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Lung biopsy cells transcriptional landscape from COVID-19 patient stratified lung injury in SARS-CoV-2 infection through impaired pulmonary surfactant metabolism

Clinical management of COVID-19 is still complicated due to the lack of therapeutic interventions to reduce the breathing problems, respiratory complications and acute lung injury – which are the major complications of most of the mild to critically affected patients and the molecular mechanisms behind these clinical features are still largely unknown. In this study, we have used the RNA-seq gene expression pattern in the COVID-19 affected lung biopsy cells and compared it with the effects observed in typical cell lines infected with SARS-CoV-2 and SARS-CoV. We performed functional overrepresentation analyses using these differentially expressed genes to signify the processes/pathways which could be deregulated during SARS-CoV-2 infection resulting in the symptomatic impairments observed in COVID-19. Our results showed that the significantly altered processes include inflammatory responses, antiviral cytokine signaling, interferon responses, and interleukin signaling etc. along with downmodulated processes related to lung’s functionality like-responses to hypoxia, lung development, respiratory processes, cholesterol biosynthesis and surfactant metabolism. We also found that the viral protein interacting host’s proteins involved in similar pathways like: respiratory failure, lung diseases, asthma, and hypoxia responses etc., suggesting viral proteins might be deregulating the processes related to acute lung injury/breathing complications in COVID-19 patients. Protein-protein interaction networks of these processes and map of gene expression of deregulated genes revealed that several viral proteins can directly or indirectly modulate the host genes/proteins of those lung related processes along with several host transcription factors and miRNAs. Surfactant proteins and their regulators SPD, SPC, TTF1 etc. which maintains the stability of the pulmonary tissue are found to be downregulated through viral NSP5, NSP12 that could lead to deficient gaseous exchange by the surface films. Mitochondrial dysfunction owing to the aberration of NDUFA10, NDUFAF5, SAMM50 etc. by NSP12; abnormal thrombosis in lungs through atypical PLAT, EGR1 functions by viral ORF8, NSP12; dulled hypoxia responses due to unusual shift in HIF-1 downstream signaling might be the causative elements behind the acute lung injury in COVID-19 patients. Our study put forward a distinct mechanism of probable virus induced lung damage apart from cytokine storm and advocate the need of further research for alternate therapy in this direction.


Introduction
The recent Coronavirus Disease (COVID-19) pandemic has affected approximately 3.5 million people across 212 countries and territories and the number active cases are still on the rise (at 30 April, 2020) [1]. So far till the writing of this article around 7% of the infected population has suffered death [1] and the fatality rate is continuously increasing due to the lack of detailed knowledge of the molecular mechanism of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and proper targeted therapeutic approaches against it.
SARS-CoV-2 is a single stranded positive sense enveloped RNA virus and belongs to the betacoronavirus genus of coronavirus [2]. It has 11 protein coding genes encompassing its ~29.9Kb genome [3]. About 90% genomic similarity was observed between SARS-CoV-2 and bat derived SARS-like coronavirus, while SARS-CoV-2 genome is ~79% and ~50% similar with that of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome related Coronavirus (MERS-CoV), respectively [2,4,5]. Lu et al. (2020) showed the considerable differences between SARS-CoV-2 and SARS-CoV genomes, as in SARS-CoV-2 there has been 380 amino acids substituted, ORF8a deleted, ORF8b elongated, and ORF3b truncated [2]. Though the genomic features are almost similar like those of SARS-CoV, SARS-CoV-2 showed some unique clinical and pathophysiological features like-prolonged incubation period [6], latency inside the host [7] etc. which are making the clinical management of this virus difficult.
Based on the clinical exhibitions of COVID-19, most of the mild to critically affected patients show respiratory complications like-moderate to severe pneumonia, which can further turn into acute respiratory distress syndrome (ARDS), sepsis, and multiple organ dysfunction (MOD) in severely ill patients [8]. Most of these clinical symptoms are associated primarily with respiratory system, specifically with lungs [9] leading to the depleted lung functionality; while the complications with other systems like-cardiovascular system, nervous system etc. were also reported in few patients [10,11]. Recently cases of pulmonary embolism in the lungs of COVID-19 patients are reported [12].
In SARS-CoV and MERS-CoV infections, increased level of pro-inflammatory cytokines were observed which in turn increased the activation and recruitment of inflammatory cells into the lung tissues, causing the acute lung injury [13]. Similarly, increased levels of many pro-inflammatory cytokines were also detected in moderate to critically affected COVID-19 patients [14], leading to the respiratory failure from ARDS. However the complex interplays between pro-inflammatory and anti-inflammatory cytokines are yet to be completely illustrated. Apart from the cytokine storm, other factors like-host innate immunity, autoimmunity against the pulmonary epithelial and endothelial cells, host genetics and epigenetic factors also play important role in the pathogenesis of SARS-CoV infection [15,16]. Moreover, the multifaceted host-virus interactions are also found to be a key player in the pathogenesis of previous coronavirus infections [17].
Previously, transcriptional responses in COVID-19 were experimentally recorded using various in vivo or in vitro approaches like-using cell lines, animal models and COVID-19 infected lungs with SARS-CoV-2 [18], Nasopharyngeal (NP) swab [19], bronchoalveolar lavage fluid of COVID-19 patients [20] etc. which might not provide the actual image of the host transcriptional responses in lung damage upon the viral infection. How the deregulation in the lung's gene expression profiles is related to the pathogenesis of the SARS-CoV-2 infection and overall pathophysiology of lung failure is not yet devised. Moreover, how the lung's functionality related pathways are modulated by SARS-CoV-2 is still elusive. As a result, designing of more targeted therapeutic approaches for the clinical management of the COVID-19 patients is still very complicated. In this regard, we have analyzed a publicly available transcriptome data from the lung biopsy of a COVID-19 patient and summarized which pathways are particularly modulated during the SARS-CoV-2 infection, and how the virus is playing a role in the deregulation of the biological processes/pathways related to lungs' overall functionality and causing acute lung injury in COVID-19 patients.
Quality of microarray experiment (data not shown) was verified by Bioconductor package "arrayQualityMetrics v3.44.0" [22]. Differentially expressed (DE) between two experimental conditions were called using Bioconductor package Limma [23]. Probe annotations were converted to genes using in-house python script basing the Ensembl gene model (Biomart 99) [24]. The highest absolute expression value was considered for the probes that were annotated to the same gene. We have considered the genes to be differentially expressed, which have FDR [25]

Analysis of RNA-seq expression data
Illumina sequenced RNA-seq raw FastQ reads were extracted from GEO database accession: GSE147507 [21]. This data include independent biological triplicates of primary human lung epithelium (NHBE) which were mock treated or infected with SARS-CoV-2 for 24hrs; two technical replicate of post-mortem lung biopsy sample of a COVID-19 deceased patient, along with lung biopsy of two different healthy person. We have checked the raw sequence quality using FastQC program (v0.11.9) [26] and found that the "Per base sequence quality", and "Per sequence quality scores" were high over threshold for all sequences (data not shown). Mapping of reads was done with TopHat (tophat v2.1.1 with Bowtie v2.4.1) [27].
Short reads were uniquely aligned allowing at best two mismatches to the human reference genome from (GRCh38) as downloaded from USCS database [28]. Sequence matched exactly more than one place with equally quality were discarded to avoid bias [29]. The reads that were not mapped to the genome were utilized to map against the transcriptome (junctions mapping). Ensembl gene model [30] (version 99, as extracted from UCSC) was used for this process. After mapping, we used SubRead package featureCount (v2.21) [31] to calculate absolute read abundance (read count, rc) for each transcript/gene associated to the Ensembl genes. For differential expression (DE) analysis we used DESeq2 (v1.26.0) with R (v3.6.2; 2019-07-05) [32] that uses a model based on the negative binomial distribution. To avoid false positive, 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 apart from adjusted p-value cut-off of ≤ 0.05 by FDR. Raw read counts of this experiment is 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)" [22]. From this analyses, in our data no outlier was detected by "Distance between arrays", "Boxplots", and "MA plots" methods and replicate samples are clustered together (Supplementary file 3).

Retrieval of the host proteins that interact with SARS-CoV and SARS-CoV-2
We have obtained the list of human proteins that forms high confidence interactions with SARS-CoV and SARS-CoV-2 proteins from conducted previously studies [33][34][35] and processed their provided proteins name into the associated HGNC official gene symbol.

Mapping of the deregulated genes in cellular pathways
We have utilized Reactome pathway browser [38] for the mapping of deregulated genes of SARS-CoV-2 infection in different cellular pathways. We then searched and targeted the pathways which are found to be enriched for lung related functionalities.

Obtaining the transcription factors which can modulate the differential gene expression
We have obtained the transcription factors (TFs) which bind to the given differentially expressed genes using a custom TFs module created using ENCODE [43], TRRUST [44], and ChEA [45] database.

Obtaining human miRNAs target genes
We extracted the experimentally validated target genes of human miRNAs from miRTarBase database [46].

Extraction of transcription factors modulate human miRNA expression
We have downloaded the experimentally validated TFs which bind to miRNA promoters and module it from TransmiR (v2.0) database which provides regulatory relations between TFs and miRNAs [47]. For miRNAs come to play role in transcriptional regulation, we have considered those TFs that are expressed (upregulated) itself and that can 'activate' or 'regulate' miRNAs, or in absence of TFs (downregulation) that could otherwise 'suppress' miRNAs.

Identification of the host epigenetic factors genes
We used EpiFactors database [48] 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) [49]. We used STRING [50] database to extract highest confidences (0.9) edges only for the protein-protein interactions to reduce any false positive connection.

Antiviral immune responses and organ specific functionalities are deregulated in lungs
During a viral respiratory infection, many pathways of the host get fine-tuned to battle with 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 [51]. These complex

Genes in lung surfactant metabolism pathway are deregulated in COVID-19 patient's lung
Pulmonary surfactant proteins play important role in maintaining the surface tension at the air-liquid interface in the alveoli for efficient gaseous exchange, and can also modulate immunological functions of lung's innate immune cells to eliminate pathogens [53].
Moreover, their role in viral infections as well as in impeding inflammatory responses and clearance of apoptotic cells in lungs are previously reported [53]. Our above analysis as indicated that surfactant metabolism could be a target of this virus, we sought to check the routes of deregulations of this pathway in SARS-CoV-2 infected lung and how they are affecting the downstream signaling processes to impede normal lung function through impaired surfactant metabolism. To achieve this goal, we have mapped the differentially expressed genes in this pathway using Reactome pathway browser [38]. We looked deeply into 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 in turn play an important role by regulating the alveolar surface tension [54]. But in COVID-19 affected lung, TTF1 and SFTPC genes are found to be downregulated, whereas SFTPB is upregulated ( Figure 3). GATA6 transcription factor promotes the transcription of SFTPA gene [55] which is involved in immune and inflammatory responses along with lowering the surface tension in the alveoli [56] and both of them are found to be upregulated in SARS-CoV-2 infected lung while the GATA6 antagonist LMCD1 was downregulated ( Figure 3). While the complex of CSF2RA and CSF2RB can bind GM-CSF to induce activation of macrophages [57] and degradation of STFPs in the alveolar macrophages [58]. We found CFSF2RA downregulated and CSF2RB Numerous genes in the hypoxic responses and HIF-1 alpha signaling were found to be abruptly regulated in the SARS-CoV-2 infected lung (Supplementary Figure 5). PLAT, a tissue plasminogen activator, have profound roles in maintaining the normal homeostasis of lung and its aberrant regulation can lead to many lung injuries [62]. In the response to hypoxia process, in PPI map of differentially expressed genes of combined GOBP module 'response to hypoxia' and SARS-CoV-2 target genes [33], this PLAT protein was found to be directly targeted by viral protein ORF8 ( Figure 5). Moreover, several indirect responses from the viral protein interactions were also revealed ( Figure 5). SARS-CoV-2 M protein can target STOM which interacts with SLC2A1. SLC2A1 can also be targeted by host miRNA miR-320a ( Figure 5). ORF8 which interacts with OS9 can modulate EGLN1 and EGLN2.  Figure 6). NSP5 can modulate NOTCH1 through HDAC2 ( Figure   6). Moreover, host miRNAs like-miR630 can downregulate TGFBR2; while miR-206, miR320a and miR-375 are downregulated so that SOX9 and WYHAZ are overexpressing ( Figure 6). Virus could hamper several growth factor signaling which are crucial for various lung injury repair mechanisms [64,65].
From the respiratory process network we can delineate that several transcription factors are deregulated which are associated in transcribing ECSIT that is directly targeted by viral ORF9c and indirectly by viral ORF8, NSP7 (Figure 7). Moreover, ECSIT itself is directly targeted by ORF9c (Figure 7). NSP12 can modulate SFTPB, SFTPC, SLC5A3, DUSP10, SAMM50 etc. by targeting TCF12 (Figure 7). 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 probable downregulation of miR-320a ( Figure 7).
Virus might be dampening the host immune response in lung by targeting ECSIT [66], as well as could dull the respiratory gaseous exchange in lung by negatively modulating the surfactant proteins [67].
Surfactant metabolism is found to be modulated by not only viral proteins but also through the aberrant host response (Figure 8) further lead to abnormal pathogenic lung injury [70].
Several epigenetic factors like-HDAC2, DNMT1, CUL2, MOV10, RBX1 and TLE1 which are involved in these processes can be targeted by different viral proteins, through which these abovementioned processed can be significantly altered. Epigenetic modulator are key modulators in balancing the normal lung pathobiology and anomalies of these regulations can lead to many lung diseases [71]. HDAC2 and DNMT1 have significant roles in chronic obstructive pulmonary disease (COPD) progression [72,73].

Discussion
Though there are a wide variety of symptoms and clinical features seen in the COVID-19 patients, almost every mild to critically affected patients showed respiratory and breathing complications which ranges from pneumonia to acute lung injury [74]. Severely ill patients are mostly supported by artificial ventilation as no therapeutic drugs are discovered yet for mitigating these complications due to the missing understandings on the molecular aspects of lung related abnormalities in COVID-19. We have identified some important respiratory and lung related processes in which we got several genes are deregulated upon the progression of SARS-CoV-2 infection. So, we prioritized these pathways to check how viral proteins might be playing a role in these aberrant regulations and searched for potential therapies/drugs for the treatment to lessen the resultant effects of the aberration.
We have compared the deregulated genes from SARS-CoV-2 infected lung with the differentially expressed genes from SARS-CoV-2 infected cell line and SARS-CoV infection, to see how host lung and SARS-CoV-2 are responding upon the infections. We found that a significant variations in the number of total deregulated genes between these. Other report also suggests the deregulation of a huge number of genes when expression anylyses are performed using host's infected cells [75]. That means cell lines infected with SARS-CoV-2 might not provide the complete outcomes of the infections. We also checked and verified the quality of our normalized reads to nullify the risk of probable poor sequencing and abnormal read normalization results; all these recommend the suitability of our generated differential expression analysis.
Several SARS-CoV-2 entry receptor (ACE2)/entry associated proteins (TMPRSS2, BSG, CTSL, DPP4) were previously discussed [76]; all of which are readily expressed in the lung, except ACE2 (Supplementary Figure 7A). 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 while the genes of the entry associated proteins were downregulated (Supplementary Figure 7B). More COVID-19 patient data have to be analyzed in concluding this striking feature.
"Cytokine storm" is a much discussed phenomenon in previously reported pathogenic human coronavirus infections which can be lethal for the host for the destruction of its own respiratory systems [77]. Similar responses can also occur in SARS-CoV-2 infection [78].
We have also observed that several inflammatory and antiviral responses are readily deregulated in the SARS-CoV-2 infected lung which could lead to the abnormalities in overall respiratory functions.
Apart from this, our study also identified dysregulations in several non-cytokine mediated lung function related vital processes, namely-response to hypoxia, lung development, respiratory process, and surfactant metabolism; aberrations in these pathways leading to lung pathobiology in COVID-19. Networks generated combining the viral-host protein interactions information suggest that viral proteins might be actively involved in these deregulations along with several host factors which were also decontrolled due to the viral infections.
Hypoxic conditions are common in respiratory infections due to reduced inhalation of oxygen [79]. Several genes which are involved in hypoxia induced responses are found to be deregulated ( Figure 5) in COVID-19 affected lung. ALDH3A1 can protect airway epithelial cells from destruction [80]. Though it is upregulated its functionalities can be impeded through viral proteins ( Figure 5). CFLAR functions in shutting down apoptotic responses by interacting with RIPK1 [81] but viral interactions with RIPK1 might prevent it ( Figure 5).
Virus can induce the transcription of ANGPTL4 by utilizing TCF12 transcription factor ( Figure 5) which in turn could cause pulmonary tissue damage [82]. Viral protein could promote the activity of EGLN1 and EGLN2 ( Figure 5) to suppress the transcription of HIFinduced genes in hypoxia [83]; on the other hand the regulation through these proteins might be hampered due to viral ineractions and 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 [84] in SARS-CoV-2 patients ( Figure 5). In hypoxia, REST is induced and can act as a negative regulator of gene expression to maintain a balance between different processes [85] which is here found downregulated and can be targeted through host miRNA miR-421 in COVID-19 ( Figure 5). GLUT1 (SLC2A1 gene) promotes increased glucose transport into hypoxic cells for its prolonged adaptation during this condition [86], but it is found to be downregulated in lung of COVID-19 patients and this can occur through miR-320a ( Figure   5). During hypoxia, TGF-beta signaling regulates inflammation and vascular responses [87]; but attenuated TGFβ expression might lead to disease severity ( Figure 5). EGR1 transcription factor can be modulated through viral proteins ( Figure 5) in preventing hypoxia induced EGR1 activation of HIF-1 alpha [88], which 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 [89]. Also, PLAT which is a crucial factor in splitting down clots [90], this function might be directly altered by SARS-CoV-2 ORF8.
Many COVID-19 patients are reported to have pulmonary embolism and thrombosis [91], this hypoxic responses could suggest the probable routes of this.
Similarly, several lung development and respiratory process genes/proteins were also found to be deregulated in the COVID-19 patient's lung (Figure 6, 7). SOX9 which is considered an important regulator for the recovery from acute lung injury [92], can be down-modulated by the virus (Figure 6). Though the host miRNAs cannot target the YWHAZ which is a prosurvival protein [93] and also can induce expression surfactant protein A2 [94], it can be indirectly modulated through viral protein NSP7 ( Figure 6). Likewise, viral protein ORF8 can indirectly modulate CHI3L1 ( Figure 6) which can suppress lung epithelium injury [95]. Virus can block TCF12 and inhibit the expression of PDGFRA and PDGFRB ( Figure 6) which could play a role in lung maturation and injury response [96]. GLI3, which exerts essential role in developing the lung, and regulating the innate immune cells [97], is downregulated in COVID-19 lungs ( Figure 6). LTBP3 can promote lung alveolarization [98] but can be modulated by SARS-CoV-2 protein NSP12 ( Figure 6). Aberration in NOTCH signaling contributes significantly in various lung diseases [99], and in SARS-CoV-2 infection NOTCH1, HES1 is found to be downregulated ( Figure 6). CD55, a member of the complement system which plays crucial role in host defense in airway epithelium [100], can be modulated by viral protein NSP12 (Figure 7). CYSLTR1 is upregulated in SARS-CoV-2 infection (Figure 7), which is correlated to COPD [101]. This protein can be modulated by viral ORF9c and ORF3a (Figure 7). ECSIT found to be directly targeted by viral ORF9c protein (Figure 7) to stop the ECSIT mediated antiviral innate immune response [66]. Several mitochondrial genes like-NDUFA10, NDUFAF5, SAMM50 are found downregulated in COVID-19 affected lung ( Figure 7); as mitochondria plays important role in cellular respiration and lung diseases [102], aberration of these might also lead to lung related complicacies. DUSP10 can regulate aberrant inflammatory response upon viral infections [103], but in SARS-CoV-2 infected lung this gene is downregulated which might have occurred through the interaction of NSP12-TCF12 interactions (Figure 7).
Pulmonary surfactant proteins are lipoproteins which mainly functions to lower the alveolar surface tension [104] as well as they can elicit some immune stimulatory roles against some respiratory pathogens [105]. Among the surfactant proteins, SP-A and SP-D mainly evoke immune responses while SP-B and SP-D play roles in maintaining the efficient respiratory gaseous exchanges [69]. Several lung diseases like-asthma, acute respiratory distress syndrome (ARDS), COPD etc. are reported to be associated with aberration in the functionalities of surfactant proteins [70,106]. In SARS-CoV-2 affected lung, production of the surfactant proteins are found to be deregulated ( Figure 8) patient's lung cells ( Figure 1E) which could lead to low accumulation of phospholipids in lungs. As phosphatidylcholine (PC) and phosphatidylglycerol (PG) are the principal phospholipids of surfactant proteins [107], impeded production of lipids will make surfactant proteins non-functional.
Considering all these, lung surfactants might be useful in the treatment of COVID-19 patients, as lung surfactant replacement therapies were previously reported to be successful in other respiratory infections and acute lung injury to reduce the lung damage of the patients [104,108,109] and also our analysis found it as an alternative from enrichment of related process deregulated genes (data not shown). Also, other drugs like-respiratory stimulants for COPD [110], sargramostim for treating pulmonary alveolar proteinosis [111], and oseltamivir in curing influenza-related lower respiratory tract complications [112] showed potential improvements in lung's and respiratory system's overall condition. Further in vitro and invivo research may be turn out to be useful for the patients who cannot tolerate painful ventilator.
From our results, we can suggest that surfactant proteins production along with other respiratory responses in lung could be deregulated. Along with the antiviral drugs to mitigate the viral responses, drugs which can improve the lung conditions in COVID-19 patients could also be considered as a treatment option for the patients. Our generated model can be useful for further experiments, as well as more insights will be gathered upon the use of surfactant therapy in laboratory using SARS-CoV-2 infected model organisms.

Conflict of Interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The authors declare no conflict of interest.

Author's Contribution
ABMMKI conceived the project, designed the workflow and performed the analyses. Both authors interpreted the results and wrote the manuscript. Both authors read and approved the final manuscript.

Funding
This project was not associated with any internal or external source of funding.

Data Availability Statement
Analyses generated data are deposited as supplementary files.    Color schemes are similar as Figure 1 and Figure 2.

Supplementary file 2:
Raw read counts expression of RNA-seq data (GEO accession: