Dataset Information

Biomarkers for Inner Ear Disorders: Scoping Review on the Role of Biomarkers in Hearing and Balance Disorders.

ABSTRACT: The diagnostics of inner ear diseases are primarily functional, but there is a growing interest in inner ear biomarkers. The present scoping review aimed to elucidate gaps in the literature regarding the definition, classification system, and an overview of the potential uses of inner ear biomarkers. Relevant biomarkers were categorized, and their possible benefits were evaluated. The databases OVID Medline, EMBASE, EBSCO COINAHL, CA PLUS, WOS BIOSIS, WOS Core Collection, Proquest Dissertations, Theses Global, PROSPERO, Cochrane Library, and BASE were searched using the keywords "biomarker" and "inner ear". Of the initially identified 1502 studies, 34 met the inclusion criteria. The identified biomarkers were classified into diagnostic, prognostic, therapeutic, and pathognomonic; many were detected only in the inner ear or temporal bone. The inner-ear-specific biomarkers detected in peripheral blood included otolin-1, prestin, and matrilin-1. Various serum antibodies correlated with inner ear diseases (e.g., anti-type II collagen, antinuclear antibodies, antibodies against cytomegalovirus). Further studies are advised to elucidate the clinical significance and diagnostic or prognostic usage of peripheral biomarkers for inner ear disorders, filling in the literature gaps with biomarkers pertinent to the otology clinical practice and integrating functional and molecular biomarkers. These may be the building blocks toward a well-structured guideline for diagnosing and managing some audio-vestibular disorders.

SUBMITTER: Gomaa NA

PROVIDER: S-EPMC7824431 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Biomarkers for Inner Ear Disorders: Scoping Review on the Role of Biomarkers in Hearing and Balance Disorders.

Gomaa Nahla A NA Jimoh Zaharadeen Z Campbell Sandra S Zenke Julianna K JK Szczepek Agnieszka J AJ

Diagnostics (Basel, Switzerland) 20201229 1

The diagnostics of inner ear diseases are primarily functional, but there is a growing interest in inner ear biomarkers. The present scoping review aimed to elucidate gaps in the literature regarding the definition, classification system, and an overview of the potential uses of inner ear biomarkers. Relevant biomarkers were categorized, and their possible benefits were evaluated. The databases OVID Medline, EMBASE, EBSCO COINAHL, CA PLUS, WOS BIOSIS, WOS Core Collection, Proquest Dissertations, ...[more]

PMID: 33383894

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Project description:Purpose: To identify orthologous genes in Xenopus that are implicated in deafness and vestibular disorders in humans and to compare RNA-Seq and microarray to determine the advantages of each technology for Xenopus transcriptomic analysis. Methods: Inner ear RNA from X. laevis stages 56-58 was isolated with the QiagenÂ® RNeasyÂ® Mini Kit. RNA quality was assessed using the Agilent 2100 Bioanalyzer. The RNA was sent to the National Center for Genome Resources, for Illumina-Solexa sequencing using the genome analyzer II and to MIT for microarray processing usign the Affymetrix GeneChipÂ® X. laevis Genome 2.0 Array. The OMIM database was mined for identification of genes causing deafness and vestibular disorder in humans. Human sequences for each of the deafness and vestibular disorders genes were downloaded from Ensembl. Blast-2.2.27+ was used to mapped the human sequences against X. tropicalis predicted proteins from JGI or to Xenopus consensus sequences downloaded from Affymetrix. The alignment of the human sequences to the predicted proteins resulted in the identification of the protein designation number. The protein designation number was used to obtain the sacaffold number and coordinates from JGI genome browser. The scaffold number and coordinates were input into Alpheus sequence variant detection pipeline to obtain the number of reads associated with each gene. The reads were log2 transformed for comparison to the microarray. In the case of the alignment of the human sequences to the Xenopus consensus sequences resulted in the PSID. The PSID was used to obtain the GCRMA intensity value. The GCRMA value and the number of reads were compared to determine which technology detected more genes. Results: Using Affymetrix GeneChipÂ® X. laevis Genome 2.0 Arrays and Illumina-Solexa sequencing methods, we determined that the transcriptional profile of the Xenopus inner ear comprises hundreds of genes that are orthologous to OMIMÂ® genes implicated in deafness and vestibular disorders in humans. Analysis of genes that mapped to both technologies showed that RNA-Seq detected more of both deafness and vestibular disorder than the Microarray. RNA-Seq and microarray detected 108 genes but RNA-Seq detected 48 genes that were below threshold criteria for microarray. While the microarray detected 11 genes that were below the expression criteria for RNA-Seq and 23 genes were below the threshold criteria for both technologies. Further analysis of the 108 genes detected by both technologies showed a minor correlation between the two technologies. Conclusions: As part of this study we identified candidate scaffold regions of the Xenopus tropicalis genome that can be used for gene mutagenesis. Furthermore, results from this study showed that the two technologies can complement each other and that a combination of both approaches can provide a more complete analysis of gene expression than either method alone. Inner ear RNA from X. laevis larval stages 56-58 was isolated and shipped to the National Center for Genome Resources, for Illumina-Solexa sequencing or to the Massachusetts Institute of Technology BioMicro Center for microarray analysis with the Affymetrix GeneChipÂ® X. laevis Genome 2.0 Array. RNA-Sequencing was completed using the Illumina-Solexa platform for sequencing by synthesis. Short-insert paired end (SIPE) libraries were prepared from total RNA according to Illuminaâ??s mRNA-Seq Sample Prep Protocol v2.0 (Illumina, San Diego, CA, USA). The resultant double-stranded cDNA concentration was measured on a NanoDrop spectrophotometer, and size and purity were determined on the 2100 Bioanalyzer using a DNA 1000 Nano kit. The cDNA libraries were cluster amplified on Illumina flowcells, sequenced on the GAII Sequencer as 36-cycle single-end reads, and processed using Illumina software v1.0. Illumina reads were aligned to the X. tropicalis genome using the algorithm for genomic mapping and alignment program (GMAP) and AlpheusÂ® Sequence Variant Detection System v3.1.

Project description:Purpose: To identify orthologous genes in Xenopus that are implicated in deafness and vestibular disorders in humans and to compare RNA-Seq and microarray to determine the advantages of each technology for Xenopus transcriptomic analysis. Methods: Inner ear RNA from X. laevis stages 56-58 was isolated with the Qiagen® RNeasy® Mini Kit. RNA quality was assessed using the Agilent 2100 Bioanalyzer. The RNA was sent to the National Center for Genome Resources, for Illumina-Solexa sequencing using the genome analyzer II and to MIT for microarray processing usign the Affymetrix GeneChip® X. laevis Genome 2.0 Array. The OMIM database was mined for identification of genes causing deafness and vestibular disorder in humans. Human sequences for each of the deafness and vestibular disorders genes were downloaded from Ensembl. Blast-2.2.27+ was used to mapped the human sequences against X. tropicalis predicted proteins from JGI or to Xenopus consensus sequences downloaded from Affymetrix. The alignment of the human sequences to the predicted proteins resulted in the identification of the protein designation number. The protein designation number was used to obtain the sacaffold number and coordinates from JGI genome browser. The scaffold number and coordinates were input into Alpheus sequence variant detection pipeline to obtain the number of reads associated with each gene. The reads were log2 transformed for comparison to the microarray. In the case of the alignment of the human sequences to the Xenopus consensus sequences resulted in the PSID. The PSID was used to obtain the GCRMA intensity value. The GCRMA value and the number of reads were compared to determine which technology detected more genes. Results: Using Affymetrix GeneChip® X. laevis Genome 2.0 Arrays and Illumina-Solexa sequencing methods, we determined that the transcriptional profile of the Xenopus inner ear comprises hundreds of genes that are orthologous to OMIM® genes implicated in deafness and vestibular disorders in humans. Analysis of genes that mapped to both technologies showed that RNA-Seq detected more of both deafness and vestibular disorder than the Microarray. RNA-Seq and microarray detected 108 genes but RNA-Seq detected 48 genes that were below threshold criteria for microarray. While the microarray detected 11 genes that were below the expression criteria for RNA-Seq and 23 genes were below the threshold criteria for both technologies. Further analysis of the 108 genes detected by both technologies showed a minor correlation between the two technologies. Conclusions: As part of this study we identified candidate scaffold regions of the Xenopus tropicalis genome that can be used for gene mutagenesis. Furthermore, results from this study showed that the two technologies can complement each other and that a combination of both approaches can provide a more complete analysis of gene expression than either method alone.

Project description:BackgroundEar and hearing care programs are critical to early detection and management of otitis media (or middle ear disease). Otitis media and associated hearing loss disproportionately impacts First Nations children. This affects speech and language development, social and cognitive development and, in turn, education and life outcomes. This scoping review aimed to better understand how ear and hearing care programs for First Nations children in high-income colonial-settler countries aimed to reduce the burden of otitis media and increase equitable access to care. Specifically, the review aimed to chart program strategies, map the focus of each program against 4 parts of a care pathway (prevention, detection, diagnosis/management, rehabilitation), and to identify the factors that indicated the longer-term sustainability and success of programs.MethodA database search was conducted in March 2021 using Medline, Embase, Global Health, APA PsycInfo, CINAHL, Web of Science Core Collection, Scopus, and Academic Search Premier. Programs were eligible or inclusion if they had either been developed or run at any time between January 2010 to March 2021. Search terms encompassed terms such as First Nations children, ear and hearing care, and health programs, initiatives, campaigns, and services.ResultsTwenty-seven articles met the criteria to be included in the review and described a total of twenty-one ear and hearing care programs. Programs employed strategies to: (i) connect patients to specialist services, (ii) improve cultural safety of services, and (iii) increase access to ear and hearing care services. However, program evaluation measures were limited to outputs or the evaluation of service-level outcome, rather than patient-based outcomes. Factors which contributed to program sustainability included funding and community involvement although these were limited in many cases.ConclusionThe result of this study highlighted that programs primarily operate at two points along the care pathway-detection and diagnosis/management, presumably where the greatest need lies. Targeted strategies were used to address these, some which were limited in their approach. The success of many programs are evaluated as outputs, and many programs rely on funding sources which can potentially limit longer-term sustainability. Finally, the involvement of First Nations people and communities typically only occurred during implementation rather than across the development of the program. Future programs should be embedded within a connected system of care and tied to existing policies and funding streams to ensure long term viability. Programs should be governed and evaluated by First Nations communities to further ensure programs are sustainable and are designed to meet community needs.

Dataset Information

Biomarkers for Inner Ear Disorders: Scoping Review on the Role of Biomarkers in Hearing and Balance Disorders.

Publications

Biomarkers for Inner Ear Disorders: Scoping Review on the Role of Biomarkers in Hearing and Balance Disorders.

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