Table 2.
Small Airway Epithelium Genes Persistently Dysregulated Despite 1 Year of Smoking Cessation
| Gene | Gene Name | Functional Category | P Value | BH-Corrected P Value*† |
Fold Change*‡ |
|---|---|---|---|---|---|
| ME1 | Malic enzyme 1 | Oxidant related | <1 × 10−16 | <1 × 10−16 | 4.34 |
| PIR | Pirin | Oxidant related | 1.11 × 10−16 | 8.92 × 10−14 | 2.93 |
| SLC2A1 | Solute carrier family 2 member 1 | Transport | 1.11 × 10−16 | 8.92 × 10−14 | 1.59 |
| TRIM16 | Tripartite motif-containing 16 | Transcription | 2.22 × 10−16 | 1.53 × 10−13 | 2.27 |
| NPAS3 | Neuronal PAS domain protein 3 | Transcription | 4.44 × 10−16 | 2.79 × 10−13 | −2.12 |
| CYP4X1 | Cytochrome P450 family 4 subfamily X member 1 | Oxidant related | 1.33 × 10−15 | 8.03 × 10−13 | −1.70 |
| WNK4 | WNK lysine-deficient protein kinase 4 | Signal transduction | 1.33 × 10−14 | 5.67 × 10−12 | −2.34 |
| RTN4RL1 | Reticulon 4 receptor-like 1 | Metabolism | 5.13 × 10−14 | 1.85 × 10−11 | −1.93 |
| GALNT6 | Polypeptide N-acetylgalactosaminyl transferase 6 | Metabolism | 2.03 × 10−13 | 6.11 × 10−11 | 2.07 |
| S100A10 | S100 calcium binding protein A10 | Signal transduction | 2.39 × 10−12 | 4.94 × 10−10 | 1.82 |
| NAV1 | Neuron navigator 1 | Unknown | 3.11 × 10−12 | 5.78 × 10−10 | 1.84 |
| NOL3 | Nucleolar protein 3 | Metabolism | 3.57 × 10−12 | 6.22 × 10−10 | 1.51 |
| CLDN10 | Claudin 10 | Transport | 9.96 × 10−12 | 1.45 × 10−9 | 2.45 |
| KDELR3 | KDEL endoplasmic reticulum protein retention receptor 3 | Transport | 1.56 × 10−11 | 2.18 × 10−9 | 2.00 |
| FAM110C | Family with sequence similarity 110, member C | Cell cycle | 6.26 × 10−11 | 6.97 × 10−9 | 1.68 |
| CHST15 | Carbohydrate sulfotransferase 15 | Metabolism | 9.70 × 10−11 | 1.02 × 10−8 | 1.58 |
| GALNT7 | GalNAc transferase 7 | Metabolism | 2.25 × 10−10 | 2.17 × 10−8 | 1.55 |
| FHOD3 | Formin homology 2 domain containing 3 | Growth/proliferation | 3.31 × 10−10 | 2.75 × 10−8 | −1.89 |
| CYP1B1 | Cytochrome P450, family 1, subfamily B, polypeptide 1 | Oxidant related | 4.04 × 10−10 | 3.25 × 10−8 | 76.06 |
| PLAG1 | PLAG1 zinc finger | Transcription | 4.62 × 10−10 | 3.59 × 10−8 | −1.51 |
| SLC29A1 | Solute carrier family 29, member 1 | Transport | 1.02 × 10−9 | 6.79 × 10−8 | −1.72 |
| KCNK6 | Potassium two pore domain channel subfamily K member 6 | Signal transduction | 1.47 × 10−9 | 9.18 × 10−8 | 1.64 |
| LOC102724094 | LOC102724094 | Unknown | 1.87 × 10−9 | 1.13 × 10−7 | 2.22 |
| LOC105378604 | Uncharacterized LOC105378604 | Unknown | 3.66 × 10−9 | 2.00 × 10−7 | −1.68 |
| MSRB1 | LDL receptor-related protein 4 | Oxidant related | 4.13 × 10−9 | 2.17 × 10−7 | 1.62 |
| PEG10 | Paternally expressed 10 | Apoptosis | 4.20 × 10−9 | 2.19 × 10−7 | −1.74 |
| S100A14 | S100 calcium binding protein A14 | Apoptosis | 5.89 × 10−9 | 2.65 × 10−7 | 1.63 |
| LRP4 | Low-density lipoprotein receptor-related protein 4 | Development | 1.35 × 10−8 | 5.63 × 10−7 | 1.86 |
| TMCC3 | Transmembrane and coiled-coil domain family 3 | Unknown | 1.45 × 10−8 | 5.85 × 10−7 | 2.01 |
| LOC284825 | Long intergenic nonprotein coding RNA 1697 | Unknown | 1.60 × 10−8 | 6.36 × 10−7 | 6.35 |
| KCNB1 | Potassium voltage-gated channel subfamily B member 1 | Transport | 1.65 × 10−8 | 6.44 × 10−7 | −1.66 |
| CDC42EP5 | CDC42 effector protein 5 | Growth/proliferation | 2.13 × 10−8 | 7.88 × 10−7 | 1.87 |
| DPP10 | Dipeptidylpeptidase 10 | Proteolysis | 2.48 × 10−8 | 8.93 × 10−7 | 1.83 |
| FOXA2 | Forkhead box A2 | Transcription | 4.87 × 10−8 | 1.56 × 10−6 | −1.67 |
| LHX6 | LIM homeobox 6 | Growth/proliferation | 5.72 × 10−8 | 1.76 × 10−6 | 1.85 |
| SIX3 | SIX homeobox 3 | Regulation | 5.73 × 10−8 | 1.76 × 10−6 | 2.67 |
| GAD1 | Glutamate decarboxylase 1 | Metabolism | 1.16 × 10−7 | 3.20 × 10−6 | 4.79 |
| LFNG | LFNG O-fucosylpeptide 3-β-N-acetylglucosaminyltransferase | Signal transduction | 2.01 × 10−7 | 4.93 × 10−6 | 1.63 |
| DPP10-AS1 | DPP10 antisense RNA 1 | Unknown | 2.33 × 10−7 | 5.58 × 10−6 | 1.75 |
| MATN2 | Matrilin 2 | Growth/proliferation | 2.60 × 10−7 | 6.08 × 10−6 | 2.42 |
| NR4A3 | Nuclear receptor subfamily 4 group A member 3 | Transcription | 3.07 × 10−7 | 7.01 × 10−6 | 1.87 |
| LOC100507560 | Uncharacterized LOC100507560 | Metabolism | 2.85 × 10−6 | 4.56 × 10−5 | −1.73 |
| PRKCB | Protein kinase C, β | Signal transduction | 5.15 × 10−6 | 7.42 × 10−5 | −3.07 |
| PDGFRL | Platelet-derived growth factor receptor-like | Proteolysis | 5.29 × 10−6 | 7.59 × 10−5 | 1.80 |
| GSTM3 | Glutathione S-transferase mu 3 | Metabolism | 2.16 × 10−5 | 0.0002 | 1.80 |
| UCHL1 | Ubiquitin C-terminal hydrolase L1 | Proteolysis | 2.76 × 10−5 | ||
| CCEPR | Cervical carcinoma expressed PCNA regulatory LncRNA | Unknown | 3.99 × 10−5 | 0.0004 | 1.52 |
| KRT40 | Keratin 40 | Unknown | 6.32 × 10−5 | 0.0006 | 1.68 |
| DAPK1 | Death-associated protein kinase 1 | Apoptosis | 0.0002 | 0.001 | −1.62 |
| FAM3B | Family with sequence similarity 3, member B | Apoptosis | 0.0002 | 0.002 | 1.52 |
| DNAJC12 | DnaJ homolog, subfamily C, member 12 | Transport | 0.0003 | 0.002 | 1.70 |
| DEFB1 | Defensin, β1 | Immune response | 0.0007 | 0.004 | 2.29 |
| KIAA1211 | KIAA1211 | Unknown | 0.002 | 0.01 | 1.62 |
| CDH2 | Cadherin 2 | Adhesion | 0.004 | 0.02 | 1.92 |
*
Calculated in the primary cohort assessed over 1 year.
†
BH correction was adjusted using Benjamini-Hochberg (BH) correction (30).
‡
A positive fold change represents upregulation in expression in smokers compared with nonsmokers; a negative fold change represents a downregulation in smokers compared with nonsmokers.