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Discerning the genetics and epigenetics of chronic rhinosinusitis Key words: Genetics, genomics, epigenetics, epigenomics, tran-
(CRS) may optimize outcomes through early diagnostics, scriptomics, GWAS, sinusitis, CRS, chronic rhinosinusitis, nasal
personalized and novel therapeutics, and early prognostication. polyps, RNA, RNA-Seq, cystic fibrosis, primary ciliary dyskinesia,
CRS associated with cystic fibrosis and primary ciliary review
dyskinesia has well-characterized genetic mutations. Most CRS
subjects, however, do not exhibit identifiable monogenic
alterations. Clustering in related individuals is seen in CRS with
nasal polyps. Spouses of subjects with CRS without nasal polyps The study of the genetics of chronic rhinosinusitis (CRS) is
also may be at increased risk of the same disease. These necessary to understand its pathogenesis. Most CRS patients do
observations generate questions on genetic and environmental not have identifiable monogenic or polygenic alterations, with
influences in CRS. Genome-wide association studies have the exception of CRS associated with cystic fibrosis (CF) or pri-
identified variations and polymorphisms between CRS and mary ciliary dyskinesia (PCD). Understanding CRS genetics,
control subjects in genes related to innate and adaptive however, may assist with screening, earlier diagnosis, prognosti-
immunity. Candidate gene and transcriptomics studies have cation, genotyping, and developing targeted therapeutics, poten-
investigated and identified genetic variations related to tially transforming the philosophy of management from treating
immunity, inflammation, epithelial barrier function, stress– symptoms to modulating specific targets.
response, antigen processing, T-cell regulation, and cytokines in CRS is a clinical diagnosis characterized by symptomatic local
CRS. Epigenetic studies have identified mechanisms through inflammation of the nose and sinuses that persists for at least 12
which environmental factors may affect these gene functions. weeks.1,2 CRS is best thought of as an umbrella diagnosis encom-
However, causality is not determined for most variations. passing many pathogenetic subtypes with differing phenotypic
Inferences drawn from these data must be measured because and endotypic characteristics. However, in clinical practice and
most investigations report unreplicated results from small study in research studies, CRS is often classified, studied, and treated
populations. Large, replicated studies in tight cohorts across according to the presence or absence of nasal polyps (NPs).
diverse populations remain a pressing need in studying CRS The etiology of CRS is poorly understood; pathogenetically,
genetics. (J Allergy Clin Immunol 2023;nnn:nnn-nnn.) the syndrome is characterized by mucociliary dysfunction.1,2
Contemporary researchers believe that in the genetically suscep-
tible host, environmental insults that result in mucoepithelial
disruption may trigger a cascade of immunopathologic responses
that become self-perpetuating and result in chronic sinonasal
mucosal inflammation.3 CRS with NP (CRSwNP) patients gener-
ally have more recalcitrant disease than patients with CRS
From athe Department of Otolaryngology Head and Neck Surgery, Mayo Clinic in Ari- without NPs (CRSsNP).4-7 At the histopathologic and molecular
zona, Phoenix; bthe Saint Louis University School of Medicine, St Louis; cthe Depart- levels, CRSwNP is classically characterized by infiltration of eo-
ment of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital sinophils and TH2 cells that produce IL-5 and other TH2 cyto-
Medical University, Beijing; dBeijing Tongren Hospital, Capital Medical University,
kines, whereas CRSsNP is associated with a predominance of
Beijing; ethe Department of Allergy, Beijing Tongren Hospital, Capital Medical Uni-
versity, Beijing; fthe Beijing Laboratory of Allergic Diseases and Beijing Key Labo- TH1-mediated inflammation. However, it is now increasingly un-
ratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing; gthe derstood that CRS phenotypes do not necessarily match these
Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Acad- classic endotypic presumptions, and the underlying pathogenetic
emy of Medical Sciences, Beijing; and hthe Division of Allergy and Immunology, processes in CRS may encompass type 1, type 2, or type 3 inflam-
Northwestern University Feinberg School of Medicine, Chicago.
Supported by National Institutes of Health grants R01 AI137174, U19 AI106683, and
mation, or a mix.3 CRS may be associated with allergy, atopy to
P01 AI145818 (to A.K.). fungi, aspirin sensitivity (leukotriene dysregulation), asthma, im-
Disclosure of potential conflict of interest: D. Lal reports consultant for GSK and receipt munodeficiency, CF, PCD, vasculitis such as eosinophilic granu-
of consulting fees. A. Kato reports a gift from Lyra Therapeutics for his research. The lomatosis with polyangiitis and granulomatosis with polyangiitis,
rest of the authors declare that they have no relevant conflicts of interest.
or unknown factors.1,2
Received for publication March 28, 2022; revised January 4, 2023; accepted for publica-
tion January 6, 2023. Causal factors in CRS are not currently detailed, with the
Corresponding author: Devyani Lal, MD, FARS, Division of Rhinology, Mayo Clinic in exception of subtypes such as CF and PCD. Familial clustering is
Arizona, 5777 E Mayo Blvd, Phoenix, AZ 85054. E-mail: lal.devyani@mayo.edu. seen in certain subtypes of CRS, especially CRSwNP,8,9 but
0091-6749/$36.00 spouses of CRS subjects also appear to be at increased relative
Ó 2023 American Academy of Allergy, Asthma & Immunology
https://doi.org/10.1016/j.jaci.2023.01.004
risk of developing the disease.9 These reports suggest that familial
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populations, may affect these studies’ reliability. Henmyr et al24 higher in those individuals with the CDHR3 allele rs6967330,
aimed to replicate 53 SNPs reported to be associated with CRS even after eliminating asthma as a confounding factor.96 Thus,
by previous CGS in a White population of European origin; how- it is plausible that CRS occurred as a result of childhood viral in-
ever, the investigators only found 7 variants in 7 genes that were fections due to certain genetic variations. In addition, the same
significantly associated with CRS susceptibility. Of these, only group also identified the GSDMB rs7216389 SNP to be higher
some SNPs in PARS2, TGFB1, and NOS1 reached the significant in CRS patients,97 and this SNP has been previously identified
threshold after multiple testing. Table E1 outlines the candidate in childhood-onset asthma and increased susceptibility to rhino-
genes investigated and implicated in the pathogenesis of CRS. virus infections.98
These include genetic variations in antigen presentation, proin-
flammatory response, type 2 inflammation, innate immunity, tis- Genome-wide association study
sue remodeling, cellular responses to stress, membrane receptors, Three recent pooling-based GWAS assessing separate pools of
and ion channels. In addition, Table E1 provides information on DNA from CRS patients and control subjects found novel genetic
whether SNPs susceptible to CRS were replicated in the study variants in several innate immunity-related genes involved in the
of Henmyr et al or of others. Table II summarizes the pathobio- pathogenesis of CRS.99-101
logic implications of the genetic variations identified.25-93 Kristjansson et al27 reported their large GWAS meta-analysis
A prospective study on children found that a variant on NP and CRS to date from the United Kingdom and Iceland
(rs6967330-A) in CDHR3 that has been previously identified as on 5,608 CRS subjects, 4,366 NP subjects, and over 700,000 con-
an asthma risk allele94 was also associated with a higher incidence trols. The findings from these studies are summarized in Table E1
of rhinovirus type C infection.95 A retrospective study on CRS and Table II. The authors showed that 10 loci (HLA-DQA1, IL33,
(n 5 343) versus controls (n 5 389) that sought to see if individ- TSLP, ALOX15, 10p14, FOXP1, CYP2S1, IL18R1, SLC22A4, and
uals with CRS had this allele also identified the odds of CRS to be MYRF) were significantly associated with NP and 2 variants
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TABLE II. Genes identified in CRS, association with major biological pathways, and disease processes
Gene/loci Function Regulation Population Disease Study
Innate immunity:
Genes encoding
HLA-MHC
class I
A1/B8 Antigen [ Associated White Asthma, NP Moloney 198025
presentation
A74 Associated European CRSwNP Luxenberger 200026
Cw*04 Cw*12, Associated Turkish NP Keles 200818
A*24 B*07, B*57
Innate immunity:
Genes encoding
HLA-MHC
class II
DRB1*04 Antigen Associated Turkish Asthma, AIA Keles 200818
presentation
DQA1 rs1391371 Associated European Genome-wide Kristjansson 201927
NP, CRS
DRA rs2395190 Associated East Asian Genome-wide Sakaue 202128
CRS
rs9268644 Korean CRSwNP Kim 201219
rs3129878
rs3129881
rs2239805
DQB1*03 Associated American Allergic fungal Schubert 200429
sinusitis and
hypertrophic
sinus disease
DR16, DQ8, DQ 9 Associated Chinese CRSwNP Zhai 200730
DRB1*03, DRB1*04 Associated Mestizo Mexican CRSwNP Jaqueline 200631
DRB1*08
Innate immunity:
Toll like
receptors (TLR)
TLR2 rs3804099 Member of TLR Associated Korean CRS Park 201132
family that with [ risk
plays a
fundamental role
in pathogen
recognition
and activation
of innate
immunity
7 other No association Canadian CRS Tewfik 200833
variations
TLR2 TLR4 3 SNPs TLR2 (2258A>G) Turkish CRSwNP Kesici 202134
and TLR4
(1196C>T)
associated
TL2, TLR4, mRNA levels Associated Korean Biofilms of Sun 201235
NF-kappaB CRS
patients
Innate immunity:
Bitter taste
receptors
TAS2R13 rs1015443 Mediates taste Associated with Canadian CRS Mfuna Endam 201436
detection
TASR249 rs12226920
TAS2R49 rs12226919
TAS2R38 rs10246939 Mediates capability Associated with United States CRSwNP and Adappa 201437; Mfuna
to taste bitter Canadian refractory Endam 201436
compounds CRS patients
Associated Polish CRS Dzaman 201637
homozygous AVI
genotype had higher
computed tomography
scores than homozygous
PAV genotypes
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AIA, Aspirin-intolerant asthma; ASA, aspirin sensitive asthma; ECM, extracellular matrix; lncRNA, long noncoding RNA; NO, nitric oxide; PGE2, prostaglandin E2; TSA, Trichostatin
A; UTR, untranslated region. [; Upregulated; Y, downregulated; Y, downregulated but mixed study results.
(HLA-DQA1 and ALOX15) associated with CRS. The loss- may also be ethnic specific. (The 1000 Genomes Project, archived
of-function variant rs34210653 (Thr560Met) in the ALOX15 online at www.genome.gov/27528684/1000-genomes-project,
gene, carried by 1 in 20 Europeans, appears to protects against was a collaboration among research groups in the United States,
NP and CRS.27 The ALOX15 gene codes for arachidonate 15- the United Kingdom, China, and Germany to produce an exten-
lipoxygenase enzyme. Arachidonate 15-lipoxygenase is activated sive catalog of human genetic variation.)
by IL-13 and promotes eotaxin-3 expression, which is involved in Kristjansson et al27 assessed the NP associations of variants re-
TH2 cells, tissue eosinophilia, and type 2 inflammation in ported to associate with eosinophil count. Of the 210 eosinophil
CRSwNP.102,103 variants, 24 associate significantly with NP in the combined Ice-
Review of the 1000 Genomes Project database revealed that land and United Kingdom data set. Of those, 7 were highly corre-
this variant rs34210653 exhibits common allele frequency lated with 1 of the 10 signals (HLA-DQA1, IL33, TSLP, ALOX15,
(0.066) in admixed American populations and intermediate 10p14, FOXP1, CYP2S1, IL18R1, SLC22A4, and MYRF) detected
frequency in European populations (0.011), but has extremely in NP. The remaining variants represent 17 novel NP-associated
low frequency or is nonpolymorphic in other populations (Afri- variants. Further analysis of the 17 NP-associated signals demon-
can, 0.002; East Asian, 0; South Asian, 0.003). This suggests that strated that 7 were NP-associated variants associated with CRS
the association of CRS and NP with the rs34210653 in ALOX15 and 13 NP-associated variants associated with asthma. All of
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FIG 1. Shared susceptible genes/loci among NPs, allergy and blood eosinophil count, as per GWAS in
European populations (visualized using PhenoGram).
the variants have effects in the same direction for both NP and in skin is also associated with ‘‘localized opacification’’ on
eosinophil count. Fig 1 presents the data from previous GWAS computed tomographic scans. Another SNP (rs10820254, located
in European populations to determine the overlapping suscepti- close to the CYLC2 gene) is associated with the ‘‘diffuse opacifica-
bility loci of CRS,27 allergy (combined phenotype of asthma, tion’’ class phenotype. Because WSB2 functions as a negative regu-
hay fever, and eczema),104 and blood eosinophil count.105 The re- lator of the IL-21 receptor (IL-21R, a molecule associated with
sults of this analysis suggest that increased circulating eosinophil microbe-related epithelial conditions such as inflammatory bowel
count may be a major common event in CRS and allergy. disease and Helicobacter pylori infection), the authors reported a
A recently published GWAS of 220 disorders/traits conducted critical role of mucosal immunity in CRS pathogenesis,52 noting
using Biobank Japan28 provided an atlas of genetic architectures in that IL-21R expression is also upregulated in atopic dermatitis pa-
non-European populations. Five loci (LINC02106, HLA-DRA, tients who experience Staphylococcus aureus colonization barrier
ANKS1A, FAM71D, and FUT2) exhibited the genome-wide signif- dysfunction.
icance for CRS in 4617 participants from East Asian populations.
However, likely as a result of the small sample size for NP (n 5
160), no associated loci were reported. Soliai et al52 published the Mapping of major biologic connections of genetic
first GWAS of CRS and its subphenotypes in the United States in variations associated with CRS
a study of a European American population with 483 CRS and To characterize the main biological connections and identify
2057 control subjects. Analysis of genotypes of all CRS subjects re- the functional pathways and networks associated with CRS
vealed 82 significant SNPs at 6 loci, but the authors could not vali- susceptibility, all associated genes reported from CGS and
date either of the 2 SNPs associated with CRS and NP in the study GWAS were integrated and analyzed. Plausible genes were
by Kristjansson et al.27 The investigators next studied CRS subphe- prioritized by the functional mapping and annotation GWAS
notypes in 646 subjects with sinus computed tomographic scans, platform as well as the Data-Driven Expression Prioritized
172 of which were part of the GWAS. The investigators validated Integration for Complex Traits (DEPCIT) package according to
2 loci that were associated with CRS in first-stage GWAS. The the CGS and GWAS data sets. To characterize the main biological
SNP (rs11068795) associated with expression of the WSB2 gene connections and networks associated with CRS susceptibility,
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FIG 2. Biologic connections and functional networks for prioritized plausible genes of CRS. Networks of
enriched gene ontology/pathway terms were constructed using Metascape. Each term is presented as a
circle node. Circle size represents the number of genes enriched; circle color represents cluster identity.
Terms with similarity score > 0.3 are linked by an edge. The shade of edge represents the degree of
correlation.
enriched ontology clusters from plausible genes were assessed seem to have higher ratios of the eosinophilic endotype than
(Fig 2). Some of the enriched pathways, such as cytokine produc- Asian populations.106 In line with this, one study reported that
tion, leukocyte activation involved in immune response, and numerous second-generation Asian patients with CRSwNP
cytokine-mediated signaling pathways, were assembled together residing in the United States had the same noneosinophilic in-
and exhibited high connectivity. Additionally, the enriched flammatory characteristic as native-born patients from Asian
pathway related to inflammatory bowel disease was also assem- countries,107 in concordance with the findings of the above 2
bled at the core, probably conferring pleiotropic effects or shared GWAS, according to which the significant genes/loci are not
genetic architecture across different inflammatory traits. Investi- shared between European and East Asian populations. It is likely
gation of these networks could help develop a comprehensive un- that these differences relate to genetic heterogeneity among
derstanding of CRS. ethnic groups.
PLAT with excessive fibrin deposition by aberrant coagulation in CRS. Most studies were conducted in small samples (ranging in
cascade may promote NP. Methylation of CpG sites 1, 2, and 3 size from 2 to 187 subjects) in Asian populations. Only 2 studies
in IL8 proximal promoter was significantly decreased in were replicated with a larger sample size by the same investi-
CRSwNP versus CRSsNP.74 DNA methylation of the CpG3 site gator.80,53 Most studies were conducted on NP tissue, with the
correlated negatively with tissue eosinophil cationic protein and exception of 2 studies that included sinonasal tissue as well as pe-
myeloperoxidase. IL-1b and TNF-a significantly increased IL- ripheral blood,78,67 and 2 miRNA studies were done exclusively
8 expression alongside CpG3 methylation reduction.74 on DC of peripheral blood.63,89
Differences in microRNA (miRNA) levels involved in type I
interferon pathway,75 transcription factor aryl hydrocarbon recep-
tor (AHR),76 transforming growth factor beta 1 (TGFB1),77,78 TRANSCRIPTOMICS
mucin-type O-glycan biosynthesis, and ciliogenesis and ciliary Bulk transcriptome analysis in whole tissue
function were also reported in NP tissue.77,79 NP tissue was In the 2000s, several investigators started to report microarray
also noted to have increased expression of IL-874 and TNF-a findings in CRS, including gene expression profiles in NP45,112
signaling49 as well as decreased expression of IL-10 in peripheral and AERD,42 and the effect of glucocorticoid treatment in
dendritic cells (DCs).63 Expression of miR-150-5p and its target NP.113 Table E3 in the Online Repository available at www.
gene, EGR2 (early growth response 2), are upregulated in CRS jacionline.org summarizes salient studies in CRS transcriptomics.
blood DCs.89 Two studies investigated and reported that Although initial studies identified novel molecules, results were
TGFB1 proliferation of NP fibroblasts could be inhibited by his- inconsistent. Liu et al45 found upregulation of prolactin-
tone deacetylase (HDAC) inhibitors.80,81 miR-19a (but not the inducible protein, statherin, lactoferrin, and DMBT1 (deleted in
other miR-17-92) was higher in DC of CRSwNP.63 Recombinant malignant brain tumors 1) in NP, while Stankovic et al42 reported
IL-4 suppressed IL-10 expression in DC, which was abolished by downregulation of them in NP. These inconsistent results may be
blocking HDAC-11 or knocking down the miR-19a gene in DC.63 related to small sample sizes and differences in specimen samples.
Both histone acetylation studies were in vitro studies investigating Liu et al used sphenoid and ethmoid tissues, whereas Stankovic
effect of HDAC inhibitors.80,81 et al used inferior turbinate and ethmoid tissue in controls. There
An early genome-wide DNA methylation assay studied blood are regional differences in the expression of many genes, including
and polyp tissue from subjects with and without aspirin hyper- lactoferrin in sinonasal mucosa. Because gene expression in con-
sensitivity (no controls).67 In NP of patients with aspirin- trol tissue influences outcomes in NP-associated genes, investiga-
intolerant asthma, hypermethylation was detected at 332 loci in tors have to pay attention to the control tissue in each study.
296 genes, and hypomethylation at 158 loci in 141 genes. In the Because the more recent transcriptomic analyses used inferior
arachidonate pathway, PGDS, ALOX5AP, and LTB4R were hypo- turbinate, uncinate, or ethmoid tissue in controls, results from
methylated, whereas PTGES was hypermethylated.67 More these studies were similar to findings by Stankovic et al.42 Stan-
recently, Kim et al55 compared NP with uncinate process tissue kovic et al also reported the first observation of upregulation of
in Korean patients. Compared to healthy controls, 397 and 387 POSTN (periostin), which is now a well-known type 2–associated
genes were hypermethylated in eosinophilic CRSwNP and non- gene in asthma and other type 2 inflammatory diseases,114,115
eosinophilic CRSwNP, respectively, and 399 and 208 genes such as CRSwNP and AERD. After this, many investigators iden-
were hypomethylated. Genes involved in cancer pathways, tified upregulation of POSTN in NP from patients with asthmatic
KRT19 (keratin 19), NR2F2 (nuclear receptor subfamily 2 group or eosinophilic CRSwNP by microarray and RNA-Seq.50,51,61 In
F member 2), and ADAMTS1 (ADAM metallopeptidase with addition to POSTN, Plager et al61 also showed the upregulation of
thrombospondin type 1 motif 1) were among the top genes whose many type 2–associated genes in NP from asthmatic CRSwNP
promoters were significantly hypomethylated in NP. including CLC (Charcot-Leyden crystal), CCR3, CCL13 (MCP-
In the Chinese population, NP was associated with down- 4), CCL18 (PARC), CCL26 (eotaxin-3), F13A1, IL1RL1, CPA3
regulated miRNAs in TGFB signaling pathway,77 enriched (carboxypeptidase A3), and CST1 (cystatin SN). This implies
messenger RNAs (mRNAs) in CCL-18 (C-C motif chemokine accumulation of eosinophils, M2 macrophages, TH2 cells, group
ligand), impaired ciliogenesis, and ciliary function.79 Increased 2 innate lymphoid cells, mast cells (MCs), and elevation of type 2
expression of enhanced type I interferon was seen in eosinophilic cytokines including IL-4 and IL-13 in NP.
CRSwNP.109 Higher methylation of the COL181 gene, which co- In East Asia, the prevalence of eosinophilic NP is lower than in
des for a subtype of collagen,56 and upregulated miRNAs in Western countries, allowing investigators to directly compare
mucin-type O-glycan biosynthesis77,66 were also reported. In 2 eosinophilic and noneosinophilic NP by transcriptome analysis.
studies investigating alternative polyadenylation in the 39 un- One study used RNA-Seq to identify upregulated genes in NP
translated region in eosinophilic CRSwNP tissue versus uncinate compared to control tissue and found 1058 and 647 upregulated
tissue, the authors found several different pathways, including genes in eosinophilic and noneosinophilic NP, respectively.50
Wnt signaling (an important pathway for immune cell mainte- Another study used microarray techniques and found 1449 and
nance and renewal), transcription, nucleolus, transcription regula- 880 upregulated genes in eosinophilic and noneosinophilic NP,
tion, apoptosis, protein targeting and transport, RNA splicing, respectively.51 The studies, both from Asia, also identified differ-
protein localization, and mRNA processing; the studies had no entially expressed genes between eosinophilic and noneosino-
healthy controls.53,54 philic NPs. Importantly, eosinophilic NP-specific genes
The greatest challenge in epigenetic data is interpreting included many of the previously identified upregulated genes in
whether identified differences play a causal role in pathogenesis, NP in the United States such as CLC, CCL26, CST1, and
occur as a result of the disease,110,111 or are just noise. Epigenetic POSTIN.42,50,51,61 Nakayama et al106 directly compared Asian
studies investigating the specific influence of environmental aller- (residing in Japan) NP with White (residing in the United States)
gens, smoking, diet, and other factors have not yet been conducted NP by RNA-Seq and found that the gene expression profile in
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eosinophilic NP strongly overlapped between the 2 populations. MCs in NP can be classified into 4 subtypes, MCT (tryptase1),
Noneosinophilic NP-specific genes including IFN-g–induced MCTC (tryptase1chymase1), intermediate MC, and proliferative
TH1 chemokines (CXCL9, CXCL10, and CXCL11), IL-17– MC; they also found that MCTC and intermediate MC play proin-
induced chemokines (CXCL5 and CCL20 [LARC]), and innate flammatory roles in eosinophilic NP. Finally, Nakayama et al106
molecules such as SAA1 (serum amyloid A1) and CHI3L1 (chiti- used scRNA-Seq to identify the original source of elevated genes
nase-3–like protein 1) were similarly elevated in both Asian in NP found by bulk RNA-Seq. Overall, scRNA-Seq reveals the
studies.50,51 This suggests that a mixed type 1 and type 3 endotype heterogeneity and novel cell populations in each cell type, detects
may be the dominant endotype in noneosinophilic NP in Asia. molecular mechanisms at the cellular level, and provides new in-
These studies also used gene enrichment analyses such as gene sights into the pathogenesis of CRS.
ontology and pathway analyses in dysregulated genes to predict
molecular mechanisms and pathogenesis of CRSwNP. Although
pathogenesis and dysregulated genes in CRSsNP were unclear Limitations of transcriptomic studies
for a longer period as a result of the heterogeneity of endotypes, Although scRNA-Seq provides comprehensive information
Klingler et al116 was recently able to identify type 1, 2, and 3 and is a useful tool to study disease pathogenesis, there are
endotype–specific genes in CRSsNP by microarray and predict some limitations. Although up to 30% to 60% of CD451 cells in
molecular mechanisms in each endotype in CRSsNP by gene NP are neutrophils and eosinophils, they were almost absent in
enrichment analysis. Overall, these results suggest that current earlier scRNA-Seq studies in NP.64,87 This weakness raises the
microarray and RNA-Seq analyses provide reproducible tran- concern that the frequency of cell types discovered by scRNA-
scriptomic results if investigators focus on the same control tissue Seq may not be accurate enough. To fill this gap, several investi-
and endotypic inflamed tissue. gators performed bulk RNA-Seq in purified eosinophils and
neutrophils from NP and peripheral blood and identified NP-
specific genes in each granulocyte.119,120 Bulk RNA-Seq is not,
Single-cell transcriptome analysis however, able to identify the heterogeneity found in other immune
Although bulk RNA-Seq provides overall transcriptional cells, including T cells, B cells, and MCs. In addition, Poposki
changes in target tissues, investigators have yet to study the et al120 noted that less than 1% contaminating cells influences
sources of these altered genes in separate assays. Single-cell the result of transcriptome analysis if these genes are highly ex-
RNA-Seq (scRNA-Seq) technology is able to fill this gap by pressed in the contaminating cells but not in target cells. Future
detecting the whole transcriptome profile of individual cells. studies will require optimizing scRNA-Seq technology for gran-
Ordovas-Montanes et al64 provided the first evidence of scRNA- ulocytes. Finally, RNA expression is frequently transient and
Seq analysis in CRS and found transcriptional changes in many may not be directly correlated with protein level. This influences
structural and inflammatory cell types in NP. This study mainly both in vivo tissue samples as well as in vitro culture studies. In-
focused on epithelial cell components and found that NP are char- vestigators need to keep this in mind when making research plans
acterized by basal cell hyperplasia, reduction of glandular cells, and analyzing data.
and an aberrant basal progenitor differentiation compared to non-
polypoid mucosa.64 Furthermore, they clearly showed that basal,
differentiating, and secretory epithelial cells received signals PATHOBIOLOGIC FUNCTIONS OF GENES
from IL-4 and/or IL-13 in NP, a finding based on the elevation ASSOCIATED WITH CRS
of canonical IL-4/IL-13 responsive genes including CST1, Table II summarizes the biologic pathways related to key ge-
CCL26, and POSTN.64 Stevens et al87 performed scRNA-Seq in netic variations and details the study population and disease asso-
whole NP tissues from patients with CRSwNP and AERD and ciation in CRS.
found that ALOX15 (15-lipooxygenase) was significantly
elevated in apical and ciliated epithelial cells from AERD NP
and that the level of ALOX15 correlated with eosinophils in NP. Innate immunity
Both bulk and single-cell transcriptome studies help us to identify Innate immunity plays a first-line role in the detection of
and confirm the direct roles of type 2 cytokines in epithelial cells. pathogens. HLA haplotype variations have importance in antigen
For example, Jackson et al65 used airway epithelial cells differen- processing and presentation (Table II). HLA genes may be asso-
tiated by air–liquid interface culture and performed scRNA-Seq ciated with immune response, cell surface receptor signaling
in control and IL-13–stimulated epithelial cells, finding a dra- pathway, immune system processes, and antigen processing and
matic change of secretory cell phenotype and also confirming presentation.10 Toll-like receptors (TLRs) recognize pathogens
the findings of Ordovas-Montanes et al64 and Stevens et al87 like bacteria, viruses, and fungi and subsequently lead to inflam-
that IL-13 induced CST1, CCL26, POSTN, and ALOX15 in secre- matory processes involving adaptive immunity. TLR2 has been
tory and ciliated epithelial cells. Other studies have focused on recognized as the main receptor for Staphylococcus aureus.
specific cell types. Ma et al117 focused on CD41 T cells in NP Although different polymorphisms in TLR have been reported
and found that TH2 cells can be classified into 2 main subpopula- in various ethnic populations in CRS compared to controls,32
tions, pathogenic TH2 cells and CD1091CRTH22 TH2 cells, these have not been replicated.32,33 Recently, bitter taste receptors
which produce both type 2 cytokines and immunosuppressive have been identified to play a role in the upper airway innate im-
IL-10. Buchheit et al68 analyzed B-linage cells and found that mune response. CRS associated with certain genotypes has been
IgG41 and IgE1 antibody secreting cells were elevated in reported to be associated with worse surgical outcomes or the
AERD NP compared to CRSwNP NP and control tissue. They need to undergo a surgical treatment, while patients homozygous
also found that IL5RA was expressed in a subset of plasma cells for the TAS2R38 allele (PAV) were less likely to require surgical
in AERD NP. Dwyer et al118 investigated MCs and found that treatment for CRS.121 An Italian study found that the
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nonfunctional phenotype was more common in CRS patients Genes in arachidonic acid metabolism and aspirin-
compared to controls, and gram-negative biofilms in CRS patients exacerbated respiratory disease
were more likely to occur in those with the nonfunctional haplo- Altered arachidonic metabolism has been implicated in aspirin-
type.38 A Polish study reported similar findings: the homozygous exacerbated respiratory disease (AERD), which is associated with a
AVI genotype had higher computed tomographic scores than the triad of CRSwNP, asthma, and aspirin sensitivity. However,
homozygous PAV genotypes, and TAS2R38 polymorphisms may CRSwNP, even in the absence of AERD, has shown to be associated
result in susceptibility to CRS.37 A replication study by Mfuna with polymorphisms in certain genes involved in arachidonic acid
Endam et al36 identified an SNP in TAS2R38 (rs10246939) in Ca- metabolism. The rs20417 variant of COX2 was found in Polish in-
nadian patients with CRSwNP and refractory CRS as well as 3 dividuals with CRSwNP.86 The rs3780894 variant of ALOX5 and
novel SNPs associated with CRS. rs17612127 in ALOX5AP were found in CRS in a Canadian popu-
The NOS family of genes encodes for enzymes involved in gen- lation.88 Additionally, rs17238773 in ALOX5AP was found in a
eration of nitric oxide, a reactive free radical involved in innate replication study in Whites.24 The rs321090 variant in CYSLTR1
immunity. In small and diverse populations, SNPs for NOS1 (receptor for cysteinyl leukotriene involved in mediating broncho-
and NOS2 have been differentially associated with CRS,24,39 constriction) was also found in the same Canadian population in
CRSwNP patients40 and CAT, the gene for catalase, was reported CRS that found SNPs in ALOX5 and ALOX5AP.88 Familial clus-
to be more active in eosinophilic CRSwNP patients.40 Other tering of AERD is not strongly supported in the literature.16
genes involved in innate immunity have been investigated.
MET, a proto-oncogene that encodes a member of the receptor
tyrosine kinase family of proteins, is involved in cellular survival, CRS and the CFTR gene
migration, and invasion. In a Canadian population, MET Several studies have found higher prevalence of CFTR muta-
(rs38850) was found to be associated with CRS.41 SNP in SER- tions in non-CF CRS patients.90-92,122,123 However, most studies
PINA1 (Serpin family A member 1; rs1243168), a gene that en- are limited in studying only the known CFTR variants, and it is
codes the inhibitor of serine protease and targets elastase, likely that several unknown variants have been missed, unless
plasmin, thrombin, trypsin, chymotrypsin, and plasminogen, gene sequencing technology is used to study these associations
has also found to be associated with CRS unresponsive to medical in CRS.
therapy in a Canadian population.43 This gene is deficient in
alpha-1-antitrypsin, an inherited condition that causes severe
lung and liver disease. LTF, the gene for lactoferrin, which plays CRS ASSOCIATED WITH CHARACTERIZED
an important role in first-line defense, has also been shown to have GENETIC DEFECTS
associations with CRSwNP in a Polish population, especially Cystic fibrosis
those with asthma or allergy.44 CF is a life-shortening, autosomal recessive disorder associated
with mutations of the CF CFTR (transmembrane conductance
regulator) gene, which is present on the long arm of chromosome
Acquired immunity
7 (7q).124 In the United States, CF is a common genetic disease,
SNPs in proinflammatory genes are detailed in Table II, as are
occurring in 1 in 2,500 to 3,500 White newborns and carried by
significant variations in genes related to type 2 inflammation.
1 in 27 individuals in North America. CF also affects people of
Additionally, polymorphisms in the IL4 gene (rs2243250) were
all races, including African American (1 in 15,000), Hispanic
found to be associated with CRSwNP in Koreans.59 Milonski
American (1 in 13,500), and Asian American (1 in 35,000).125
et al58 also found the tissue mRNA levels of IL4, 1L13, and
The frequency of CF, however, appears to be decreasing, and
POSTN to be higher in CRS versus controls. In a Chinese popu-
the longevity of subjects has greatly improved.126 The CFTR
lation, TSLP polymorphisms were higher in CRSwNP,69 and in
gene codes for the CFTR protein, which is a chloride and bicar-
a Belgian population, IL33 polymorphisms were higher in
bonate channel in exocrine glands. CFTR mutations can lead to
CRSwNP versus controls.71 ILIRL1, which serves as the receptor
increased mucus viscosity, leading to associations with CRS,
for IL-33, has been associated with several polymorphisms
bronchiectasis, pancreatic insufficiency, and liver disease.124
(rs10204137, rs10208293, rs13431828, rs2160203, and
Phe508 is the most common mutation, seen in up to 90 percent
rs4988957) in a Canadian population with CRS.72 FCER1A, a re-
of CF patients in the United States.127,128 Compared to controls,
ceptor for IgE, had polymorphisms (rs2427827) in CRSwNP in an
genetic mutations in the CFTR gene are more commonly seen
Indian population.23
in CRS patients without diagnosed CF,123 and CFTR heterozy-
gotes have a higher risk of developing CRS.129 In addition,
Genes involved in tissue remodeling CFTR dysfunction may occur as a result of smoking, infection,
Aberrant tissue remodeling has been implicated as one of the or hypoxia.129 In a systematic review and meta-analysis of 6
pathophysiologic mechanisms in CRS. Polymorphisms in TGFB1 studies from the United States and Europe, Yong et al123 found
in CRS (rs11466315 in Korean and rs1800469 in White popula- that the pooled prevalence of CFTR mutations in patients with
tions) have been reported.24,62 Polymorphisms in matrix metallo- CRS was 5.65% and that of the Phe508 mutation was 4.22%.
protein MMP9 (rs3918242) have been identified in CRSwNP with These rates were significantly higher than the estimated preva-
aspirin-intolerant asthma in Turkish48 and CRSwNP in Chinese83 lence of CFTR carrier status of 3% to 4% in the general popula-
populations. In addition, rs2274756 in MMP9 has been identified tion, raising the possibility that these mutations may confer
in Chinese subjects with CRSwNP83 and MMP1 (rs1799750) in susceptibility to CRS. However, overall, the study was limited
CRSwNP in a Polish population.82 Studies undertaken to find as- by the lack of stringent inclusion criteria for CRS.
sociations between MMP283 and SERPINE1 (PAI1)85 have not An international web consortium, CFTR2 (cftr2.org/), devoted
shown any significant associations. to the collection of mutations in the CFTR gene, has identified over
16 LAL ET AL J ALLERGY CLIN IMMUNOL
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2000 CFTR mutations, with at least 300 variants now known to be which is a monogenic disorder, PCD can result from mutations in
disease causing. CFTR mutations are grouped into 6 major classes 1 or more of over 40 genes (Table IV). These mutations ultimately
according to their effect on CFTR protein synthesis and function result in structural abnormalities and dysfunction of the motile
(Table III).124,127,130-133 Although some mutations fall clearly cilia with hallmark ultrastructural defect (absence of the outer
into one class, others lead to several functional defects—for or inner dynein arm with microtubular disorganization).140 Unex-
example, the CFTR mutation Phe508del, which is the archetypal pected neonatal respiratory distress in full-term infants, persistent
misfolding class II mutation, also affects gating and stability. wet cough from early infancy, bronchiectasis, CRS, and middle
The class of mutation, the presence of modifier genes, as well as ear effusion with conductive hearing impairment should raise
the presence of complex alleles (ie, 2 or more mutations on the concern for PCD. Fifty percent of PCD patients have situs inver-
same allele that interact to modify protein quantity or function) sus and are commonly infertile.140 Mutations in the DNAH5 gene
impact disease severity. Therefore, even in Phe508del homozy- are the most frequently reported, followed by DNAI1. Different
gotes, additional CFTR mutations in promoter, intronic, and mutations are associated with variable phenotypes. A biallelic
exonic regions are associated with disease severity, which also pathogenic mutation or hemizygous X-linked mutation in a
might affect responsiveness to new CFTR modulators.124 known PCD gene can confirm PCD diagnosis.141,142 Most PCD
Some studies have found that the genotype of CF has a is inherited in an autosomal recessive fashion, although rare
relationship with the presence or absence of polyps. Of 45 X-linked (PIH1D3 and OFD1 gene mutations) and autosomal
patients, 62.5% Phe508 homozygotes had NPs, versus 42.1% of dominant (FOXJ1 mutations) inheritances are also known.140
heterozygotes. However, there was no association of genotype The top 5 implicated genes for PCD differ by ethnicity.139 Addi-
with severity of CF.134 Another study did not find high-risk geno- tionally, about 30% to 35% of patients with PCD have no identifi-
types to be associated with more severe sinonasal disease.135 able genetic mutations. Genes related to PCD are large and
Similarly, Weinstock et al136 did not find an association of high- therefore can have several mutations, all of which are not patho-
and low-risk genotypes with the presence of nasal polyposis, genic. These factors, along with the lack of a comprehensive data-
extent of sinus surgery, or recurrence. It has been shown that base of all genetic mutations that can cause PCD, limit the
IFRD1 gene polymorphisms affect lung disease severity in CF, sensitivity of genetic testing. There is no clear correlation be-
as well as increase the risk of developing nasal polyposis.137 tween severity of CRS and the type of ciliary abnormality in
Why some CF patients develop CRSwNP while others develop PCD, and no studies have been undertaken to correlate type and
CRSsNP needs to be further studied; the genetic underpinnings severity of CRS and PCD genotype. Additionally, PCD genotype
of CRS in CF are not completely understood. has not been found to be a predictor for endoscopic sinus surgery
CFTR modulators are compounds that can target CFTR protein in a retrospective study including 54 pediatric PCD subjects.143
dysfunction.124,128 Ivacaftor is a CFTR potentiator that increases Recently, polymorphisms in the taste receptor TAS2R38 have
the probability of the chloride channel remaining in an open state. been implicated in susceptibility to respiratory infections in
Lumacaftor is a corrector that improves availability of the CFTR PCD.144 The genomics of PCD is still poorly characterized, and
protein at the cell membrane and is especially useful in Phe508 personalized therapy in PCD is not yet on the horizon.
mutations. Triple modulator combinations (ivacaftor combined
with 2 corrector compounds with different mechanisms of action)
significantly restored Phe508del CFTR function on Phe508del Limitations of genetic studies
homozygotes as well as those with a single copy of Phe508del While studying the role of genomics and epigenomics in CRS
combined with nonmodulable mutations in clinical trials.124 is progressing rapidly, interpretation of data remains a challenge,
The understanding of genetics of CF have allowed for the use of and each type of genetic study has its limitations. Further, CRS
gene editing to potentially treat CF patients.138 Without a clear demonstrates high heterogeneity in clinical features, diversity of
understanding of the genetic basis of CRS, however, the ability immunologic profiles, and significant influence from ancestry and
to create such precision approaches may not be possible. current environments. Contemporary data suggest that individual
patients may have highly heterogenous inflammatory profiles
with varying admixtures of type 1, type 2, and type 3 responses.1,2
Primary ciliary dyskinesia Given this background, interpretation of CRS genetic studies
PCD is a rare syndrome affecting 1:10,000 to 15,000 Euro- must be nuanced through our contemporary understanding of
peans. Consanguinity and closed genetic pool populations, such CRS heterogeneity. Comparing CRS with controls and defining
as Arabs, have higher prevalence of PCD.139,140 In contrast to CF, each study group and phenotype precisely are imperative to
J ALLERGY CLIN IMMUNOL LAL ET AL 17
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TABLE IV. Genetic mutations in PCD and association with situs inversus
Type of defect Genes involved in mutation Situs inversus
Defects of outer dynein arm composure Heavy chains DNAH5 and DNAH11, intermediate chains Yes
DNAI1 and DNAI2, light chains DNAL1 and NME8 result in
dysfunction of outer dynein arms
Defects in outer dynein arm docking complexes (ODA-DC) and CCDC114, 1472 ARMC4, 73 CCDC151, TTC25 Yes
targeting
Abnormal cytoplasmic dynein preassembly factors (dynein DNAAF1, DNAAF2, DNAAF3, DNAAF4 (DYX1C1), DNAAF5 Yes
axonemal assembly factors [DNAAFs]) (HEATR2), LRRC6, ZMYND10, SPAG1, C21ORF59,
DNAAF6 (PIH1D3), CFAP300 cause PCD with combined
outer and inner dynein arm defects
Tubular disorganization CCDC39, CCDC40 Yes
Defects in radial spoke components RSPH1, RSPH4A, RSPH9, RSPH3, DNAJB13 No
Defects in central pair associated proteins HYDIN100, STK36 No
Isolated nexin link defects DRC1, CCDC65,GAS8 No
Reduced generation of multiple motile cilia (respiratory cells MCIDAS (major regulator of ciliogenesis in multiciliated cells; No
usually lack any motile cilia or show only very few motile respiratory cells usually lack any motile cilia or show only
cilia) very few motile cilia), CCNO (mutations result in a very low
number of cilia covering the airway cells; cilia can still have
normal cilia motility)
Motile ciliopathies with subtle or no respiratory disease MNS1, DNAH9, CFAP53, ENKUR Maybe
The following genes are autosomal recessive: ARMC4, C21orf59, CCDC103, CCDC114, CCDC151, CCDC39, CCDC40, CCDC65, CCNO, CFAP221, CFAP298, CFAP300,
DNAAF1, DNAAF2, DNAAF3, DNAAF4, DNAAF5, DNAAF11 (LRRC6) DNAH11, DNAH5 (most common), DNAH8, DNAH9, DNAH11, DNAI1 (second most common), DNAI2,
DNAJB13, DNAL1, DRC1, GAS8, GAS2L2, HYDIN, LRRC56, MCIDAS, NME8, ODAD1, ODAD2, ODAD3 (CCDC151), RSPH1, RSPH3, RSPH4A, RSPH9, SPAG1, SPEF2,
STK36, TTC25, ZMYND10. The following genes are X-linked recessive: OFD1, PIH1D3, RPGR. The following gene is autosomal dominant: OFD1.
TABLE V. Research needs and future directions for genetic studies in CRS
d Development of large biobanking alliances nationally and internationally with well-characterized cohorts that are based on histology, inflammation, and
molecular-driven endotyping of CRS.
d Identification of CFTR gene variations in non-CF CRS.
d Identification of PCD genotypes in non-PCD CRS.
d Further study of genetic diseases, such as AAT deficiency, that have not been adequately studied in CRS and need attention. AAT is characterized by mu-
tations in the SERPINA1 gene. In homozygotes, mutations are known to lead to early-onset panacinar emphysema and chronic obstructive pulmonary
disease. AAT belongs to the serine protease inhibitor group that critically regulate various inflammatory cascades, with a major role in the neutralization of
neutrophil proteases, in particular neutrophil elastase.157
d Machine learning applications for studying large populations, association of comorbid conditions, and identification of theratypes and integrated multio-
mics.158
d Multiomics study with application of machine learning for calculating heritability and developing a polygenic risk score to make risk predictions and prog-
nostications for disease onset, severity, and therapeutic responsiveness.158,159
d Optimizing scRNA-Seq technology. Although up to 30% to 60% of CD451 cells in NP are neutrophils and eosinophils, they were almost absent in earlier
scRNA-Seq studies in NP.64,87 Future studies will require optimizing the technology for granulocytes.
AAT, Alpha-1-antitrypsin.
genetic studies.145 In the absence of clear cutoffs between normal sinusitis in that they were more likely to have maternal history
and disease states, genetic studies may yield results that may not of asthma, to be skin test positive to Alternaria, and to report
be relevant. eczema, allergic rhinitis, wheeze, asthma, a higher number of
Another major drawback is the cross-sectional nature of colds during childhood, and increased total serum IgE levels at
genetic studies, which can only offer input on association, not 9 months of age. In those with late-onset adult sinusitis, there
causation. Indeed, most studies in the literature, with notable were no significant differences in these characteristics compared
exceptions, offer a genetic snapshot in time and may not account to those without sinusitis. However, the diagnosis of adult sinus-
for certain individuals who are normal at the time of study and itis in this study was made according to a history of whether or not
may miss individuals who are predisposed and progress to the patient had undergone a sinus x-ray, as advised by a commu-
develop CRS over the course of their lives. Prospective studies nity physician.146 Additionally, in a retrospective review, Chang
in the literature are rare. Chang et al146 studied early-life risk fac- et al96 found CRS to be higher in those individuals with
tors for CRS. They created a longitudinal birth cohort study that CDHR3 allele rs6967330 (previously identified by Bønnelykke
enrolled over 1000 individuals at birth and followed them into et al94 in a pediatric study to be associated with higher incidence
adulthood. The investigators found that the strongest risk factor of asthma and rhinovirus type C infection95). Thus, childhood
of having adult ‘‘sinusitis’’ was physician-diagnosed sinusitis at viral infections may predispose people to development of CRS
age 6. The group with early-onset CRS (childhood sinusitis as a result of certain genetic variations. Longitudinal studies
with development of adult CRS) differed from those without may be far more valuable at understanding the causation and
18 LAL ET AL J ALLERGY CLIN IMMUNOL
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pathophysiology of CRS than most cross-sectional studies, which in CRS. However, causality is not determined for most of these
at best imply association. This also implies that longitudinal reported variations. Inferences from these data must be measured
studies may be critical to further understanding CRS because most investigations report unreplicated results from small
pathogenesis. study populations. Large, replicated studies in tight cohorts across
Reproducibility remains a concern for GWAS of CRS.52 Of diverse ethnic and geographical populations is a pressing need in
note, the finding by Kristjansson et al27 of only 2 genome-wide studying CRS genetics. With the exception of some GWAS,
significant loci despite genotyping approximately 10,000 cases genetic studies have mostly been conducted in Asia. Given the
suggests that substantial clinical heterogeneity could have variabilities in genetic composition and the environmental insults
masked other risk loci, as use of diagnosis codes for inclusion across the globe, broad generalization to other populations should
may have captured a range of conditions with overlapping symp- await confirmation through large population-based replication
toms. Use of phenotypic classifications that are based on the pres- studies. Future investigations into specific genetic biomarkers
ence or absence of NPs to study genetics must be supplanted by will also clarify the heritability of CRS. As the physiologic and
use of biomarkers to subtype disease and study genetic profiles. pathobiological roles of these genes become better understood,
For example, eosinophilic CRSwNP and noneosinophilic novel diagnostic and therapeutic tools will become available for
CRSwNP have distinct mRNA and miRNA profiles.50,51,147,148 risk prediction as well as novel and targeted drug therapy; further,
Most candidate gene and epigenetic studies reported in CRS we will gain the ability to alter the risk of CRS by using gene-based
are nonreplicated and have been primarily conducted on small therapy or epigenetic reprogramming.
populations in Asia, where the population may have genetic and
environmental influences distinct from other global populations. We thank Angela Donaldson (Mayo Clinic, Jacksonville, Fla) for review of
Ideally, longitudinal replication studies involving repeated ob- the report.
servations, as well as replication across different study designs
and well-characterized cohorts in large populations, should be
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