RFX transcription factors control a miR-150/PDAP1 axis that restrains the proliferation of human T cells.

Michele Chirichella,Niccolò Bianchi,Francesco Gualdrini,Elena Foli,Emina Džafo,Amy Kenyon,Gioacchino Natoli,Silvia Monticelli,Paula M Oliver

doi:10.1371/journal.pbio.3001538

Abstract

Within the immune system, microRNAs (miRNAs) exert key regulatory functions. However, what are the mRNA targets regulated by miRNAs and how miRNAs are transcriptionally regulated themselves remain for the most part unknown. We found that in primary human memory T helper lymphocytes, miR-150 was the most abundantly expressed miRNA, and its expression decreased drastically upon activation, suggesting regulatory roles. Constitutive MIR150 gene expression required the RFX family of transcription factors, and its activation-induced down-regulation was linked to their reduced expression. By performing miRNA pull-down and sequencing experiments, we identified PDGFA-associated protein 1 (PDAP1) as one main target of miR-150 in human T lymphocytes. PDAP1 acted as an RNA-binding protein (RBP), and its CRISPR/Cas-9–mediated deletion revealed that it prominently contributed to the regulation of T-cell proliferation. Overall, using an integrated approach involving quantitative analysis, unbiased genomics, and genome editing, we identified RFX factors, miR-150, and the PDAP1 RBP as the components of a regulatory axis that restrains proliferation of primary human T lymphocytes.

Highlights

Through their ability to target a variety of mRNAs and regulate their translation and stability, microRNAs modulate all aspects of the biology of T lymphocytes, including cell differentiation, activation, and proliferation [1,2]
To identify and accurately quantify miRNAs that are expressed by ex vivo isolated primary human T cells, we performed NanoString digital profiling of CD4+ naive, central memory (TCM), and effector memory (TEM) T-cell subsets isolated from 4 independent donors
While miR-150 expression was substantially similar among subsets, a few moderately expressed miRNAs were preferentially expressed in memory T cells compared to naive cells, while miR-181a was instead preferentially expressed in naive compared to memory T lymphocytes (S1B Fig)

Summary

Introduction

Through their ability to target a variety of mRNAs and regulate their translation and stability, microRNAs (miRNAs) modulate all aspects of the biology of T lymphocytes, including cell differentiation, activation, and proliferation [1,2]. The effect of any given miRNA is dependent on its expression level relative to that of its targets [3,4] and on the specific context and cell-specific usage of target sites in the 30 untranslated region (UTR) of mRNAs [5], resembling the cell type–specific regulation of gene expression mediated by transcription factors. The quantitative analysis of miRNA expression in different T-cell subsets and in response to T cell. A regulatory axis restraining human T cell proliferation to SM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Methods

Results

Conclusion