A Low-Producing Haplotype of Interleukin-6 Disrupting CTCF Binding Is Protective against Severe COVID-19

Abstract

Interleukin6 (IL-6) is a key driver of hyperinflammation in COVID-19, and its level strongly correlates with disease progression. To investigate whether variability in COVID-19 severity partially results from differential <i>IL-6</i> expression, functional single-nucleotide polymorphisms (SNPs) of <i>IL-6</i> were determined in Chinese COVID-19 patients with mild or severe illness. An Asian-common <i>IL-6</i> haplotype defined by promoter SNP rs1800796 and intronic SNPs rs1524107 and rs2066992 correlated with COVID-19 severity. Homozygote carriers of <i>C-T-T</i> variant haplotype were at lower risk of developing severe symptoms (odds ratio, 0.256; 95% confidence interval, 0.088 to 0.739; <i>P </i>= 0.007). This protective haplotype was associated with lower levels of <i>IL-6</i> and its antisense long noncoding RNA <i>IL-6-AS1</i> by <i>cis</i>-expression quantitative trait loci analysis. The differences in expression resulted from the disturbance of stimulus-dependent bidirectional transcription of the <i>IL-6</i>/<i>IL-6-AS1</i> locus by the polymorphisms. The protective rs2066992-<i>T</i> allele disrupted a conserved CTCF-binding locus at the enhancer elements of <i>IL-6-AS1</i>, which transcribed antisense to <i>IL-6</i> and induces <i>IL-6</i> expression in inflammatory responses. As a result, carriers of the protective allele had significantly reduced <i>IL-6-AS1</i> expression and attenuated <i>IL-6</i> induction in response to acute inflammatory stimuli and viral infection. Intriguingly, this low-producing variant that is endemic to present-day Asia was found in early humans who had inhabited mainland Asia since ∼40,000 years ago but not in other ancient humans, such as Neanderthals and Denisovans. The present study suggests that an individual's <i>IL-6</i> genotype underlies COVID-19 outcome and may be used to guide IL-6 blockade therapy in Asian patients. <b>IMPORTANCE</b> Overproduction of cytokine interleukin-6 (IL-6) is a hallmark of severe COVID-19 and is believed to play a critical role in exacerbating the excessive inflammatory response. Polymorphisms in <i>IL-6</i> account for the variability of IL-6 expression and disparities in infectious diseases, but its contribution to the clinical presentation of COVID-19 has not been reported. Here, we investigated <i>IL-6</i> polymorphisms in severe and mild cases of COVID-19 in a Chinese population. The variant haplotype <i>C-T-T</i>, represented by rs1800796, rs1524107, and rs2066992 at the <i>IL-6</i> locus, was reduced in patients with severe illness; in contrast, carriers of the wild-type haplotype <i>G</i>-<i>C</i>-<i>G</i> had higher risk of severe illness. Mechanistically, the protective variant haplotype lost CTCF binding at the <i>IL-6</i> intron and responded poorly to inflammatory stimuli, which may protect the carriers from hyperinflammation in response to acute SARS-CoV-2 infection. These results point out the possibility that <i>IL-6</i> genotypes underlie the differential viral virulence during the outbreak of COVID-19. The risk loci we identified may serve as a genetic marker to screen high-risk COVID-19 patients.