The Current State of Proteomics and Metabolomics for Inner Ear Health and Disease

Characterising inner ear disorders represents a significant challenge due to a lack of reliable experimental procedures and identified biomarkers. It is also difficult to access the complex microenvironments of the inner ear and investigate specific pathological indicators through conventional techniques. Omics technologies have the potential to play a vital role in revolutionising the diagnosis of ear disorders by providing a comprehensive understanding of biological systems at various molecular levels. These approaches reveal valuable information about biomolecular signatures within the cochlear tissue or fluids such as the perilymphatic and endolymphatic fluid. Proteomics identifies changes in protein abundance, while metabolomics explores metabolic products and pathways, aiding the characterisation and early diagnosis of diseases. Although there are different methods for identifying and quantifying biomolecules, mass spectrometry, as part of proteomics and metabolomics analysis, could be utilised as an effective instrument for understanding different inner ear disorders. This study aims to review the literature on the application of proteomic and metabolomic approaches by specifically focusing on Meniere's disease, ototoxicity, noise-induced hearing loss, and vestibular schwannoma. Determining potential protein and metabolite biomarkers may be helpful for the diagnosis and treatment of inner ear problems.

From bench to bedside: Advancing towards therapeutic treatment of vestibular schwannomas

Vestibular schwannomas are rare intracranial tumors originating from Schwann cells of the vestibular nerve. Despite their benign nature, these tumors can exert significant mass effects and debilitating symptoms, including gradual hearing loss, vertigo, facial nerve dysfunction, and headaches. Current clinical management options encompass wait-and-scan, surgery, radiation therapy, and off-label medication. However, each approach exhibits its own challenges and harbors limitations that underscore the urgent need for therapeutic treatments. Over the past 2 decades, extensive elucidation of the molecular underpinnings of vestibular schwannomas has unraveled genetic anomalies, dysregulated signaling pathways, downstream of receptor tyrosine kinases, disrupted extracellular matrix, inflammatory tumor microenvironment, and altered cerebrospinal fluid composition as integral factors in driving the development and progression of the disease. Armed with this knowledge, novel therapeutic interventions tailored to the unique molecular characteristics of those conditions are actively being pursued. This review underscores the urgency of addressing the dearth of Food and Drug Administration-approved drugs for vestibular schwannoma, highlighting the key molecular discoveries and their potential translation into therapeutics. It provides an in-depth exploration of the evolving landscape of therapeutic development, which is currently advancing from bench to bedside. These ongoing efforts hold the promise of significantly transforming the lives of vestibular schwannoma patients in the future.

Characterization of vestibular schwannoma tissues using liquid chromatography-tandem mass spectrometry analysis of specific peptide fragments separated by in-sample tryptic protein digestion followed by mathematical analysis

Vestibular schwannoma is the most common benign neoplasm of the cerebellopontine angle. Its first symptoms include hearing loss, tinnitus, and vestibular symptoms, followed by cerebellar and brainstem symptoms, along with palsy of the adjacent cranial nerves. However, the clinical picture has unpredictable dynamics and currently, there are no reliable predictors of tumor behavior. Hence, it is desirable to have a fast routine method for analysis of vestibular schwannoma tissues at the molecular level. The major objective of this study was to verify whether a technique using in-sample specific protein digestion with trypsin would have the potential to provide a proteomic characterization of these pathological tissues. The achieved results showed that the use of this approach with subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of released peptides allowed a fast identification of a considerable number of proteins in two differential parts of vestibular schwannoma tissue as well as in tissues of control healthy samples. Furthermore, mathematical analysis of MS data was able to discriminate between pathological vestibular schwannoma tissues and healthy tissues. Thus, in-sample protein digestion combined with LC-MS/MS separation and identification of released specific peptides followed by mathematical analysis appears to have the potential for routine characterization of vestibular schwannomas at the molecular level. Data are available via ProteomeXchange with identifier PXD045261.

Potential Molecular Biomarkers of Vestibular Schwannoma Growth: Progress and Prospects

Vestibular schwannomas (VSs, also known as acoustic neuromas) are relatively rare benign brain tumors stem from the Schwann cells of the eighth cranial nerve. Tumor growth is the paramount factor for neurosurgeons to decide whether to choose aggressive treatment approach or careful follow-up with regular magnetic resonance imaging (MRI), as surgery and radiation can introduce significant trauma and affect neurological function, while tumor enlargement during long-term follow-up will compress the adjacent nerves and tissues, causing progressive hearing loss, tinnitus and vertigo. Recently, with the deepening research of VS biology, some proteins that regulate merlin conformation changes, inflammatory cytokines, miRNAs, tissue proteins and cerebrospinal fluid (CSF) components have been proposed to be closely related to tumor volume increase. In this review, we discuss advances in the study of biomarkers that associated with VS growth, providing a reference for exploring the growth course of VS and determining the optimal treatment strategy for each patient.

Proteomic Imaging of Vestibular Schwannomas and Normal Nerves. Histopathologic Correlations

OBJECTIVES

Proteomic analysis of vestibular schwannoma (VS), non-vestibular schwannoma (NVS), and normal nerve (NN) using mass spectrometry and imaging of matrix assisted laser desorption ionization-time of flight (MALDI-TOF).

METHODS

Retrospective, qualitative, and descriptive study on VS, NVS, and NN. Samples were provided by our Tumor Bank. They were analyzed histologically then sprayed by acid matrix. The laser beam of MALDI performed desorption-ionization of the sample. A mass spectrogram (MS) was drawn depending on time of flight of ionized peptides, and MALDI-imaging was obtained which is a summation color spectrum depending on sample's peptide content. The slice was reexamined histologically and results compared with MALDI-imaging.

RESULTS

Fifty schwannomas were sampled, of which 27 exploitable: 22 VS (17 Antoni type A and five type B) and five NVS (all Antoni type B). Eleven NN were analyzed. Among the 22 VS, near-total correlation between MALDI-imaging and pathology was found in two cases (9.1%), partial correlation in four (18.2%), and no correlation in 16 (72.7%); correlations were more frequent in VS of the Antoni type B. MS showed a peptide spike at 2,000 m/z in 7 (31.8%) and 5,000 m/z in 21 (95.5%). Among the five NVS, near-total correlation was found in three cases (60%), partial correlation in one (20%), and no correlation in one (20%). MS showed a peptide spike at 2,000 m/z in two (40%) and 5,000 m/z in all (100%). Among the 11 NN, near-total correlation was found in nine cases (81.8%), partial correlation in one (9.1%), and no correlation in one (9.1%). MS showed no peptide spike at 2,000 or 5,000 m/z. Behind homogeneous areas on histology, there was great heterogeneity on MALDI-imaging and MS, regarding VS and NVS, but not NN.

CONCLUSIONS

There was a lack of correlation between MALDI-imaging and pathology in VS (except Antoni type B) as compared with NVS and NN. The lack of correlation in VS of the type A as compared with type B VS and NVS could be attributed to the overexpression of degeneration-associated proteins/peptides in VS of the type B as well as NVS that are better correlated with histologic findings. The two peptide spikes detected in schwannoma and not in NN opens up the prospect of tumor biomarkers identifiable by sequencing. The proteomic polymorphism found in VS and NVS was absent on histology which is a new morphologic characteristic of schwannoma. Further studies should be performed in the future to confirm the benefit and usefulness of the MALDI in the analysis of VS and NVS.

Protein profiling of cerebrospinal fluid from patients undergoing vestibular schwannoma surgery and clinical significance

Vestibular schwannoma (VS) is a common disease in the region of the cerebellopontine angle in the posterior cranial fossa. Large VS and its surgical management usually lead to severe cranial nerve dysfunction and affect the patient's quality of life. We aimed to find some possible progression markers of VS. Here, we sought to characterize the cerebrospinal fluid (CSF) proteome of patients with different VS grades and recurrence to identify biomarkers predictive of VS growth or recurrence. CSF was collected intraoperatively prior to removal of untreated VS, including grade I-V and recurrence. Isobaric tags for relative and absolute quantitation-based proteomic analysis of CSF from 43 VS patients and 3 control patients was used to identify candidate proteins. Ninety-three overlapping proteins were found to display differential expression in grade I, II, III, IV, and V VS patients compared with the control group. Nine proteins were chosen for validation with enzyme-linked immunosorbent assay. VS was distinguished from control patients based on the expression patterns of six proteins (ATP-binding cassette subfamily A member 3 [ABCA3], secretogranin-1 [SCG1], Krueppel-like factor 11 [KLF11], voltage-dependent calcium channel subunit alpha-2/delta-1 [CA2D1], brain acid soluble protein 1 [BASP1], and peroxiredoxin-2 [PRDX2]. ABCA3 and KLF11 were positively correlated with the size of early-phase of VS, while BASP1 and PRDX2 showed a negative correlation. ABCA3, CA2D1, and KLF11 were upregulated, while BASP1 and PRDX2 were downregulated in the CSF from VS recurrence. But SCG1 was increased only at early-phase. These data suggest that increased ABCA3 and KLF11 and decreased BASP1 and PRDX2 in CSF are associated with VS growth at the early phase or recurrence.

Hearing Response Following Internal Auditory Canal Decompression in Neurofibromatosis Type 2

BACKGROUND

Hearing response following an osteodural decompression of the internal auditory canal (IAC) is controversial.

OBJECTIVE

To evaluate the course of auditory brainstem responses (ABRs) and the early hearing response during the first year following IAC decompression for small to medium-sized vestibular schwannomas occurring in neurofibromatosis type 2 (NF2).

METHODS

Retrospective chart review of middle fossa craniotomy for IAC osteodural decompression in NF2-related vestibular schwannomas.

RESULTS

Twelve NF2 patients were operated on from 2011 to 2016 for IAC decompression. All had NF2 according to the Manchester criteria. All had a progressive change of their ABRs documented from the diagnosis of NF2 over a mean period of 6.25 [0.36;10.9] yr. Treatment was proposed to stop hearing progression based on the speech discrimination scores (SDSs; n = 4) or for hearing maintenance (n = 8). In patients with prior hearing progression, hearing responses were observed in 3 of the 4 patients during the first year. One patient kept on progressing. In the hearing maintenance group, the SDSs remained stable. SDSs improved from 85% [20-100] to 92.5% [60-100] on average (n = 12) and from 55% [20-80] to 77.5% [50-100] in the hearing progression group (n = 4). ABRs improved in 4 patients following decompression.

CONCLUSION

IAC decompression allows early objective hearing responses in select patients. We suggest that the procedure should be offered to patients with hearing progression based on their SDSs and/or associated progressive increases in their wave III and V latencies on ABRs.

Multiplex assay for multiomics advances in personalized-precision medicine

Building the future of precision medicine is the main focus in cancer domain. Clinical trials are moving toward an array of studies that are more adapted to precision medicine. In this domain, there is an enhanced need for biomarkers, monitoring devices, and data-analysis methods. Omics profiling using whole genome, epigenome, transcriptome, proteome, and metabolome can offer detailed information of the human body in an integrative manner. Omes profiles reflect more accurately real-time physiological status. Personalized omics analyses both disease as a whole and the main disease processes, for a better understanding of the individualized health. Through this, multi-omic approaches for health monitoring, preventative medicine, and personalized treatment can be targeted simultaneously and can lead clinicians to have a comprehensive view on the diseasome.