Table 3.
SF-3–030 Pretreatment Modulates the Profile of Proteins Involved in Multiple Pathways in the Lung
| Gene | Annotation | Function | Abundance Ratio |
|---|---|---|---|
| A. Group 1: Proteins Upregulated by HDM and Inhibited by SF-3–030 | |||
| Immunoglobulin production and aminoglycan metabolism | |||
| Gtf3c1 | General transcription factor 3C polypeptide 1 | 5S class rRNA transcription by RNA polymerase III | 0.001 |
| Ighm | Immunoglobulin heavy constant mu | Antigen processing and presentation | 0.375 |
| Hexb | β-hexosaminidase subunit β | Astrocyte cell migration | 0.620 |
| Ighv5-15 | Immunoglobulin heavy variable 5-15 | B-cell receptor signaling pathway | 0.399 |
| Ighv1-43 | Immunoglobulin heavy variable V1-43 | 0.684 | |
| Ighv1-4 | Immunoglobulin heavy variable 1-4 | 0.550 | |
| Anxa8 | Annexin A8 | Blood coagulation | 0.458 |
| Gpnmb | Transmembrane glycoprotein NMB | Bone mineralization | 0.526 |
| Chil4 | Chitinase-like protein 4 | Carbohydrate metabolic process | 0.770 |
| Pds5b | Sister chromatid cohesion protein PDS5 homolog B | Cell division | 0.175 |
| Selenot | Thioredoxin reductase-like selenoprotein T | Cell redox homeostasis | 0.001 |
| Hba-a1 | α globin 1 | Cellular oxidant detoxification | 0.720 |
| Hcn3 | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 | Cellular response to dopamine | 0.001 |
| Tbc1d4 | TBC1 domain family member 4 | Cellular response to insulin stimulus | 0.001 |
| Igkv6-32 | Immunoglobulin kappa variable 6-32 | Immune response | 0.671 |
| Igkv6-23 | Immunoglobulin kappa variable 6-23 | 0.300 | |
| Igkv6-17 | Immunoglobulin kappa variable 6-17 | 0.507 | |
| Igkv6-13 | Immunoglobulin kappa variable 6-13 | 0.224 | |
| Igkv4-78 | Immunoglobulin kappa variable 4-78 | 0.001 | |
| Igkv4-58 | Immunoglobulin kappa variable 4-58 | 0.001 | |
| Igkv4-57-1 | Immunoglobulin kappa variable 4-57-1 | 0.488 | |
| Vbp1 | Prefoldin subunit 3 | Microtubule-based process | 0.356 |
| Pip4p2 | Type 2 phosphatidylinositol 4,5-bisphosphate 4-phosphatase | Negative regulation of phagocytosis | 0.001 |
| Ints9 | Integrator complex subunit 9 | snRNA processing | 0.001 |
| B. Group 2: Proteins Upregulated by HDM and Further Upregulated by SF-3–030 | |||
| Cellular response to chemical stimulus | |||
| Retnlg | Resistin-like γ | Myeloid dendritic cell chemotaxis | 1.392 |
| Rac2 | Ras-related C3 botulinum toxin substrate 2 | Actin cytoskeleton organization | 1.346 |
| Arg1 | Arginase-1 | Adaptive immune response | 1.311 |
| Iglc1 | Immunoglobulin lambda constant 1 | B-cell receptor signaling pathway | 4.077 |
| Ighv9-4 | Immunoglobulin heavy variable 9-4 | 2.055 | |
| Ighv6-3 | Immunoglobulin heavy variable 6-3 | 2.361 | |
| Ighv2-6 | Immunoglobulin heavy variable 2-6 | 1.700 | |
| Ighv1-62-2 | Immunoglobulin heavy variable 1-62-2 | 1.957 | |
| Pcna | Proliferating cell nuclear antigen | Base-excision repair, gap filling | 1.488 |
| Fryl | FRY-like transcription coactivator | Cell morphogenesis | 2.723 |
| Mt1 | Metallothionein-1 | Cellular metal ion homeostasis | 2.796 |
| Mt2 | Metallothionein-2 | Cellular response to cadmium ion | 1.710 |
| Ear2 | Eosinophil cationic protein 2 | Chemotaxis | 1.636 |
| Ear1 | Eosinophil cationic protein 1 | 1.775 | |
| Ear6 | Ear6 protein | 1.439 | |
| C. Group 3: Proteins Downregulated by HDM and Upregulated by SF-3–030 | |||
| Regulation of developmental process | |||
| Ophn1 | Oligophrenin-1 | Actin cytoskeleton reorganization | 5.317 |
| S1pr1 | Sphingosine 1-phosphate receptor 1 | 1,000 | |
| Amfr | E3 ubiquitin-protein ligase AMFR | Aging | 1.863 |
| Ntn4 | Netrin-4 | Animal organ morphogenesis | 1,000 |
| Myh8 | Myosin-8 | ATP metabolic process | 1,000 |
| Dock4 | Dedicator of cytokinesis protein 4 | Cell chemotaxis | 1,000 |
| Dnajc7 | DnaJ homolog subfamily C member 7 | Chaperone cofactor-dependent protein refolding | 1,000 |
| Snx27 | Sorting nexin-27 | Endocytic recycling | 1,000 |
| Unc13d | Protein unc-13 homolog D | Exocytosis | 2.911 |
| Taf15 | TAF15 RNA polymerase II, TATA box binding protein | Gene expression | 1,000 |
| Igkv1-88 | Immunoglobulin kappa chain variable 1-88 | Immune response | 1,000 |
| Sart1 | U4/U6.U5 tri-snRNP–associated protein 1 | Maturation of 5S rRNA | 1,000 |
| Cenpq | Centromere protein Q | Metaphase plate compression? | 1,000 |
| Comtd1 | Catechol O-methyltransferase domain-containing protein 1 | Methylation | 1,000 |
| Snrpb2 | U2 small nuclear ribonucleoprotein B | mRNA splicing via spliceosome | 1,000 |
| Ctdsp1 | Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 | Negative regulation of G1/S transition of mitotic cell cycle | 1,000 |
| Rgs22 | Regulator of G-protein signaling 22 | Negative regulation of signal transduction | 1,000 |
| Nat10 | RNA cytidine acetyltransferase | Negative regulation of telomere maintenance via telomerase | 1,000 |
| Arap3 | Arf-GAP with Rho-GAP domain, ANK repeat, and PH domain-containing protein 3 | Positive regulation of GTPase activity | 1,000 |
| Fastk | Fas-activated serine/threonine kinase | Regulation of mitochondrial mRNA stability | 1,000 |
| D. Group 4: Proteins Downregulated by HDM and Further Downregulated by SF-3–030 | |||
| Cell–matrix adhesion | |||
| Itga2b | Integrin α-IIb | Cell–matrix adhesion | 0.587 |
Definition of abbreviations: ATP = adenosine triphosphate; rRNA = ribosomal RNA; snRNA = small nuclear RNA; LC-MS/MS = liquid chromatography with tandem mass spectrometry.
Protein abundance was determined by label-free quantification using LC-MS/MS. Proteins are categorized on the basis of pathway regulation between HDM versus HDM + SF-3–030 groups in four distinct groups: proteins that were upregulated by HDM that were (A) inhibited by SF-3–030 and (B) further upregulated by SF-3–030 and genes downregulated by HDM that were (C) upregulated by SF-3–030 and (D) further downregulated by SF-3–030. n = 3–4.