Genome-wide association study for acute otitis media in children identifies FNDC1 as disease contributing gene

Prevalence of Gram positive bacteria in the affected individuals of Otitis media with effusion from the indigenous population of Southern Punjab, Pakistan: first report

Otitis media with effusion (OME) is a type of otitis media (OM) characterized by the presence of fluid behind intact tympanic membrane and is one of the most common diseases of early childhood. It is an infectious disease associated with the presence of many pathogenic bacteria in the middle ear of affected individuals. This study was aimed to determine the prevalence of Gram-positive bacteria from the middle ear of OME patients in the population of Southern Punjab, Pakistan. The incidence of OME under comprehensive healthcare setting was investigated in patients who consulted at the department of ear, throat and nose, Bahawal Victoria Hospital (BVH), Bahawalpur, from December, 2019 to May, 2021. Ear swabs were taken from affected and normal individuals. After culturing bacteria from the ear swabs, microscopic analysis and biochemical tests were performed to characterize the cultured Gram-positive bacteria. Out of 352 patients examined, 109 (30.9%) patients had OME. Age of the participants ranged from 14 to 50 years; individuals between the ages of 14 and 22 years had the highest infection rates, while individuals between 40 and 50 years had the lowest rate of infection. Tympanic membrane perforation, fever, cough, sore throat, ear pain and hearing problem showed association with symptoms of OME. Microscopic analysis and biochemical characterization showed the presence of streptococci and staphylococci in all the studied samples. The most frequently isolated bacteria were Streptococcus pneumoniae, Streptococcus pyogenes, and Staphylococcus aureus with percentage of 53.3%, 20% and 13.3% respectively. Enterococcus faecalis (6.6%) and Staphylococcus epidermidis (6.6%) were also identified in the studied samples. This study will help in the better medical administration of OME affected individuals.

Rs420137, rs386360 and rs7763726 polymorphisms in fibronectin type III domain containing 1 are associated with susceptibility to coronary heart disease: Analysis in the Han population

Background

Numerous genetic studies have shown that genes are related to the pathogenesis of coronary heart disease (CHD). The main aim of this study was to confirm whether fibronectin type III domain containing 1 (FNDC1) polymorphisms correlate with the risk of CHD.

Methods

In this study, in order to assess the association between three FNDC1 single nucleotide polymorphisms (SNPs) and the risk of CHD, we conducted a case-control study involving 630 patients with CHD and 568 healthy controls using Agena MassARRAY (Agena Bioscience, San Diego, CA, USA). Genotype distribution in case and control groups was analyzed by Chi square test. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by logistic regression models adjusted for age, sex, smoking, and alcohol consumption to assess the correlation between SNPs and CHD risk.

Results

Our results indicated that FNDC1-rs420137, -rs386360, and -rs7763726 played important roles in enhancing the risk of CHD. Subgroup analysis revealed that rs420137 increased the susceptibility to CHD in males, smokers, and patients aged ≤62 years. Rs360 had an increased risk of CHD in males, patients at aged ≤62 years, smokers, and non-drinkers. Furthermore, the association of rs7763726 with increased CHD risk was also observed in males, patients aged ≤62 years, smokers, and drinkers. Last but not least, these three SNPs we selected were protective factors against hypertension in CHD individuals.

Conclusion

Our research suggest that FNDC1-rs420137, -rs386360, and -rs7763726 variants may be regarded as novel biomarkers for predicting CHD risk and other specific mechanisms of action of CHD need to be further studied.

NELL-1 in Genome-Wide Association Studies across Human Diseases

Neural epidermal growth factor-like (EGFL)-like protein (NELL)-1 is a potent and key osteogenic factor in the development and regeneration of skeletal tissues. Intriguingly, accumulative data from genome-wide association studies (GWASs) have started unveiling potential broader roles of NELL-1 beyond its functions in bone and cartilage. With exploration of the genetic variants of the entire genome in large-scale disease cohorts, GWASs have been used for establishing the connection between specific single-nucleotide polymorphisms of NELL1, in addition to osteoporosis, metabolic diseases, inflammatory conditions, neuropsychiatric diseases, neurodegenerative disorders, and malignant tumors. This review summarizes the findings from GWASs on the manifestation, significance level, implications on function, and correlation of specific NELL1 single-nucleotide polymorphisms in various disorders in humans. By offering a unique and comprehensive correlation between genetic variants and plausible functions of NELL1 in GWASs, this review illustrates the wide range of potential effects of a single gene on the pathogenesis of multiple disorders in humans.

Use of a Network-Based Method to Identify Latent Genes Associated with Hearing Loss in Children

Hearing loss is a total or partial inability to hear. Approximately 5% of people worldwide experience this condition. Hearing capacity is closely related to language, social, and basic emotional development; hearing loss is particularly serious in children. The pathogenesis of childhood hearing loss remains poorly understood. Here, we sought to identify new genes potentially associated with two types of hearing loss in children: congenital deafness and otitis media. We used a network-based method incorporating a random walk with restart algorithm, as well as a protein-protein interaction framework, to identify genes potentially associated with either pathogenesis. A following screening procedure was performed and 18 and 87 genes were identified, which potentially involved in the development of congenital deafness or otitis media, respectively. These findings provide novel biomarkers for clinical screening of childhood deafness; they contribute to a genetic understanding of the pathogenetic mechanisms involved.

Ear Infection Trajectories and Academic, Behavioral, and Quality-of-Life Outcomes: A Population-Based Longitudinal Study

OBJECTIVE

The purpose of this study was to investigate (1) typical trajectories of parent-reported ear infections throughout childhood and (2) their associations with child outcomes.

METHOD

Design and participants: Two parallel cohorts assessed biennially from 2004 to 2014 spanning ages 0-1 to 10-11 years (B cohort, n = 3721) and ages 4-5 to 14-15 years (K cohort, n = 3489) in the Longitudinal Study of Australian Children. Ear infection: Parent-reported ongoing ear infections (B: waves 1-6; K: waves 1, 2, 4, and 5). Outcomes (wave 6): National academic standardized test, teacher-reported learning, parent- and teacher-reported behavior, and self-reported quality of life. Analysis: Latent class models identified ear infection trajectories. Linear regression quantified associations between trajectories and outcomes.

RESULTS

Four probability trajectories of ear infections emerged in both cohorts: "consistently low" (B 86.2%, K 87.0%), "moderate to low" (5.5%, 9.7%), "low to moderate" (7.0%, 1.5%), and "consistently high" (1.4%, 1.8%). In K cohort, the "consistently high" group had the worst outcomes (effect sizes 0.2-0.8 SDs), with effect sizes largest for psychosocial and language outcomes. "Moderate to low" and "low to moderate" groups showed marginal to no academic associations, although behavior and quality-of-life scores were 0.2 to 0.3 SDs poorer than the "consistently low" group. Similar but attenuated associations were seen in B cohort.

CONCLUSION

Sizable adverse adolescent outcomes follow parent reports of persistent ongoing ear infections throughout childhood. Despite a possibility of reverse causation, this suggests that cumulative rather than age-specific ear infections are most important to outcomes. Clinicians may generally be reassuring about ongoing ear infections limited to either early or middle childhood but should proactively identify and manage the small subgroup whose early infections persist throughout the elementary school years.

Comparative Proteomic Analysis to Investigate the Pathogenesis of Oral Adenoid Cystic Carcinoma

Adenoid cystic carcinoma (ACC) belongs to salivary gland malignancies commonly occurring in an oral cavity with a poor long-term prognosis. The potential biomarkers and cellular functions acting on local recurrences and distant metastases remain to be illustrated. Proteomics is the core content of precision medicine research, which provides accurate information for early detection of cancer, benign and malignant diagnosis, classification and personalized medication, efficacy monitoring, and prognosis judgment. To obtain a comprehensive regulation network and supply clues for the treatment of oral ACC (OACC), we utilized mass spectrometry-based quantitative proteomics to analyze the protein expression profile in paired tumor and adjacent normal tissues. We identified a total of 40,547 specific peptides and 4454 differentially expressed proteins (DEPs), in which HAPLN1 was the most upregulated protein and BPIFB1 was the most downregulated. Then, we annotated the functions and characteristics of DEPs in detail from the aspects of gene ontology, subcellular structural localization, KEGG, and protein domain to thoroughly understand the identified and quantified proteins. Glycosphingolipid biosynthesis and glycosaminoglycan degradation pathways showed the biggest difference according to KEGG analysis. Moreover, we confirmed 20 proteins from the ECM-receptor signaling pathway by a parallel reaction monitoring quantitative detection and 19 proteins were quantified. This study provides useful insights to analyze DEPs in OACC and guide in-depth thinking of the pathogenesis from a proteomics view for anticancer mechanisms and potential biomarkers.

FNDC1 Polymorphism (rs3003174 C > T) Increased the Incidence of Coronary Artery Aneurysm in Patients with Kawasaki Disease in a Southern Chinese Population

Background

A large number of studies demonstrated that the key to the occurrence and development of Kawasaki disease (KD) is the over-activation of immune cells and the generation of various inflammatory factors, leading to the imbalance of the immune system. Recently, mutations in the FNDC1 gene have been shown to be associated with inflammatory responses. However, there have been no reports on the relationship between FNDC1 gene and KD so far.

Methods

We enrolled 1611 controls and 1459 patients with KD, including 372 patients with coronary artery aneurysm (CAA) and 179 patients with coronary artery lesion (CAL). The relationship between FNDC1 rs3003174 polymorphism and KD with CAA or without CAA was investigated.

Results

This study showed no evidence that the association between FNDC1 rs3003174 C>T polymorphism and KD susceptibility was statistically significant (CT versus CC: adjusted odds ratio (OR) =0.897, 95% confidence interval (CI) =0.769–1.045, P=0.162; TT versus CC: adjusted OR=0.995, 95% CI=0.786–1.260, P=0.968; dominant model: adjusted OR=0.916, 95% CI=0.792–1.059, P=0.235; and recessive model: adjusted OR=1.055, 95% CI=0.845–1.316, P=0.638). However, our further stratified analysis in the control and KD group bore out that the incidence of TT genotype of FNDC1 rs3003174 C > T polymorphism was higher than that of CC/CT genotype in KD patients stratified by CAA (adjusted OR=1.437, 95% CI=1.034–1.996, P=0.031). Moreover, a stratified analysis of age and gender in KD patients indicated that the rs3003174 TT genotype increased the risk of CAA formation in aged ≦60 months (CC/CT vs TT: adjusted OR=1.580, 95% CI=1.106–2.259, P=0.012) and male (CC/CT vs TT: adjusted OR=1.653, 95% CI=1.101–2.481, P=0.015) KD patients.

Conclusion

The results of this study demonstrated that the FNDC1 rs3003174 C>T polymorphism may be a hazard factor in the formation of CAA in KD patients that was not disclosed before.

The transcriptional landscape of the cultured murine middle ear epithelium in vitro

Otitis media (OM) is the most common paediatric disease and leads to significant morbidity. Although understanding of underlying disease mechanisms is hampered by complex pathophysiology, it is clear that epithelial abnormalities underpin the disease. The mechanisms underpinning epithelial remodelling in OM remain unclear. We recently described a novel in vitro model of mouse middle ear epithelial cells (mMEECs) that undergoes mucociliary differentiation into the varied epithelial cell populations seen in the middle ear cavity. We now describe genome wide gene expression profiles of mMEECs as they undergo differentiation. We compared the gene expression profiles of original (uncultured) middle ear cells, confluent cultures of undifferentiated cells and cells that had been differentiated for 7 days at an air liquid interface (ALI). >5000 genes were differentially expressed among the three groups of cells. Approximately 4000 genes were differentially expressed between the original cells and day 0 of ALI culture. The original cell population was shown to contain a mix of cell types, including contaminating inflammatory cells that were lost on culture. Approximately 500 genes were upregulated during ALI induced differentiation. These included some secretory genes and some enzymes but most were associated with the process of ciliogenesis. The data suggest that the in vitro model of differentiated murine middle ear epithelium exhibits a transcriptional profile consistent with the mucociliary epithelium seen within the middle ear. Knowledge of the transcriptional landscape of this epithelium will provide a basis for understanding the phenotypic changes seen in murine models of OM.

Summary: This paper presents a genome wide transcriptional analysis of murine middle ear epithelial cells as they undergo differentiation to a mucociliary phenotype representative of the native middle ear epithelium.

FNDC1 Promotes the Invasiveness of Gastric Cancer via Wnt/β-Catenin Signaling Pathway and Correlates With Peritoneal Metastasis and Prognosis

Background

Gastric cancer (GC) has a high morbidity and mortality rate, with peritoneal metastasis (PM) identified as the main site of metastasis. Our previous study found that FNDC1 has a higher frequency of mutations in patients with PM by high-throughput sequencing assay, suggesting that it may be associated with GC invasion and PM, however the specific mechanism remains unclear.

Methods

First, the correlation between FNDC1 and PM and prognosis of GC was clarified by bioinformatics and clinicopathological analysis. Next, the effect of FNDC1 expression on the invasion and metastasis ability of GC was investigated in vivo and in vitro. Finally, the signaling pathways involved in the regulation of FNDC1 were explored.

Results

FNDC1 was highly expressed in GC and was associated with PM and poor prognosis. FNDC1 was also associated with epithelial-mesenchymal transition (EMT) in GC cells. Through in vivo and in vitro experiments, it was clarified that knockdown of FNDC1 could inhibit the proliferation, invasion, and migration of GC cells. In addition, it was elucidated that FNDC1 promotes EMT through the Wnt/β-catenin signaling pathway.

Conclusion

FNDC1 may be associated with the invasion of GC and PM after surgery. FNDC1 was highly expressed in GC tissues and cell lines, while significantly associated with poor DFS and OS in GC patients. Both univariate and multivariate analyses suggested that the expression of FNDC1 was an independent factor for GC. Knockdown of FNDC1 also significantly inhibited the proliferation, migration, and activity of GC cells. FNDC1 may promote EMT in GC cells through the regulation of Wnt/β-catenin signaling pathway. FNDC1 has the potential to be used as a predictor of PM and may also be studied in depth as a therapeutic target for GC, which has potential clinical utility and is worthy of further validation.

Genomics of Otitis Media (OM): Molecular Genetics Approaches to Characterize Disease Pathophysiology

Otitis media (OM) is an infective and inflammatory disorder known to be a major cause of hearing impairment across all age groups. Both acute and chronic OM result in substantial healthcare utilization related to antibiotic prescription and surgical procedures necessary for its management. Although several studies provided evidence of genetics playing a significant role in the susceptibility to OM, we had limited knowledge about the genes associated with OM until recently. Here we have summarized the known genetic factors that confer susceptibility to various forms of OM in mice and in humans and their genetic load, along with associated cellular signaling pathways. Spotlighted in this review are fucosyltransferase (FUT) enzymes, which have been implicated in the pathogenesis of OM. A comprehensive understanding of the functions of OM-associated genes may provide potential opportunities for its diagnosis and treatment.

Panel 3: Genomics, precision medicine and targeted therapies

OBJECTIVE

To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media.

DATA SOURCES

PubMed articles published since the last meeting in June 2015 up to June 2019.

REVIEW METHODS

A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members.

CONCLUSION

Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media.

IMPLICATIONS FOR PRACTICE

In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics.

Overexpression of FNDC1 Relates to Poor Prognosis and Its Knockdown Impairs Cell Invasion and Migration in Gastric Cancer

The distribution and content of fibronectin is closely related to the occurrence and development of tumors. Fibronectin is widely involved in cell migration, adhesion, proliferation, hemostasis, and tissue repair. Fibronectin type III domain containing 1, as a primary component of the structural domain of fibronectin, is closely related to the occurrence of some cancers. However, the molecular mechanism of fibronectin type III domain containing 1 in gastric cancer has not been elaborated. In this study, we analyzed the expression and prognosis of fibronectin type III domain containing 1 by collecting data from Oncomine and GEPIA database. The expression of fibronectin type III domain containing 1 in gastric cancer cells was detected by quantitative real-time polymerase chain reaction in vitro. After knockdown of fibronectin type III domain containing 1 by small interfering RNA, the proliferation, invasion, and migration of AGS (human gastric adenocarcinoma cell line) cells and the function of epithelial–mesenchymal transition were measured by Cell Counting Kit-8, colony formation, transwell, and Western blot. The results showed that fibronectin type III domain containing 1 was highly expressed in gastric cancer tissues and its overexpression was significantly correlated with the prognosis of gastric cancer. In vitro, experiments revealed that knockdown of fibronectin type III domain containing 1 could inhibit the proliferation, migration, and invasion of gastric cancer cells, possibly by changing the epithelial–mesenchymal transition pathway. The findings elaborated the biological role of fibronectin type III domain containing 1 in gastric cancer and potential mechanism of action, possibly providing a new insight for future clinical diagnosis or even molecular therapy.

Current Understanding of Host Genetics of Otitis Media

The pathogenesis of otitis media (OM), an inflammatory disease of the middle ear (ME), involves interplay between many different factors, including the pathogenicity of infectious pathogens, host immunological status, environmental factors, and genetic predisposition, which is known to be a key determinant of OM susceptibility. Animal models and human genetics studies have identified many genes and gene variants associated with OM susceptibility: genes that encode components of multiple signaling pathways involved in host immunity and inflammatory responses of the ME mucosa; genes involved in cellular function, such as mucociliary transport, mucin production, and mucous cell metaplasia; and genes that are essential for Eustachian tube (ET) development, ME cavitation, and homeostasis. Since our last review, several new mouse models with mutations in genes such as CCL3, IL-17A, and Nisch have been reported. Moreover, genetic variants and polymorphisms in several genes, including FNDC1, FUT2, A2ML1, TGIF1, CD44, and IL1-RA variable number tandem repeat (VNTR) allele 2, have been identified as being significantly associated with OM. In this review, we focus on the current understanding of the role of host genetics in OM, including recent discoveries and future research prospects. Further studies on the genes identified thus far and the discovery of new genes using advanced technologies such as gene editing, next generation sequencing, and genome-wide association studies, will advance our understanding of the molecular mechanism underlying the pathogenesis of OM and provide new avenues for early screening and developing effective preventative and therapeutic strategies to treat OM.

Identification of Novel Genes and Biological Pathways That Overlap in Infectious and Nonallergic Diseases of the Upper and Lower Airways Using Network Analyses

Previous genetic studies on susceptibility to otitis media and airway infections have focused on immune pathways acting within the local mucosal epithelium, and outside of allergic rhinitis and asthma, limited studies exist on the overlaps at the gene, pathway or network level between the upper and lower airways. In this report, we compared [1] pathways identified from network analysis using genes derived from published genome-wide family-based and association studies for otitis media, sinusitis, and lung phenotypes, to [2] pathways identified using differentially expressed genes from RNA-sequence data from lower airway, sinus, and middle ear tissues, in particular cholesteatoma tissue compared to middle ear mucosa. For otitis media, a large number of genes (n = 1,806) were identified as differentially expressed between cholesteatoma and middle ear mucosa, which in turn led to the identification of 68 pathways that are enriched in cholesteatoma. Two differentially expressed genes CR1 and SAA1 overlap in middle ear, sinus, and lower airway samples and are potentially novel genes for otitis media susceptibility. In addition, 56 genes were differentially expressed in both tissues from the middle ear and either sinus or lower airways. Pathways that are common in upper and lower airway diseases, whether from published DNA studies or from our RNA-sequencing analyses, include chromatin organization/remodeling, endocytosis, immune system process, protein folding, and viral process. Taken together, our findings from genetic susceptibility and differential tissue expression studies support the hypothesis that the unified airway theory wherein the upper and lower respiratory tracts act as an integrated unit also applies to infectious and nonallergic airway epithelial disease. Our results may be used as reference for identification of genes or pathways that are relevant to upper and lower airways, whether common across sites, or unique to each disease.

Environmental determinants associated with acute otitis media in children: a longitudinal study

BACKGROUND

Acute otitis media (AOM) is a common pediatric disease and frequent reason for antibiotic treatment. We aimed to identify environmental and host factors associated with AOM and assess which determinants were associated with AOM at specific ages.

METHODS

This study among 7863 children was embedded in the Generation R Study: a population-based prospective cohort study from fetal life onwards. Data on outcome and possible determinants were collected using questionnaires until 6 years. We used generalized estimating equation models to examine associations with AOM with longitudinal odds at different ages, considering correlations between repeated measurements.

RESULTS

Male gender increased odds of AOM in children at 2, 3, and 4 years but not at other ages. Postnatal household smoking, presence of siblings, and pet birds increased odds of AOM. Breastfeeding decreased AOM odds, most notably in the first 2 months of life. No association was found for season of birth, maternal age, ethnicity, aberrant birth weight for gestational age, prenatal smoking, furry pets, and daycare attendance.

CONCLUSIONS

Risk of childhood AOM varies with age. Significant association with AOM was found for gender and breastfeeding at specific ages and for household smoking, presence of siblings, and pet birds at all the studied ages.

Recent Perspectives on Gene-Microbe Interactions Determining Predisposition to Otitis Media

A comprehensive understanding about the pathogenesis of otitis media (OM), one of the most common pediatric diseases, has the potential to alleviate a substantial disease burden across the globe. Advancements in genetic and bioinformatic detection methods, as well as a growing interest in the microbiome, has enhanced the capability of researchers to investigate the interplay between host genes, host microbiome, invading bacteria, and resulting OM susceptibility. Early studies deciphering the role of genetics in OM susceptibility assessed the heritability of the phenotype in twin and triplet studies, followed by linkage studies, candidate gene approaches, and genome-wide association studies that have helped in the identification of specific loci. With the advancements in techniques, various chromosomal regions and genes such as FBXO11, TGIF1, FUT2, FNDC1, and others have been implicated in predisposition to OM, yet questions still remain as to whether these implicated genes truly play a causative role in OM and to what extent. Meanwhile, 16S ribosomal RNA (rRNA) sequencing, microbial quantitative trait loci (mbQTL), and microbial genome-wide association studies (mGWAS) have mapped the microbiome of upper airways sites and therefore helped in enabling a more detailed study of interactions between host polymorphisms and host microbiome composition. Variants of specific genes conferring increased OM susceptibility, such as A2ML1, have also been shown to influence the microbial composition of the outer and middle ear in patients with OM, suggesting their role as mediators of disease. These interactions appear to impact the colonization of known otopathogens (Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis), as well as Neisseria, Gemella, Porphyromonas, Alloprevotella, and Fusobacterium populations that have also been implicated in OM pathogenesis. Meanwhile, studies demonstrating an increased abundance of Dolosigranulum and Corynebacterium in healthy patients compared to those with OM suggest a protective role for these bacteria, thereby introducing potential avenues for future probiotic treatment. Incorporating insights from these genetic, microbiome, and host-pathogen studies will allow for a more robust, comprehensive understanding of OM pathogenesis that can ultimately facilitate in the development of exciting new treatment modalities.

Updated Guidelines for the Management of Acute Otitis Media in Children by the Italian Society of Pediatrics: Prevention

BACKGROUND

In recent years, new information has been acquired regarding the diagnosis, treatment and prevention of acute otitis media (AOM). The Italian Pediatric Society, therefore, decided to issue an update to the Italian Pediatric Society guidelines published in 2010.

METHODS

The search was conducted on Pubmed, and only those studies regarding the pediatric age alone, in English or Italian, published between January 1, 2010 and December 31, 2018, were included. Each study included in the review was assessed using the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) methodology. The quality of the systematic reviews was evaluated using the A MeaSurement Tool to Assess systematic Reviews (AMSTAR) 2 appraisal tool. The guidelines were formulated using the GRADE methodology by a multidisciplinary panel of experts.

RESULTS

The importance of eliminating risk factors (passive smoking, environmental pollution, use of pacifier, obesity, limitation of day-care center attendance) and the promotion of breastfeeding and hygiene practices (nasal lavages) was confirmed. The importance of pneumococcal vaccination in the prevention of AOM was reiterated with regard to the prevention of both the first episode of AOM and recurrences. Grommets can be inserted in selected cases of recurrent AOM that did not respond to all other prevention strategies. Antibiotic prophylaxis is not recommended for the prevention of recurrent AOM, except in certain carefully selected cases. The use of complementary therapies, probiotics, xylitol and vitamin D is not recommended.

CONCLUSIONS

The prevention of episodes of AOM requires the elimination of risk factors and pneumococcal and influenza vaccination. The use of other products such as probiotics and vitamin D is not supported by adequate evidence.

Rutin suppresses FNDC1 expression in bone marrow mesenchymal stem cells to inhibit postmenopausal osteoporosis

A previous study revealed that rutin is the main component of Eucommia flavonoids that exerts a protective effect against osteopenia. The bone density and trabecular bone number of osteoporosis model rats can be significantly improved after treatment with rutin. Further study using whole gene expression profiling revealed that FNDC1, a fibronectin type III domain-containing protein, may be a novel bone metabolism-related factor that is decreased in rutin-treated rats. The mechanism underlying the effects of rutin treatment on osteoporosis is important to explore. Micro-CT, western blotting, quantitative PCR, transmission electron microscopy, and Alizarin Red mineralization staining assays were performed to evaluate bone density, FNDC1 expression and autophagy to determine whether FNDC1 might play a significant role in rutin-inhibited trabecular bone loss in rats. FNDC1 expression was high in the osteoporosis group, whereas rutin treatment facilitated FNDC1 downregulation. In addition, rutin promoted bone marrow mesenchymal stem cell autophagy by inhibiting phosphorylated Akt in osteoporosis. In summary, our study shows that rutin could regulate FNCD1 level and autophagy through the Akt/mTOR signaling pathway to provide a novel therapeutic strategy for osteoporosis.

Target Genes of Autism Risk Loci in Brain Frontal Cortex

Autism spectrum disorder (ASD) is a complex neuropsychiatric disorder. A number of genetic risk loci have been identified for ASD from genome-wide association studies (GWAS); however, their target genes in relevant tissues and cell types remain to be investigated. The frontal cortex is a key region in the human brain for communication and cognitive function. To identify risk genes contributing to potential dysfunction in the frontal cortex of ASD patients, we took an in silico approach integrating multi-omics data. We first found genes with expression in frontal cortex tissue that correlates with ASD risk loci by leveraging expression quantitative trait loci (eQTLs) information. Among these genes, we then identified 76 genes showing significant differential expression in the frontal cortex between ASD cases and controls in microarray datasets and further replicated four genes with RNA-seq data. Among the ASD GWAS single nucleotide polymorphisms (SNPs) correlating with the 76 genes, 20 overlap with histone marks and 40 are associated with gene methylation level. Thus, through multi-omics data analyses, we identified genes that may work as target genes of ASD risk loci in the brain frontal cortex.

A2ML1 and otitis media: novel variants, differential expression, and relevant pathways

A genetic basis for otitis media is established, however, the role of rare variants in disease etiology is largely unknown. Previously a duplication variant within A2ML1 was identified as a significant risk factor for otitis media in an indigenous Filipino population and in US children. In this report exome and Sanger sequencing was performed using DNA samples from the indigenous Filipino population, Filipino cochlear implantees, US probands, Finnish, and Pakistani families with otitis media. Sixteen novel, damaging A2ML1 variants identified in otitis media patients were rare or low-frequency in population-matched controls. In the indigenous population, both gingivitis and A2ML1 variants including the known duplication variant and the novel splice variant c.4061 + 1 G>C were independently associated with otitis media. Sequencing of salivary RNA samples from indigenous Filipinos demonstrated lower A2ML1 expression according to the carriage of A2ML1 variants. Sequencing of additional salivary RNA samples from US patients with otitis media revealed differentially expressed genes that are highly correlated with A2ML1 expression levels. In particular, RND3 is upregulated in both A2ML1 variant carriers and high-A2ML1 expressors. These findings support a role for A2ML1 in keratinocyte differentiation within the middle ear as part of otitis media pathology and the potential application of ROCK inhibition in otitis media.

Identification of Target Genes at Juvenile Idiopathic Arthritis GWAS Loci in Human Neutrophils

Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease among children which could cause severe disability. Genomic studies have discovered substantial number of risk loci for JIA, however, the mechanism of how these loci affect JIA development is not fully understood. Neutrophil is an important cell type involved in autoimmune diseases. To better understand the biological function of genetic loci in neutrophils during JIA development, we took an integrated multi-omics approach to identify target genes at JIA risk loci in neutrophils and constructed a protein-protein interaction network via a machine learning approach. We identified genes likely to be JIA risk loci targeted genes in neutrophils which could contribute to JIA development.

Overexpression of FNDC1 in Gastric Cancer and its Prognostic Significance

Objectives: The aims of this study were to compare the expression of fibronectin type III domain containing 1 (FNDC1) in gastric cancer (GC) and normal gastric tissue, to explore the prognostic significance of FNDC1 expression in patients with gastric adenocarcinoma, and to analyze FNDC1-related signaling pathways. Methods: The expression level of FNDC1 was initially predicted using the Oncomine and Cancer Genome Atlas databases. A Kaplan-Meier plotter database was mined to examine the clinical prognostic significance of FNDC1 mRNA in patients with GC. Subsequently, immunohistochemistry was used to measure FNDC1 protein expression levels in tissue from 90 cases of GC and paired adjacent normal tissue. Kaplan-Meier univariate and Cox multivariate survival analyses were used to determine the prognostic role of FNDC1 expression. Results: Bioinformatic data indicated that FNDC1 mRNA expression levels were significantly highly expressed in GC compared with normal gastric tissue (all P < 0.05), and patients with GC with high FNDC1 mRNA expression levels had remarkably lower overall survival (all P < 0.01). Immunohistochemical results revealed that expression levels of FNDC1 protein were significantly increased in GC compared with normal gastric tissue (P < 0.001). Additionally, Kaplan-Meier univariate and Cox multivariate survival analyses indicated that increased expression of FNDC1 was an independent predictor of poor prognosis in patients with GC (all P < 0.05). Conclusions: FNDC1 was highly expressed in GC, and high expression of FNDC1 was an independent predictor of poor prognosis in patients with GC. FNDC1 co-expressed genes were largely enriched in extracellular matrix-receptor interactions, which are closely related to tumor metastasis.

High FNDC1 expression correlates with poor prognosis in gastric cancer

Gastric cancer is a common human cancer worldwide. Fibronectin is an important extracellular matrix protein that has been implicated in many cancers and is known to be associated with proliferation and migration. Fibronectin type III domain containing 1 (FNDC1) contains a major component of the structural domain of fibronectin. The objectives of the present study were to measure FNDC1 expression in gastric cancer tissues and evaluate its value as a potential prognostic marker for gastric cancer. FNDC1 protein expression was analyzed by immunohistochemistry in 98 samples of gastric cancer tissue and 25 adjacent normal tissues. The associations between FNDC1 level and various clinicopathological characteristics were assessed, and the correlation between FNDC1 expression levels and prognosis of patients with gastric cancer was analyzed using a Kaplan-Meier analysis. It was demonstrated that FNDC1 expression in gastric cancer tissues and adjacent tissues was significantly different. FNDC1 expression levels were significantly higher in gastric cancer tissues compared with normal gastric tissues (P<0.001). Among the clinicopathological characteristics evaluated, clinical stage (P<0.001), T classification (P<0.001), N classification (P<0.001) and pathological differentiation (P=0.044) were significantly associated with high FNDC1 expression. Higher FNDC1 expression level was significantly correlated with poorer survival. The present findings suggest that FNDC1 expression levels may be a promising prognostic biomarker for gastric cancer.

A mouse-to-man candidate gene study identifies association of chronic otitis media with the loci TGIF1 and FBXO11

Chronic otitis media with effusion (COME) is the most common cause of hearing loss in children, and known to have high heritability. Mutant mouse models have identified Fbxo11, Evi1, Tgif1, and Nisch as potential risk loci. We recruited children aged 10 and under undergoing surgical treatment for COME from 35 hospitals in the UK, and their nuclear family. We performed association testing with the loci FBXO11, EVI1, TGIF1 and NISCH and sought to replicate significant results in a case-control cohort from Finland. We tested 1296 families (3828 individuals), and found strength of association with the T allele at rs881835 (p = 0.006, OR 1.39) and the G allele at rs1962914 (p = 0.007, OR 1.58) at TGIF1, and the A allele at rs10490302 (p = 0.016, OR 1.17) and the G allele at rs2537742 (p = 0.038, OR 1.16) at FBXO11. Results were not replicated. This study supports smaller studies that have also suggested association of otitis media with polymorphism at FBX011, but this is the first study to report association with the locus TGIF1. Both FBX011 and TGIF1 are involved in TGF-β signalling, suggesting this pathway may be important in the transition from acute to chronic middle ear inflammation, and a potential molecular target.

Epidemiology of Acute Otitis Media in the Postpneumococcal Conjugate Vaccine Era

OBJECTIVES

To study the epidemiology of acute otitis media (AOM), especially the otitis-prone condition, during the pneumococcal conjugate vaccines 7 and 13 era.

METHODS

Six hundred and fifteen children were prospectively managed from 6 to 36 months of life during a 10-year time frame (June 2006-June 2016). All clinical diagnoses of AOM were confirmed by tympanocentesis and bacterial culture of middle ear fluid.

RESULTS

By 1 year of age, 23% of the children experienced ≥1 episode of AOM; by 3 years of age, 60% had ≥1 episodes of AOM, and 24% had ≥3 episodes. The peak incidence occurred at 6 to 12 months of life. Multivariable analysis of demographic and environmental data revealed a significantly increased risk of AOM associated with male sex, non-Hispanic white race, family history of recurrent AOM, day care attendance, and early occurrence of AOM. Risk factors for stringently defined (tympanocentesis-confirmed) otitis proneness, in which children suffered at least 3 episodes of AOM in a 6-month period or at least 4 within a year, were male sex, day care attendance, and family history of AOM, whereas breastfeeding in the first 6 months of life was protective. Stringently defined otitis prone children were also likely to experience their first AOM episode at a younger age. The proportion of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis causing AOM had dynamic changes during the past decade.

CONCLUSIONS

We conclude that the epidemiology but not the risk factors for AOM have undergone substantial changes since the introduction of pneumococcal conjugate vaccines.

A genome-wide association study reveals candidate genes for the supernumerary nipple phenotype in sheep (Ovis aries)

Genome-wide association studies (GWASs) have been widely applied in livestock to identify genes associated with traits of economic interest. Here, we conducted the first GWAS of the supernumerary nipple phenotype in Wadi sheep, a native Chinese sheep breed, based on Ovine Infinium HD SNP BeadChip genotypes in a total of 144 ewes (75 cases with four teats, including two normal and two supernumerary teats, and 69 control cases with two teats). We detected 63 significant SNPs at the chromosome-wise threshold. Additionally, one candidate region (chr1: 170.723-170.734 Mb) was identified by haplotype-based association tests, with one SNP (rs413490006) surrounding functional genes BBX and CD47 on chromosome 1 being commonly identified as significant by the two mentioned analyses. Moreover, Gene Ontology enrichment for the significant SNPs identified by the GWAS analysis was functionally clustered into the categories of receptor activity and synaptic membrane. In addition, pathway mapping revealed four promising pathways (Wnt, oxytocin, MAPK and axon guidance) involved in the development of the supernumerary nipple phenotype. Our results provide novel and important insights into the genetic mechanisms underlying the phenotype of supernumerary nipples in mammals, including humans. These findings may be useful for future breeding and genetics in sheep and other livestock.

Common variants upstream of MLF1 at 3q25 and within CPZ at 4p16 associated with neuroblastoma

Neuroblastoma is a cancer of the developing sympathetic nervous system that most commonly presents in young children and accounts for approximately 12% of pediatric oncology deaths. Here, we report on a genome-wide association study (GWAS) in a discovery cohort or 2,101 cases and 4,202 controls of European ancestry. We identify two new association signals at 3q25 and 4p16 that replicated robustly in multiple independent cohorts comprising 1,163 cases and 4,396 controls (3q25: rs6441201 combined P = 1.2x10^-11, Odds Ratio 1.23, 95% CI:1.16–1.31; 4p16: rs3796727 combined P = 1.26x10^-12, Odds Ratio 1.30, 95% CI: 1.21–1.40). The 4p16 signal maps within the carboxypeptidase Z (CPZ) gene. The 3q25 signal resides within the arginine/serine-rich coiled-coil 1 (RSRC1) gene and upstream of the myeloid leukemia factor 1 (MLF1) gene. Increased expression of MLF1 was observed in neuroblastoma cells homozygous for the rs6441201 risk allele (P = 0.02), and significant growth inhibition was observed upon depletion of MLF1 (P < 0.0001) in neuroblastoma cells. Taken together, we show that common DNA variants within CPZ at 4p16 and upstream of MLF1 at 3q25 influence neuroblastoma susceptibility and MLF1 likely plays an important role in neuroblastoma tumorigenesis.

Neuroblastoma is an embryonal tumor of the developing sympathetic nervous system that accounts for 12% of childhood cancer deaths. Approximately 1–2% of cases are inherited in an autosomal dominant fashion. These familial cases often harbor germline mutations in ALK or PHOX2B. However, the vast majority of neuroblastomas appear to arise sporadically. We are studying sporadic neuroblastoma through an ongoing genome-wide association study (GWAS). To date, this effort has identified single nucleotide polymorphisms (SNPs) within or upstream of CASC15 and CASC14, BARD1, LMO1, DUSP12, HSD17B12, DDX4/IL31RA, HACE1, LIN28B, and TP53, along with a common copy number variation (CNV) within NBPF23 at chromosome 1q21.1, each being highly associated with neuroblastoma. Here, we report on genome-wide association study (GWAS) comprising 3,264 neuroblastoma patients and 8,598 control subjects. We identify two new association signals at 3q25 and 4p16 (3q25: rs6441201 combined P = 1.2x10^-11, Odds Ratio 1.23, 95% CI:1.16–1.31; 4p16: rs3796727 combined P = 1.26x10^-12, Odds Ratio 1.30, 95% CI: 1.21–1.40). The 3q25 signal resides upstream of the MLF1 gene and the 4p16 signal maps to the CPZ gene. We further demonstrate that neuroblastoma cells homozygous for the risk allele at 3q25 express higher levels of MLF1 and that silencing of MLF1 in neuroblastoma cells results in significant growth inhibition.

A novel microRNA-1207-3p/FNDC1/FN1/AR regulatory pathway in prostate cancer

Prostate cancer (PCa) is the second most common cause of cancer-specific deaths in the U.S. Unfortunately, the underlying molecular mechanisms for its development and progression remain unclear. Studies have established that microRNAs (miRNAs) are dysregulated in PCa. The intron-derived microRNA-1207-3p (miR-1207-3p) is encoded at the non-protein coding gene locus PVT1 on the 8q24 human chromosomal region, an established PCa susceptibility locus. However, miR-1207-3p in PCa had not previously been investigated. Therefore, we explored if miR-1207-3p plays any regulatory role in PCa. We discovered that miR-1207-3p is significantly underexpressed in PCa cell lines in comparison to normal prostate epithelial cells, and that increased expression of microRNA-1207-3p in PCa cells significantly inhibits proliferation, migration, and induces apoptosis via direct molecular targeting of fibronectin type III domain containing 1 (FNDC1). Our studies also revealed significant overexpression of FNDC1, fibronectin (FN1) and the androgen receptor (AR) in human PCa cell lines as well as tissues, and FNDC1, FN1, and AR positively correlate with aggressive PCa. These findings, recently published in Experimental Cell Research, are the first to describe a novel miR-1207-3p/FNDC1/FN1/AR novel regulatory pathway in PCa.