title: RNA-sequencing study of peripheral blood monocytes in chronic periodontitis.
abstract: BACKGROUND
  Monocytes are an important cell type in chronic periodontitis (CP) by interacting with oral bacteria and mediating host immune response. The aim of this study was to reveal new functional genes and pathways for CP at monocyte transcriptomic level.
  
  
  METHODS
  We performed an RNA-sequencing (RNA-seq) study of peripheral blood monocytes (PBMs) in 5 non-smoking moderate to severe CP (case) individuals vs. 5 controls. We took advantage of a microarray study of periodontitis to support our findings. We also performed pathway-based analysis on the identified differentially expressed (DEx) transcripts/isoforms using DAVID (Database for Annotation, Visualization and Integrated Discovery).
  
  
  RESULTS
  Through differential expression analyses at both whole gene (or whole non-coding RNA) and isoform levels, we identified 380 DEx transcripts and 5955 DEx isoforms with a PPEE (posterior probability of equal expression) of <0.05. Pervasive up-regulation of transcripts at isoform level in CP vs. control individuals was observed, suggesting a more functionally active monocyte transcriptome for CP. By comparing with the microarray dataset, we identified several CP-associated novel genes (e.g., FACR and CUX1) that have functions to interact with invading microorganisms or enhance TNF production on lipopolysaccharide stimulation. DAVID analysis of both the RNA-seq and the microarray datasets leads to converging evidence supporting "endocytosis", "cytokine production" and "apoptosis" as significant biological processes in CP.
  
  
  CONCLUSIONS
  As the first RNA-seq study of PBMs for CP, this study provided novel findings at both gene (e.g., FCAR and CUX1) and biological process level. The findings will contribute to better understanding of CP disease mechanisms.
authors.affiliation: Center of Genomics and Bioinformatics, Dept. of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States. Electronic address: yliu8@tulane.edu.
authors.forename: Yao-Zhong
authors.initials: YZ
authors.lastname: Liu
authors.affiliation: Dept. of Periodontics, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, LA, United States. Electronic address: pmaney@lsuhsc.edu.
authors.forename: Pooja
authors.initials: P
authors.lastname: Maney
authors.affiliation: Dept. of Periodontics, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, LA, United States.
authors.forename: Jyoti
authors.initials: J
authors.lastname: Puri
authors.affiliation: Center of Genomics and Bioinformatics, Dept. of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States.
authors.forename: Melody
authors.initials: M
authors.lastname: Baddoo
authors.affiliation: Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States.
authors.forename: Michael
authors.initials: M
authors.lastname: Strong
authors.affiliation: Dept. of Biomedical Engineering, Tulane University School of Science and Engineering, United States.
authors.forename: Yu-Ping
authors.initials: YP
authors.lastname: Wang
authors.affiliation: Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States.
authors.forename: Erik
authors.initials: E
authors.lastname: Flemington
authors.affiliation: Center of Genomics and Bioinformatics, Dept. of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States.
authors.forename: Hong-Wen
authors.initials: HW
authors.lastname: Deng
mesh_terms: D000328:Adult; D015703:Antigens, CD / Q000235:genetics; D055113:Chronic Periodontitis / Q000097:blood / Q000235:genetics*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D008875:Middle Aged; D009000:Monocytes / Q000378:metabolism; D009687:Nuclear Proteins / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020033:Protein Isoforms / Q000235:genetics; D012333:RNA, Messenger / Q000097:blood*; D011961:Receptors, Fc / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D014157:Transcription Factors; D059467:Transcriptome
chemical_list: D015703:Antigens, CD; C080632:CUX1 protein, human; C036832:Fc(alpha) receptor; D018398:Homeodomain Proteins; D009687:Nuclear Proteins; D020033:Protein Isoforms; D012333:RNA, Messenger; D011961:Receptors, Fc; D012097:Repressor Proteins; D014157:Transcription Factors
keywords: Apoptosis; CUX1; Cytokine; Endocytosis; FCAR; Monocytes; Periodontitis; RNA sequencing analysis
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