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Mouse methylation profiles for leukocyte cell types, and estimation of leukocyte fractions in inflamed gastrointestinal DNA samples

Author

Listed:
  • Kazuhiro Nishiyama
  • Hitomi Nishinakamura
  • Hideyuki Takeshima
  • Liu Yuyu
  • Chihiro Takeuchi
  • Naoko Hattori
  • Haruna Takeda
  • Satoshi Yamashita
  • Mika Wakabayashi
  • Kotomi Sato
  • Kazutaka Obama
  • Toshikazu Ushijima

Abstract

Precise analysis of tissue DNA and RNA samples is often hampered by contaminating non-target cells whose amounts are highly variable. DNA methylation profiles are specific to cell types, and can be utilized for assessment of the fraction of such contaminating non-target cells. Here, we aimed 1) to identify methylation profiles specific to multiple types of mouse leukocytes, and 2) to estimate the fraction of leukocytes infiltrating inflamed tissues using DNA samples. First, genome-wide DNA methylation analysis was conducted for three myeloid-lineage cells and four lymphoid-lineage cells isolated by fluorescence-activated cell sorting after magnetic-activated cell sorting from leukocytes in the spleen. Clustering analysis using CpG sites within enhancers separated the three myeloid-lineage cells and four lymphoid-lineage cells while that using promoter CpG islands (TSS200CGIs) did not. Among the 266,108 CpG sites analyzed, one CpG site was specifically hypermethylated (β value ≥ 0.7) in B cells, and four, seven, 183, and 34 CpG sites were specifically hypomethylated (β value

Suggested Citation

  • Kazuhiro Nishiyama & Hitomi Nishinakamura & Hideyuki Takeshima & Liu Yuyu & Chihiro Takeuchi & Naoko Hattori & Haruna Takeda & Satoshi Yamashita & Mika Wakabayashi & Kotomi Sato & Kazutaka Obama & Tos, 2023. "Mouse methylation profiles for leukocyte cell types, and estimation of leukocyte fractions in inflamed gastrointestinal DNA samples," PLOS ONE, Public Library of Science, vol. 18(10), pages 1-13, October.
    • Handle: RePEc:plo:pone00:0290034
    DOI: 10.1371/journal.pone.0290034
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    1. Matthew D. Schultz & Yupeng He & John W. Whitaker & Manoj Hariharan & Eran A. Mukamel & Danny Leung & Nisha Rajagopal & Joseph R. Nery & Mark A. Urich & Huaming Chen & Shin Lin & Yiing Lin & Inkyung J, 2015. "Human body epigenome maps reveal noncanonical DNA methylation variation," Nature, Nature, vol. 523(7559), pages 212-216, July.
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