Differential interferon-α subtype immune signatures suppress SARS-CoV-2 infection
Schuhenn J.
1*
,
Meister T.L.
2*
, Todt D.
2,3
, Bracht T.
4,5
,
Schork K.
4,6
,
Billaud J.-N.
7
,
Elsner C.
1
, Heinen N
2
, Karakoese Z.
1
, Haid S.
8
, Kumar S.
9
,
Brunotte L.
9, 10
,
Eisenacher M.
4,6
,
Chen J.
11
, Yuan Z
11
, Pietschmann T.
8, 12, 13
, Wiegmann B.
14
, Beckert H.
15
,
Taube C.
15
, Le-Trilling VTK.
1
, Trilling M.
1
,
Krawczyk A.
1,16
, Ludwig S.
9, 10
, Sitek B.
4,5
,
Steinmann E.
2
, Dittmer U.
1
, Sutter K.
1*#
and Pfaender S.
2*#
Affiliation:
1
University Hospital Essen, University Duisburg-Essen, Institute for Virology, Essen,
Germany
2
Ruhr-University-Bochum, Molecular and Medical Virology, Bochum, Germany
3
European Virus Bioinformatics Center (EVBC), Jena, Germany
4
Ruhr-University-Bochum, Medizinisches Proteom-Center, Bochum, Germany
5
University Hospital Knappschaftskrankenhaus Bochum, Department of Anesthesia, Intensive
Care Medicine and Pain Therapy, Bochum, Germany
6
Ruhr-University Bochum, Center for Protein Diagnostics (PRODI), Medical Proteome
Analysis, Bochum, Germany
7
Qiagen Digital Insights, Redwood City, California, United States
8
Twincore, Department of Experimental Virology, Hannover, Germany
9
Westfaelische Wilhelms-University, Institute of Virology Muenster, Münster, Germany
10
Interdisciplinary Centre for Clinical Research, University of Muenster, Muenster, Germany
11
MOE & NHC Key Laboratory of Medical Molecular Virology, School of Basic Medical
Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
12
Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-
Straße 1, 30625 Hannover, Germany
13
German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 30625
Hannover, Germany
14
Hannover Medical School, Department for Cardiothoracic, Transplantation and Vascular
Surgery, Hannover, Germany
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15
University Medical Center Essen - Ruhrlandklinik, Department of Pulmonary Medicine,
Experimental Pneumology, Essen, Germany
16
University Hospital Essen, Department of Infectious Diseases, West German Centre of
Infectious Diseases, Essen, Germany
* Equally contributing author
#
Correspondence: Kathrin.sutter@uni-due.de; Stephanie.pfaender@rub.de
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Summary
1
Type I interferons (IFN-I) exert pleiotropic biological effects during viral infections, balancing
2
virus control versus immune-mediated pathologies and have been successfully employed for
3
the treatment of viral diseases. Humans express twelve IFN-alpha (α) subtypes, which activate
4
downstream signalling cascades and result in distinct patterns of immune responses and
5
differential antiviral responses. Inborn errors in type I IFN immunity and the presence of anti-
6
IFN autoantibodies account for very severe courses of COVID-19, therefore, early
7
administration of type I IFNs may be protective against life-threatening disease. Here we
8
comprehensively analysed the antiviral activity of all IFNα subtypes against SARS-CoV-2 to
9
identify the underlying immune signatures and explore their therapeutic potential. Prophylaxis
10
of primary human airway epithelial cells (hAEC) with different IFNα subtypes during SARS-
11
CoV-2 infection uncovered distinct functional classes with high, intermediate and low antiviral
12
IFNs. In particular IFNα5 showed superior antiviral activity against SARS-CoV-2 infection.
13
Dose-dependency studies further displayed additive effects upon co-administered with the
14
broad antiviral drug remdesivir in cell culture. Transcriptomics of IFN-treated hAEC revealed
15
different transcriptional signatures, uncovering distinct, intersecting and prototypical genes of
16
individual IFNα subtypes. Global proteomic analyses systematically assessed the abundance of
17
specific antiviral key effector molecules which are involved in type I IFN signalling pathways,
18
negative regulation of viral processes and immune effector processes for the potent antiviral
19
IFNα5. Taken together, our data provide a systemic, multi-modular definition of antiviral host
20
responses mediated by defined type I IFNs. This knowledge shall support the development of
21
novel therapeutic approaches against SARS-CoV-2.
22
23
Keywords: Type I IFN, IFNα subtypes, SARS-CoV-2, COVID-19, antiviral treatment,
24
remdesivir, therapy, ISG
25
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The copyright holder for this preprintthis version posted May 20, 2021. ; https://doi.org/10.1101/2021.05.20.444757doi: bioRxiv preprint
Main
26
Without the capacity to produce or recognize interferons (IFN), mammalian hosts rapidly
27
succumb in case of viral infections. Accordingly, humans with loss-of-function mutations in
28
the IFN signalling pathway even fail to control attenuated viruses. Therefore., IFNs are
29
indispensable mediators of the first immediate intrinsic cellular defences against invading
30
pathogens, such as viruses. So far, three different types of IFNs, types I, II and III, have been
31
identified and classified based on their genetic, structural, and functional characteristics as well
32
as receptor usages
1-3
. Type I IFNs are among the first line of antiviral defence due to the
33
ubiquitous expression of the surface receptor IFNAR consisting of two subunits IFNAR1 and
34
IFNAR2. In humans, the type I IFN family comprises IFNβ, IFNε, IFNκ, IFNω and twelve
35
IFNα subtypes. The latter code for the distinct human IFNα proteins: IFNα1, -2, -4, -5, -6, -7, -
36
8, -10, -14, -16, -17 and -21, encoded by 14 nonallelic genes including one pseudogene and two
37
genes that encode identical proteins (IFNα13 and IFNα1). The overall identity of the IFNα
38
proteins ranges from 75 to 99% amino acid sequence identity
1,4
. Despite their binding to the
39
same cellular receptor, their antiviral and antiproliferative potencies differ considerably
5-10
. As
40
a general event in terms of signal transduction, IFNα subtypes engage the IFNAR1/2 receptor
41
and initiate a signal transduction cascade resulting in the phosphorylation of receptor-associated
42
janus tyrosine kinases culminating in downstream signalling events including the activation of
43
IFN-stimulated gene factor 3 (ISGF3) consisting of phosphorylated STAT1 and STAT2 and
44
the IFN regulatory factor 9. ISGF3 binding to the IFN-stimulated response elements (ISRE), in
45
promotor regions of various genes, initiates the transcriptional activation of a large number of
46
IFN-stimulated genes (ISGs), which elicit direct antiviral, anti-proliferative and
47
immunoregulatory properties
11
. It is largely elusive, why different IFNα proteins exhibit
48
distinct effector functions. Different receptor affinities and/or interaction interfaces within the
49
IFNAR have been discussed which may account for the observed variability in the biological
50
activity
12,13
. Furthermore, the dose, the cell type, the timing and the present cytokine milieu
51
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might further affect the IFN effector response
14
. In the absence of specific antiviral drugs,
52
treatment of patients with type I IFNs is often considered as first therapeutic response, given its
53
successful clinical application against viral infections
15,16
. Recently, type III IFNs (IFN-lambda,
54
IFNλ) received significant attention and are currently explored in clinical trials
17
. IFNλ binds
55
to the type III IFN receptor, which is preferentially expressed on epithelial cells and certain
56
myeloid cells
18
, resulting in restricted cell signalling and compartmentalized activity.
57
Especially at epithelial surface barriers, IFNλ mount an effective local innate immune response,
58
by conferring viral control and inducing immunity without generating systemic activation of
59
the immune system which could trigger pathologic inflammatory responses. Signal transduction
60
cascades of type I and type III IFNs are considered to be rather similar resulting in overlapping
61
ISG signatures, however, type I IFN signalling leads to a more rapid induction and decline of
62
ISG expression
19
.
63
The outbreak of novel viruses, as exemplified by the recent emergence of Severe Acute
64
Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), causing the disease COVID-19 has
65
emphasised the urgent need for fast and effective therapeutic strategies. Indeed, type I IFN
66
treatment is currently explored as emergency treatment against COVID-19 in various clinical
67
trials
20-22
, and it was already shown that SARS-CoV-2 is sensitive to type I IFNs
23
and ISGs
24
.
68
Given their large genome size, CoVs have evolved a variety of strategies circumventing the
69
host innate immune reaction, including evasion strategies targeting type I IFN signalling
23,25-27
.
70
Along those lines, recent studies showed significantly decreased interferon activity in COVID-
71
19 patients who developed more severe disease
28
, highlighting the importance of IFN in
72
controlling viral infection. Against viruses, pegylated IFNα2 is approved and frequently
73
administered in clinical settings. However, common side effects include the occurrence of flu-
74
like symptoms, haematological toxicity, elevated transaminases, nausea, fatigue, and
75
psychiatric sequelae, which often result from systemic activation of the immune system
29
.
76
Given the described distinct biological properties of IFNα subtypes, we comprehensively
77
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The copyright holder for this preprintthis version posted May 20, 2021. ; https://doi.org/10.1101/2021.05.20.444757doi: bioRxiv preprint
