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Lung transcriptome of a COVID-19 patient and systems biology predictions suggest impaired surfactant production which may be druggable by surfactant therapy

An incomplete understanding of the molecular mechanisms behind impairment of lung pathobiology by COVID-19 complicates its clinical management. In this study, we analyzed the gene expression pattern of cells obtained from biopsies of COVID-19-affected patient and compared to the effects observed in typical SARS-CoV-2 and SARS-CoV-infected cell-lines. We then compared gene expression patterns of COVID-19-affected lung tissues and SARS-CoV-2-infected cell-lines and mapped those to known lung-related molecular networks, including hypoxia induced responses, lung development, respiratory processes, cholesterol biosynthesis and surfactant metabolism; all of which are suspected to be downregulated following SARS-CoV-2 infection based on the observed symptomatic impairments. Network analyses suggest that SARS-CoV-2 infection might lead to acute lung injury in COVID-19 by affecting surfactant proteins and their regulators SPD, SPC, and TTF1 through NSP5 and NSP12; thrombosis regulators PLAT, and EGR1 by ORF8 and NSP12; and mitochondrial NDUFA10, NDUFAF5, and SAMM50 through NSP12. Furthermore, hypoxia response through HIF-1 signaling might also be targeted by SARS-CoV-2 proteins. Drug enrichment analysis of dysregulated genes has allowed us to propose novel therapies, including lung surfactants, respiratory stimulants, sargramostim, and oseltamivir. Our study presents a distinct mechanism of probable virus induced lung damage apart from cytokine storm.


Antiviral immune responses and organ specific functions are dysregulated in lungs.
During respiratory virus infections, many host pathways are fine-tuned to battle against the invading pathogen; on the other side, the infecting viruses also try to hijack and modulate host pathways for immune evasion and survival inside the host 22 . These complex interactions lead to the disease complexity, causing several critical pathophysiological conditions in host's respiratory system 22 . To explore which particular biological processes/pathways are dysregulated in SARS-CoV-2 infection, we first identified the dysregulated-genes in both SARS-CoV and SARS-CoV-2 infections and performed comparative functional enrichment analyses 23 .
As expected, enrichment analyses revealed biological processes related to antiviral inflammatory responses, and viral processes were overrepresented in all three infection models (Fig. 1A). Several biological processes, such as negative regulation of viral replication, immune system process, response to hypoxia, and heart development were only enriched in the SARS-CoV-2 infection models (Fig. 1A). However, few pivotal processes were uniquely enriched for the dysregulated genes from COVID-19-affected lung, namely viral transcription, adaptive immune response, brain development, lung development, and respiratory gaseous exchange by respiratory system (Fig. 1A).
Similarly, enrichment using the 'Bioplanet' 24 module suggests host antiviral immune responses through various inflammatory cytokine signaling pathways, apoptosis, and interferon-I signaling in all of these infection models (Fig. 1B,C). While, HIF-1 signaling, heart development, asthma, and type-II interferon signaling pathways were found in both SARS-CoV-2 infection data (Fig. 1B, Supplementary Fig. 2). Intriguingly, some pathways, such as disease associated with surfactant metabolism, ROS/RNS production, fatty acyl-CoA biosynthesis, ER-phagosome pathway, and inflammasomes, were only found in the SARS-CoV-2-infected lung (Fig. 1C, Supplementary Fig. 2). Functional enrichment using the 'DisGeNet' 25 module revealed that the dysregulated genes of SARS-CoV and SARS-CoV-2 infections are also involved in other diseases, namely viral disease, lung diseases, asthma, pneumonitis, and hypoxia (Fig. 1D, Supplementary Fig. 2). Interestingly, several cholesterol biosynthesis pathways were found to be dysregulated only in the lung biopsy of COVID-19 patient (Fig. 1E, Supplementary Fig. 2). As cholesterol in lung plays important roles in maintaining normal lung physiology and protection against many diseases 26 , downregulation of these indicates possible association with lung-related comorbidities of COVID-19 patients.
These enrichment analyses suggest that several pathways related to lung's function are likely dysregulated directly or indirectly by the infecting SARS-CoV-2 virus. While hunting for more definitive clues on which particular processes are being modulated during SARS-CoV-2 infection, we again performed enrichment analysis with our in-house combined module (Supplementary file 4). This enrichment analysis revealed several important lung-function-related processes only for the dysregulated genes from the COVID-19 patient's lung. These includued, lung development, pulmonary surfactant metabolism disease or dysfunction, respiratory processes, regulation of respiratory gaseous exchange, and some antiviral responses (Fig. 2, Supplementary Fig. 3). We also exported a list of significantly enriched terms in color-coded heatmaps. Intriguingly, while equating the expression of these enriched genes, we discovered that genes of these key lung-related processes are significantly altered in SARS-CoV-2-infected lungs compared to the SARS-CoV-2-infected NHBE cells and SARS-CoV infection model ( Supplementary Fig. 4). www.nature.com/scientificreports/ for efficient gaseous exchange at the air-liquid interface in the alveoli, and can also modulate functions of lung's innate immune cells to eliminate pathogens 27 . Additionally, they have been shown to impede inflammatory responses and the clearance of apoptotic cells in lungs following viral infection 27 . Taking cue from the results of previous section, it was apparent that surfactant metabolism could be a potential target of viral modulation. Therefore, we sought to decipher the probable routes of SARS-CoV-2-induced dysregulations of this pathway and its downstream signaling. To attain this, we mapped the differentially expressed genes into this pathway using the Reactome pathway browser 28 . Next, we scrutinized the mechanisms of this pathway to elucidate the probable alterations happening in COVID-19-affected lung.
In normal lung, TTF1-CCDC59 complex can transactivate SFTPB and SFTPC gene expression, which play an important role by regulating the alveolar surface tension 29 . But in COVID-19-affected lung, TTF1 and SFTPC genes were found to be downregulated, whereas SFTPB was upregulated (Fig. 3). GATA6 transcription factor promotes the transcription of SFTPA gene 30 which is involved in immune and inflammatory responses, and lowers the surface tension in the alveoli 31 . Both GATA6 and SFTPA genes were upregulated in SARS-CoV-2-infected lung, while the GATA6 antagonist LMCD1 was downregulated (Fig. 3). The CSF2RA-CSF2RB complex can bind GM-CSF to induce activation of macrophages 32 and helps in the degradation of STFPs in the alveolar macrophages 33 . We found CFSF2RA downregulated and CSF2RB upregulated in the lung of the COVID-19-affected patient (Fig. 3). Pro-SFTPB and Pro-SFTPC are cleaved by NAPSA, CTSH, and PGA3-5 to produce active SFTPB and SFTPC 34,35 . Surprisingly, NAPSA was dysregulated in the COVID-19-affected lung (Fig. 3). Overall, the transcription of surfactant genes, production of active surfactant proteins, and their turnover may be dysregulated in the COVID-19 patient's lung, which could have resulted in the severely lethal disease complications. As these mechanisms are found to be altered upon SARS-CoV-2 infections, the virus may be positively facilitating these anomalies.
Host proteins which interact with the virus are involved in different respiratory-function-related pathways and diseases. In previously reported human coronavirus infections, SARS and MERS coronaviruses are often found to commandeer host machineries, suppressing host immune responses and other important biological processes for their continued existence within the infected cells 36 . We performed functional enrichment analyses using previously reported SARS-CoV and SARS-CoV-2 host factor proteins 37-39 www.nature.com/scientificreports/ to illuminate the pathways which may be targeted by viral proteins, causing the lung injuries in COVID-19 patients.
As anticipated, the enrichment analyses showed association of both SARS-CoV and SARS-CoV-2 infections with several immune signaling pathways, such as interleukin signaling, interferon signaling, apoptosis, and inflammasomes ( Fig. 4A,C). However, this approach also revealed several vital pathways for respiratory function such as HIF-1 signaling, and hypoxic and oxygen homeostasis regulation of HIF-1 alpha (Fig. 4A,C). Using the DisGenNet module 25 , lung disease, asthma, hyperoxia, respiratory failure, and pulmonary hypertension were found to be enriched (Fig. 4B). These results enlightened that SARS-CoV-2 is likely utilizing its proteins to modulate normal lung's physiological and immune responses, which we further explored by linking these viralhost protein-protein interactions (PPI) to our previously identified essential lung processes.

SARS-CoV-2 proteins and host epigenetic regulators can modulate the functions of lung and other respiratory processes.
Results from the previous sections rationalized that both the dysregulated genes in COVID-19-affected lung and SARS-CoV-2 interacting proteins are involved in several respiratory functions. Hence, we produced several functional networks of dysregulated genes, viral protein-host protein interactions, and host epigenetic regulators involved in those processes to gain insight on virus-mediated deregulations and the resulting pathophysiological effects of COVID-19. We have mainly addressed four broad biological processes that can significantly affect COVID-19 patients: response to hypoxia, lung development, respiratory processes, and surfactant metabolism.
Numerous genes in hypoxia response and HIF-1 alpha signaling were abruptly dysregulated in the SARS-CoV-2-infected lung ( Supplementary Fig. 5). This included PLAT, a tissue plasminogen activator with profound roles in lung homeostasis, whose aberrant regulation can lead to many lung injuries 40 . In the PPI map of differentially-expressed genes of the GOBP 41 module 'response to hypoxia' and SARS-CoV-2 target genes 37 , this PLAT protein was found to be directly targeted by viral protein ORF8 (Fig. 5). Moreover, several indirect responses from the viral protein interactions were also revealed ( Fig. 5). SARS-CoV-2 M protein can target STOM which interacts with SLC2A1. SLC2A1 can also be targeted by host miRNA miR-320a (Fig. 5). SLC2A1 encoding GLUT1 protein is upregulated by hypoxic responses in alveolar epithelial cells 42 .
Viral ORF8 interaction with OS9 can modulate EGLN1 and EGLN2, which might disrupt the functions of the EGLN-HIF oxygen sensing system 43 . KCNMA1 was found to interact with host proteins ATP1B1 and PRKACA that interact with viral M and NSP13 proteins, respectively (Fig. 5). ORF9c may modulate EDNRA indirectly through F2RL1 (Fig. 5) and can alter the vasoconstrictor effect resulting from EDNRA 44 . PML functions might be altered through the viral N and MOV10 proteins' interaction. Functions of SLCBA1 may be modulated by NSP13 through PRKACA (Fig. 5). NSP7 can regulate ALDH3A1 which can affect CYP1A1 and NR4A2 (Fig. 5). NSP5 interacting HDAC2 can curb PML and REST which have hypoxia responsive functions 45,46 (Fig. 5). NSP12 can modulate a wide range of hypoxia functions related proteins, namely TGFBR2, MECP2, MTHFR, CBFA2T3, EGR1, and ANGPTL4 by interacting with the transcription factor TCF12 (Fig. 5). NSP12 through RIPK1 interactions can dampen the apoptosis regulating function of CFLAR 47 (Fig. 5). Apart from this, several host miRNAs could possibly downregulate the expression of some genes, namely-miR-320a, miR-3188, miR-3661, miR-217, miR-421 and miR-429 (Fig. 5). These viral mediated deviations found in the hypoxia responses might be a decisive factor in the lung injury found in COVID-19 patients 48 .
From the respiratory process network, we can delineate that several transcription factors are dysregulated. Many of these are associated with ECSIT that can directly interact with viral ORF9c and indirectly by viral ORF8, and NSP7 (Fig. 7A). Moreover, ECSIT itself is directly targeted by ORF9c (Fig. 7A). NSP12 can modulate SFTPB, SFTPC, SLC5A3, DUSP10, and SAMM50 by targeting TCF12 (Fig. 7A). Also, in this network we have observed suppressive actions of miRNAs-miR-206, miR-217, miR-375 on NR4A2 and NDST1; as well as upregulation of YWHAZ due to the probable downregulation of miR-320a (Fig. 7A). Virus might be dampening the host immune response in the lung by targeting ECSIT 51 and by diminishing, respiratory gaseous exchange by negatively modulating the surfactant proteins 52 .
Surfactant metabolism is found to be modulated not only by viral proteins, but also through irregular host responses (Fig. 7B). Viral proteins NSP12 and NSP5 can target transcription factor TCF12 and epigenetic regulator HDAC2, respectively, which in turn modulate important members of surfactant metabolism process, namely-TTF1, CCDC59, SFTPB, SFTPC, CSF2RA, CSF2RB, NAPSA, SFTPD, and DMBT1 (Fig. 7B). These can also be modulated through CKAP4 which is observed to interact with viral M, NSP2, NSP9, E, and ORF8 proteins (Fig. 7B). Furthermore, we have observed that viral M and S proteins can interact with proteins of this process both directly and indirectly (Supplementary Fig. 6). Host miRNA miR-421 was found to downregulate LMCD1; while miR-137, miR-375, and miR-429 fail to modulate CCDC59 and GATA6 because of their probable inactivation/suppression by differential expression of the regulating TFs (Fig. 7B). As SFTPD and SFTPC are downregulated along with several regulatory partners, their primary function of immunomodulation and  www.nature.com/scientificreports/ efficient air exchange in lung 53,54 might be seriously hindered by the viral proteins; which could further lead to pathogenic lung injury 55 . SARS-CoV-2 proteins can target several epigenetic factors, such as HDAC2, DNMT1, CUL2, MOV10, RBX1 and TLE1, to alter the above-mentioned processes. Epigenetic factors play a key role in balancing normal lung pathobiology, and anomalies in their regulation can lead to many lung diseases 56 . For instance, HDAC2 and DNMT1 have significant roles in chronic obstructive pulmonary disease (COPD) progression 57,58 . Drug enrichment suggests lung surfactant replacement therapy as a potential treatment option. Our results pointed towards the probable SARS-CoV-2 directed dysregulation in several important respiratory processes and surfactant metabolism pathway in COVID-19-affected lung. We then sought to dig out possible therapies/drugs for the improvement of the lung and respiratory conditions of COVID-19-affected patients. In this regard, we performed drug enrichment analysis for differentially expressed genes present in the combined module terms 'response to hypoxia' , 'lung development' , 'respiratory process' and 'surfactant metabolism pathway' using the WebGestalt functional enrichment tool 59 . We have found significant enrichment scores for lung surfactants, respiratory stimulants, sargramostim, and oseltamivir (Fig. 8, Supplementary Fig. 7).

Discussion
Though there are a wide variety of symptoms and clinical features seen in COVID-19 patients, almost every mild-to-critically affected patient showed respiratory and breathing complications, ranging from pneumonia to acute lung injury 60 . Severely ill patients are greatly supported by artificial ventilation, as no therapeutic drugs for mitigating these complications have been discovered. This is due to the lack of understanding on the molecular aspects of lung-related abnormalities in COVID-19. We have identified dysregulated genes related to respiratory and lung-related processes upon the SARS-CoV-2-infection. We have prioritized these pathways and searched for potential therapies/drugs for the treatment which could lessen the resultant effects of gene dysregulation.
Several SARS-CoV-2 entry receptor (ACE2)/entry associated proteins (TMPRSS2, BSG, CTSL, and DPP4) have been previously described 61 . All of these viral entry associated factors are readily expressed in the lung, except ACE2 (Supplementary Fig. 8A). While analyzing the expression profiling in SARS-CoV-2-infected lung, we discovered a quite unexpected scenario. Astoundingly, in COVID-19-affected lung, ACE2 was upregulated www.nature.com/scientificreports/ while the genes of the entry associated proteins were downregulated ( Supplementary Fig. 8B). More COVID-19 patient data must be analyzed to validate this striking finding. "Cytokine storm" is a much discussed phenomenon in previously reported pathogenic human coronavirus infections that can be lethal for the host due to the destruction of its own respiratory systems 62 . Similar responses can also occur following SARS-CoV-2 infection 63 . We observed that several inflammatory and antiviral responses are readily dysregulated in the SARS-CoV-2-infected lung that could lead to the abnormalities in overall respiratory functions.
Apart from this, our study identified dysregulation in several lung function related vital processes, namelyresponse to hypoxia, lung development, respiratory process, and surfactant metabolism; alterations in these pathways lead to abnormal lung pathobiology in COVID-19. Networks generated from combining the viral-host protein interactions suggest that viral proteins might be actively involved in these dysregulations along with several host factors, which might also be decontrolled due to the viral infections.
Hypoxic conditions are common in respiratory infections due to reduced oxygenation of the blood 64 . Several genes involved in hypoxia-induced responses were found to be dysregulated (Fig. 5) in the COVID-19-affected lung. ALDH3A1 can protect airway epithelial cells from destruction 65 . Though it is upregulated, its functions can be impeded through viral proteins (Fig. 5). CFLAR functions in shutting down apoptotic responses by interacting with RIPK1 47 , but viral interactions with RIPK1 might prevent this (Fig. 5). SARS-CoV-2 can induce the transcription of ANGPTL4 by utilizing TCF12 transcription factor (Fig. 5) which in turn could cause pulmonary tissue damage 66 . Viral proteins could promote the activity of EGLN1 and EGLN2 (Fig. 5) to suppress the transcription of HIF-induced genes in hypoxia 67 ; on the other hand the regulation through these proteins might be hampered due to viral interactions. Moreover, the constant overexpression of HIF-mediated inflammatory genes could also occur, which could lead to inflammation-induced lung damage. Severe hypoxia-induced responses can occur through the downregulation of MECP2 68 in SARS-CoV-2 patients (Fig. 5). In hypoxia, REST is induced and can act as a negative regulator of gene expression to maintain a balance between different processes 45 , that were found to be downregulated and can be targeted through miR-421 in COVID-19 (Fig. 5). GLUT1 (SLC2A1 gene) promotes increased glucose transport into hypoxic cells for its prolonged adaptation during this condition 69 , but it was found to be downregulated in lung of COVID-19 patient and this can occur through miR-320a (Fig. 5). During hypoxia, TGFβ signaling regulates inflammation and vascular responses 70 ; but attenuated TGFβ expression might lead to increased disease severity (Fig. 5). EGR1 transcription factor can be modulated through viral proteins (Fig. 5) that might prevent the hypoxia induced EGR1 activation of HIF-1 alpha 71 . This probable route of viral-mediated HIF-1 signaling inhibition could curb the whole hypoxia induced survival responses. Moreover, defective hypoxia response can occur due to the overactivity of EGR1 that can result in anomalous thrombosis 72 . Also, PLAT is a crucial factor in splitting down clots 73 ; this function might be directly targeted by SARS-CoV-2 ORF8 (Fig. 5). Many COVID-19 patients were reported to have pulmonary embolism and thrombosis 74 , which could be the effect of altered hypoxic responses. www.nature.com/scientificreports/ Similarly, several lung development and respiratory process genes/proteins were found to be dysregulated in the COVID-19 patient's lung (Fig. 6, 7). SOX9, an important regulator for the recovery from acute lung injury 75 , can be down-modulated by the virus (Fig. 6). Though the host miRNAs cannot target the YWHAZ pro-survival protein 76 , they can induce expression surfactant protein A2 77 , which might be indirectly modulated through viral protein NSP7 (Fig. 6). Likewise, viral protein ORF8 can indirectly modulate CHI3L1 (Fig. 6) that normally suppresses lung epithelium injury 78 . Virus can block TCF12 and inhibit the expression of PDGFRA and PDGFRB (Fig. 6) which could play a role in lung maturation and injury response 79 . GLI3, which exerts essential role in developing the lung and regulating the innate immune cells 80 , is downregulated in COVID-19 lungs (Fig. 6). LTBP3 can promote lung alveolarization 81 , but can be modulated by SARS-CoV-2 protein NSP12 (Fig. 6). Abnormal NOTCH signaling contributes significantly in various lung diseases 82 , and in SARS-CoV-2 infection NOTCH1 and HES1 are found downregulated (Fig. 6). CD55, a member of the complement system which plays crucial role in host defense in airway epithelium 83 , can be modulated by viral protein NSP12 (Fig. 7A). CYSLTR1 is upregulated in SARS-CoV-2 infection (Fig. 7A), which is correlated to COPD 84 . This protein can be modulated by viral ORF9c and ORF3a (Fig. 7A). ECSIT was found to directly interact with viral ORF9c (Fig. 7A) which might stop ECSIT-mediated antiviral innate immune response 51 . Several mitochondrial genes, for instance NDUFA10, NDUFAF5, and SAMM50 were downregulated in COVID-19-affected lung (Fig. 7A). As mitochondria plays important role in cellular respiration and lung diseases 85 , aberrant expression of these genes might also lead to lung-related complications. DUSP10 can regulate unusual inflammatory responses upon viral infections 86 , but in SARS-CoV-2-infected lung this gene was found downregulated, possibly through NSP12-TCF12 interactions (Fig. 7A).
Pulmonary surfactant proteins are lipoproteins that mainly function to lower the alveolar surface tension 87 and can elicit immune stimulatory roles against some respiratory pathogens 88 . Among the surfactant proteins, SP-A and SP-D mainly evoke immune responses, while SP-B and SP-D play roles in maintaining efficient respiratory gas exchange 54 . Several lung diseases including asthma, acute respiratory distress syndrome (ARDS), COPD are reportedly associated with aberration in the function of surfactant proteins 55,89 . In SARS-CoV-2-affected lung, production of the surfactant proteins is found to be dysregulated (Fig. 7B). Viral protein NSP5 can recruit HDAC2 and downregulate the expression of TTF1 which is needed for the expression of SP-B and SP-C (Fig. 7B). SP-A and SP-D can be targeted indirectly by several viral proteins (Fig. 7B) which might dampen the production of surfactant proteins in lungs, thus complicating the disease condition. The CSF2RA-CSF2RB complex modulate the surfactant recycling that maintains the overall balance of surfactant content 33 . We found that CSF2RA is dysregulated in SARS-CoV-2-infected lung, which could lead to abnormal surfactant recycling (Fig. 7B). While performing enrichment analysis, we witnessed a significant downregulation of several cholesterol biosynthesis pathways in COVID-19 patient's lung cells (Fig. 1E) that could lead to low accumulation of phospholipids in lungs. As phosphatidylcholine (PC) and phosphatidylglycerol (PG) are the principal phospholipids of surfactant proteins 90 , disrupted production of lipids might make surfactant proteins non-functional.
Considering all these, lung surfactants might be useful in the treatment of COVID-19 patients, as lung surfactant therapies were previously reported to be successful in other respiratory infections and acute lung injury to reduce the lung damage of the patients 87,91,92 . Also, other drugs including respiratory stimulants for COPD 93 , sargramostim for treating pulmonary alveolar proteinosis 94 , and oseltamivir in curing influenza-related lower respiratory tract complications 95 showed potential for improving the lung's and respiratory system's overall condition.
From our results, we can suggest that surfactant protein production along with other respiratory responses in lung could be dysregulated in COVID-19. However, further experimental proteomic analyses of this dysregulation are required for the functional implications of this study. Along with the antiviral drugs to mitigate the viral responses, drugs that can improve lung conditions in COVID-19 could also be considered as a treatment option for the patients. Our generated results can be useful for obtaining greater insight on the probable dampened  Analysis of RNA-seq expression data. Illumina sequenced RNA-seq raw FastQ reads were extracted from GEO database 96 , accession: GSE147507. This data includes independent biological triplicates of primary human lung epithelium (NHBE) cell lines which were mock treated or infected with SARS-CoV-2 for 24hrs. This data also contains two technical replicate of post-mortem lung biopsy sample of a deceased COVID-19 patient, along with lung biopsy samples of two different healthy persons as control. We have checked the raw sequence quality using FastQC program (v0.11.9) 101 , and found that the "Per base sequence quality" and "Per sequence quality scores" were high over the threshold for all sequences (data not shown). Mapping of reads was done with TopHat (tophat v2.1.1 with Bowtie v2.4.1) 102 . Short reads were uniquely aligned allowing at best two mismatches to the human reference genome (GRCh38) as downloaded from UCSC database 103 . Sequences matched exactly more than once with equal quality were discarded to avoid bias 104 107 that uses a model based on the negative binomial distribution. To avoid false positives, we considered only those transcripts where at least 10 reads are annotated in at least one of the samples used in this study and also applied a minimum Log2 fold change of 0.5 for to be differentially expressed transcripts apart from adjusted p-value cut-off of ≤ 0.05 by FDR. Raw read counts of this experiment are provided in supplementary file 2. To assess the fidelity of the RNA-seq data used in this study and normalization method applied here, we checked the normalized Log2 expression data quality using R/Bioconductor package "arrayQualityMetrics (v3.44.0)" 97 . From this analysis, in our data no outlier was detected by "Distance between arrays", "Boxplots", and "MA plots" methods and replicate samples were clustered together (Supplementary file 3).

Retrieval of the host proteins that interact with SARS-CoV and SARS-CoV-2 proteins.
We have obtained the list of human proteins that form high confidence interactions with SARS-CoV and SARS-CoV-2 proteins from previously conducted studies [37][38][39] and processed their provided protein names into the associated HGNC official gene symbol.
Functional enrichment analysis. We utilized Gitools (v1.8.4) for enrichment analysis and heatmap generation 23 . We have utilized the Gene Ontology Biological Processes (GOBP) 41 , Reactome pathway 28 , Bioplanet pathways 24 , HumanCyc database 108 , DisGeNet 25 , KEGG pathway 109 modules, and a custom in-house built combined module (Supplementary file 4) for the overrepresentation analysis. This combined module was generated from related modules with few genes to a parent term/process which otherwise would have been left out from analysis due to statistical stringency cutoff (module with at least 10 genes are selected) during enrichment analysis. Resulting p-values were adjusted for multiple testing using the Benjamin and Hochberg's method of False Discovery Rate (FDR) 100 .

Mapping of the differentially expressed genes from SARS-CoV-2-infected lung onto biological pathways.
We utilized the Reactome pathway browser 28 for the mapping of dysregulated genes of SARS-CoV-2 infection onto different biological pathways. We then focused on the pathways which were found to be enriched for lung-related functions.
Obtaining the transcription factors which can modulate the differential gene expression. We obtained the transcription factors (TFs) which bind to a given differentially expressed gene using a custom TFs module created using ENCODE 110 , TRRUST 111 , and ChEA 112 databases.
Obtaining human miRNAs target genes. We extracted the experimentally validated target genes of human miRNAs from miRTarBase database 113 .
Extraction of transcription factors modulate human miRNA expression. We downloaded experimentally validated TFs which bind to miRNA promoters and modules from TransmiR (v2.0) database which provides regulatory relations between TFs and miRNAs 114 . Because miRNAs play roles in transcriptional regu- www.nature.com/scientificreports/ lation, we considered TFs that are expressed (upregulated) and can 'activate' or 'regulate' miRNAs, or in the absence of TFs (downregulation), those could otherwise 'suppress' miRNAs.
Identification of the host epigenetic factors genes. We used the EpiFactors database 115 to find human genes related to epigenetic activity.

Construction of biological networks. Construction, visualization and analysis of biological networks
with differentially expressed genes, their associated transcription factors, associated human miRNAs, and interacting viral proteins were executed in the Cytoscape software (v3.8.0) 116 . We used the STRING 117 database to extract only the highest confidences (0.9) edges for protein-protein interactions to reduce any false positive connection.
Drug enrichment analysis. We used the WebGestalt tool 59 for predicting potential drugs targeting the given differentially expressed genes. We selected the drugs based on FDR (BH) ≤ 0.05 100 , using both DrugBank 118 and GLAD4U 119 drug database combined.

Data availability
Publicly available data were utilized. Analyses generated data are deposited as supplementary files.