Amplification of mitochondrial DNA from archival temporal bone specimens

Detection of mitochondrial DNA deletions in the cochlea and its structural elements from archival human temporal bone tissue

Large-scale deletions of mitochondrial DNA (mtDNA) have been associated with aging and disease in post-mitotic tissues. These post-mitotic tissues, including skeletal muscle, heart and brain, are heavily dependent on intact functional mitochondria. The cochlear tissues are known to contain an abundance of mitochondria. This observation stimulated a search for mtDNA deletions in the cochlea and its elements using a sensitive nested PCR methodology and long range PCR to explain the functional deficits observed in age-related hearing loss. The presence of the so-called "common" deletion (CD) was detected in cochlear tissue from two individuals with age-related hearing loss, 73 and 78 years of age. Three additional deletions, that to our knowledge have not been previously reported, were also identified in these two individuals, including a 5354 bp deletion flanked with a 3 bp repeat, a 9682 bp deletion flanked by a 10 bp repeat and a 5142 bp deletion without a flanking repeat. The 9682 and 5142 bp deletions were also detected in an individual 39 years of age with normal hearing, however, these two deletions were not detected in a normal hearing individual 9 years of age. In contrast, the 5354 bp deletion was detected in all four of the individuals studied. To localize the deletions within the cochlea, the cochlear elements were removed by laser capture microdissection (LCM) and the mtDNA from these tissues was studied. The 5142 and 5354 bp deletions were detected in the organ of corti, spiral ligament, and ganglion cells, but not in the stria vascularis. These findings correlate with the reduction in the number of spiral ganglion cells and outer hair cells, and the normal stria vascularis volume observed in this individual. All four of these deletions involve the cytochrome c oxidase (COX) subunit III gene, encoded by mtDNA. These observations suggest that multiple mtDNA deletions may contribute to a deficit in mitochondrial function in the cochlea and result in hearing loss if a level of physiological significance is reached.

Polyester wax: a new embedding medium for the histopathologic study of human temporal bones

BACKGROUND

Celloidin and paraffin are the two common embedding mediums used for histopathologic study of the human temporal bone by light microscopy. Although celloidin embedding permits excellent morphologic assessment, celloidin is difficult to remove, and there are significant restrictions on success with immunostaining. Embedding in paraffin allows immunostaining to be performed, but preservation of cellular detail within the membranous labyrinth is relatively poor.

OBJECTIVES/HYPOTHESIS

Polyester wax is an embedding medium that has a low melting point (37 degrees C), is soluble in most organic solvents, is water tolerant, and sections easily. We hypothesized that embedding in polyester wax would permit good preservation of the morphology of the membranous labyrinth and, at the same time, allow the study of proteins by immunostaining.

METHODS

Nine temporal bones from individuals aged 1 to 94 years removed 2 to 31 hours postmortem, from subjects who had no history of otologic disease, were used. The bones were fixed using 10% formalin, decalcified using EDTA, embedded in polyester wax, and serially sectioned at a thickness of 8 to 12 mum on a rotary microtome. The block and knife were cooled with frozen CO2 (dry ice) held in a funnel above the block. Sections were placed on glass slides coated with a solution of 1% fish gelatin and 1% bovine albumin, followed by staining of selected sections with hematoxylin and eosin (H&E). Immunostaining was also performed on selected sections using antibodies to 200 kD neurofilament and Na-K-ATPase.

RESULTS

Polyester wax-embedded sections demonstrated good preservation of cellular detail of the organ of Corti and other structures of the membranous labyrinth, as well as the surrounding otic capsule. The protocol described in this paper was reliable and consistently yielded sections of good quality. Immunostaining was successful with both antibodies.

CONCLUSION

The use of polyester wax as an embedding medium for human temporal bones offers the advantage of good preservation of morphology and ease of immunostaining. We anticipate that in the future, polyester wax embedding will also permit other molecular biologic assays on temporal bone sections such as the retrieval of nucleic acids and the study of proteins using mass spectrometry-based proteomic analysis.

Detection of mitochondrial DNA from human inner ear using real-time polymerase chain reaction and laser microdissection

CONCLUSIONS

In this study we were able to amplify and analyze extremely small amounts of template DNA from only a few individually dissected cells. We anticipate that this approach will facilitate the detection and analysis of mitochondrial (mt) DNA mutations in specific cell types in the inner ear, which should shed new light on genetic disorders leading to hearing loss.

OBJECTIVE

To isolate mtDNA from selected tissues in the inner ear. Although several methods for extracting DNA from formalin-fixed, celloidin-embedded, archival human temporal bones have been reported, the isolation of DNA from the inner ear by means of laser microdissection has not been previously demonstrated.

MATERIAL AND METHODS

This was a retrospective study. Temporal bones were obtained from subjects with no known otological history at autopsy. The combined method of laser microdissection and real-time polymerase chain reaction was used to isolate mtDNA from selected tissues in the inner ear.

RESULTS

mtDNA could be isolated from the stria vascularis, spiral ligament, spiral ganglion cells and organ of Corti.

Correlation of cochlear blood supply with mitochondrial DNA common deletion in presbyacusis

OBJECTIVE

To study the relationships between cochlear hypoxia, mitochondrial (mt) DNA4977 deletion and metabolic features of mtDNA in presbyacusis.

MATERIAL AND METHODS

Sixty-seven temporal bones from a presbyacusis group, an age-matched control group and a young and middle-aged control group were involved in the experiment. Nested and tri-nested polymerase chain reactions (PCRs) were applied to test for the presence of the mtDNA4977 deletion. Computer imaging processing was used to measure blood vessel parameters in the internal acoustic meatus (IAM).

RESULTS

The mtDNA4977 deletion was detected in 17/34 ears in the presbyacusis group, 4/19 ears in the age-matched control group and 0/14 ears in the young and middle-aged control group. In the presbyacusis group, the lumen of the vasa nervorum of the IAM showed a more severe narrowing in cases with than without the mtDNA4977 deletion.

CONCLUSION

The high incidence of the mtDNA4977 deletion in the temporal bones of presbyacusis patients suggests a correlation between the mtDNA4977 deletion and presbyacusis. Hypoxia of the cochlea may cause the mtDNA4977 deletion and other mtDNA mutants and furthermore may cause a reduction in mitochondrial oxidative phosphorylation and decreased function of the acoustic neural system. The symptoms of presbyacusis may occur when the function of the acoustic neural system is impaired as a result of abnormal mtDNA metabolism reaching a particular threshold.

Deoxyribonucleic acid contamination in archival human temporal bones: a potentially significant problem

HYPOTHESIS

Contamination of archival human temporal bones with extraneous deoxyribonucleic acid may represent a potentially significant problem in the analysis of nucleic acids isolated from archival specimens.

BACKGROUND

During the past decade, there has been growing interest in the development of molecular biologic techniques that can be applied to the investigation of pathologic changes in archival human temporal bones. The impetus for the development of these techniques is in part related to the fact that the temporal bone collections represent a repository of archival material compiled over decades, which is not available from living patients.

METHODS

An archival human temporal bone specimen from a male patient with the Mohr-Tranebjaerg syndrome (formerly called DFN-1) and a well-characterized mutation was analyzed for the presence of the mutation by a standard method for extraction, isolation, amplification, and sequencing of deoxyribonucleic acid. The experiment was repeated four times.

RESULTS

The deoxyribonucleic acid sequence from three of four extractions was normal. The known mutation was easily and repeatedly demonstrated in a blood sample from the same individual. Because Mohr-Tranebjaerg syndrome is X-linked, there is only one allele, and therefore there is no potential endogenous source to account for the normal sequence that was amplified. Contamination of the tissue sections by extraneous deoxyribonucleic acid presumably occurred during acquisition and processing of the temporal bone.

CONCLUSIONS

Contamination of archival temporal bones with exogenous deoxyribonucleic acid is a significant potential problem that must be considered in the interpretation of the results of deoxyribonucleic acid retrieved from archival sections. The authors recommend collecting blood samples from temporal bone donors in the future to ensure the availability of a reliable source of deoxyribonucleic acid.

Temporal bone histopathology in connexin 26-related hearing loss

OBJECTIVE

Mutations in GJB2, a gene that encodes a gap junction protein, Connexin 26 (Cx26), are responsible for approximately one third of sporadic severe-to-profound or profound congenital deafness and half of severe-to-profound or profound autosomal recessive nonsyndromic hearing loss (ARNSHL). Mouse mutants homozygous for knockouts of this gene are nonviable, precluding histopathologic studies of the associated inner ear pathology in this animal model. Therefore, we studied archival temporal bone sections to identify temporal bone donors with Cx26-related deafness.

STUDY DESIGN

Temporal bone donors with a history of congenital severe-to-profound or profound deafness were identified in the registry of the Temporal Bone Library at the University of Iowa. Histological findings were interpreted in a blinded fashion. DNA extracted from two celloidin-embedded mid-modiolar sections from each temporal bone was screened for the 35delG Cx26 mutation. The entire coding region of Cx26 was screened for other deafness-causing mutations if the 35delG mutation was detected.

RESULTS

Of five temporal bone donors with congenital severe-to-profound deafness, one donor was found to have Cx26-related deafness. This individual was a Cx26 compound heterozygote, carrying the 35delG mutation and a noncomplementary Cx26 missense mutation on the opposing allele. Microscopic evaluation of this temporal bone showed no neural degeneration, a good population of spiral ganglion cells, near-total degeneration of hair cells in the organ of Corti, a detached and rolled-up tectorial membrane, agenesis of the stria vascularis, and a large cyst in the scala media in the region of the stria vascularis.

CONCLUSION

This study is the first to report the temporal bone histopathology associated with Cx26-related deafness. Preservation of neurons in the spiral ganglion suggests that long-term successful habilitation with cochlear implants may be possible in persons with severe-to-profound or profound Cx26-related deafness.

Amplification of RNA from archival human temporal bone sections

BACKGROUND

The amplification of DNA from celloidin-embedded human temporal bone sections by polymerase chain reaction (PCR) has been applied to some auditory diseases, such as herpes zoster oticus and hearing loss caused by the mutations of mitochondrial DNA. However, few studies have reported detection of RNA from temporal bone sections.

OBJECTIVES

Because RNA analysis from temporal bone sections may elucidate the development of the diseases in the auditory, vestibular, and facial nerves, the authors investigated whether RNA in these sections can be amplified by reverse transcription (RT)-PCR.

METHODS

Sections that were formalin-fixed, decalcified, and embedded between 1972 and 1986 were used. Nucleic acid was extracted from the celloidin-embedded temporal bone sections and subjected to RT-PCR. Human alpha-tubulin RNA was reverse transcribed to cDNA and amplified by nested PCR using two sets of primers that were designed to distinguish cDNA from genomic DNA based on the presence of an intron between the primers.

RESULTS

Human alpha-tubulin RNA was detected in 11 of 14 temporal bone sections (79%) by RT-PCR. RNA was detected in even the oldest sections, which were processed in 1972.

CONCLUSIONS

These results indicate that RNA can be analyzed from archival celloidin-embedded human temporal bone sections.

Molecular temporal bone pathology: IV. Analysis of DNA template length using mitochondrial PCR primers

The focus of this study was to identify, via molecular biology techniques, the length of the DNA templates present in individual archival celloidin-embedded human temporal bone sections. Earlier studies have suggested that the maximum template length present in these tissues is on the order of 471 base pair (bp). Polymerase chain reaction (PCR) amplification of 92 bp, 121 bp, 471 bp, and 609 bp regions of mitochondrial DNA (mtDNA), extracted from single archival celloidin-embedded human temporal bone sections, was used to assess the length of the template DNA extracted. These data are crucial to determine the limits of applying PCR technology to amplify specific genomic DNA targets located within the human inner ear. The results described should be of value to those investigators extracting DNA from archival individual human temporal bone sections for polymerase chain reaction assays of specific genetic alterations or infectious agents associated with temporal bone pathologies.

Molecular temporal bone pathology: I. Historical foundation

The application of molecular biology techniques to temporal bone research is resulting in rapid changes in our understanding of the fundamental mechanisms of auditory, facial nerve, and vestibular function. The use of the polymerase chain reaction, cDNA libraries, and in situ hybridization histochemistry, the determination of genetic defects, and the manipulation of transgenic animals are the molecular biology tools that are available to approach these research problems. Knowledge of the molecular pathology that results in the otologic and neuro-otologic dysfunction many of our patients experience is currently in its infancy. A review of the historical foundation of temporal bone pathology and the evolution of the application of cell and molecular biology methods to archival celloidin-embedded human temporal bone material is presented.

Temporal bone analysis of patients with presbycusis reveals high frequency of mitochondrial mutations

Presbycusis is a histologically and genetically heterogenous group of disorders, which lead to progressive, primarily sensorineural hearing loss with aging. Acquired mitochondrial DNA defects have been proposed as important determinants of aging, particularly in neuro-muscular tissues. The spiral ganglion and membranous labyrinth from archival temporal bones of 5 patients with presbycusis were examined for mutations within the mitochondrially-encoded cytochrome oxidase II gene. When compared to controls, results indicate that mitochondrial mutations in the peripheral auditory system occur commonly with age-related hearing loss, that there is great individual variability in both quantity and location of mutation accumulation, and that at least a proportion of presbycusis patients have a highly significant load of mutations in auditory tissue. This work supports the hypothesis that acquired mitochondrial mutations are a determinant of hearing loss in a subgroup of presbycusis patients.

Association of mitochondrial DNA deletions and cochlear pathology: a molecular biologic tool

The purpose of these experiments was to develop a method of isolation, amplification, and identification of cochlear mitochondrial DNA (mtDNA) from minute quantities of tissue. Additionally, studies were designed to detect mtDNA deletions (mtDNA del) from the cochlea that previously have been amplified from other organ systems and tissues. MtDNA del have been associated with many pathologies, including neurological disorders, sensorineural hearing loss, ischemia, cardiomyopathies, and aging. DNA was extracted from rat and human tissues, and polymerase chain reaction was used to amplify mtDNA sequences. A 360 base pair (bp) cytochrome-b gene product and the highly conserved ND1-16S ribosomal ribonucleic acid regions found only in mtDNA were amplified from all tissues. Preliminary studies have identified a 4834 bp mtDNA del in aged rats and a corresponding 4977 bp mtDNA del in aged humans. Additionally, preliminary results in human archival temporal bone studies reveal the presence of the 4977-bp mtDNA deletion in two out of three patients with presbycusis. The deletion was not evident in age-matched control patients without a history of presbycusis. This technique of mtDNA identification makes it possible to investigate specific mtDNA defects from a single cochlea, promoting the study of hereditary hearing loss and presbycusis at a molecular biologic level.