Abstract Chronic rhinosinusitis with nasal polyps (CRSwNP) is a common upper respiratory tract complication where the pathogenesis is largely unknown. Herein, we investigated the transcriptome profile in nasal mucosa biopsies of CRSwNP patients and healthy individuals. We further integrated the transcriptomics data with genes located in chromosomal regions containing genome-wide significant gene variants for COVID-19. Among the most significantly upregulated genes in polyp mucosa were CCL18, CLEC4G, CCL13 and SLC9A3. Pathways involving “Ciliated epithelial cells” were the most differentially expressed molecular pathways when polyp mucosa and non-polyp mucosa from the same patient was compared. Natural killer T-cell (NKT) and viral pathways were the most statistically significant pathways in the mucosa of CRSwNP patients compared with those of healthy control individuals. Upregulated genes in polyp mucosa, located within the genome-wide associated regions of COVID-19, included LZTFL1, CCR9, SLC6A20, IFNAR1, IFNAR2 and IL10RB. Interestingly, the second most over-expressed gene in our study, CLEC4G, has been shown to bind directly to SARS-CoV-2 spike's N-terminal domain and mediate its entry and infection. Our results on altered expression of genes related to cilia and viruses point to the de-regulation of viral defenses in CRSwNP patients, and may give clues to future intervention strategies. Subject terms: Biochemistry, Biological techniques, Cell biology, Genetics, Biomarkers, Diseases, Molecular medicine Introduction The human nasal mucosa is the main portal of entry and a critical site of infection of respiratory pathogens. Chronic rhinosinusitis with nasal polyps (CRSwNP) is a common upper respiratory tract complication in humans^[44]1. CRSwNP is a condition defined by chronic inflammation of the nasal cavity and the paranasal sinuses combined with bilateral polyps in the middle meatus of the nose. CRSwNP is difficult to treat, and recurrences are frequent, despite medical treatment and surgical interventions. The clinical management of CRSwNP is largely ineffective partly due to the limited understanding of the underlying pathogenic factors. Therefore, understanding the mechanisms that underlie CRSwNP pathogenesis is essential to help identify targets and/or pathways for therapeutic interventions. Despite several hypotheses over the years, the pathogenesis of CRSwNP remains unclear^[45]2. Studies have shown an increased frequency of positive family history among those affected^[46]1,[47]3,[48]4 and there is a five-fold increased risk of having CRSwNP among first-degree relatives to subjects with the disease, indicating that genetic mechanisms are important^[49]1. Studies of gene expression in nasal polyps have shown significantly altered expression levels of several genes when comparing nasal polyp tissue to nasal mucosa from unaffected individuals^[50]5–[51]11. A previous study based on gene expression microarray of six nasal polyp samples from patients with CRSwNP and six tissue samples from control subjects, suggested induction of type 2 inflammation and eosinophil migration, such as CCL13, CCL18, CCL8 and genes related to antimicrobial defense responses^[52]12. Similarly, using microarray technology, whole gene expression has been studied in several chronic respiratory sinusitis (CRS) populations^[53]13–[54]16. A few previous whole transcriptome RNA sequencing analyses of CRSwNP tissue have also been performed^[55]17–[56]19. A report from Wang et al. examined specifically patients with CRSwNP and comorbid asthma, where they analysed ten patients with CRSwNP and asthma, ten patients with CRSwNP-alone and nine healthy control individuals. This study identified the HISLA Gene “HIF1A Stabilizing Long Noncoding RNA” (alias LINC01146) as a hub lncRNA dysregulated in CRSwNP patients, with and without asthma, compared with controls^[57]17. Another RNA sequencing study collected mucosal tissue samples from six CRS without nasal polyps (CRSsNP), six CRSwNP, and six control patients. Additional matched polyp samples were also collected from the six CRSwNP patients. In their study, CRSwNP polyp tissue showed an upregulation of B-cell mediated immune responses and a reduced expression of genes related to epithelial morphogenesis and homeostasis. Finally, the largest transcriptome analysis of CRSwNP so far has been performed by Peng et al.^[58]19 who performed RNA sequencing analysis on 44 CRSwNP patients and 41 control subjects. This study reported the transcript signatures of CRSwNP as genes involved in cilia dysfunction, interferon signaling, viral responses, inflammation and abnormal metabolism of extracellular matrix (ECM)^[59]19. Despite the growing body of reports on differentially expressed genes and pathways associated with CRSwNP, the complex disease mechanism and pathways underlying CRSwNP remain elusive and require further investigation. Given that, the aim of this study was to add to the knowledge of the transcriptome profile in CRSwNP using 50 nasal mucosa biopsies, integrate genome wide genetic risk variants and specifically investigate genes located within genome-wide significant regions in COVID-19. Materials and methods Ethical statement The study was done in accordance with the principles expressed in the Declaration of Helsinki and was approved by the Regional Ethics Committee in Gothenburg, Sweden. A written informed consent was obtained from all participants in the study. The confidentiality of the personal data from all participants was ensured throughout the study. Biological materials Polyp tissue was collected from 16 CRSwNP patients with a mean age of 60 years (range 35–73) and a total of ten males and six females. Two types of control tissues were used: adjacent non-polyp tissue from inferior/middle turbinates of the 16 CRSwNP patients, and inferior/middle turbinates from 18 healthy controls with no history of sinus disease with a mean age of 59.8 years (range 40–84) and a total of eight males and ten females. The patient and control populations show a somewhat uneven distribution for gender, with 38% females in CRSwNP patients and 63% females in the controls. For females the age ranged from 38 to 76 years old with a median age of 63. Male age ranged from 35 to 84 with a median of 57. Control patient age ranged from 40 to 84 years old with a median age of 60 and CRSwNP patient age ranged from 35 to 73 with a median of 60. All biopsies were immediately put in RNA later preservative fluid (ThermoFisher, San Diego, CA, USA). The diagnosis of CRS was based on the definition of the European Position Paper on Rhinosinusitis and Nasal Polyps guidelines^[60]20. All CRSwNP patients were treated locally in their nasal cavity with corticosteroids as recommended by the current Rhinosinusitis and Nasal Polyps 2012 guidelines^[61]20. The study was carried out in accordance with the Declaration of Helsinki and was approved by the Local Ethics Committee in Gothenburg, Sweden (Date for approval 2012-12-30, Dnr 829-12). RNA extraction and cDNA synthesis The 50 tissue samples from CRSwNP patients and healthy controls were directly put in RNA later medium (Thermo Fisher Scientific Inc., CA, USA) and processed for extraction and purification of total RNA using the Kingfisher RNA kit together with the Kingfisher instrument (Thermo Fisher Scientific Inc., CA, USA) according to the manufacturer’s instructions. The quantity and quality of isolated RNA was determined using the NanoDrop 2000 Spectrophotometer (Thermo Fischer Scientific) and 2200 TapeStation Automated Electrophoresis System (Agilent Technologies). Samples with an RNA integrity number of greater than 6.0 were chosen for sequencing, with the exception of one polyp sample at RIN 4 which was included. Whole genome RNA sequencing Preparation of libraries was carried out using the TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold (Illumina, Inc., San Diego, CA), using 60–1000 ng of total RNA input. The Novaseq 6000 platform was used (Illumina, Inc., San Diego, CA) and 100 bp paired-end reads were generated by Clinical Genomics (Gothenburg, Sweden). Adapters and low-quality tail were trimmed from reads prior to read alignment. Clean sequence reads aligned to the human genome were used to assemble transcripts, estimate the abundance of these transcripts and detect differential expression among samples. For mRNA and lncRNA analyses, the reference genome build GRCh38/hg38 was chosen as the annotation references. Fragments per kilo-base of exon per million