Periodontal status.Probing depth (mm)AgeGenderMMMMMFFFPatient characteristicsPatientF-a-Gene Expression in PeriodontitisFigure 1. H E and CD3-stained order PD1-PDL1 inhibitor 1 paraffin-embedded gingival biopsies obtained from one representative patient with periodontitis. A. H E staining of inflammatory cells in periodontitis-affected sections. B. H E staining of inflammatory cells in healthy gingival sections. C. Staining of the T-cell marker CD3 in periodontitis-affected sections. D. Staining of the T-cell marker CD3 in healthy sections. E, epithelium, C, BIBS39 web connective tissue. doi:10.1371/journal.pone.0046440.gImmunohistochemical stainings in gingival tissueFor staining of the T cell marker CD3, interferon regulatory factor 4 (IRF4) and chemokine (C-C motif) ligand 18 (CCL18), gingival tissues were rinsed in phosphate buffered saline (PBS) with 0.1 Saponin (PBS-Saponin buffer) for 10 min. After an antigen retrieval procedure, 10 mM Tris, 1 mM EDTA (pH 9.0) for CD3 and 0.01 M Citrate acid (pH 6.0) for IRF4 and CCL18, sections were blocked in 1 H2O2 in PBS-Saponin for 60 min at room temperature (RT) for CD3 and for 45 min at RT for IRF4 and CCL18. Subsequently, tissues were rinsed in PBS-Saponin for 10 min and further treated with 3 bovine serum albumin (BSA) diluted in PBS-Saponin for 30 min at RT. The expression of CD3, IRF4 and CCL18 was investigated using CD3 polyclonal rabbit antibody (1 mg/ml, PBS-Saponin) from Dako Sweden AB (Stockholm, Sweden), IRF4 polyclonal rabbit antibody (0.5 mg/ml, PBSSaponin) from Atlas antibodies (Stockholm, Sweden) and CCL18 
polyclonal rabbit anti-human antibody (0.5 mg/ml, PBS-Saponin) from Sigma-Aldrich (St. Louis, MO, USA). Normal rabbit IgG from R D systems (MN, USA) was used as negative control. After incubation with primary antibody, sections were blocked with 1 normal goat serum in PBS for 15 min. Afterwards, sections were incubated with a biotinylated secondary antibody provided in the Vectastain ABC-Elite Complex Kit (Vector labs, Burlingame, CA, USA) followed by application of the Elite ABC solution for 40 min at RT in the dark. Thereafter, sections were washed with PBS and the peroxidase activity was visualized with 0.3 (v/v) in DAB buffer containing 0.1 (v/v) H2O2. Finally, the slides were washed with distilled water, dehydrated through an ethanol series (70 , 95 , 99.9 ) into xylene, mounted, and photographed using a light microscope. For CD3 stainings, the amount of positive cells was evaluated by three blinded observers, using a relative scale from 0 to 3, and statistical differences between periodontitisaffected and healthy biopsies were tested using the Wilcoxon signed-rank test.RNA extractionRNA was extracted from gingival biopsies using steel-bead matrix tubes and a tabletop Fast-Prep homogenizer by two sequential centrifugations for 20 s at speed 6.5 (Qbiogene, Irvie, CA, USA). The RNA was purified on RNeasy Spin Columns (Qiagen, Valencia, CA, USA), treated with DNAse H to ensure degradation of DNA, and thereafter eluated in RNase-free water. The average RNA yield was 15.6 mg. RNA quality was assessed using the RNA 6000 NanoLabChip Kit of the Bioanalyzer system from Agilent Technologies (Santa Clara, CA, USA).Transcriptome sample preparation for sequencingA total amount of 2? mg per sample was used as input material for the RNA sample preparations. All samples had RIN values above 8. The samples were bar-coded and prepared according to the protocol (Cat# RS-930-1001) from the manufacturer (Illumina, San Di.Periodontal status.Probing depth (mm)AgeGenderMMMMMFFFPatient characteristicsPatientF-a-Gene Expression in PeriodontitisFigure 1. H E and CD3-stained paraffin-embedded gingival biopsies obtained from one representative patient with periodontitis. A. H E staining of inflammatory cells in periodontitis-affected sections. B. H E staining of inflammatory cells in healthy gingival sections. C. Staining of the T-cell marker CD3 in periodontitis-affected sections. D. Staining of the T-cell marker CD3 in healthy sections. E, epithelium, C, connective tissue. doi:10.1371/journal.pone.0046440.gImmunohistochemical stainings in gingival tissueFor staining of the T cell marker CD3, interferon regulatory factor 4 (IRF4) and chemokine (C-C motif) ligand 18 (CCL18), gingival tissues were rinsed in phosphate buffered saline (PBS) with 0.1 Saponin (PBS-Saponin buffer) for 10 min. After an antigen retrieval procedure, 10 mM Tris, 1 mM EDTA (pH 9.0) for CD3 and 0.01 M Citrate acid (pH 6.0) for IRF4 and CCL18, sections were blocked in 1 H2O2 in PBS-Saponin for 60 min at room temperature (RT) for CD3 and for 45 min at RT for IRF4 and CCL18. Subsequently, tissues were rinsed in PBS-Saponin for 10 min and further treated with 3 bovine serum albumin (BSA) diluted in PBS-Saponin for 30 min at RT. The expression of CD3, IRF4 and CCL18 was investigated using CD3 polyclonal rabbit antibody (1 mg/ml, PBS-Saponin) from Dako Sweden AB (Stockholm, Sweden), IRF4 polyclonal rabbit antibody (0.5 mg/ml, PBSSaponin) from Atlas antibodies (Stockholm, Sweden) and CCL18 polyclonal rabbit anti-human antibody (0.5 mg/ml, PBS-Saponin) from Sigma-Aldrich (St. Louis, MO, USA). Normal rabbit IgG from R D systems (MN, USA) was used as negative control. After incubation with primary antibody, sections were blocked with 1 normal goat serum in PBS for 15 min. Afterwards, sections were incubated with a biotinylated secondary antibody provided in the Vectastain ABC-Elite Complex Kit (Vector labs, Burlingame, CA, USA) followed by application of the Elite ABC solution for 40 min at RT in the dark. Thereafter, sections were washed with PBS and the peroxidase activity was visualized with 0.3 (v/v) in DAB buffer containing 0.1 (v/v) H2O2. Finally, the slides were washed with distilled water, dehydrated through an ethanol series (70 , 95 , 99.9 ) into xylene, mounted, and photographed using a light microscope. For CD3 stainings, the amount of positive cells was evaluated by three blinded observers, using a relative scale from 0 to 3, and statistical differences between periodontitisaffected and healthy biopsies were tested using the Wilcoxon signed-rank test.RNA extractionRNA was extracted from gingival biopsies using steel-bead matrix tubes and a tabletop Fast-Prep homogenizer by two sequential centrifugations for 20 s at speed 6.5 (Qbiogene, Irvie, CA, USA). The RNA was purified on RNeasy Spin Columns (Qiagen, Valencia, CA, USA), treated with DNAse H to ensure degradation of DNA, and thereafter eluated in RNase-free water. The average RNA yield was 15.6 mg. RNA quality was assessed using the RNA 6000 NanoLabChip Kit of the Bioanalyzer system from Agilent Technologies (Santa Clara, CA, USA).Transcriptome sample preparation for 
sequencingA total amount of 2? mg per sample was used as input material for the RNA sample preparations. All samples had RIN values above 8. The samples were bar-coded and prepared according to the protocol (Cat# RS-930-1001) from the manufacturer (Illumina, San Di.
