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  • Buschur, Kristina L.Univ Pittsburgh, Dept Computat & Syst Biol, Sch Med, Pittsburgh, PA 15260 USA.;Joint CMU Pitt PhD Program Computat Biol, Pittsburgh, PA 15213 USA.;Columbia Univ, Div Gen Med, Med Ctr, New York, NY USA.;New York Genome Ctr, New York, NY USA. (author)

Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis

  • Article/chapterEnglish2023

Publisher, publication year, extent ...

  • 2023-01-25
  • Springer Nature,2023
  • printrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:kth-324462
  • https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-324462URI
  • https://doi.org/10.1186/s12931-023-02316-6DOI

Supplementary language notes

  • Language:English
  • Summary in:English

Part of subdatabase

Classification

  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • QC 20230303
  • BackgroundChronic obstructive pulmonary disease (COPD) varies significantly in symptomatic and physiologic presentation. Identifying disease subtypes from molecular data, collected from easily accessible blood samples, can help stratify patients and guide disease management and treatment.MethodsBlood gene expression measured by RNA-sequencing in the COPDGene Study was analyzed using a network perturbation analysis method. Each COPD sample was compared against a learned reference gene network to determine the part that is deregulated. Gene deregulation values were used to cluster the disease samples.ResultsThe discovery set included 617 former smokers from COPDGene. Four distinct gene network subtypes are identified with significant differences in symptoms, exercise capacity and mortality. These clusters do not necessarily correspond with the levels of lung function impairment and are independently validated in two external cohorts: 769 former smokers from COPDGene and 431 former smokers in the Multi-Ethnic Study of Atherosclerosis (MESA). Additionally, we identify several genes that are significantly deregulated across these subtypes, including DSP and GSTM1, which have been previously associated with COPD through genome-wide association study (GWAS).ConclusionsThe identified subtypes differ in mortality and in their clinical and functional characteristics, underlining the need for multi-dimensional assessment potentially supplemented by selected markers of gene expression. The subtypes were consistent across cohorts and could be used for new patient stratification and disease prognosis.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Riley, CraigUniv Pittsburgh, Dept Med, Div Pulm Med, Pittsburgh, PA USA. (author)
  • Saferali, AabidaBrigham & Womens Hosp, Channing Div Network Med, Boston, MA USA. (author)
  • Castaldi, PeterBrigham & Womens Hosp, Channing Div Network Med, Boston, MA USA. (author)
  • Zhang, GraceUniv Pittsburgh, Dept Computat & Syst Biol, Sch Med, Pittsburgh, PA 15260 USA. (author)
  • Aguet, FrancoisBroad Inst MIT & Harvard, Cambridge, MA USA. (author)
  • Ardlie, Kristin G.Broad Inst MIT & Harvard, Cambridge, MA USA. (author)
  • Durda, PeterUniv Vermont, Larner Coll Med, Dept Pathol & Lab Med, Burlington, VT USA. (author)
  • Craig Johnson, W.Univ Washington, Dept Biostat, Seattle, WA USA. (author)
  • Kasela, SilvaNew York Genome Ctr, New York, NY USA.;Columbia Univ, Dept Syst Biol, New York, NY USA. (author)
  • Liu, YongmeiDuke Univ, Duke Mol Physiol Inst, Dept Med,Med Ctr, Div Cardiol, Durham, NC USA. (author)
  • Manichaikul, AniUniv Virginia, Ctr Publ Hlth Genom, Charlottesville, VA USA. (author)
  • Rich, Stephen S.Univ Virginia, Ctr Publ Hlth Genom, Charlottesville, VA USA. (author)
  • Rotter, Jerome I.UCLA Med Ctr, Inst Translat Genom & Populat Sci, Lundquist Inst Biomed Innovat Harbor, Dept Pediat, Torrance, CA USA. (author)
  • Smith, JoshUniv Washington, Northwest Genome Ctr, Seattle, WA USA. (author)
  • Taylor, Kent D.UCLA Med Ctr, Inst Translat Genom & Populat Sci, Lundquist Inst Biomed Innovat Harbor, Dept Pediat, Torrance, CA USA. (author)
  • Tracy, Russell P.Univ Vermont, Larner Coll Med, Dept Pathol & Lab Med, Burlington, VT USA.;Univ Vermont, Larner Coll Med, Dept Biochem, Burlington, VT USA. (author)
  • Lappalainen, TuuliKTH,Genteknologi,Science for Life Laboratory, SciLifeLab,New York Genome Ctr, New York, NY USA.;Columbia Univ, Dept Syst Biol, New York, NY USA(Swepub:kth)u1o81n30 (author)
  • Graham Barr, R.Columbia Univ, Div Gen Med, Med Ctr, New York, NY USA. (author)
  • Sciurba, FrankUniv Pittsburgh, Dept Med, Div Pulm Med, Pittsburgh, PA USA. (author)
  • Hersh, Craig P.Brigham & Womens Hosp, Channing Div Network Med, Boston, MA USA. (author)
  • Benos, Panayiotis V.Univ Pittsburgh, Dept Computat & Syst Biol, Sch Med, Pittsburgh, PA 15260 USA.;Joint CMU Pitt PhD Program Computat Biol, Pittsburgh, PA 15213 USA.;Univ Florida, Dept Epidemiol, 2004 Mowry Rd, Gainesville, FL 32603 USA. (author)
  • Univ Pittsburgh, Dept Computat & Syst Biol, Sch Med, Pittsburgh, PA 15260 USA.;Joint CMU Pitt PhD Program Computat Biol, Pittsburgh, PA 15213 USA.;Columbia Univ, Div Gen Med, Med Ctr, New York, NY USA.;New York Genome Ctr, New York, NY USA.Univ Pittsburgh, Dept Med, Div Pulm Med, Pittsburgh, PA USA. (creator_code:org_t)

Related titles

  • In:Respiratory Research: Springer Nature24:11465-99211465-993X

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