Modelling Nonalcoholic Steatohepatitis In Vivo—A Close Transcriptomic Similarity Supports the Guinea Pig Disease Model
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals
2.2. Liver Samples and Histology
2.3. Guinea Pig Hepatic RNA Sequencing
2.4. Transcriptome Analyses
2.5. Protein–Protein Association Network
2.6. Translational Aspects of the Guinea Pig Model
2.7. Correlation Analysis of Gene Expression and Fibrosis Quantification
2.8. Statistical Analysis
3. Results
3.1. Guinea Pig NASH Development and Disease Stage
3.2. The Hepatic Transcriptome Clearly Distinguishes Guinea Pigs with NASH from Controls
3.3. The Guinea Pig NASH Transcriptome Is Similar to That of Humans with Early-Stage NASH
3.4. Guinea Pig NASH Transcriptome Resembles Human Advanced NASH
3.5. Identification of Potential New Biomarkers of Fibrosis Deposition
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Preclinical Model | Sex | Species: Strain | Weeks on Diet | Histological Phenotype |
---|---|---|---|---|
Guinea pig | Female | Guinea pig: Dunkin-Hartley | 25 | NASH with fibrosis. Histological scoring: NASH CRN [10] |
DIAMOND [32] | Male | Mouse: B6/129 (isogenic cross between C57BL/6J and 129S1/SvImJ) | 52 | NASH with fibrosis Histological scoring: NASH CRN [10] |
WD1 [30] | Male | Mouse: C57BL/6N | 12 | NAFLD No histological scoring. Positive α-sma liver stain and picrosirius red indicative of activated hepatic stellate cells and fibrosis, respectively |
WD2 [31] | Male | Mouse: C57BL/6J | 20 | NAFLD. No histological scoring |
Group | Control (n = 6) | NASH (n = 6) |
---|---|---|
Steatosis 1 | 0 | 3 ** |
Ballooning 1 | 0 | 2 (1–2) * |
Inflammation 1 | 0 (0–1) | 3 ** |
Fibrosis 1 | 0 | 3 ** |
Relative fibrosis area 2 | 1.39 ± 0.24 | 7.48 ± 1.81 *** |
Gene Name (Full Name) | Log2 Fold Change | Adjusted p-Value | Function |
---|---|---|---|
ADAMDEC1 (ADAM like decysin 1) | 8.01 | 4.94 ×10−60 | Secreted protein invovled in dendritic cell maturation. |
ADGRG3 (adhesion G protein-coupled receptor 3) | 7.66 | 3.79 × 10−40 | GPCR possibly invovled tumor angiogenesis. |
KRT23 (keratin 23) | 10.97 | 1.53 × 10−35 | Member of keratin family of intermediate filaments responsible for structural integrity of epithelial cells. |
ATP6V0A4 (ATPase H + transporting V0 subunit a4) | 9.02 | 3.01 × 10−32 | Vacuolar ATPase mediating acidification of intracellular compartments necessary for protein sorting, zymogen activation, receptor-mediated endocytosis and synaptic vesicle protein gradient generation. |
TMEM213 (transmembrane protein 213) | 10.12 | 1.28 × 10−29 | No listed function. |
CIB4 (calcium and integrin binding family member 4) | −9.70 | 1.82 × 10−26 | No listed function. |
PAK6 (p21 (RAC1) activated kinase 6) | 9.38 | 5.69 × 10−26 | p21 stimulated serine/threonine kinase involved in cytoskeleton rearrangement, apoptosis and MAP kinase signalling pathway. |
TMC1 (transmembrane channel like 1) | 9.27 | 1.82 × 10−25 | No listed function. |
CCL7 (C–C motif chemokine ligand 7) | 9.09 | 2.30 × 10−25 | Encodes MCP3-a secreted chemokine recruiting macrophages during inflammation, and also a substrate of MMP2. |
PTPRN (protein tyrosine phosphatase receptor type N) | 9.23 | 2.58 × 10−24 | Signalling molecule regulating processes such as cell growth, differentiation, mitotic cycle, and oncogenic transformation. |
VSIG1 (V-set and immunoglobulin domain containing 1) | 8.26 | 1.06 × 10−22 | Encodes a member of the junctional adhesion molecule (JAM) family. |
SLC34A2 (solute carrier family 34 member 2) | 8.49 | 1.13 × 10−20 | pH-sensitive sodium-dependent phosphate transporter |
DSG4 (desmoglein 4) | 8.15 | 2.78 × 10−19 | Desmosomal cadherin possibly playing a role in cell–cell adhesion in epithelial cells. |
TNFSF18 (TNF super family member 18) | 7.74 | 1.92 × 10−17 | Cytokine belonging to the TNF ligand family that plays a role in T-lymphocyte survival and the interaction between endothelial cells and T lymphocytes. |
MTHFD2 (methylenetetrahydrofolate dehydrogenase (NADP + dependent) 2, methenyltetrahydrofolate cyclohydrolase) | 7.63 | 6.53 × 10−17 | Nuclear encoded mitochondrial bifunctional enzyme with methylenetetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclohydrolase activities. |
SPOCK1 (SPARC (osteonectin), cwcv and kazal-like domains proteoglycan 1) | 7.72 | 8.38 × 10−17 | Seminal plasma proteoglycan containing chondroitin and heperan sulfate chains. |
ECT2 (epithelial cell transforming 2) | 8.43 | 5.94 × 10−16 | Guanine nucleotide exchange factor, expressed at high levels in mitotic cells in the regenerating liver. |
SPTA1 (spectrin alpha, erythrocytic 1) | 7.99 | 7.35 × 10−15 | Molecular scaffold protein that links the plasma membrane to the actin cytoskeleton and determines the cell shape. |
STAR (steroidogenic acute regulatory protein) | 8.36 | 2.48 × 10−14 | Involved in the acute regulation of steroid hormone synthesis by enhancing the conversion of cholesterol into pregnolone. |
KEL (Kell metalloendopeptidase (Kell blood group)) | 7.66 | 1.34 × 10−12 | Encodes a type II transmembrane glycoprotein of the Kell blood group antigen. |
Gene | Pearson’s ρ | p Value | GPLog2FC | HLog2FC | Function 1 | Secreted | Role in NASH | Cell-Specific Expression 2 |
---|---|---|---|---|---|---|---|---|
ACKR3 | All: 0.91 NASH: 0.87 | All: 4.54 × 10−5 NASH: 0.025 | 1.36 | HNASH1: ND HNASH2: 0.69 | GPCR, orphan receptor | NO | ? | Endothelial cells |
BIRC3 | All: 0.88 NASH: 0.82 | All: 1.77 × 10−4 NASH: 0.045 | 1.1 | HNASH1: 1.9 HNASH2: 0.7 | Inhibits apoptosis | NO | YES (hypoxia induced) [39] | Immune cells, cholangiocytes, endothelial cells, and hepatocytes |
CHST11 | All: 0.95 NASH: 0.87 | All: 1.42 × 10−6 NASH: 0.023 | 1.16 | HNASH1: −0.35 HNASH2: 0.19 | Promotes synthesis of chondroitin (ECM) | NO | ? | Immune cells |
EMP3 | All: 0.93 NASH: 0.81 | All: 9.41 × 10−6 NASH: 0.049 | 1.5 | HNASH1: 0.98 HNASH2: 0.19 | Membrane protein, cell proliferation | NO | ? | Immune cells |
FZD7 | All: 0.87 NASH: 0.83 | All: 2.22 × 10−4 NASH: 0.041 | 1.2 | HNASH1: ND HNASH2: 0.6 | Wnt signalling | NO | YES in HCC [40] | Cholangiocytes, HSC |
RGS14 | All: −0.83 NASH: −0.80 | All: 8.26 × 10−4 NASH: 0.053 | −1.58 | HNASH1: −0.3 HNASH2: −0.2 | Regulates GPCR (increases microtubule assembly) | NO | ? | Immune cells |
RHBDF1 | All: 0.96 NASH: 0.92 | All: 4.11 × 10−7 NASH: 0.010 | 1.17 | HNASH1: 0.6 HNASH2: 0.03 | Regulates ADAM17 and release of TNF-α | NO | ? | Cholangiocytes |
SERPINB9 | All: 0.9 NASH: 0.84 | All: 6.19 × 10−5 NASH: 0.037 | 1.4 | HNASH1: −0.7 HNASH2: 0.5 | Inhibits activity of granzyme B | YES | YES [41] | Immune cells, endothelial cells, stellate cells, and myofibroblasts, macrovascular endothelial cells |
VWF | All: 0.97 NASH: 0.86 | All: 7.52 × 10−8 NASH: 0.027 | 1.46 | HNASH1: −0.03 HNASH2: 0.5 | Platelet aggregation | YES | YES [42,43] | Macrovascular endothelial cells |
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Skat-Rørdam, J.; Ipsen, D.H.; Seemann, S.E.; Latta, M.; Lykkesfeldt, J.; Tveden-Nyborg, P. Modelling Nonalcoholic Steatohepatitis In Vivo—A Close Transcriptomic Similarity Supports the Guinea Pig Disease Model. Biomedicines 2021, 9, 1198. https://doi.org/10.3390/biomedicines9091198
Skat-Rørdam J, Ipsen DH, Seemann SE, Latta M, Lykkesfeldt J, Tveden-Nyborg P. Modelling Nonalcoholic Steatohepatitis In Vivo—A Close Transcriptomic Similarity Supports the Guinea Pig Disease Model. Biomedicines. 2021; 9(9):1198. https://doi.org/10.3390/biomedicines9091198
Chicago/Turabian StyleSkat-Rørdam, Josephine, David H. Ipsen, Stefan E. Seemann, Markus Latta, Jens Lykkesfeldt, and Pernille Tveden-Nyborg. 2021. "Modelling Nonalcoholic Steatohepatitis In Vivo—A Close Transcriptomic Similarity Supports the Guinea Pig Disease Model" Biomedicines 9, no. 9: 1198. https://doi.org/10.3390/biomedicines9091198