Genome-wide analysis of HDAC inhibitor-mediated modulation of microRNAs and mRNAs in b cells induced to undergo class-switch DNA recombination and plasma cell differentiation

Helia N. Sanchez, Tian Shen, Dawn Garcia, Zhao Lai, Paolo Casali, Hong Zan

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

Antibody responses are accomplished through several critical B cell-intrinsic processes, including somatic hypermutation (SHM), class-switch DNA recombination (CSR), and plasma cell differentiation. In recent years, epigenetic modifications or factors, such as histone deacetylation and microRNAs (miRNAs), have been shown to interact with B-cell genetic programs to shape antibody responses, while the dysfunction of epigenetic factors has been found to lead to autoantibody responses. Analyzing genome-wide miRNA and mRNA expression in B cells in response to epigenetic modulators is important for understanding the epigenetic regulation of B-cell function and antibody response. Here, we demonstrate a protocol for inducing B cells to undergo CSR and plasma cell differentiation, treating these B cells with histone deacetylase (HDAC) inhibitors (HDIs), and analyzing mRNA and microRNA expression. In this protocol, we directly analyze complementary DNA (cDNA) sequences using next-generation mRNA sequencing (mRNA-seq) and miRNA-seq technologies, mapping of the sequencing reads to the genome, and quantitative reverse transcription (qRT)-PCR. With these approaches, we have defined that, in B cells induced to undergo CSR and plasma cell differentiation, HDI, an epigenetic regulator, selectively modulates miRNA and mRNA expression and alters CSR and plasma cell differentiation.

Original languageEnglish (US)
Article numbere55135
JournalJournal of Visualized Experiments
Volume2017
Issue number127
DOIs
StatePublished - Sep 20 2017

Keywords

  • B cell
  • Class-switch DNA recombination
  • Flow cytometry
  • Histone deacetylase (HDAC) inhibitors (HDIs)
  • Immunology
  • Issue 127
  • MicroRNA
  • MiRNA-seq
  • MRNA
  • MRNA-seq
  • Plasma cell differentiation

ASJC Scopus subject areas

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

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