Fig 2: Up-regulated ISG expression and suppressed MCF7 and T47D proliferation upon HNRNPC repression mediated via the interferon beta signaling pathway A–CIn the siRNA-transfected MCF7 (left) or T47D cells (right), the interferon signaling pathway was blocked at different stages by means of IFNß neutralization (A), IFNAR2 neutralization (B), or JAK-STAT inhibition (C). The expressions of the ISGs were measured by qPCR. Each sample has three replicates. Data represent mean ± SD.D, EGrowth curves of the MCF7 (D) or T47D cells (E) upon HNRNPC knock-down but with the interferon response blocked with the IFNß antibody. Each sample has three replicates. Data represent mean ± SD.FGrowth curves of the MCF7 (left) or T47D (right) cells upon HNRNPC knock-down and JAK-STAT inhibition with ruxolitinib (5 µM). siNC: non-targeting siRNA as a negative control, siLMNA: siRNA for LMNA as another negative control, siHN-1: siRNA sequence 1 for HNRNPC, siHN-2: siRNA sequence 2 for HNRNPC. Each sample has three replicates. Data represent mean ± SD.

Fig 3: Human metapneumovirus (hMPV)-mediated suppression of cathelicidin antimicriobial peptide (CAMP) is largely interferon-independent. (A–D) Monocyte-derived macrophages (MDMs) were mock-infected (N.I.), infected with hMPV (hMPV) or pretreated with BX795 before hMPV infection (BX795 + hMPV) for 24 h. mRNA expression of IFN-ß (A), IL-28A/B (B), IL-29 (C), and ISG54 (D) was assessed by quantitative real-time PCR (qRT-PCR). (E) Same set-up for hMPV infection and BX795 pretreatment as (A–D), concomitant with or without 1,25(OH)2D3 treatment. CAMP mRNA expression was assessed by qRT-PCR. (F) MDMs were mock-infected (N.I.), infected with hMPV (hMPV) or pretreated with IFNAR2 neutralizing antibody (aIFNAR) before hMPV infection (hMPV + aIFNAR) for 24 h. mRNA expression of ISG54 was assessed by qRT-PCR. (G) Same set-up for hMPV infection and aIFNAR pretreatment as (F), concomitant with or without 1,25(OH)2D3 treatment. CAMP mRNA expression was assessed by qRT-PCR. Error bars represent SD for triplicates. **p < 0.01, ***p < 0.001. Data are representative of at least three independent experiments from different donors.

Fig 4: Therapeutics reduced expression of a representative list of interferon stimulated genes- ISGs (DDX58, IFIH1, IFITM3, IRF7) or inflammatory markers (IL6) (matched to figure 1).Relative expression of interferon inducible or inflammatory genes in treated or untreated MISTRG6- hACE2 mice infected with SARS-CoV-2 mice at 14dpi or 28dpi. Uninfected baseline expression values are presented as reference. The distribution of cells that preferentially express these genes is overlayed on the tSNE plots showing 14dpi and 28dpi human immune cells. IFITM3 and IL6 were particularly enriched in macrophage/monocyte clusters, while IRF7, DDX58 and IFIH1 were enriched in multiple immune cells such as T cells, B cells, and myeloid cells. Normalized to HPRT1. DDX58: uninfected n=3; CTRL-infected: 14dpi n=8, 28dpi n=: 5; Dex 14dpi n=3, 28dpi n= 6; RDV 14 and 28dpi n=3; anti-IFNAR2 14 and 28 dpi n=3, anti-IFNAR2+ Remdesivir 14 and 28dpi n=5 biologically independent mice examined over at least 2 independent experiments. IFIH1: uninfected n=5; CTRL-infected: 14dpi n =11, 28dpi n=: 3; Dex 14 and 28dpi n=4; RDV 14 and 28dpi n=3; anti-IFNAR2 14 and 28 dpi n=3, anti-IFNAR2+ Remdesivir 14 dpi n=4 and 28dpi n=5 biologically independent mice examined over at least 2 independent experiments. IFITM3: uninfected n=4; CTRL-infected: 14dpi n =7, 28dpi n=: 4; Dex 14 and 28dpi n=4; RDV 14 and 28dpi n=3; anti-IFNAR2 14 and 28 dpi n=3, anti-IFNAR2+ Remdesivir 14 and 28dpi n=4 biologically independent mice examined over at least 2 independent experiments. IRF7: uninfected n=4; CTRL-infected: 14dpi n =7, 28dpi n=: 5; Dex 14 and 28dpi n=4; RDV 14 and 28dpi n=3; anti-IFNAR2 14 and 28 dpi n=3, anti-IFNAR2+ Remdesivir 14dpi n=4, 28dpi n=5 biologically independent mice examined over at least 2 independent experiments. IL6: uninfected n=5; CTRL-infected: 14dpi n =9, 28dpi n=: 4; Dex 14dpi n=3, 28dpi n=4; RDV 14 and 28dpi n=3; anti-IFNAR2 14 and 28 dpi n=3, anti- IFNAR2+ Remdesivir 14dpi n=4, 28dpi n=5 biologically independent mice examined over at least 2 independent experiments. Unpaired, two-tailed t-test.

Fig 5: Targeting viral replication and the downstream interferon response attenuates the hyperactive immune/inflammatory response (matched to figure 1).a. Representative gating strategy of human immune cells in the lungs of SARS-CoV-2 infected MISTRG6-hACE2 mice. Cells isolated from lungs or bronchioalveolar lavage (BAL) were stained with antibodies against human CD45, HLA-DR, CD68, CD16, CD14, CD206, CD86, CD11B, CD11C, CD123, CD3, and mouse CD45. Cell numbers were calculated using counting beads.b. Human immune cells (numbers) in BAL (14dpi) or lungs (14 and 28dpi) of SARS-Cov-2 infected MISTRG6-hACE2 mice treated with dexamethasone (Dex), Remdesivir (RDV), anti-IFNAR2 or a combined therapy of Remdesivir (RDV) and anti-IFNAR2. 14dpi, BAL: CTRL-infected n=5, Dex; RDV anti-IFNAR2 n=3; anti-IFNAR2+RDV n=4 biologically independent mice examined over 2 independent experiments. 14dpi, Lung: CTRL-infected n=7; Dex, RDV, anti-IFNAR2, anti-IFNAR2+RDV n=4 biologically independent mice examined over 3 independent experiments. 28dpi, lung: CTRL infected n=5, Dex n=4, RDV n=3, anti-IFNAR2 n=3, anti-IFNAR2+RDV n=6 biologically independent mice examined over 3 independent experiments. Means with individual datapoints plotted. Unpaired, two-tailed t-test. P<0.0001=8.19×10-5.c. Representative flow cytometry plots and frequencies of alveolar macrophages (AMs) (middle: hCD206hihCD86+hCD68+) or inflammatory macrophages (bottom: hCD206lo/-hCD86+hCD68+) in 14dpi or 28dpi lungs of treated or untreated MISTRG6-hACE2 mice. 14dpi: CTRL infected n=5, Dex n=4, RDV n=4, anti-IFNAR2 n=4, anti-IFNAR2+RDV n=4 biologically independent mice examined over at least 2 independent experiments. 28dpi: CTRL infected n=5, Dex n=4, RDV n=3, anti-IFNAR2 n=3, anti-IFNAR2+RDV n=6 biologically independent mice examined over 3 independent experiments. Means with individual datapoints. Unpaired, two-tailed t-test. P<0.0001=4.67×10-5.d. Frequencies (left) and numbers (right) of lung pDCs at 14dpi. CTRL-infected n=6, Dex n=4, RDV, anti-IFNAR2 n=3, anti-IFNAR2+RDV n=6 mice examined over at least 2 experiments. Means with datapoints. Unpaired, two-tailed t-test. P<0.0001=7.29×10-5.e. IFNA transcript levels measured by qPCR in treated or control untreated MISTRG6-hACE2 mice infected with SARS-CoV-2: Uninfected n=5; CTRL infected: 4dpi n=8, 14dpi n =9, 28dpi n=: 6; Dex 14dpi n=4, Dex 28dpi= 4; RDV 14 and 28dpi n=3, anti-IFNAR2 14 and 28dpi n=3, anti-IFNAR2+ Remdesivir 14 and 28dpi n=4 biologically independent mice examined over at least 2 independent experiments. Normalized to HPRT1. Violin plots with individual datapoints. Unpaired, two-tailed t test.f. Representative histograms and frequencies of HLA-DR+ activated T cells in treated or control mice. 14dpi: CTRL-infected n=5, Dex, RDV, anti-IFNAR2, anti-IFNAR2+RDV n=4; 28dpi: CTRL infected, Dex, anti-IFNAR2+RDV n=4, RDV, anti-IFNAR2 n=3 biologically independent mice examined over 3 independent experiments. Means with datapoints. Unpaired, two-tailed t-test.Some of the data associated with dexamethasone therapy used here as a control have been reported19.