Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung

Epigenetics. 2018;13(3):264-274. doi: 10.1080/15592294.2018.1441650. Epub 2018 May 10.

Abstract

Gene regulatory analysis of highly diverse human tissues in vivo is essentially constrained by the challenge of performing genome-wide, integrated epigenetic and transcriptomic analysis in small selected groups of specific cell types. Here we performed genome-wide bisulfite sequencing and RNA-seq from the same small groups of bronchial and alveolar cells isolated by laser capture microdissection from flash-frozen lung tissue of 12 donors and their peripheral blood T cells. Methylation and transcriptome patterns differed between alveolar and bronchial cells, while each of these epithelia showed more differences from mesodermally-derived T cells. Differentially methylated regions (DMRs) between alveolar and bronchial cells tended to locate at regulatory regions affecting promoters of 4,350 genes. A large number of pathways enriched for these DMRs including GTPase signal transduction, cell death, and skeletal muscle. Similar patterns of transcriptome differences were observed: 4,108 differentially expressed genes (DEGs) enriched in GTPase signal transduction, inflammation, cilium assembly, and others. Prioritizing using DMR-DEG regulatory network, we highlighted genes, e.g., ETS1, PPARG, and RXRG, at prominent alveolar vs. bronchial cell discriminant nodes. Our results show that multi-omic analysis of small, highly specific cells is feasible and yields unique physiologic loci distinguishing human lung cell types in situ.

Keywords: RNA sequencing; alveolar cell; bronchial cell; laser capture microdissection; whole-genome bisulfite sequencing.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alveolar Epithelial Cells / metabolism
  • Cell Lineage / genetics
  • DNA Methylation / genetics*
  • Epigenesis, Genetic
  • GTP Phosphohydrolases / genetics
  • Gene Regulatory Networks / genetics
  • Genome, Human / genetics
  • Humans
  • Laser Capture Microdissection
  • Lung / cytology
  • Lung / metabolism*
  • PPAR gamma / genetics*
  • Promoter Regions, Genetic
  • Proto-Oncogene Protein c-ets-1 / genetics*
  • Retinoid X Receptor gamma / genetics*
  • Signal Transduction
  • T-Lymphocytes / metabolism
  • Transcriptome / genetics
  • Whole Genome Sequencing

Substances

  • ETS1 protein, human
  • PPAR gamma
  • Proto-Oncogene Protein c-ets-1
  • Retinoid X Receptor gamma
  • GTP Phosphohydrolases