Table 1. Genes whose expression was modulated in the lungs of wood mice infected with vM3.MR compared with those infected with vM3.stop.
| Symbol | Description | Tissue/cell specificity | Biological processa | Ratiob |
|---|---|---|---|---|
| Upregulated in vM3.MR-infected wood mice | ||||
| Immune/inflammatory response | ||||
| Igha | Immunoglobulin heavy constant α | Lymph node, intestine | Mucosal immune response | 2.6 |
| Ighg1 | Immunoglobulin heavy constant gamma 1 | Lymph node | Humoral immune response mediated by circulating Ig | 4.5 |
| Ighg2b | Immunoglobulin heavy constant gamma 2B | Lymph node | Humoral immune response mediated by circulating Ig | 2.4 |
| Ighm | Immunoglobulin heavy constant mu | Lymph node | Humoral immune response mediated by circulating Ig | 2.8 |
| Ighm | Immunoglobulin heavy constant mu | Lymph node | Humoral immune response mediated by circulating Ig | 3 |
| Ighv1–72 | Immunoglobulin heavy variable 1–72 | Lymph node, small intestine | Humoral immune response mediated by circulating Ig | 2.7 |
| Igk-V8 | Immunoglobulin κ chain | B cells, lymph node | Humoral immune response mediated by circulating Ig | 5.7 |
| Igkv8–30 | Immunoglobulin κ chain variable 8–30 | B cells, lymph node | Humoral immune response mediated by circulating Ig | 3.4 |
| Igkc | Immunoglobulin κ constant | B cells, lymph node | B-cell differentiation | 2.4 |
| Oas2 | 2'-5' Oligoadenylate synthetase 2 | Macrophage | Immune response/Rnase L induction | 2 |
| C1qb | Complement component 1, q subcomponent, β polypeptide | Macrophage, microglia, spleen, lymph nodes | Complement activation, classical pathway | 2.1 |
| Itgb6 | Integrin β 6 | Kidney, lung, skeletal muscle | Cell adhesion/signaling/inflammation | 3.1 |
| Cell signaling | ||||
| Dusp1 | Dual specificity phosphatase 1 | Macrophage, lung, dendritic cell | Inactivation of MAPK activity | 2 |
| Rem1 | Rad- and gem-related GTP-binding protein 1 | Myoblasts | Signal transduction | 2 |
| Map3k4 | Mitogen-activated protein kinase kinase kinase 4 | Ubiquitous | Intracellular protein kinase cascade | 4.8 |
| Tprkb | Tp53rk-binding protein | liver, kidney, eye | protein catabolic process | 2.3 |
| Ywhaq | Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide | Embryonal stem cells, neuronal tissue | Signal transduction | 2 |
| Regulation of expression | ||||
| Crx | Cone-rod homeobox-containing gene | Retina | Regulation of transcription | 3.5 |
| Myb | Myeloblastosis oncogene | Myeloid progenitor, T cell | G1/S transition of mitotic cell cycle | 2.2 |
| Bcas2 | Breast carcinoma amplified sequence 2 | Embryonal stem cells | mRNA processing | 2.3 |
| Paip1 | Polyadenylate-binding protein-interacting protein 1 | stem cell, pro-B cell | Positive regulation of translation | 7.4 |
| Cell adhesion/morphogenesis | ||||
| Vcl | Vinculin | Lung, mast cells | Focal adhesion plaque formation | 3 |
| Cdh15 | Cadherin 15 | Muscle | Cell adhesion | 2.6 |
| Npnt | Nephronectin | Lung, kidney | Cell–cell adhesion mediated by integrin | 2.8 |
| Parva | Parvin, α | Osteoblasts, stem cells, lung | Cell adhesion | 2.9 |
| Lung/respiratory tract | ||||
| Bpifa1 | BPI fold-containing family A, member 1 | Lung, heart | 17.6 | |
| Bpifb1 | BPI fold-containing family B, member 1 | Lung, stomach | 7.3 | |
| Scgb1a1 | Secretoglobin, family 1A, member 1 | Lung | 10.3 | |
| Scgb3a2 | Secretoglobin, family 3A, member 2 | Lung | 3.2 | |
| Detoxification | ||||
| Cyp2f2 | Cytochrome P450, family 2, subfamily f, polypeptide 2 | Lung, lacrimal gland, salivary gland, liver | Response to toxinoxidation-reduction process | 2.2 |
| Cyp2a4 | Similar to cytochrome P450, family 2, subfamily a, polypeptide 4 | Lacrimal gland | Oxidation-reduction process | 12.8 |
| Myeloid cell activation | ||||
| Snca | Synuclein, α | Bone marrow, neuronal tissue | Myeloid leukocyte activation | 2.1 |
| Trim10 | Tripartite motif-containing 10 | Bone marrow | Myeloid cell haemopoiesis | 4.5 |
| Ion transport | ||||
| Slc4a1 | Solute carrier family 4 (anion exchanger), member 1 | Bone marrow | Anion transport | 2.2 |
| Lrrc26 | Leucine-rich repeat containing 26 | Salivary gland, lacrimal gland | Ion transport | 2 |
| Miscellaneous | ||||
| Ap2a2 | Adaptor protein complex AP-2, α 2 subunit | CD4 T cell, granulocytes | Endocytosis | 3 |
| Bc1 | Brain cytoplasmic RNA 1 | Translational repressor activity | 2.7 | |
| Mus81 | MUS81 endonuclease homolog (yeast) | Adipose tissue, muscle | DNA repair | 2.1 |
| Mccc2 | Methylcrotonoyl-Coenzyme A carboxylase 2 (β) | Adipose tissue, liver, kidney | Coenzyme A metabolic process | 2 |
| Spa17 | Sperm autoantigenic protein 17 | Testis | Ciliary or flagellar motility | 2.1 |
| Myl4 | Myosin, light polypeptide 4 | Heart, lung | Muscle contraction | 2.5 |
| Agr2 | Anterior gradient homolog 2 | Intestine, lacrymal gland | ER secreory pathway | 4.2 |
| Agr3 | Anterior gradient homolog 3 | Lung, testis | ER secreory pathway | 10 |
| Downregulated in vM3.MR-infected wood mice | ||||
| Regulation of expression | ||||
| Rnpc3 | RNA-binding region (RNP1, RRM) containing 3 | Ubiquitous | Regulation of alternative mRNA splicing, via spliceosome | 2.5 |
| Malat1 | Metastasis-associated lung adenocarcinoma transcript 1 (non-coding RNA) | Adrenal gland | Regulation of alternative mRNA splicing, via spliceosome | 2.2 |
| Malat1 | Metastasis-associated lung adenocarcinoma transcript 1 (non-coding RNA) | Regulation of alternative mRNA splicing, via spliceosome | 3.0 | |
| Nsa2 | NSA2 ribosome biogenesis homolog | B cells, mast cells and macrophages | rRNA processing | 4.3 |
| Ddx6 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 | B cells, T cells | Cytoplasmic mRNA processing body assembly | 2.0 |
| C1d | C1D nuclear receptor co-repressor | Myeloid, dendritic cells, osteoblasts | Regulation of transcription | 2.9 |
| Mtf1 | Metal response element-binding transcription factor 1 | Lacrimal gland, testis | Regulation of transcription | 2.7 |
| Ankrd1 | Ankyrin repeat domain 1 (cardiac muscle) | Heart | Regulation of transcription | 2.2 |
| Fubp1 | Far upstream element (FUSE)-binding protein 1 | Embryonal stem cells, T cells, B cells | Regulation of transcription | 6.0 |
| Nfic | Nuclear factor I/C | Muscle, adipose tissue | Regulation of transcription | 3.3 |
| Yap1 | Yes-associated protein 1 | Embryonal Stem cells, placenta | Regulation of transcription | 2.0 |
| Hist1h1c | Histone cluster 1, H1c | Pancreas, intestine, osteoblast | Chromatin organization | 4.0 |
| Srp9 | Signal recognition particle 9 | Lacrimal gland, prostate | Negative regulation of translational elongation | 3.0 |
| Ion transport | ||||
| Slc39a8 | Solute carrier family 39 (metal ion transporter), member 8 | Lung, uterus, cornea | Zinc ion transport | 2.0 |
| Nipal2 | NIPA-like domain containing 2 | Salivary, lacrimal glands | Magnesium ion transport | 5.9 |
| Mfsd7c | Major facilitator superfamily domain containing 7C | Placenta | Haeme transport | 2.0 |
| Sln | Sarcolipin | Macrophage, thymocyte | Regulation of calcium ion transport | 7.3 |
| Atp6v0b | ATPase, H+ transporting, lysosomal V0 subunit B | Macrophage, microglia | Proton transport | 2.0 |
| Cell signaling | ||||
| Rnd3 | Rho family GTPase 3 | Dendritic cell, fibroblast, osteoblast | Small GTPase-mediated signal transduction | 3.0 |
| Calm1 | Calmodulin 1 | Ubiquitous | Response to calcium ion | 7.0 |
| Leprot | Leptin receptor overlapping transcript | Mast cell, macrophage, osteoblast | Negative regulation of JAK-STAT cascade | 2.0 |
| Igbp1 | Immunoglobulin (CD79A)-binding protein 1 | Granulocytes | Negative regulation of stress-activated MAPK cascade | 2.4 |
| Camk1d | Calcium/calmodulin-dependent protein kinase ID | Dendritic cells, neuronal tissue | Protein modification process | 2.0 |
| Immune/inflammatory response | ||||
| Igk-V1 | Immunoglobulin κ chain variable 1 (V1) | Intestine, spleen, B cell | 2.4 | |
| Bcap29 | B-cell receptor-associated protein 29 | B cells, macrophage, testis | Apoptosis/intracellular transport | 3.0 |
| Sod2 | Superoxide dismutase 2, mitochondrial | Macrophage, microglia | Response to reactive oxygen species | 5.0 |
| Retnla | Resistin like α | Adipose tissue, lung | Hormone activity/Inflammatory response | 2.1 |
| Tbk1 | TANK-binding kinase 1 | Macrophage | Positive regulation of interferon-α/β | 2.0 |
| Cell adhesion/morphogenesis | ||||
| Itgav | Integrin α V | Macrophage, osteoblast | Cell adhesion/phagocytosis | 4.8 |
| Sirpa | Signal-regulatory protein α | Macrophage | Phagocytosis | 2.5 |
| Sytl1 | Synaptotagmin-like 1; similar to synaptotagmin-like 1 | Salivary, lacrimal glands | Exocytosis | 4.7 |
| Cyfip1 | Cytoplasmic FMR1-interacting protein 1 | Macrophage, microglia | Cell morphogenesis | 6.8 |
| Cell cycle | ||||
| Cdc123 | Cell division cycle 123 | Ubiquitous | G1 phase of mitotic cell cycle | 6.6 |
| Commd5 | COMM domain containing 5 | Macrophage | Cell cycle arrest | 2.2 |
| Miscellaneous | ||||
| Zdhhc12 | zinc finger, DHHC domain containing 12 | macrophage | 3.0 | |
| Ssfa2 | Sperm-specific antigen 2 | epidermis, mast cells, macrophage | 2.7 | |
| Ndufa2 | NADH dehydrogenase (ubiquinone) 1 α subcomplex, 2 | Ubiquitous | Electron transport chain | 2.0 |
| Tpm3 | Tropomyosin 3, γ | NK cells, mast cells | Nervous system development | 2.4 |
| Pgk1 | Phosphoglycerate kinase 1 | Macrophage, skeletal muscle | Glucose catabolic process | 3.8 |
| Bgn | Biglycan | Osteoblast, fibroblast, lung | Extracellular matrix | 11.7 |
| 2700089E24Rik | RIKEN cDNA 2700089E24 gene | Salivary gland, mammary gland | 4.3 | |
| Ckap4 | Cytoskeleton-associated protein 4 | Osteoblast, fibroblast | 2.7 | |
| Ttn | Titin | Heart, mammary gland, skeletal muscle | Sarcomere organization | 3.9 |
| Mb | Myoglobin | Ubiquitous | Oxygen transport | 2.7 |
| Acaa1a | Acetyl-Coenzyme A acyltransferase 1A | Liver, kidney | Fatty acid metabolic process | 4.2 |
| Hsd17b7 | Hydroxysteroid (17-β) dehydrogenase 7 | Ovary, liver, macrophage | Steroid biosynthetic process | 4.8 |
a
Gene symbol, description, tissue/cell specificity, and Biological Process were annotated using DAVID (http://david.abcc.ncifcrf.gov/)56, 57 and BioGPS (http://biogps.org/).58
b
Ratio of the normalized signal intensities obtained after Affymetrix genechip analysis for animals infected with vM3.MR vs vM3.stop. Only genes (probe sets) showing greater than twofold change in value and with a P<0.001 with respect to Present or Absent flags are represented.Bolded values are transcripts that were significantly upregulated and the focus of this manuscript.