[Title]
Epigenetic scars in regulatory T cells are retained after successful treatment of chronic hepatitis C with direct-acting antivirals

[Author]

So-Young Kim1,†, June-Young Koh1,2,†, Dong Hyeon Lee3,†, Hyung-Don Kim1, Seong Jin Choi1, Yun Yeong Ko4, Ha Seok Lee1, Jeong Seok Lee1,2, In Ah Choi5, Eun Young Lee6, Hye Won Jeong5, Min Kyung Jung4, Su-Hyung Park1, Jun Yong Park7,*, Won Kim3,*, Eui-Cheol Shin1,4,*

1Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
2GENOME INSIGHT Inc., Daejeon 34051, Republic of Korea
3Department of Internal Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul National University College of Medicine, Seoul 07061, Republic of Korea
4The Center for Viral Immunology, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
5Department of Internal Medicine, Chungbuk National University College of Medicine, Cheongju 28644, Republic of Korea
6Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
7Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
†These authors contributed equally to this work.
*Corresponding author:
Eui-Cheol Shin, M.D., Ph.D.,

[Journal] 

Journal of Hepatology, In Press Journal Pre-Proof, Published online: June 13, 2024


[Abstract]

Background & Aims

Chronic hepatitis C virus (HCV) infection results in abnormal immunological alterations, which are not fully normalized after viral elimination by direct-acting antiviral (DAA) treatment. Here we longitudinally examined phenotypic, transcriptomic, and epigenetic alterations in peripheral blood regulatory T (T_REG) cells from patients with chronic HCV infection according to DAA treatment.

Methods

Patients with chronic genotype 1b HCV infection who achieved sustained virologic response (SVR) by DAA treatment and age-matched healthy donors were recruited. Phenotypic characteristics of T_REG cells were investigated through flow cytometry analysis. Moreover, transcriptomic and epigenetic landscape of T_REG cells were analyzed using RNA-seq and ATAC-seq analysis.

Results

The T_REG cell population—especially the activated T_REG cell subpopulation—was expanded in peripheral blood during chronic HCV infection, and this expansion was sustained even after viral clearance. RNA-seq analysis revealed that viral clearance did not abrogate the inflammatory features of these T_REG cells, such as T_REG activation and TNF signal. Moreover, ATAC-seq analysis showed inflammatory imprinting in the epigenetic landscape of T_REG cells from patients, which remained after treatment. These findings were further confirmed by intracellular cytokine staining, demonstrating that T_REG cells exhibited inflammatory features and TNF production in chronic HCV infection that were maintained after viral clearance.

Conclusions

Overall, our results showed that during chronic HCV infection, the expanded T_REG cell population acquired inflammatory features at phenotypic, transcriptomic, and epigenetic levels, which were maintained even after successful viral elimination by DAA treatment. Further studies are warranted to examine the clinical significance of sustained inflammatory features in the T_REG cell population after recovery from chronic HCV infection.

Impact and implications

During chronic HCV infection, several immune components are altered both quantitatively and qualitatively. The recent introduction of DAAs led to a high cure rate of chronic HCV infection. Nevertheless, we have demonstrated that inflammatory features of T_REG cells are maintained at phenotypic, transcriptomic, and epigenetic levels even after successful DAA treatment. Further in-depth studies are required to investigate the long-term clinical outcomes of patients who have recovered from chronic HCV infection.

Graphical abstract