Simultaneous Epigenetic and Gene Expression Profiling at Single Cell Resolution Uncovers Stem-Like Treg Subsets Induced With Oligonucleotide Expansion in Humans

Overview

Journal Immune Netw

Date 2025 Jan 13

PMID 39801740

Authors

Hyo Jeong Nam

Jeong-Ryeol Gong

Yong-Hee Kim

Thuy Nguyen-Phuong

Nari Byun

Jeong Heon Yoon

Yong Chan Kim

Hyunwoo Chung

Brian Hyohyoung Lee

Haeyoon Kwon

Woochan Lee

Sung-Jun Kang

Kyunghyuk Park

Bukyoung Cha

Jong-Il Kim

Hyun Je Kim

Affiliations

Soon will be listed here.

Abstract

Tregs play a central role in maintaining immune tolerance. Recent progress in the clinical application of Tregs underscores their potential for cell therapy. Nevertheless, a notable hurdle remains in producing functional Tregs . There is also a lack of detailed studies evaluating the function of Tregs during their expansion process. Our prior investigation showed that the expansion with oligonucleotides produces FoxP3Helios subsets. To investigate how oligonucleotides in culture media influence on gene expression and epigenetic states at single cell resolution, we sorted Tregs from healthy individuals and profiled oligonucleotide-expanded and non-expanded Tregs. We discovered a subset of Tregs, specifically enriched in expanded Tregs (seTregs), through oligonucleotide-induced expansion. seTregs showed an enhancement in both stem-like characteristics and functional attributes. Through analysis of histone modification data and gene regulatory networks, we elucidated (Helios) as a pivotal transcription factor in generating these cell subsets. We believe these findings offer insights into evaluating functional regulation of expanded Tregs aimed at manufacturing Treg-based cell therapies.

References

Getnet D, Grosso J, Goldberg M, Harris T, Yen H, Bruno T . A role for the transcription factor Helios in human CD4(+)CD25(+) regulatory T cells. Mol Immunol. 2010; 47(7-8):1595-600. PMC: 3060613. DOI: 10.1016/j.molimm.2010.02.001. View

Fornes O, Castro-Mondragon J, Khan A, van der Lee R, Zhang X, Richmond P . JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2019; 48(D1):D87-D92. PMC: 7145627. DOI: 10.1093/nar/gkz1001. View

Kim Y, Bhairavabhotla R, Yoon J, Golding A, Thornton A, Tran D . Oligodeoxynucleotides stabilize Helios-expressing Foxp3+ human T regulatory cells during in vitro expansion. Blood. 2012; 119(12):2810-8. PMC: 3327459. DOI: 10.1182/blood-2011-09-377895. View

Mijnheer G, Lutter L, Mokry M, van der Wal M, Scholman R, Fleskens V . Conserved human effector Treg cell transcriptomic and epigenetic signature in arthritic joint inflammation. Nat Commun. 2021; 12(1):2710. PMC: 8113485. DOI: 10.1038/s41467-021-22975-7. View

Schep A, Wu B, Buenrostro J, Greenleaf W . chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat Methods. 2017; 14(10):975-978. PMC: 5623146. DOI: 10.1038/nmeth.4401. View

Sugita K, Hanakawa S, Honda T, Kondoh G, Miyachi Y, Kabashima K . Generation of Helios reporter mice and an evaluation of the suppressive capacity of Helios(+) regulatory T cells in vitro. Exp Dermatol. 2015; 24(7):554-6. DOI: 10.1111/exd.12711. View

Kim H, Barnitz R, Kreslavsky T, Brown F, Moffett H, Lemieux M . Stable inhibitory activity of regulatory T cells requires the transcription factor Helios. Science. 2015; 350(6258):334-9. PMC: 4627635. DOI: 10.1126/science.aad0616. View

Thornton A, Lu J, Korty P, Kim Y, Martens C, Sun P . Helios and Helios Treg subpopulations are phenotypically and functionally distinct and express dissimilar TCR repertoires. Eur J Immunol. 2019; 49(3):398-412. PMC: 6402968. DOI: 10.1002/eji.201847935. View

Sakaguchi S, Sakaguchi N, Asano M, Itoh M, Toda M . Immunologic self-tolerance maintained by activated T cells expressing IL-2 receptor alpha-chains (CD25). Breakdown of a single mechanism of self-tolerance causes various autoimmune diseases. J Immunol. 1995; 155(3):1151-64. View

10.

Chinen T, Kannan A, Levine A, Fan X, Klein U, Zheng Y . An essential role for the IL-2 receptor in T cell function. Nat Immunol. 2016; 17(11):1322-1333. PMC: 5071159. DOI: 10.1038/ni.3540. View

11.

Kartha V, Duarte F, Hu Y, Ma S, Chew J, Lareau C . Functional inference of gene regulation using single-cell multi-omics. Cell Genom. 2022; 2(9). PMC: 9534481. DOI: 10.1016/j.xgen.2022.100166. View

12.

Stuart T, Srivastava A, Madad S, Lareau C, Satija R . Single-cell chromatin state analysis with Signac. Nat Methods. 2021; 18(11):1333-1341. PMC: 9255697. DOI: 10.1038/s41592-021-01282-5. View

13.

Khattri R, Cox T, Yasayko S, Ramsdell F . An essential role for Scurfin in CD4+CD25+ T regulatory cells. Nat Immunol. 2003; 4(4):337-42. DOI: 10.1038/ni909. View

14.

Devi-Marulkar P, Fastenackels S, Karapentiantz P, Goc J, Germain C, Kaplon H . Regulatory T cells infiltrate the tumor-induced tertiary lymphoïd structures and are associated with poor clinical outcome in NSCLC. Commun Biol. 2022; 5(1):1416. PMC: 9789959. DOI: 10.1038/s42003-022-04356-y. View

15.

Elkord E, Abd Al Samid M, Chaudhary B . Helios, and not FoxP3, is the marker of activated Tregs expressing GARP/LAP. Oncotarget. 2015; 6(24):20026-36. PMC: 4652984. DOI: 10.18632/oncotarget.4771. View

16.

Schmidl C, Hansmann L, Lassmann T, Balwierz P, Kawaji H, Itoh M . The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations. Blood. 2014; 123(17):e68-78. DOI: 10.1182/blood-2013-02-486944. View

17.

Polansky J, Schreiber L, Thelemann C, Ludwig L, Kruger M, Baumgrass R . Methylation matters: binding of Ets-1 to the demethylated Foxp3 gene contributes to the stabilization of Foxp3 expression in regulatory T cells. J Mol Med (Berl). 2010; 88(10):1029-40. PMC: 2943068. DOI: 10.1007/s00109-010-0642-1. View

18.

Ma S, Zhang B, LaFave L, Earl A, Chiang Z, Hu Y . Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin. Cell. 2020; 183(4):1103-1116.e20. PMC: 7669735. DOI: 10.1016/j.cell.2020.09.056. View

19.

Luo Y, Xu C, Wang B, Niu Q, Su X, Bai Y . Single-cell transcriptomic analysis reveals disparate effector differentiation pathways in human T compartment. Nat Commun. 2021; 12(1):3913. PMC: 8222404. DOI: 10.1038/s41467-021-24213-6. View

20.

Ohkura N, Yasumizu Y, Kitagawa Y, Tanaka A, Nakamura Y, Motooka D . Regulatory T Cell-Specific Epigenomic Region Variants Are a Key Determinant of Susceptibility to Common Autoimmune Diseases. Immunity. 2020; 52(6):1119-1132.e4. DOI: 10.1016/j.immuni.2020.04.006. View