Transcriptomic analysis of pathways regulated by toll-like receptor 4 in a murine model of chronic pulmonary inflammation and carcinogenesis

Bauer, Alison K; Fostel, Jennifer; Degraff, Laura M; Rondini, Elizabeth A; Walker, Christopher; Grissom, Sherry F; Foley, Julie; Kleeberger, Steven R

doi:10.1186/1476-4598-8-107

Molecular Cancer

Table 1 Representative gene expression changes increased in BALBLsp-d compared to BALB mice.

From: Transcriptomic analysis of pathways regulated by toll-like receptor 4 in a murine model of chronic pulmonary inflammation and carcinogenesis

Gene Symbol	Gene Name	Affymetrix Probe ID	Major GO Category(ies)
Angiogenesis
Hbegf ^†	heparin-binding EGF-like growth factor	1418349_at	angiogenesis; blastocyst growth
Mmp19 ^†	matrix metallopeptidase 19	1421977_at	angiogenesis; peptidoglycan metabolic process
Timp1 ^†	tissue inhibitor of metallo-proteinase 1	1460227_at	erythrocyte maturation
Cell cycle and cell growth
Cdkn1a ^†	cyclin-dependent kinase inhibitor 1A (P21)	1424638_at	regulation of progression through cell cycle; response to DNA damage stimulus
*Ereg* ^†‡	epiregulin	1419431_at	regulation of progression through cell cycle; angiogenesis
Mina	myc induced nuclear antigen	1451042_a_at	regulation of cell proliferation
Myc ^†	myelocytomatosis oncogene	1424942_a_at	regulation of progression through cell cycle; release of cytochrome c from mitochondria
Socs3	suppressor of cytokine signaling 3	1455899_x_at	regulation of cell growth; regulation of protein amino acid phosphorylation
Cell shape and morphogenesis
Krt19	keratin 19	1417156_at	cytoskeleton organization and biogenesis
Tnc ^†	tenascin C	1416342_at	cell adhesion
Tuba1c	tubulin, alpha 1C	1416128_at	microtubule-based process and movement
Inflammatory and immune response
Il6 ^†	interleukin 6	1450297_at	neutrophil apoptosis
Lif ^†	leukemia inhibitory factor	1421207_at	immune response; tyrosine phosphorylation of stat3 protein
Spp1 ^†	secreted phosphoprotein 1	1449254_at	ossification; anti-apoptosis
Protein synthesis and turnover
Eif1a	eukaryotic translation initiation factor 1A	1419736_a_at	translation and initiation
Hras1 ^†	Harvey rat sarcoma virus oncogene 1	1422407_s_at	translation; endocytosis
Nola1	nucleolar protein family A, member 1	1418305_s_at	rRNA processing; ribosome biogenesis and assembly
Nola2	nucleolar protein family A, member 2	1416605_at	rRNA processing; translation
Nol5A	nucleolar protein 5	1450986_at	ribosome biogenesis and assembly
Nmd3	NMD3 homolog	1437238_x_at	ribosomal large subunit export from nucleus
Rps6ka3	ribosomal protein S6 kinase polypeptide 3	1427299_at	protein amino acid phosphorylation; ribosome biogenesis and assembly
Protein targeting
Afp ^†	alpha fetoprotein	1416646_at	ovulation; transport
Bcl3 ^†	B-cell leukemia/lymphoma 3	1418133_at	protein import into nucleus, translocation; follicular dendritic cell differentiation
Bnip1	BCL2/adenovirus E1B interacting protein 1, NIP1	1427908_at	ER to Golgi vesicle-mediated transport; apoptosis
Nup62	Nucleoporin 62	1438917_x_at	protein targeting; transport
Transcription, processing, and chromatin structure
Bhlhb8	basic helix-loop-helix domain containing, class B, 8	1449233_at	regulation of transcription, DNA-dependent
Ddx39	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39	1423643_at	mRNA processing; RNA splicing
Hmga1 ^†	high mobility group AT-hook 1	1416184_s_at	DNA packaging; transcription
Lmna	lamin A	1425472_a_at	nuclear membrane organization and biogenesis
Pparg ^†	peroxisome proliferator activated receptor gamma	1420715_a_at	negative regulation of transcription from RNA polymerase II promoter

These genes were identified in profile "BHT-1day_up" (A) and profile "BHT-1day_down" (B) below the p value set for the DAVID analysis (p < 0.0003)*; see Additional file 2, Table S1 for the complete profile gene lists.
*These genes were identified after bioinformatic analysis filtering first on biological patterns using both Genespring and Spotfire Software followed by filtering on GO biological categories using the DAVID Bioinformatics Database. ^†These genes were upregulated ≥ 2-fold in BALB^Lsp-dvs. BALB 1 day following protocol 1 (chronic BHT) (P < 0.05). ^‡Significant interaction effects between strain (BALB vs BALB^Lpsdmice) and treatment (oil, 1 or 3 days following 4BHT) (p < 0.05). Bolded genes are those genes in common with the gene list identified for Protocol 2 (see Table 2).

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ISSN: 1476-4598

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