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

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

doi:10.4110/in.2024.24.e39

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

Immune Netw. 2024 Oct 24;24(6):e39. doi: 10.4110/in.2024.24.e39. eCollection 2024 Dec.

Authors

Hyo Jeong Nam^{1

2}, Jeong-Ryeol Gong³, Yong-Hee Kim^{1

4}, Thuy Nguyen-Phuong^{1

2}, Nari Byun^{1

2

5}, Jeong Heon Yoon⁵, Yong Chan Kim⁵, Hyunwoo Chung¹, Brian Hyohyoung Lee^{1

2}, Haeyoon Kwon⁶, Woochan Lee⁷, Sung-Jun Kang^{1

2}, Kyunghyuk Park⁷, Bukyoung Cha⁷, Jong-Il Kim^{1

7}, Hyun Je Kim^{1

2

7

8}

Affiliations

¹ Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.
² Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul 03080, Korea.
³ Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea.
⁴ Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
⁵ Teraimmune, Inc., Gaithersburg, MD 20878, USA.
⁶ Department of Medicine, Seoul National University College of Medicine, Seoul 03080, Korea.
⁷ Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 03080, Korea.
⁸ Department of Dermatology, Seoul National University Hospital, Seoul 03080, Korea.

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 in vitro. There is also a lack of detailed studies evaluating the function of Tregs during their ex vivo expansion process. Our prior investigation showed that the ex vivo expansion with oligonucleotides produces FoxP3^highHelios^high 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 in vitro 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 IKZF2 (Helios) as a pivotal transcription factor in generating these cell subsets. We believe these findings offer insights into evaluating functional regulation of in vitro expanded Tregs aimed at manufacturing Treg-based cell therapies.

Keywords: Epigenetics; Regulatory T cell; Transcriptomics.