SNP rs10748643 determines CD39 expression in T and NK cells through altering NFIC binding affinity rather than interfering RNA splicing

Fengqin Fang^1*Chenxin Gan¹Qian Wu¹Jorg J Goronzy²Yongchun Zhang^3,4Lingjie Li⁵Huiming Sheng¹

• ¹Tongren Hospital of Shanghai Jiao Tong University School of Medicine, Shanghai, China
• ²Mayo Clinic Minnesota, Rochester, United States
• ³School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
• ⁴School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;, Shanghai, China
• ⁵Shanghai Jiao Tong University School of Medicine, Shanghai, China

NTPDase-1 CD39, a dominant component of purinergic signaling, is proven being the critical regulator of tissue microenvironment and cellular function particularly for T cells. We repeatedly use SNP rs10748643 genotype as a tag of CD39 expression in T cells in many studies. However, no study is done yet to profile the impact of the SNP mutation on CD39 expression in all immune cells. In this study, we reveal that SNP rs10748643 mainly determines CD39 expression in T and NK cells. In contrast, it has the least influence on monocytes, B cells and granulocytes. These immune cells demonstrate constitutive CD39 expression, which is different from T and NK cells. We applied bioinformatic tools and bench experiments to disclose the underlying mechanism. We found that the amount of each variant is barely affected by SNP mutation in B cells, whereas almost all variants are significantly impacted by SNP mutation in T cells. Such discrepancy in T and B cells do not support the hypothesis that SNP rs10748643 interferes with the splicing efficiency of CD39 mRNA. MicroRNA regulation was also excluded. Transcriptional factor regulation was emphasized because conserved motif sequence of NFIC exactly covers the SNP site. Using CUT&Tag technology, we found the binding affinity of NFIC decreases when SNP mutates from A to G, causing the reduced inhibition of NFIC on CD39 expression in T cells. NFIC inducer may be another potential approach to restrain CD39 expression for improving the immunosuppressive microenvironment.