Allelic bias contributes to heterogeneous phenotypes of NK cell deficiency [PBMC]

While monogenic variants in CDC45-MCM-GINS (CMG) replisome proteins cause human natural killer cell deficiencies (NKD), family members with the same inherited variants often have variable clinical and cellular phenotypes. Using iPSCs from two siblings with the same hereditary compound heterozygous GINS4 variants but variable disease expressivity, we modeled cell proliferation dynamics and the effect of GINS4 variants on NK cell development from pluripotent stem cells. Cell cycle impairment and increased apoptosis were detected in NK cells from patient-derived iPSCs following NK cell lineage commitment but not in pluripotent cells. While this effect was detected in cell lines from both siblings, the efficiency of NK cell differentiation was variable and correlated with differential clinical severity of NKD. Further investigation of allelic expression of inherited GINS4 variants demonstrated equal biallelic expression of GINS4 in pluripotent cells and primary CD34+ progenitors. However, allelic bias in lineage committed NK cells led to over- or under-representation of more damaging inherited GINS4 heterozygous variants that tracked with differential cellular and clinical severity. This study identifies allelic bias as an epigenetic factor that contributes to the phenotypic variations of monogenic diseases and further defines the etiology of NK cell-lineage specific immunodeficiency arising from CMG variants. Overall design: PBMCs were stained with PE-Cy7 CD34 (RRID:AB_2629726, Biolegend, 343616), APC CD14 (RRID:AB_314190, Biolegend, 301808), Pacific Blue CD19 (RRID:AB_2073118, Biolegend, 302232), Alexa488 CD56 (RRID:AB_2564093, Biolegend, 362518), BUV CD3 BD (RRID:AB_2870222, Biosciences, 612940). T cells, NK cells, CD34+ cells and B cells were isolated and directly processed. 2~10 X 104 cells were lysed, and RNA was collected with NucleoSpin RNA XS kit (Takara, 740902) according to the manufacturer's protocol. RNA quality control was performed using the Agilent 2100 Bioanalyzer System. Libraries were generated with SMARTer stranded RNA-Seq kit (Takara, 634839) and sequenced on NovaSeq 6000 (Illumina).