外文文献中耳炎生物信息学的最新进展Panel 2- recent advance in otitis media bioinformatics

Contents lists available at ScienceDirect International Journal of Pediatric Otorhinolaryngology journal homepage Panel 2 recent advance in otitis media bioinformatics Diego Preciado Jian Dong Li Kensei Komatsu Arwa Kurabi Gustavo Nino Stephanie Val Shyan Vijayasekaran Oren Ziv Ann Hermansson A R T I C L E I N F O Keywords Otitis media Bioinformatics Proteomics microRNA Genomics Transcriptome A B S T R A C T Objectives To update the medical literature on recent large scale studies employing bioinformatics data analysis tools in otitis media OM disease models with a principal focus on developments in the past 5 years Data sources Pubmed indexed peer reviewed articles Review methods Comprehensive review of the literature using the following search terms genomics in fl ammasome microRNA proteomics transcriptome bioinformatics with the term otitis media and middle ear Included articles published in the English language from January 1 2015 April 1 2019 Implications for practice Large scale bioinformatics tools over the past fi ve years lend credence to the paradigm of innate immune response playing a critical role in host defense against bacteria contributing to Otitis Media OM progression from acute to chronic In total genomic miRNAomic and proteomic analyses all point to the need for a tightly regulated innate immune and infl ammatory response in the middle ear Currently there is an urgent need for developing novel therapeutic strategies to control immunopathology and tissue damage im prove hearing and enhance host defense for both acute and chronic OM based on full understanding of the basic molecular pathogenesis of OM 1 Introduction the usage of bioinformatics to impact the treatment of human disease Over the past decade or so an unprecedented volume of biological data has been produced by large scale big data eff orts such as the human genome project advances in mass spectrometric based pro teomics analyses next generation genetic sequencing epigenetics as well as projects in other organisms such as the elucidation of health and disease microbiomes The huge demand for analysis and inter pretation of these data is being managed by the evolving science of bioinformatics Bioinformatics is defi ned as the application of tools of computation and analysis to the capture and interpretation of biological data and is essential for the understanding applicability and man agement of data in modern biology and medicine In general the OM fi eld has lagged relative to other respiratory and infectious disease arenas in terms of large scale profi ling of molecular genetic and bac terial processes during disease progression This is largely due to the fact that OM is a ubiquitous disease process in which discovery and advances span through multiple medical specialties and global geo graphical regions The amount of federal funded dollars going to OM basic research is markedly less than other infectious disease entities Relatively mundane and widely available surgical techniques such as tympanostomy tube placement are considered eff ective treatments Yet OM accounts for the primary reason for antibiotics prescriptions and surgical procedures in the US representing a burden of more than 2 billion annually to the US healthcare system 1 2 Critically there are no medications proven eff ective to reduce mucous accumulation in the ear leaving only watchful waiting or surgery as treatment options Beyond concerns related to over utilization of general anesthesia for small children the over usage of antibiotics to treat OM with the ex panding emergence of resistant pathogens represents a signifi cant so cietal problem As such there is a critical gap to identify novel ther apeutic approaches for these children In general the genetic and molecular underpinnings of OM disease progression from acute to chronic are only recently being elucidated Knowledge gained from large scale descriptive studies will serve the goal of uncovering much needed novel management strategies The goal of this review is to up date the latest literature in the OM and upper airway fi eld which taps into bioinformatics to further our understanding of OM progression focusing on the latest knowledge in genomics miRNAomics pro teomics microbiomics and transcriptomics https doi org 10 1016 j ijporl 2019 109834 The goal of this report will be to compile the latest literature on bioinformatic studies or knowledge meaning the usage of big data to further the understanding and treatment of otitis media Corresponding author Division of Pediatric Otolaryngology Children s National Health System 111 Michigan Av NW Washington DC 20010 United States E mail address DPreciad childrensnational org D Preciado International Journal of Pediatric Otorhinolaryngology xxx xxxx xxxx 0165 5876 2019 Elsevier B V All rights reserved Please cite this article as Diego Preciado et al International Journal of Pediatric Otorhinolaryngology https doi org 10 1016 j ijporl 2019 109834 2 Methods A comprehensive review of the biomedical literature was conducted by the 2019 International Symposium for Otitis Media Symposium Research Conference panel 2 Bioinformatics members Pub med was used as the search engine Given instructions provided to the Panel by the symposium organizers each Panel member conducted an in dependent search engine query on the basis of his her area of expertise Collectively the following search terms were employed genomics infl ammasome microRNA proteomics transcriptome microbiome bioinformatics with the term otitis media and middle ear Included articles for this state of the art review mostly focused on those pub lished in the English language from January 1 2015 April 1 2019 3 Genomic associations in otitis media disease susceptibility Classic studies in twins reveal a substantial heritable component to recurrent acute otitis media rAOM and chronic otitis media with ef fusion cOME 3 5 To delineate this genetic component for OM susceptibility initial widely cited studies by researchers in the United Kingdom identifi ed candidate gene from two mouse models of severe spontaneous OM 6 7 The mutations underlying these mouse models mapped to the Evi1 gene and the Fbxo11 gene Another group in Wes tern Australia evaluated an association between polymorphisms in the human homologues EVI1 and FBXO11 and susceptibility to rAOM or cOME in a cohort of families treated by the authors The Western Australian Family Study of OM and in a unique cohort of children followed longitudinally since birth for 20 years the Western Australian Pregnancy Cohort Study or Raine study 8 Using bioinformatics analyses these studies showed that the association at FBXO11 was in dependent of associated environmental risk factors for OM i e day care attendance allergy As both EVI1 and FBXO11 proteins appear to in teract in the transforming growth factor TGF signaling pathway these data confi rm a genetic basis for susceptibility to severe OM and suggest this might be mediated by variants at FBXO11 that result in infl ammatory dysfunction by altering regulation of the TGF pathway Two classic studies into genome wide linkage scans using multi case families of Caucasian origin identifi ed specifi c regions of the genome harboring putative susceptibility genes The fi rst identifi ed two regions of linkage on chromosome 10q26 3 and 19q13 43 and a further region on 3p25 3 after conditioning on the linked regions suggesting epistatic interactions 9 The second identifi ed two diff erent regions of linkage on 17q12 and 10q22 3 10 Whilst the region of 19q13 43 has since been refi ned 11 12 there has been no replication of any of these re gions in independent studies and the causal genes underlying them have yet to be identifi ed Notably in the past fi ve years a Finnish group evaluated 35 can didate genes in 624 cases and 778 controls identifi ed strong association of the TLR4 gene region with risk of childhood OM The TLR4 gene region identifi ed a novel and previously unrecognized risk haplotype in OM cases defi ned by the minor alleles of rs13209060 rs13209057 and rs503071713 The association was strongest in children who had their fi rst OM episode at younger than 6 months which is in accordance with several clinical studies showing that these children will be otitis prone in over 80 and in children who had undergone multiple tympa nostomy tube insertions This suggested that the more severe phenotype of OM has the strongest connection with the TLR4 TCG risk haplotype which further supported a role of TLR4 in OM pathogenesis The p value of the association in the subset of patients with multiple tube insertions was of the order of 10 5 which is one of the most signifi cant associations so far reported in OM candidate gene studies TLR4 is thought to play a major role in innate immunity against the pathogens causing OM The major microbial ligand of TLR4 is LPS a bacterial cell wall component of Gram negative bacteria TLR4 also recognizes other microbial antigens such as pneumococcal pneumolysin TLR4 has a role in the up regulation of TLR2 which recognizes the peptidoglycan of Gram positive bacteria TLR4 is thus important for the innate immune response against the major pathogens causing OM Haemophilus in fl uenzae MoraxellacatarrhalisandGram positiveStreptococcus pneumoniae TLR4 also recognizes endogenous ligands such as heat shock proteins and proteolytically cleaved fi brinogen which may po tentially contribute to the pathogenesis of OM Of note is that TLR4 knock out mice have decreased pathogen clearance and prolonged in fl ammation in the middle ear during experimental OM further sup porting a connection between TLR4 and OM risk 14 15 They were unable to replicate this association in a UK cohort or in two US cohorts This may refl ect the heterogeneous nature of OM and diff erences in diff erent experimental models and that inter action of environmental and host factors may modulate which genetic factors contribute to overall predisposition to OM 13 Similarly by performing single nu cleotide polymorphism SNP analyses a number of groups found that polymorphisms in TLRs along with other regulatory and infl ammatory cytokines IL 10 IL 1 IL 1 IL 8 genes are also associated with OM susceptibility 16 18 Further highlighting the importance of host epithelial and innate immunity in OM responses recent large scale genetic susceptibility studies in an indigenous Filipino population and in US children em ploying novel exome and Sanger sequencing along with bioinformatic data analyses reported a strong association of variants within A2ML1 as signifi cant risk factors for OM Sixteen novel damaging A2ML1 variants identifi ed in OM 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 1G C were independently associated with OM 19 This report suggests a role for A2ML1 in epithelial diff er entiation within the middle ear as part of OM pathology and the po tential application of ROCK inhibition in otitis media Another recent study from the same multi institutional group identifi ed variants of the fucose transferase FUT2 gene to also be associated with OM predis position 20 Notably OM bacterial pathogens were shown to activate FUT2 suggesting that upon bacterial stimulation middle ear glyco proteins such as mucins rich in specifi c glycan fucoses are produced in turn predictably interacting with neutrophils and other innate immune cells in the middle ear driving their innate immune defense function 4 The role of MicroRNA responses in airway middle ear infl ammation Beyond genetic association large scale analyses the recent dis covery of short sequence RNAs as potent regulators of gene transcrip tion has opened a whole new fi eld of molecular research into epigenetic mechanisms of disease susceptibility MicroRNAs miRs are small RNA molecules approximately 22 nucleotides long that can negatively control their target gene expression post transcriptionally There are currently more than 460 human miRNAs known and the total number is predicted to be much larger Although there is no question about the biological importance of miRs as key post transcriptional regulators of gene expression understanding the function of a single miR or clusters of miRs using bioinformatics tools may be challenging First multiple miRs and targets are often involved simultaneously Second miR pro fi les just as mRNA transcripts are cell and context specifi c 21 22 Third as further detailed below the presence of non canonical miRNA mRNA binding and diverse mechanisms of miRNA action e g mRNA decay make the traditional bioinformatics approach of identifying seeding sites in specifi c 3 untranslated regions 3 UTRs 23 in suffi cient to understand or predict overall miR functional eff ects The traditional approach of examining the eff ect of a particular miR or a set of candidate miRs begins with the identifi cation of predicted targets This process usually involves bioinformatics tools for in silico analyses of miRNA mRNA interactions based on 3 UTRs mediated silencing of gene expression at the post transcriptional level 23 The probability algorithm is usually built based on the perfect complementarity of the D Preciado et al International Journal of Pediatric Otorhinolaryngology xxx xxxx xxxx 2 miR seed region the sequence spanning nucleotides 2 to 7 of the 5 end of the mature miR with the seed match at the 3 UTR which is a highly evolutionarily conserved region 23 These bioinformatics tools are often linked to simultaneous mRNA profi les to refi ne possible miR targets downregulated genes However this target based approach has become problematic as it does not encompass the diverse me chanisms of action of miRs in cell biology Indeed miRs aff ect multiple non canonical targets indirectly or directly using imperfect base pair matching 24 25 Multiple reports have also established the ability of miRs to target protein coding sequences CDS and not only those lo cated in 3 UTR regions 25 26 In fact some seeding sequences for miRs are only functional when present in CDS 26 More importantly it is also clear now that in addition to post transcriptional silencing the molecular eff ects of miRs include mRNA decay 24 Specifi cally miRs promote mRNA decay by recruiting deadenylases and decapping factors onto the target mRNAs through a mechanism mediated by GW182 TNRC624 These miRNA driven complexes deprotect mRNA ends thus leading to mRNA decay by both 5 3 and 3 5 RNA exonucleases 24 Notably prior studies comparing eff ects in mRNA levels by RNA seq and translation effi ciency by ribosome profi ling have demonstrated that miR induced mRNA decay is the dominant functional consequence in mammalian cells 24 27 Specifi c to middle ear and respiratory tract the role of miRs in disease progression is only recently being studied The presence of ex tracellular miRs secreted for cell to cell re programming in distinct areas of the respiratory tract have now been profi led 28 29 This mechanism of action of some miRs is increasingly recognized as a powerful way to amplify and or sustain autocrine and or paracrine eff ects of a single or clusters of miRs 28 30 Given that miR packaging and exporting is a highly complex and regulated process the determi nation of the key miRs in a given sample needs to account for the in fl uence of secreted miRs For instance that human respiratory and middle ear secretions contain a baseline population of secreted miRs microRNome has been recently described 28 29 These miRs likely exert a homeostatic infl uence on the gene expression of neighboring cells Notably acute disturbances e g viral or bacterial infection can alter this baseline secretory microRNome and consequently may aff ect gene expression of homing and recruited immune cells Thus it is clear now that in addition to intracellular miRs it may be required to assess secretory miRs when analyzing samples in the respiratory system In deed extracellular miRs are in direct contact with airway cells e g epithelium and immune cells and thus may have a crucial regulatory eff ect in cellular function via autocrine and or paracrine actions at baseline and in response to diff erent stimuli Relevant to the middle ear miR 378 was recently identifi ed as the miRNA most robustly induced in middle ear exosomes upon NTHi bacterial exposure 31 Notably miR 378 has been reported to mediate a robust increased expression of MUC5AC vascular endothelial growth factor VEGF interleukin 8 IL 8 and Ang 1 in lung epithelial cell lines 32 suggesting that its presence in the middle ear may similarly be driving a mucogenic re sponse A separate recent report explored the role of anti infl ammatory miRNAs molecules namely miR 146 in the middle ear Findings sug gested that miR 146 intracellular levels correlate to increased middle ear mucosal thickness and infl ammation 33 Relevant to OM genetic susceptibility studies is the fact that miR 146 exerts an anti in fl ammatory role by shutting off the transcription of TLRs 34 To further elucidate the role of these recently profi led middle miR signatures miR bioinformatics tools must integrate intracellular and extracellular miR population with experimental data to identify the functionally dominant miR mRNA networks e g TF co regulatory networks in a particular cell system The later can be then used to elucidate miR mechanisms of action in a cell and context specifi c manner and thus provide novel and powerful insights into the pivotal role of miRs in biological processes 5 Middle ear cell responses to bacterial stimulation what do broad profi ling studies tell us As demonstrated by the genetic and miRNA studies described above many of the genes or molecular mediators involved in OM disease progression appear to be regulated by bacteria Along these lines a number of recent studies have