Epigenetic silencing of V(D)J recombination is a major determinant for selective differentiation of mucosal-associated invariant t cells from induced pluripotent stem cells

Abstract

Mucosal-associated invariant T cells (MAITs) are innate-like T cells that play a pivotal role in the host defense against infectious diseases, and are also implicated in autoimmune diseases, metabolic diseases, and cancer. Recent studies have shown that induced pluripotent stem cells (iPSCs) derived from MAITs selectively redifferentiate into MAITs without altering their antigen specificity. Such a selective differentiation is a prerequisite for the use of MAITs in cell therapy and/or regenerative medicine. However, the molecular mechanisms underlying this phenomenon remain unclear. Here, we performed methylome and transcriptome analyses of MAITs during the course of differentiation from iPSCs. Our multi-omics analyses revealed that recombination-activating genes (RAG1 and RAG2) and DNA nucleotidylexotransferase (DNTT) were highly methylated with their expression being repressed throughout differentiation. Since these genes are essential for V(D)J recombination of the T cell receptor (TCR) locus, this indicates that nascent MAITs are kept from further rearrangement that may alter their antigen specificity. Importantly, we found that the repression of RAGs was assured in two layers: one by the modulation of transcription factors for RAGs, and the other by DNA methylation at the RAG loci. Together, our study provides a possible explanation for the unaltered antigen specificity in the selective differentiation of MAITs from iPSCs.

Reprogramming and redifferentiation of mucosal-associated invariant T cells reveals tumor inhibitory activity

“…Since iNKT cells and MAIT cells belong to a family of innate-like T cells harboring semi-invariant TCR, the expression of the machinery relevant to TCR rearrangements may be repressed during differentiation in vitro. In accordance with this notion, transcripts for the machinery, such as Rag1, Rag2, and Dntt, were found to be repressed in human MAIT-iPSCs concomitant with epigenetic silencing upon differentiation (Saito et al, 2017). Therefore, further studies are warranted to clarify whether the same corollary applies to the murine system.…”

DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling

“…proteomic, miRNA and DNA methylation data) and it is the functional core of RDA step, DECO is greatly suitable to be applied on these platforms. In fact, there are many publications in the last decade reporting its use for proteomics differential analysis due to its simplicity, performance and dealing with variability of proteomic data (Basken et al , 2018; Jeannin et al , 2018; Kuzniar et al , 2017; Margolin et al , 2009; Pagel et al , 2015; Ting et al , 2009), for miRNA differential analysis (Mastriani et al , 2018; Thomou et al , 2017; Xue et al , 2017), and there are also many successful publications where LIMMA have been applied for differential analysis of CpG methylation levels in different biological scenarios (Johnson et al , 2017; Martorell-Marugan et al , 2019; Saito et al , 2017; Stefan et al , 2014; Wockner et al , 2014). For all these reasons, we think the workflow followed by DECO can be of great help for better disease stratification and biomarker identification.…”

Mucosal-Associated Invariant T Cells in Regenerative Medicine

“…There is quasi-exclusive generation of reMAIT cells from MAIT-iPSCs, which indicates that configuration of the rearranged invariant TCRα chain locus specific for MAIT cells (TRAV1-2-TRAJ33) has a pivotal role in reMAIT cell fate determination during differentiation. Differentiation of reMAIT cells from MAIT-iPSCs does not accompany expression of the genes relevant to TCR rearrangement such as recombination-activating genes 1 and 2 and DNA nucleotidylexotransferase ( 77 ). Absence of these genes will inhibit further rearrangement of MAIT cell-specific TCR, which, in turn, preserves the identity of MAIT cells.…”

“…Absence of these genes will inhibit further rearrangement of MAIT cell-specific TCR, which, in turn, preserves the identity of MAIT cells. Intriguingly, expression is silenced at both the epigenetic and transcriptional levels, further highlighting the role of rearranged TRAV1-2-TRAJ33 ( 77 ). reMAIT cells resemble MAIT cells in peripheral blood in that they express the invariant TCR (TRAV1-2-TRAJ33), CD161 high , IL-18Rα high , CCR6 high , CXCR3 + , CXCR5 + , and CD95 (Fas) high with little expression of CCR7 (Figure 1 ).…”

“…Because reMAIT cells derived from MAIT-iPSCs harbor a phenotype quasi-identical to MAIT cells and produce cytokines and chemokines as MAIT cells upon adoptive transfer, it is conceivable that reMAIT cells are ready to be used in cell therapy. This view is further underpinned by the fact that reMAIT cells are devoid of machinery responsible for TCR rearrangement such as recombination-activating genes ( 77 ). The last criterion can be met through the use of autologous MAIT cells for MAIT-iPSC preparation and supported by adoptive transfer of reMAIT cells into immunocompromised mice to observe maturation of reMAIT cells and cytokine and chemokine production in vivo .…”