Figures
- FIGURE 1
Combining datasets. a) Clustering of samples before the batch effect removal procedure (Distance-Weighted Discrimination; DWD) was performed. b) Clustering of samples after DWD. c) Clustering of samples after removing GSE8790 and samples from two control mice that clustered with the samples obtained from smoke-exposed mice. Samples were clustered using average linkage and Spearman correlation distance.
- FIGURE 2
Genes differentially expressed between the smoke-exposed mice in each model and the control group. Increasing fold changes are highlighted with the increasing level of shading. In each category the genes are sorted by the fold-change values obtained from GSE18344. The colour coding is different for the all fold changes and fold change ≥2.
- FIGURE 3
Functional interaction network based on the 234 differentially expressed genes. a) Functional network with annotated gene clusters. Each cluster is contained within a separate NTA: grey oval, with the ID superimposed on it. b) Expression of the gene clusters in each of the mouse models. Clusters containing at least one upregulated gene are marked in pink; clusters containing at least one downregulated gene are marked in green; clusters containing both up- and downregulated genes are marked in grey. Clusters not containing any differentially expressed genes are marked by black contour. Models are sorted based on the total particulate matter used in the model: from lowest (lower left corner) to highest (upper right corner).
- FIGURE 4
Clusters from the functional network. a) Models clustered by the numbers of differentially expressed genes in each of the clusters. Numbers of the differentially expressed genes are indicated on the heatmap. Branches of the vertical dendrogram are named using the cluster IDs (0–16). Each cluster is functionally annotated based on the Pathway Enrichment and Gene Ontology analyses (see table 3). Cluster 9 is marked by “–” since it did not show any significant representation of any of the known processes. #: cluster contained both up- and downregulated genes. b) Correlation between total particulate matter (TPM) and number of differentially regulated clusters across mouse models. *: indicates mouse models. TLR: Toll-like receptor; MHC: major histocompatibility complex; NOD: nucleotide-binding oligomerisation domain. r2 =0.9348, p-value = 0.0072.
- FIGURE 5
Regulation of clusters in human datasets. a) Expression of the gene clusters in each human cohort. Clusters containing at least one upregulated gene are marked in pink; clusters containing at least one downregulated gene are marked in green; clusters containing both up- and downregulated genes are marked in grey. Clusters not containing any differentially expressed genes are marked by black contour. b) Models clustered by the numbers of differentially expressed genes in each of the clusters across human data and mouse models. Numbers of the differentially expressed genes are indicated on the heatmap. Branches of the vertical dendrogram are named using the cluster IDs (0–16). Each cluster is functionally annotated based on the Pathway Enrichment and Gene Ontology analyses (see table 3). Cluster 9 is marked by “–” since it did not show any significant representation of any of the known processes. #: cluster contained both up- and downregulated genes. c) Correlation between total particulate matter (TPM) and number of differentially regulated clusters across mouse models and human datasets. Human datasets are marked by horizontal lines indicating the number of regulated clusters in each dataset. *: indicates mouse models. Laval: Laval University; GRNG: Groningen; UBC: University of British Columbia; TLR: Toll-like receptor; MHC: major histocompatibility complex; NOD: nucleotide-binding oligomerisation domain.
Tables
- TABLE 1
Mouse datasets downloaded from Gene Expression Omnibus (GEO)
GEO accession [ref.] Exposure duration weeks Strain Sex Age weeks Samples TPM µg·L−1 Cigarette GSE8790 [9] 6 A/J Male 8 3 RA/3 CS 90 2R4F GSE33561 [11] 6–7 AKR/J Male 6–8 3 RA/3 CS 90 2R4F GSE33512 [7] 16 C57BL/6 Male 12 4 RA/4 CS 100–120 1R3F GSE52509 [10] 16 C57BL/6 Female 8–10 3 RA/3 CS 500 3R4F GSE17737 12 C57BL/6 Female NA 5 FA/5 CS NA NA GSE55127 [6] 8 BALB/C Female 6–8 5 RA/5 CS >600 3R4F# GSE18344 [8] 8 CD-1 Female 13 4 RA/4 CS 750 2R4F TPM: total particulate matter; RA: room air; FA: forced air; CS: cigarette smoke; NA: not applicable. #: filters removed.
- TABLE 2
Functional annotation of the gene clusters
Cluster Genes in cluster Function derived from Pathway Enrichment
and Gene Ontology analysesGene list 0 6 TLR signalling: unfolded protein response DNAJB1, DNAJC5B, HSPA1A, HSPB1, SAA1, TLR2 10 2 TLR signalling CD86, CXCL9 1 6 Chemokines: signalling CCL17, CCL22, CCL4, CCR1, CXCL13, CXCL5 7 3 Chemokines: activity CCL2, CCL3, CCL7 11 2 Chemokines: NOD-like receptor signalling CXCL1, CXCL2 2 5 Muscle contraction ACTN2, MYH6, MYL1, TCAP, TNNI3 3 5 Integrins CD14, ITGAM, ITGAX, ITGB2, SPON2 4 4 Circadian clock ARNTL, DBP, NR1D1, PER1 5 3 Osteoclast differentiation CLEC5A, TREM2, TYROBP 6 3 Interleukins: FC-epsilon receptor I signalling FCER1G, FCGR2B, IL12B 14 2 Interleukins IL1R2, IL1RN 8 3 p53 pathway IGF1, IGFBP3, IGFBP6 9 3 – AHRR, ARNT2, MAFB 12 2 Class I MHC mediated antigen processing and presentation CYBA, NCF4 13 2 Immune response (complement pathway) C1QA, C1QB 15 2 Glutathione metabolism GCLC, GCLM 16 2 Heterotrimeric G-protein signalling pathway-Gq alpha and Go alpha mediated pathway RGS1, RGS16 There were no pathways or processes significantly represented by cluster 9. TLR: Toll-like receptor; NOD: nucleotide-binding oligomerisation domain; MHC: major histocompatibility complex.
- TABLE 3
Clinical characteristics of subjects
Variables Groningen LAVAL UBC Never-smokers Current smokers Never-smokers Current smokers Never-smokers Current smokers Subjects 12 45 27 82 17 88 Male/female 5 (42%)/7 23 (51%)/22 6 (22%)/21 37 (45%)/45 8 (47%)/9 54 (61%)/34 Age years 48.3±15.4 57.5±8.7 55.8±11.6 63±9.2 59.6±14.6 62±9.4 Smoking pack-years 0 37.9±17.4 0 53±21.8 0 53.7±27.1 FEV1 % pred 98.6±9.38 (7) 73.3±19.8 (17) 94.1±13.2 (4) 75.1±14.4 (1) 105.4±33.1 (7) 76.4±18.2 (7) FVC % pred 98.8±7.3 (7) 87.1±16.3 (18) 96.5±12.5 (6) 87. 1±13.5 (5) 99.1±31.2 (6) 86.7±15.7 (7) Data are presented as mean±sd, unless otherwise stated. The number of missing values is shown in parentheses. LAVAL: Laval University; UBC: University of British Columbia; FEV1: forced expiratory volume in 1 s; FVC: forced vital capacity.
Supplementary material
Please note: supplementary material is not edited by the Editorial Office, and is uploaded as it has been supplied by the author.
Files in this Data Supplement:
