Table 1.

Genetic associations between HLA variation, presence of Anti-La/SSA autoantibodies and epigenetic IFN signature.

HLA Alleles	SS ~ HLA		SSA ~ HLA		epigIFN ~ HLA		epigIFN ~ HLA + SSA		SS ~ HLA (positive epigIFN)		SS ~ HLA (negative epigIFN)
	beta.HLA	P.HLA	beta.HLA	P.HLA	beta.HLA	P.HLA	beta.HLA	P.HLA	beta.HLA	P.HLA	beta.HLA	P.HLA
DRB1_0301	1.14	2.07E-07	0.27	1.02 x 10–04	− 0.17	9.16 x 10–05	− 0.06	0.142	1.40	7.14 x 10–09	− 0.30	0.470
DQB1_0201	1.16	1.39E-07	0.29	2.03 x 10–05	− 0.18	6.55 x 10–05	− 0.05	0.210	1.44	2.58 x 10–09	− 0.29	0.493

β reflects the additive effect of allele dosage for different HLA alleles and P is the associated significance level. The association between HLA genetic variation, SS and SSA was determined by means of logistic regression adjusted by sex and age. The association between HLA genetic variation and epigIFN was determined by linear regression models adjusted by sex, age, cell proportions and batch effects.

epigIFN refers to the epigenetic IFN signature. DNA methylation at IFI44L gene (cg13452062) was used as a proxy for epigIFN. Patients exhibiting DNAm > 0.8 were classified as negative epigIFN. Patients exhibiting DNAm < 0.8 were classified as positive epigIFN.