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Epigenetic signature and key transcriptional regulators of human antigen-specific type 1 regulatory T cells

Alma-Martina Cepika, et al. (BioRxiv) DOI: 10.1101/2024.03.07.582969

Epigenetic signature and key transcriptional regulators of human antigen-specific type 1 regulatory T cells


  • Type 1 regulatory T cells

  • Epigenetics

  • Adoptive cell therapy

Main Findings

This study provides intriguing insights into the unique characteristics of antigen-specific type 1 regulatory T cells, known as Tr1 cells, sparking interest in their potential applications. Tr1 cells, a subset of regulatory T cells (Tregs), hold immense promise in the immune system. Unlike natural Tregs originating in the thymus, Tr1 cells are induced from peripheral CD4+ T cells in response to antigens. Their therapeutic potential lies in their ability to be differentiated in vitro to induce antigen-specific tolerance, making them a valuable tool for treating autoimmune diseases and in transplantation settings. However, the epigenetic landscape and transcription factors (TFs) that govern the differentiation and function of these cells have remained elusive.

The study reveals that antigen-specific Tr1 cells have a distinct epigenetic signature, differentiating them from natural Tregs and conventional CD4+ T cells. Using integrative analysis, the researchers identified unique transcription factors, including IRF4, BATF, and MAF. These transcription factors were found to play non-redundant roles in controlling Tr1 cell differentiation, suppressive functions, and the expression of various proteins, providing a more detailed understanding of the mechanisms underlying Tr1 cell biology. The findings from this study are of paramount importance as they enhance our understanding of Tr1 cell biology, a crucial step in the development and optimization of Tr1 cell-based therapies. The research also paves the way for further exploration of Tr1 cells in diverse settings, such as in solid tumors and in patients who have undergone allogeneic hematopoietic stem cell transplantation.


This study does not exhibit clear limitations, as the researchers have taken commendable steps to identify these findings. However, we would recommend some ideas to help clarify certain study aspects:

1. In Figure 3E, the authors presented an in vitro investigation of transcription factors (TFs), revealing that IRF4 exhibited two top peaks in both the Tr1 cells and the control group. Given that IRF4 is a critical transcriptional regulator in T cells, including Tr1 cells:

  • Evaluate how the dual expression profiles of IRF4 correspond to the traits and roles of Tr1 cells.

  • Investigate whether one subpopulation conforms more closely to the defining features of Tr1 cells than the other.

2. In Figure 4G, the author effectively demonstrates a significant impairment in the suppressive function of IRF4 KO T-allo10 cells, indicating that IRF4 plays a regulatory role in the suppressive capacity of Tr1 cells. However, we believe it is crucial to include more details about the suppressive function of IRF4 KO-T-allo10 cells by implementing the following:

  • Rescue Experiment: Conduct a rescue experiment by reintroducing IRF4 into IRF4 KO T-allo10 cells to observe if the suppressive function is restored. This approach would confirm the specific role of IRF4 in regulating the suppressive capacity of these cells.

  • Co-culture Assays: Under various conditions, perform co-culture assays with IRF4 KO T-allo10 cells and effector T cells (CD4, CD8, etc.) to assess the direct suppressive effects. This methodology can help identify the functional deficits in the KO cells.

  • Signaling Pathway Analysis: Investigate key signalling pathways in IRF4 KO T-allo10 cells to understand how the absence of IRF4 affects cellular mechanisms and functions related to immune suppression

3. In Figure 5, the author proficiently illustrates the comparative analysis between Cluster 1 and Cluster 3, elucidating the differences and identifying the cluster that more closely approximates the characteristics of Tr1 cells. However, to enhance the interpretability and facilitate a more profound understanding among readers, it is recommended that this section be revised to include a more precise and detailed figure. This revision should aim to clarify the distinctions and emphasize the key features that align with Tr1 cells, thereby ensuring that data presentation is comprehensive and accessible to a broader scientific audience.

4. Since the study paves the way for new research into Tr1 cells, it would be intriguing to determine whether these cells also exist in other diseases, such as allergies, infections, and autoimmune disorders. Additionally, it would be valuable to investigate whether they exhibit the same signature as those identified in hematopoietic stem cell transplantation (HSCT) and tumors.

5. Although the study and investigations are comprehensive, a persistent question arises: How can these findings be translated into clinical practice? We recommend providing a more detailed description of how these findings can be translated.  This should include outlining potential pathways for applying the research to patient care, discussing the steps necessary to validate these results in clinical settings, and exploring how they might influence treatment strategies and health outcomes.


  • Unique Epigenetic Signature: The preprint reveals a unique epigenetic signature for antigen-specific type 1 regulatory T cells (Tr1 cells), distinguishing them from other T cell subsets. This is novel because it provides new molecular markers to identify and study Tr1 cells.

  • Identification of Key Transcription Factors: The study identifies key transcription factors (IRF4, BATF, MAF) that regulate the differentiation, phenotype, and function of Tr1 cells. This is significant because these factors offer potential targets for modulating Tr1 cells in therapeutic settings.

  • Functional Genomics in Tr1 Cells: The research employs functional genomics to demonstrate the non-redundant roles of the identified transcription factors. This approach is novel and offers a comprehensive understanding of the molecular mechanisms governing Tr1 cell biology.

  • Molecular Fingerprinting: The preprint uses the Tr1-specific transcription factor signature as a molecular fingerprint to track Tr1 cells in clinical settings, such as in recipients of allogeneic hematopoietic stem cell transplantation and in solid tumors. This is novel because it provides a tool for monitoring and potentially predicting clinical outcomes

How does the result of the preprint matter for general immunologists and/or patients?

  • The results enhance the understanding of immune regulation by providing insights into the specific mechanisms through which Tr1 cells maintain immune tolerance, which is important for general immunologists studying immune homeostasis and tolerance.

  • The results have direct implications for developing Tr1 cell-based therapies, which could benefit patients with transplant recipients and cancer patients by promoting immune tolerance and preventing adverse immune responses.


Reviewed by Osamah Al-Rubaye  as part of a cross-institutional journal club between the Vanderbilt University Medical Center (VUMC), the Max-Delbrück Center Berlin, the Ragon Institute Boston (Mass General, MIT, Harvard), the Medical University of Vienna and other life science institutes in Vienna.

The author declares no conflict of interests in relation to their involvement in the review.

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