C9orf72 Intermediate Repeats Confer Genetic Risk for Severe COVID-19 Pneumonia Independently of Age

Abstract

A cytokine storm, autoimmune features and dysfunctions of myeloid cells significantly contribute to severe coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Genetic background of the host seems to be partly responsible for severe phenotype and genes related to innate immune response seem critical host determinants. The C9orf72 gene has a role in vesicular trafficking, autophagy regulation and lysosome functions, is highly expressed in myeloid cells and is involved in immune functions, regulating the lysosomal degradation of mediators of innate immunity. A large non-coding hexanucleotide repeat expansion (HRE) in this gene is the main genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), both characterized by neuroinflammation and high systemic levels of proinflammatory cytokines, while HREs of intermediate length, although rare, are more frequent in autoimmune disorders. C9orf72 full mutation results in haploinsufficiency and intermediate HREs seem to modulate gene expression as well and impair autophagy. Herein, we sought to explore whether intermediate HREs in C9orf72 may be a risk factor for severe COVID-19. Although we found intermediate HREs in only a small portion of 240 patients with severe COVID-19 pneumonia, the magnitude of risk for requiring non-invasive or mechanical ventilation conferred by harboring intermediate repeats >10 units in at least one C9orf72 allele was more than twice respect to having shorter expansions, when adjusted for age (odds ratio (OR) 2.36; 95% confidence interval (CI) 1.04-5.37, p = 0.040). The association between intermediate repeats >10 units and more severe clinical outcome (p = 0.025) was also validated in an independent cohort of 201 SARS-CoV-2 infected patients. These data suggest that C9orf72 HREs >10 units may influence the pathogenic process driving more severe COVID-19 phenotypes.

Keywords: C9orf72; COVID-19; SARS-CoV-2; autophagy; genetic risk; innate immunity; intermediate alleles.

Figure 1

(a) Histogram showing the distribution and frequency (%) (Y-axis) of the number of C9orf72 hexanucleotide repeats (X-axis) in ALS (black bars) and COVID-19 (white bars) patients’ alleles. (b) Frequency (%) and number (n) of intermediate alleles for each repeat length >8 repeat units in ALS and COVID-19 patients. Both for ALS and COVID-19 patients, the % and n for repeat length > 8 units are in red; for COVID-19 patients, % and n with a clear difference in comparison with ALS patients are also highlighted in red.

Figure 2

Results of univariate logistic regression analysis between COVID-19 cases and ALS patients at each intermediate allele size > 8 units. The blue line represents odds ratio (OR), the dark red line p-value, and the dotted gray line represents p = 0.05 significance level.

Figure 3

Histogram showing the distribution and frequency (%) (Y-axis) of the number of C9orf72 hexanucleotide repeats (X-axis) in patients’ alleles in severe COVID-19 patients who received mechanical ventilation (MV) or non-invasive ventilation (NIV) (white bars) and non-hospitalized SARS-CoV-2 infected subjects (asymptomatic or with very mild symptoms) (black bars).