DNA microarray gene expression analysis of a vocal fold polyp and granuloma

Microarray-based characterization of differential gene expression during vocal fold wound healing in rats

The vocal fold (VF) mucosa confers elegant biomechanical function for voice production but is susceptible to scar formation following injury. Current understanding of VF wound healing is hindered by a paucity of data and is therefore often generalized from research conducted in skin and other mucosal systems. Here, using a previously validated rat injury model, expression microarray technology and an empirical Bayes analysis approach, we generated a VF-specific transcriptome dataset to better capture the system-level complexity of wound healing in this specialized tissue. We measured differential gene expression at 3, 14 and 60 days post-injury compared to experimentally naïve controls, pursued functional enrichment analyses to refine and add greater biological definition to the previously proposed temporal phases of VF wound healing, and validated the expression and localization of a subset of previously unidentified repair- and regeneration-related genes at the protein level. Our microarray dataset is a resource for the wider research community and has the potential to stimulate new hypotheses and avenues of investigation, improve biological and mechanistic insight, and accelerate the identification of novel therapeutic targets.

Assessment of fine needle aspiration feasibility and specimen adequacy for molecular diagnostics of benign vocal fold lesions

OBJECTIVES/ HYPOTHESIS

The use of molecular testing is becoming more significant for the diagnosis and classification of disease. The application of fine-needle aspiration (FNA) biopsy as the means of sampling lesions in union with molecular testing could be a powerful combination in laryngology. The objectives of this study were to investigate 1) if FNA was feasible to sample benign vocal fold lesions; 2) if FNA samples provided sufficient RNA quality for molecular analysis; and 3) if gene expression of FNA samples matched paired surgical excised specimens.

STUDY DESIGN

Prospective cross-sectional.

METHODS

Fifteen vocal fold specimens were obtained from adult patients undergoing routine surgical removal for benign vocal fold lesions using FNA and surgical excision. Comparisons were made between FNA and excision biopsies for RNA quality. Correlative analysis was completed for RNA expression of nine genes, including decorin (DCN), connective tissue growth factor (CTGF), vascular endothelial growth factor (VEGF), collagen type VI alpha 3 (COL6A3), superoxide dismutase 1 (SOD1), glutathione S-transferase (GST2), collagen type I alpha 2 (COL1A2), ATP binding cassette (ABC), and procollagen I alpha 1 (COL1A1).

RESULTS

FNA and excision samples demonstrated similar RNA quality (P > 0.05). Per gene expression, four out of nine genes were moderately correlated between the paired samples (P < 0.05).

CONCLUSIONS

FNA of the vocal fold lamina propria is technically feasible to perform. Further improvement in the FNA technology is desirable to optimize RNA quality for reliable gene expression analysis.

Fundamental approaches in molecular biology for communication sciences and disorders

PURPOSE

This contemporary tutorial will introduce general principles of molecular biology, common deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein assays and their relevance in the field of communication sciences and disorders.

METHOD

Over the past 2 decades, knowledge of the molecular pathophysiology of human disease has increased at a remarkable pace. Most of this progress can be attributed to concomitant advances in basic molecular biology and, specifically, the development of an ever-expanding armamentarium of technologies for analysis of DNA, RNA, and protein structure and function. Details of these methodologies, their limitations, and examples from the communication sciences and disorders literature are presented. Results/Conclusions The use of molecular biology techniques in the fields of speech, language, and hearing sciences is increasing, facilitating the need for an understanding of molecular biology fundamentals and common experimental assays.

Genetic and environmental effects on vocal symptoms and their intercorrelations

PURPOSE

Recently, Simberg et al. (2009) found genetic effects on a composite variable consisting of 6 vocal symptom items measuring dysphonia. The purpose of the present study was to determine genetic and environmental effects on the individual vocal symptoms in a population-based sample of Finnish twins.

METHOD

The sample comprised 1,728 twins (125 monozygotic and 108 dizygotic twin pairs) born between 1961 and 1989, who completed a questionnaire concerning 6 vocal symptoms. Values for additive genetic, dominant genetic, shared environmental, and nonshared environmental components were computed separately for all symptoms. Multivariate analyses to determine genetic and environmental associations between the vocal symptoms were also performed.

RESULTS

Variance was explained by significant additive genetic effects (27%) in only one of the vocal symptoms, namely, voice gets low or hoarse, whereas the variance of one of the vocal symptoms, voice gets strained or tires, could be explained by nonshared environmental influence alone. Multivariate analyses showed that the correlations for most of the symptom combinations were significant.

CONCLUSIONS

Both genetic and environmental components influence vocal symptoms. Genetic and environmental influences seem to be differently balanced in different vocal symptoms. Genetic effects are moderate, whereas environmental effects seem to be the most important factor contributing to the presence of vocal symptoms.

Cross-sample validation provides enhanced proteome coverage in rat vocal fold mucosa

The vocal fold mucosa is a biomechanically unique tissue comprised of a densely cellular epithelium, superficial to an extracellular matrix (ECM)-rich lamina propria. Such ECM-rich tissues are challenging to analyze using proteomic assays, primarily due to extensive crosslinking and glycosylation of the majority of high M_r ECM proteins. In this study, we implemented an LC-MS/MS-based strategy to characterize the rat vocal fold mucosa proteome. Our sample preparation protocol successfully solubilized both proteins and certain high M_r glycoconjugates and resulted in the identification of hundreds of mucosal proteins. A straightforward approach to the treatment of protein identifications attributed to single peptide hits allowed the retention of potentially important low abundance identifications (validated by a cross-sample match and de novo interpretation of relevant spectra) while still eliminating potentially spurious identifications (global single peptide hits with no cross-sample match). The resulting vocal fold mucosa proteome was characterized by a wide range of cellular and extracellular proteins spanning 12 functional categories.

Translational systems biology and voice pathophysiology

OBJECTIVES/HYPOTHESIS

Personalized medicine has been called upon to tailor healthcare to an individual's needs. Evidence-based medicine (EBM) has advocated using randomized clinical trials with large populations to evaluate treatment effects. However, due to large variations across patients, the results are likely not to apply to an individual patient. We suggest that a complementary, systems biology approach using computational modeling may help tackle biological complexity in order to improve ultimate patient care. The purpose of the article is: 1) to review the pros and cons of EBM, and 2) to discuss the alternative systems biology method and present its utility in clinical voice research.

STUDY DESIGN

Tutorial.

METHODS

Literature review and discussion.

RESULTS

We propose that translational systems biology can address many of the limitations of EBM pertinent to voice and other health care domains, and thus complement current health research models. In particular, recent work using mathematical modeling suggests that systems biology has the ability to quantify the highly complex biologic processes underlying voice pathophysiology. Recent data support the premise that this approach can be applied specifically in the case of phonotrauma and surgically induced vocal fold trauma, and may have particular power to address personalized medicine.

CONCLUSIONS

We propose that evidence around vocal health and disease be expanded beyond a population-based method to consider more fully issues of complexity and systems interactions, especially in implementing personalized medicine in voice care and beyond.

Exploring genetic and environmental effects in dysphonia: a twin study

PURPOSE

To explore the existence of genetic effects as well as the interaction between potential genetic effects and a voice-demanding occupation on dysphonia.

METHOD

One thousand seven hundred and twenty-eight Finnish twins (555 male; 1,173 female) born between 1961 and 1989 completed a questionnaire concerning vocal symptoms and occupation. The zygosity determination resulted in 125 monozygotic and 108 dizygotic full twin pairs. A composite variable called dysphonia was formed by summing 6 vocal symptoms based on the results of a factor analysis. Twin model fitting was used to explore the contribution of genetic and environmental effects on the dysphonia variable.

RESULTS

Individual differences in dysphonia were explained by genetic effects (35%) and nonshared environmental effects (65%). Shared environmental effects were estimated at 0%. Also, the authors found that for the participants who worked in voice-demanding occupations, the causes of dysphonia were more environmental, whereas the etiology of the symptoms was more strongly affected by genes in the participants with less voice-demanding occupations. However, this gene-environment interaction was not statistically significant.

CONCLUSION

Both genetic and environmental factors have an impact on the etiology of voice problems. Environmental factors, either independently or interacting with genetic factors, seem to play the key role, especially if the person has a voice-demanding occupation.

Differential gene expression profiling of vocal fold polyps and Reinke's edema by complementary DNA microarray

OBJECTIVES

Our purpose was to determine whether complementary DNA (cDNA) microarray analysis (MA) can establish distinct gene expression profiles for 2 phenotypically similar vocal fold lesions: Reinke's edema (RE) and polyps. Established transcript profiles can provide insight into the molecular and cellular processes involved in these diseases.

METHODS

Eleven RE specimens and 17 polyps were analyzed with MA for 8,745 genes. Further MA profiling was attempted within each lesion group to identify molecular markers for reflux exposure and smoking. Prediction analysis was used to predict lesion classification for 2 unclassified samples. A real-time polymerase chain reaction was performed to corroborate MA transcript levels for selected significant genes.

RESULTS

Sixty-five genes were found to differentiate RE and polyps (p = .0088). For RE, 19 genes were differentiated for reflux exposure (p = .016). No genes were found to differentiate smokers from nonsmokers. For polyps, no genes were found to differentiate for reflux (p = .16) and smoking (p = .565). Categorization of unclassified lesions was possible with a minimum of 13 genes.

CONCLUSIONS

We demonstrate the feasibility of benign lesion classification based on MA. Microarray analysis is useful not only for improving diagnosis and classification of such lesions, but also for potentially generating prognostic indicators and targets for therapy.

Fine needle aspiration: a novel application in laryngology

Fine needle aspiration (FNA) has had an early start in medicine and has been heavily used in the United States since the 1980s. It is regarded as a highly effective means to sample mass lesions, serving as the first diagnostic procedure in many instances. FNA is safe, less invasive than biopsy, and reduces the risk of scar formation. Its main limitations can be overcome through effective training and practiced technique. In laryngology, the development of new and diversified therapeutic and diagnostic strategies depends on the development of equally appropriate diagnostic tools. FNA has the potential to be a relatively easy procedure that can be performed under local anesthesia, increasing the otolaryngologist's armamentarium. Combining the FNA procedure with technology now available, secondary to advances in genomic science, rather than cytology and H&E stains, provides the means of obtaining clinically useful information about benign and malignant disease for clinicians and researchers. This paper provides a review of the traditional FNA procedure. It offers an introduction to the future applicability of FNA to office-based laryngology. Lastly, this paper familiarizes the reader with the genomic principles being used for this procedure.

Advances in our understanding of the Reinke space

PURPOSE OF REVIEW

Normal vocal fold vibration depends critically upon the composition of the Reinke space or the lamina propria extracellular matrix. Alterations in the normal composition of the extracellular matrix result in a loss of normal vibratory function. In this article, the present literature on the Reinke space in normal and disease states is reviewed including publications in the multidisciplinary fields of biomechanics, histology, molecular biology, and tissue engineering.

RECENT FINDINGS

With recent technology advances, the etiology for benign lesions has been investigated with computer models and bioreactors. Particular extracellular matrix constituents in various benign vocal fold lesions--fibronectin, fibromodulin and hyaluronan--appear to be involved in altering the viscoelastic properties of the Reinke space. Significant basic science approaches to the investigation of the characterization of the Reinke space in vocal fold scarring has produced several potential future treatment avenues. Tissue-engineering approaches for regeneration of the Reinke space are the most recent addition to the literature showing promising research directions.

SUMMARY

Voice disorders represent a significant clinical problem. Research attempting to discover the underlying molecular and genetic regulation and homeostasis of the extracellular matrix of the Reinke space are essential. Effective future clinical interventions must be based upon the knowledge of how genetic and biologic features are disturbed in vocal diseases and how they relate to vocal symptoms.