAS1, OASL, EEF1A1, IFIT1, EIF3A | |||
Ribonucleotide binding, nucleoside phosphate binding, anion binding (9%) | TAP2, EEF1A1, ATP1A1 | |||
Signaling receptor binding (9%) | TAP2, TFF1, ISG15 | |||
Cation binding (6%) | CP, ATP1A1 | |||
Enzyme binding (6%) | NOXO1, ISG15 | |||
Active/ion transmembrane transporter activity (6%) | TAP2, ATP1A1 | |||
Transferase activity, transferring phosphorus-containing groups (6%) | OAS1, OASL | |||
Hydrolase activity, acting on acid anhydrides (6%) | TAP2, EEF1A1 | |||
Inorganic molecular entity transmembrane transporter activity (3%) | ATP1A1 | |||
Oxidoreductase activity, oxidizing metal ions (3%) | CP | |||
Nucleoside binding, translation factor activity, RNA binding (3%) | EEF1A1 | |||
mRNA binding, receptor tyrosine kinase binding, structural molecule activity, translation initiation factor activity (3%) | EIF3A | |||
Oxidoreductase activity, glutathione peroxidase activity, acting on peroxide as acceptor (3%) | GPX1 | |||
Growth factor binding (3%) | IGFBP1 | |||
Integrin binding, cell adhesion molecule binding (3%) | ISG15 | |||
Enzyme activator activity, phospholipid binding (3%) | NOXO1 | |||
Amide transmembrane transporter activity (3%) | TAP2 | |||
Signaling receptor activator activity (3%) | TFF1 | |||
Metal ion (copper ion/zinc ion) binding (3%) | LOC100686073 | |||
Gene Ontology (GO) Analysis of DEGs (Annotated for Cellular Component) | ||||
GO-Terms | Genes | |||
Intracellular organelle (15%) | TAP2, OASL, RPS24, IGFBP1, ISG15 | |||
Integral component of membrane (12%) | TAP2, ATP1A1, NOXO1, DLA-12 | |||
Membrane-bounded organelle (12%) | TAP2, OASL, IGFBP1, ISG15 | |||
Intracellular non-membrane-bounded organelle (9%) | OASL, RPS24, ISG15 | |||
Plasma membrane (6%) | ATP1A1, NOXO1 | |||
Endoplasmic reticulum (6%) | DLA-12, TAP2 | |||
Nucleus, cytosol, cytoplasm (6%) | EIF3A, LOC100686073 | |||
Host cell (3%) | IFIT1 | |||
Golgi apparatus (3%) | IGFBP1 | |||
Cytosolic ribosome, ribosomal subunit (3%) | ISG15 | |||
Intrinsic component of plasma membrane, plasma membrane protein complex (3%) | NOXO1 | |||
Oxidoreductase complex (3%) | NOXO1 | |||
Intracellular organelle lumen (3%) | OASL | |||
TAP complex, MHC class I peptide loading complex (3%) | TAP2 | |||
Endoplasmic reticulum subcompartment, nuclear outer membrane-endoplasmic reticulum membrane network, intrinsic component of organelle membrane (3%) | TAP2 | |||
Integral component of lumenal side of endoplasmic reticulum membrane, phagocytic vesicle membrane (3%) | DLA-12 | |||
Lysosome (3%) | LOC100686073 | |||
Membrane, cytoskeleton, microtubule, nucleolus, nucleoplasm, postsynaptic density, multi-eIF complex, eukaryotic 43S/48S preinitiation complex, eukaryotic translation initiation factor 3 complex, eIF3e/eIF3m (3%) | EIF3A |
Probe Set ID | Gene Description | Gene Symbol | LPS Treated vs. Control IBD Colonoids (Log-Ratio M) | LPS Treated vs. Control IBD Enteroids (Log-Ratio M) | LPS Treated vs. Control Tumor-Adjacent Organoids (Log-Ratio M) |
---|---|---|---|---|---|
CfaAffx.14226.1.S1_s_at | DEAD (Asp-Glu-Ala-Asp) box polypeptide 60 | DDX60 | 0.515 | 0.267 | 0.499 |
CfaAffx.18742.1.S1_at | Eukaryotic translation initiation factor 3 subunit A | EIF3A | 0.306 | 0.185 | 0.215 |
Cfa.15462.1.A1_at | Metallothionein-1 | LOC100686073 | −0.522 | −0.489 | −0.556 |
Details about 20 DEGs Exhibiting Opposite Trend (Upregulated in IBD Enteroids and Downregulated in IBD Colonoids and Vice Versa) between IBD Enteroids and Colonoids Following LPS Stimulation | ||||
---|---|---|---|---|
Probe Set ID | Gene Description | Gene Symbol | LPS Treated IBD Colonoids vs. Control IBD Colonoids (Contrast 3) (log2 M) | LPS Treated IBD Enteroids vs. Control IBD Enteroids (Contrast 2) (log2 M) |
Cfa.11069.1.A1_s_at | Splicing factor 3a subunit 1 | SF3A1 | 0.39123732 | −0.689723 |
Cfa.12226.1.A1_at | Double-headed protease inhibitor, submandibular gland | LOC111092171 | 0.13751692 | −0.3472223 |
Cfa.6267.3.S1_s_at | Cysteine rich protein 1 | CRIP1 | 0.43971334 | −0.3231234 |
Cfa.758.1.S1_at | Annexin A1 | ANXA1 | 0.57352154 | −0.2534974 |
Cfa.1341.1.S1_s_at | Integral membrane protein 2B | ITM2B | 0.09784959 | −0.2300856 |
Cfa.11085.1.A1_at | Regulator of G-protein signaling 2 | RGS2 | 0.40545754 | −0.2130524 |
Cfa.3290.1.S1_at | Kruppel-like factor 6 | KLF6 | 0.50830344 | −0.2017464 |
CfaAffx.22128.1.S1_at | S100 calcium binding protein P | S100P | 0.17803743 | −0.1172426 |
Cfa.5123.1.A1_at | Eukaryotic translation initiation factor 3, subunit F | EIF3F | 0.20471796 | −0.1131341 |
Cfa.14421.1.S1_at | Guanine nucleotide binding protein (G protein), gamma 5 | GNG5 | 0.22490961 | −0.1044874 |
Cfa.415.1.S1_at | Catenin (cadherin-associated protein), beta 1 | CTNNB1 | 0.09870051 | −0.0672268 |
CfaAffx.5204.1.S1_s_at | Cytochrome c, somatic | CYCS | −0.3244678 | 0.117936 |
CfaAffx.17908.1.S1_s_at | Mitochondrial import receptor subunit TOM20 homolog | TOMM20 | −0.6786731 | 0.18335565 |
Cfa.9946.1.S1_at | General transcription factor IIA, 2 | GTF2A2 | −0.4167318 | 0.19831684 |
CfaAffx.727.1.S1_x_at | FAM168A, family with sequence similarity 168, member A | FAM168A | −0.4299426 | 0.20356136 |
CfaAffx.16356.1.S1_s_at | LOC608756, similar to 60 kDa heat shock protein, mitochondrial precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock protein 60) (HSP-60) (Mitochondrial matrix protein P1) (P60 lymphocyte protein) (HuCHA60) | HSPD1 | −0.5398836 | 0.21506239 |
Cfa.1128.1.S1_at | KPNA2, karyopherin alpha 2 (RAG cohort 1, importin alpha 1) | KPNA2 | −0.2790694 | 0.24160302 |
Cfa.6212.1.A1_at | Mitochondrial 28S ribosomal protein S21 | MRPS21 | −0.5480801 | 0.40259764 |
Cfa.12820.2.A1_a_at | Cysteine-rich, angiogenic inducer, 61 | CYR61 | −0.574112 | 0.60011614 |
CfaAffx.386.1.S1_x_at | 40S Ribosomal protein S20 | RPS20 | −0.7323368 | 0.70095917 |
Gene Ontology (GO) Analysis of DEGs (Annotated for Biological Process) | ||||
GO-Terms | Genes | |||
Cellular metabolic process (14%) | RPS20, CYCS, EIF3F, MRPS21, LOC111092171, ANXA1, ITM2B, GTF2A2, SF3A1, HSPD1 | |||
Primary (nitrogen compound, organic substance) metabolic process (13%) | RPS20, EIF3F, MRPS21, LOC111092171, ANXA1, ITM2B, GTF2A2, SF3A1, HSPD1 | |||
Biosynthetic process (7%) | RPS20, EIF3F, MRPS21, ITM2B, GTF2A2 | |||
Regulation of cellular process (7%) | LOC111092171, ANXA1, GNG5, ITM2B, HSPD1 | |||
Regulation of metabolic process/negative regulation of cellular process (6%) | LOC111092171, ANXA1, ITM2B, HSPD1 | |||
Macromolecule localization and establishment (4%) | TOMM20, ANXA1, KPNA2 | |||
Cell communication, signal transduction, cellular response to stimulus (4%) | ANXA1, GNG5, HSPD1 | |||
Cellular component organization or biogenesis (4%) | TOMM20, ANXA1, SF3A1 | |||
Regulation of molecular function (4%) | LOC111092171, ANXA1, HSPD1 | |||
Negative regulation of metabolic process (4%) | LOC111092171, ANXA1, ITM2B | |||
Cell death (4%) | CYCS, ANXA1, HSPD1 | |||
Cell population proliferation, regulation of multicellular organismal process, cytokine production, leukocyte activation, regulation of biological quality, positive regulation of immune system process, response to stress, regulation of immune system process, immune effector process, regulation of response to stimulus, cell activation, immune response, cell adhesion, positive regulation of cellular process, multicellular organism development, positive regulation of multicellular organismal process, immune system development, positive regulation of metabolic process, anatomical structure development (3%) | ANXA1, HSPD1 | |||
Regulation of hydrolase activity (3%) | LOC111092171, HSPD1 | |||
Response to chemical, positive regulation of response to stimulus (3%) | ANXA1, HSPD1 | |||
Negative regulation of catalytic activity (3%) | LOC111092171, ANXA1 | |||
Cellular localization (3%) | TOMM20, KPNA2 | |||
Transmembrane transport (1%) | TOMM20 | |||
Response to endogenous stimulus/external stimulus, negative regulation of transport/response to stimulus/immune system process/multicellular organismal process (1%) | ANXA1 | |||
Cell motility, tissue migration, movement of cell or subcellular component, anatomical structure formation involved in morphogenesis, actin filament-based process, cell cycle process, cell–cell signaling (1%) | ANXA1 | |||
Developmental growth, cellular developmental process, export from cell, Vesicle-mediated transport, positive regulation of locomotion/transport (1%) | ANXA1 | |||
Taxis, localization of cell, leukocyte migration/homeostasis, myeloid cell homeostasis (1%) | ANXA1 | |||
Regulation of developmental process/localization/locomotion/signaling, positive/negative regulation of developmental process (1%) | ANXA1 | |||
Oxidation–reduction process (1%) | CYCS | |||
Production of molecular mediator of immune response, somatic diversification of immune receptors (1%) | HSPD1 | |||
Protein folding, positive regulation of catalytic activity (1%) | HSPD1 | |||
Biological process involved in symbiotic interaction, response to abiotic/biotic stimulus (1%) | HSPD1 | |||
Gene Ontology (GO) Analysis of DEGs (Annotated for Molecular Function) | ||||
GO-Terms | Genes | |||
Nucleic acid binding (15%) | RPS20, EIF3F, SF3A1, HSPD1 | |||
Cation binding (12%) | CYCS, ANXA1, S100P | |||
Enzyme inhibitor activity (8%) | LOC111092171, ANXA1 | |||
Nucleotide/ribonucleotide/nucleoside phosphate/anion binding (8%) | ITM2B, HSPD1 | |||
Peptide binding (8%) | TOMM20, ITM2B | |||
Ion transmembrane transporter activity (4%) | TOMM20 | |||
Phospholipid binding, calcium-dependent protein binding (4%) | ANXA1 | |||
Electron transfer activity, tetrapyrrole binding (4%) | CYCS | |||
Translation initiation factor binding, translation factor activity, RNA binding (4%) | EIF3F | |||
G-protein beta-subunit binding (4%) | GNG5 | |||
Lipopolysaccharide/apolipoprotein binding (4%) | HSPD1 | |||
Protein–lipid complex binding, enzyme binding, chaperone binding (4%) | HSPD1 | |||
p53 binding (4%) | HSPD1 | |||
Nuclear import signal receptor activity (4%) | KPNA2 | |||
Peptidase regulator activity (4%) | LOC111092171 | |||
Signaling receptor binding (4%) | S100P | |||
Active/amide/protein transmembrane transporter activity (4%) | TOMM20 | |||
Unfolded protein binding (4%) | TOMM20 | |||
Gene Ontology (GO) Analysis of DEGs (Annotated for Cellular Component) | ||||
GO-Terms | Genes | |||
Intracellular organelle (16%) | RPS20, TOMM20, CYCS, MRPS21, ANXA1, ITM2B, GTF2A2, SF3A1, HSPD1 | |||
Membrane-bounded organelle (13%) | TOMM20, CYCS, ANXA1, ITM2B, GTF2A2, SF3A1, HSPD1 | |||
Intracellular organelle lumen (7%) | CYCS, ANXA1, GTF2A2, HSPD1 | |||
Plasma membrane (7%) | ANXA1, ITM2B, GNG5, HSPD1 | |||
Mitochondrion (5%) | TOMM20, CYCS, HSPD1 | |||
Intracellular non-membrane-bounded organelle (5%) | RPS20, MRPS21, ANXA1 | |||
Intracellular vesicle, cytoplasmic vesicle (5%) | ANXA1, ITM2B, HSPD1 | |||
Integral component of membrane (5%) | TOMM20, ITM2B, HSPD1 | |||
Organelle envelope (4%) | TOMM20, CYCS | |||
Organelle membrane (4%) | TOMM20, ITM2B | |||
Extracellular organelle, plasma membrane region, endosome, extracellular exosome (4%) | ANXA1, HSPD1 | |||
Intrinsic component of organelle membrane (4%) | TOMM20, ITM2B | |||
Extrinsic component of plasma membrane (4%) | ANXA1, GNG5 | |||
Plasma membrane bounded cell projection, cilium, apical plasma membrane, external side of plasma membrane (2%) | ANXA1 | |||
Supramolecular polymer (2%) | ANXA1 | |||
Plasma membrane protein complex, extrinsic component of cytoplasmic side of plasma membrane, GTPase complex (2%) | GNG5 | |||
Nuclear DNA-directed RNA polymerase complex, RNA polymerase complex, RNA polymerase II (holoenzyme), RNA polymerase II transcription regulator complex, transferase complex (2%) | GTF2A2 | |||
Lipopolysaccharide receptor complex, secretory granule, Clathrin-coated pit (2%) | HSPD1 | |||
Golgi apparatus (2%) | ITM2B | |||
Ribosomal subunit (2%) | RPS20 | |||
Spliceosomal complex, small nuclear ribonucleoprotein complex (2%) | SF3A1 | |||
Outer membrane, Mitochondria-associated endoplasmic reticulum membrane, outer mitochondrial membrane protein complex (2%) | TOMM20 |
Probe Set ID | Gene Description | Gene Symbol | LPS Treated vs. Control Tumor-Adjacent Organoids (Log-Ratio M) | LPS Treated vs. Control IBD Colonoids (Log-Ratio M) | LPS Treated vs. Control IBD Enteroids (Log-Ratio M) |
---|---|---|---|---|---|
Cfa.6267.3.S1_s_at | Cysteine rich protein 1 (CRIP1) | CRIP1 | −0.238149286 | 0.43971334 | −0.3231234 |
Cfa.758.1.S1_at | Annexin A1 | ANXA1 | 0.309584226 | 0.57352154 | −0.2534974 |
Cfa.11085.1.A1_at | Regulator of G-protein signaling 2 | RGS2 | −0.302506821 | 0.40545754 | −0.2130524 |
Group Comparison * | Probe Set ID | Symbol | Name | Pathway |
---|---|---|---|---|
LPS Treated IBD sunek Colonoids vs. Control IBD Colonoids | CfaAffx.13209.1.S1_s_at | CP | Ceruloplasmin [EC:1.16.3.1] | Porphyrin metabolism, ferroptosis |
Cfa.6996.1.A1_at | ENPP6 | Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 [EC:3.1.4.-] | Ether lipid metabolism | |
Control IBD Colonoids vs. Control IBD Enteroids | CfaAffx.13785.1.S1_at, Cfa.6413.1.A1_at | CA1 | Carbonic anhydrase [EC:4.2.1.1] | Nitrogen metabolism |
Cfa.20798.1.S1_at, Cfa.3774.1.A1_s_at | ANPEP (LOC112653425) | Aminopeptidase N [EC:3.4.11.2] | Glutathione metabolism, renin–angiotensin system, hematopoietic cell lineage | |
CfaAffx.4748.1.S1_at | BAAT | Bile acid-CoA:amino acid N-acyltransferase [EC:2.3.1.65 3.1.2.2] | Primary bile acid biosynthesis, taurine and hypotaurine metabolism, Biosynthesis of unsaturated fatty acids, Peroxisome, Bile secretion | |
Control IBD Enteroids vs. Control Tumor Enteroids | CfaAffx.13785.1.S1_at, Cfa.6413.1.A1_at | CA1 | Carbonic anhydrase [EC:4.2.1.1] | Nitrogen metabolism |
Cfa.20798.1.S1_at, Cfa.3774.1.A1_s_at | ANPEP (LOC112653425) | Aminopeptidase N [EC:3.4.11.2] | Glutathione metabolism, renin–angiotensin system, hematopoietic cell lineage | |
Cfa.20396.1.S1_at | BACE2 | Beta-site APP-cleaving enzyme 2 (memapsin 1) [EC:3.4.23.45] | Alzheimer’s disease | |
CfaAffx.4748.1.S1_at | BAAT | Bile acid-CoA:amino acid N-acyltransferase [EC:2.3.1.65 3.1.2.2] | Primary bile acid biosynthesis, taurine and hypotaurine metabolism, biosynthesis of unsaturated fatty acids, peroxisome, bile secretion | |
LPS treated IBD colonoids vs. LPS treated IBD enteroids | CfaAffx.13785.1.S1_at, Cfa.6413.1.A1_at | CA1 | Carbonic anhydrase [EC:4.2.1.1] | Nitrogen metabolism |
Cfa.18640.1.S1_at | ACSL5 | Acyl-CoA synthetase long chain family member 5 [EC:6.2.1.3] | Fatty acid biosynthesis, fatty acid degradation, fatty acid metabolism, PPAR signaling pathway, ferroptosis, Thermogenesis, adipocytokine signaling pathway | |
Cfa.6996.1.A1_at | ENPP6 | Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 [EC:3.1.4.-] | Ether lipid metabolism | |
CfaAffx.4748.1.S1_at | BAAT | Bile acid-CoA:amino acid N-acyltransferase [EC:2.3.1.65 3.1.2.2] | Primary bile acid biosynthesis, taurine and hypotaurine metabolism, biosynthesis of unsaturated fatty acids, peroxisome, bile secretion | |
LPS treated IBD enteroids vs. LPS treated tumor enteroids | CfaAffx.13785.1.S1_at, Cfa.6413.1.A1_at | CA1 | Carbonic anhydrase [EC:4.2.1.1] | Nitrogen metabolism |
Cfa.18640.1.S1_at | ACSL5 | Acyl-CoA synthetase long chain family member 5 [EC:6.2.1.3] | Fatty acid biosynthesis, fatty acid degradation, fatty acid metabolism, PPAR signaling pathway, ferroptosis, thermogenesis, adipocytokine signaling pathway | |
Cfa.6996.1.A1_at | ENPP6 | Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 [EC:3.1.4.-] | Ether lipid metabolism | |
CfaAffx.4748.1.S1_at | BAAT | Bile acid-CoA:amino acid N-acyltransferase [EC:2.3.1.65 3.1.2.2] | Primary bile acid biosynthesis, taurine and hypotaurine metabolism, biosynthesis of unsaturated fatty acids, peroxisome, bile secretion | |
Common genes between IBD enteroids and colonoids following LPS stimulation | Cfa.2878.1.A1_s_at | CP | Ceruloplasmin [EC:1.16.3.1] | Porphyrin metabolism, ferroptosis |
CfaAffx.21951.1.S1_s_at | EEF1A1 | Eukaryotic translation elongation factor 1 alpha 1 (eEF1A1) | Nucleocytoplasmic transport, legionellosis, leishmaniasis | |
CfaAffx.2163.1.S1_at | TAP2 (ABCB3) | ATP-binding cassette, subfamily B (MDR/TAP), member 3 [EC:7.4.2.14] | ABC transporters, phagosome, antigen processing and presentation, human cytomegalovirus infection, Herpes simplex virus 1 infection, Epstein–Barr virus infection, human immunodeficiency virus 1 infection, primary immunodeficiency | |
CfaAffx.17868.1.S1_at | GPX1 | Glutathione peroxidase 1 [EC 1.11.1.9] | Glutathione metabolism, arachidonic acid metabolism |
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Sahoo, D.K.; Borcherding, D.C.; Chandra, L.; Jergens, A.E.; Atherly, T.; Bourgois-Mochel, A.; Ellinwood, N.M.; Snella, E.; Severin, A.J.; Martin, M.; et al. Differential Transcriptomic Profiles Following Stimulation with Lipopolysaccharide in Intestinal Organoids from Dogs with Inflammatory Bowel Disease and Intestinal Mast Cell Tumor. Cancers 2022, 14, 3525. https://doi.org/10.3390/cancers14143525
Sahoo DK, Borcherding DC, Chandra L, Jergens AE, Atherly T, Bourgois-Mochel A, Ellinwood NM, Snella E, Severin AJ, Martin M, et al. Differential Transcriptomic Profiles Following Stimulation with Lipopolysaccharide in Intestinal Organoids from Dogs with Inflammatory Bowel Disease and Intestinal Mast Cell Tumor. Cancers. 2022; 14(14):3525. https://doi.org/10.3390/cancers14143525
Chicago/Turabian StyleSahoo, Dipak Kumar, Dana C. Borcherding, Lawrance Chandra, Albert E. Jergens, Todd Atherly, Agnes Bourgois-Mochel, N. Matthew Ellinwood, Elizabeth Snella, Andrew J. Severin, Martin Martin, and et al. 2022. "Differential Transcriptomic Profiles Following Stimulation with Lipopolysaccharide in Intestinal Organoids from Dogs with Inflammatory Bowel Disease and Intestinal Mast Cell Tumor" Cancers 14, no. 14: 3525. https://doi.org/10.3390/cancers14143525