Tissue microarrays in the study of non-neoplastic disease of the nervous system

Preparation, construction and high-throughput automated analysis of human brain tissue microarrays for neurodegenerative disease drug development

A major challenge in the treatment of neurodegenerative disorders is the translation of effective therapies from the lab to the clinic. One approach to improve this process is the use of human brain tissue microarray (HBTMA) technology to aid in the discovery and validation of drug targets for brain disorders. In this protocol we describe a platform for the production of high-quality HBTMAs that can be used for drug target discovery and validation. We provide examples of the use of this platform and describe detailed protocols for HBTMA design, construction and use for both protein and mRNA detection. This platform requires less tissue and reagents than single-slide approaches, greatly increasing throughput and capacity, enabling samples to be compared in a more consistent way. It takes 4 d to construct a 60 core HBTMA. Immunohistochemistry and in situ hybridization take a further 2 d. Imaging of each HBTMA slide takes 15 min, with subsequent high-content analysis taking 30 min-2 h.

Tissue microarray (TMA) use in post mortem neuropathology

BACKGROUND

Tissue microarrays (TMAs), where each block (and thus section) contains multiple tissue cores from multiple blocks potentially allow more efficient use of tissue, reagents and time in neuropathology.

NEW METHOD

The relationship between data from TMA cores and whole sections was investigated using 'virtual' TMA cores. This involved quantitative assessments of microglial pathology in white matter lesions and motor neuron disease, alongside qualitative TDP-43 inclusion status in motor neuron disease cases. Following this, a protocol was developed for TMA construction.

RESULTS

For microglial pathology we found good concordance between virtual cores and whole sections for volume density using one 1.75 mm core (equivalent to a 2 mm core after accounting for peripheral tissue loss). More sophisticated microglial cell size and measures required two cores. Qualitative results of pTDP-43 pathology showed use of one 1.75 mm core gave a 100 % sensitivity and specificity within grey matter, and 88.3 % sensitivity and 100 % specificity within white matter. A method of producing the TMAs was suitable for immunohistochemistry both manually and by autostainer, with the minimal core loss from the microscope slide.

COMPARISON WITH EXISTING METHODS

TMAs have been used infrequently in post mortem neuropathology research. However, we believe TMAs give comparable tissue assessment results and can be constructed, sectioned and stained with relative ease.

CONCLUSIONS

We found TMAs could be used to assess both quantitative (microglial pathology) and qualitative pathology (TDP-43 proteinopathy) with greatly reduced quantities of tissue, time and reagents. These could be used for further work to improve data acquisition efficiency.

Making a Tissue Microarray

Tissue microarray (TMA) is a widely used, high-throughput, cost-effective, and tissue and reagent-conserving method of performing molecular analysis. Multiple donor tissue cores are procured and transferred into a recipient TMA block for simultaneous differential and comparative molecular profiling under theoretically identical performance conditions. Described herein is a discussion of the theory behind the TMA, an overview of the concepts and principles of TMA design and construction, a brief summary of its advantages and disadvantages, and a sample protocol of TMA construction.

Assessing fibrinogen extravasation into Alzheimer's disease brain using high-content screening of brain tissue microarrays

BACKGROUND

Tissue microarrays are commonly used to evaluate disease pathology however methods to automate and quantify pathological changes are limited.

NEW METHOD

This article demonstrates the utility of the VSlide scanner (MetaSystems) for automated image acquisition from immunolabelled tissue microarray slides, and subsequent automated image analysis with MetaXpress (Molecular Devices) software to obtain objective, efficient and reproducible data from immunolabelled tissue microarray sections.

RESULTS

Significant increases in fibrinogen immunolabelling were observed in 29 Alzheimer's disease cases compared to 28 control cases analysed from a single tissue microarray slide. Western blot analysis also demonstrated significant increases in fibrinogen immunolabelling in 6 Alzheimer's cases compared to 6 control cases. The observed changes were also validated with gold standard blinded manual H-scoring.

COMPARISON WITH EXISTING METHOD

VSlide Metafer software offers a 'tissue microarray acquisition' plugin for easy mapping of tissue cores with their original position on the tissue microarray map. High resolution VSlide images are compatible with MetaXpress image analysis software. This article details the coupling of these two technologies to accurately and reproducibly analyse immunolabelled tissue microarrays within minutes, compared to the gold standard method of manual counting using H-scores which is significantly slower and prone to inter-observer variation.

CONCLUSIONS

Here, we couple brain tissue microarray technology with high-content screening and automated image analysis as a powerful way to address bottle necks in data generation and improve throughput, as well as sensitivity to study biological/pathological changes in brain disease.

Tissue microarray construction for salivary gland tumors study

OBJECTIVE

To describe and discuss the design, building and usefulness of tissue microarray (TMA) blocks for the study of salivary gland tumors (SGTs).

STUDY DESIGN

Two hundred thirty-eight formalin-fixed, paraffin-embedded SGTs were arranged in blocks of TMA using a manual tissue arrayer. Three representative cores of 1.0, 2.0 or 3.0mm were taken from each original block and their characteristics were analyzed and described.

RESULTS

It was created 12 TMA blocks that presented highly representative neoplastic cylinders. However, those neoplasias rich in cystic spaces such as mucoepidermoid carcinoma and Warthin tumor presented more difficulties to be sampled, as the neoplastic tissue available was scarce. Tissue damage and loss during TMA construction was estimated as 3.7%.

CONCLUSION

Representative areas of SGTs, with relatively small loss of tissue, can be obtained with the construction of TMA blocks for molecular studies. However, tumors rich in cystic spaces present more difficulties to be adequately sampled.

Use of tissue microarray to facilitate oncology research

HPV-positive oropharyngeal squamous cell carcinomas (OSCC) represent a distinct disease entity from traditional OSCC. We hypothesized that for HPV DNA-positive cases, p16 expression status differentiates the biologically relevant ones.We determined HPV16DNA viral load in a cohort of 79 oropharyngeal squamous cell cancers by real-time polymerase chain reaction (PCR). We used cervical cancer as a disease model for HPV-initiated epithelial cancer. In cervical cancer, p53 and Rb expression is reduced, while p16 expression is increased. We used TMA technology to facilitate interrogation of this cohort for p53, Rb, and p16 protein expression using a quantitative, in situ method of protein analysis (AQUA analysis). Our results indeed delineate three biologically and clinically distinct types of oropharyngeal squamous cell cancers based on HPV-DNA determination and p16 expression status: one class of HPV-negative/p16-nonexpressing (HPV-negative), one class of HPV-positive/p16-nonexpressing (HPV-inactive), and one class of HPV positive/p16-expressing (HPV-active) oropharyngeal tumors. We demonstrated that only the HPV-active tumors share a similar molecular phenotype to cervical cancers, and are the ones associated with favorable prognosis.

Human postmortem brain tissue and 2-mm tissue microarrays

The authors constructed tissue microarray (TMA) blocks from human postmortem brain including numerous core samples measuring 2 mm in diameter from various anatomic regions. These TMA sections were then processed using various stainings and pretreatment techniques to evaluate their properties. The loss of core samples ranged from 2% to 100% and was significantly influenced by the type of glass slide used; it was lowest (2-8%) with SuperFrost Plus slides. The losses were not significantly altered when applying the most demanding pretreatment procedures or using human brain tissue with a long postmortem delay. A slight influence on the quality and the repeatability of some of the IHC stainings was seen by the postmortem delay, by the brain region, or by the glass slide used. One special feature of the constructed brain TMA block including many anatomic brain regions is that persons who lack skills in neuroanatomy can identify various brain structures simply by following the x-y coordinates. Thus, the applications of this brain TMA block in neurologic research by scientists with different skill bases remain to be determined.

Brief Report: S6 Ribosomal Protein Phosphorylation in Autistic Frontal Cortex and Cerebellum: a Tissue Array Analysis

Few autistic brain samples are available for study, limiting investigations into molecular and histopathological abnormalities associated with this common disease. To facilitate distribution of samples, we have constructed a tissue array containing cerebral and cerebellar cores from 5 autistic children, 1 girl with Rett syndrome, and 5 age-matched controls. To demonstrate the utility of this resource, we examined phosphorylation of the S6 ribosomal protein, a signaling event regulated by the genes mutated in tuberous sclerosis and Cowden disease. We hypothesized that the molecular pathways altered in these inherited conditions associated with autism might be dysregulated in sporadic autistic cases as well. However, no consistent alterations in S6 phosphorylation were detected in autistic tissues compared to controls in the brain regions analyzed.

Human brain tissue microarrays as a platform to investigate diseases of the nervous system

We constructed tissue microarray (TMA) blocks containing post-mortem human brain tissue from subjects with clinically and neuropathologically verified Alzheimer's disease (AD), corticobasal degeneration (CBD), progressive supranuclear palsy, Lewy body disease, multisystem atrophy (MSA) as well as an age matched control. Fifteen donor blocks were merged into two TMA blocks containing 72, 2-mm punch core samples with representative brain regions generally affected in degenerative disorders. Hyperphosphorylated-gamma, alpha-synuclein and beta-amyloid-related pathologies were estimated. The diseases were easily recognized by evaluating the two TMA sections and the results assessing TMA sections were comparable with the assessment of the whole brain sections. The assessment of TMA sections revealed concomitant multifocal alpha-synuclein pathology in AD, mild tau-involvement in the case of MSA and a slight AD-type pathology in the case of CBD. These findings emphasize the importance of searching for a variety of pathologies in "the whole brain" rather than restricting the examination to a few vulnerable regions. Furthermore, the TMA methodology clearly reduced the number of sections needed for evaluating the whole brain, it increased the amount of research material generated and furthermore no detailed neuroanatomical knowledge was required for assessment of data.

Brain deposition of beta-amyloid is a common pathologic feature in HIV positive patients

BACKGROUND

We planned to analyze the prevalence and distribution of beta-amyloid deposition in the HIV+ brain in the HAART era. Our working hypothesis is that long term survival, aging and the secondary effects of HAART may contribute to increased beta-amyloid accumulation in this patient population.

METHODS

Paraffin embedded archival brain autopsy tissues were assessed by immunocytochemistry for beta-amyloid. Detailed in-vivo neuro-behavioral assessments and ApoE genotyping were available for a subset of the studied population.

RESULTS

Immunoreactivity with the antibodies 4G8 and 6E10 was found predominantly in neuronal soma and dystrophic axonal processes. Extracellular, often perivascular plaques were also identified in many cases.

CONCLUSIONS

We propose that prolonged HAART and aging may contribute to an overall increase in amyloid deposition, potentially mediated by inhibition of insulin degradation enzyme (IDE) or disruption of the axonal transport of the amyloid precursor protein.

Insulin signaling pathways in cortical dysplasia and TSC-tubers: tissue microarray analysis

To evaluate the possible roles of the Akt/PKB-mTOR-p70S6K-S6 and cap-dependent translation (eIF4G) pathways in the pathogenesis of tuberous sclerosis complex (TSC)-associated cortical tubers and focal cortical dysplasia (FCD), we performed qualitative and semiquantitative immunohistochemical evaluation on surgically resected corticectomy specimens to detect phosphorylated molecules as activated downstream targets of the signaling pathways. A tissue microarray paraffin block was constructed from 63 archival specimens of surgically resected TSC tubers, FCDs with balloon cells, cortical dysplasia without balloon cells, and histologically normal-appearing neocortex obtained from cases with Rasmussen encephalitis, cystic-gliotic encephalopathy, and temporal lobe epilepsy. Abnormal neuroglial cells were positive for phospho-S6 and phospho-eIF4G with various staining intensities in FCDs and TSC tubers. Both proteins were much less abundantly expressed in normal-appearing neocortex. Phospho-mTOR expression was observed in neurons in all groups. The expression of phospho-S6 and phospho-eIF4G was associated with dysplastic lesions (p < 0.05), and the cytoplasmic phospho-p70S6K expression was most specific for and abundant in TSC tubers and much less prominent in other groups (p < 0.01). These results suggest that constitutive activation of cytoplasmic p70S6K plays a pivotal role in the pathogenesis of TSC tubers and that FCDs possess a distinct mechanism for activation of S6 and eIF4G.

Expression profiling by high-throughput immunohistochemistry

Immunohistochemistry (IHC) provides valuable information on expression of proteins within tissues at a cellular and subcellular level. Recent developments in the practice of IHC now make it possible to contemplate using this technique as a high-throughput expression profiling system. Advances have been made in creation and use of tissue microarrays, in automated IHC and in image capture/analysis. Each of these technologies are reviewed and issues surrounding their use considered. The success of high-throughput IHC is also dependent on both generation and screening of appropriate antibodies. Antibody-related issues which are likely to affect the success of high-throughput IHC, such as specificity, sensitivity, fixation choice, etc., are also considered.

Brain tissue microarrays in dementia research: white matter microvascular pathology in Alzheimer's disease

Tissue microarrays (TMA) consist of up to 1000 cylindrical tissue cores from different donor paraffin blocks relocated into one recipient block, allowing for efficient histopathological studies by fluorescence in situ hybridization, RNA in situ hybridization or immunohistochemistry. On the background of the increasing interest of the TMA technique in cancer research and the suggestion of its application also in studies of non-neoplastic intracranial disorders, the technique was applied to pathologic white matter in AD brains. Eight cases with AD and concomitant white matter pathology were neuropathologically diagnosed on whole brain coronal slides. The TMA technique was used to grade severity of white matter pathology and to quantify small vessels with traditional staining and immunohistochemical markers. These measurements were compared with the whole brain neuropathological assessment. The technique produced good results with preserved tissue structures as confirmed by the whole brain evaluation. Severity of white matter pathology evaluated on the TMA cores correlated negatively with small vessel quantities, and statistically significant differences in vessel quantities paralleled different grades of white matter pathology. It is concluded that the TMA technique could be further utilized in studies of dementing disorders, and may have its advantages in large, clinically well-characterized materials (e.g. in quantitative mapping of white matter changes).

A novel frozen brain tissue array technique: immunohistochemical detection of neuronal paraneoplastic autoantibodies

We introduce a modification of the tissue microarray technique in which several frozen brain tissue specimens are collected to a single frozen brain array block. In the present application, we use it for the detection of neuronal paraneoplastic anti-Hu autoantibodies. Representative samples from 15 different brain regions were collected according to a standard neuropathological autopsy protocol. Cryostat sections from each block were cut and conventionally stained. From representative areas, cylinder tissue samples from each specimen were punched and then arrayed into a recipient array block. Using the cryostat sections of this brain array, autoantibodies from seven anti-Hu-positive patient sera (confirmed by immunoblotting) were screened by immunohistochemistry. Neuronal architecture was well preserved and immunohistochemical staining was comparable to that of conventional cryostat sections. Because of the variable staining pattern in different brain areas, two anti-Hu-positive sera could be detected immunohistochemically by the one brain array. With the present array technique, it is possible to characterize the variable staining patterns of neuronal paraneoplastic autoantibodies in different locations of the human brain. The frozen brain array also allows the detection of RNA and DNA targets involved in neurological diseases.

Brain banking in the United States

Many of us who conduct research based on disorders that uniquely affect the human nervous system are involved directly or indirectly with brain banks. Brain banking is by its very nature a multi-disciplinary endeavor that requires close collaboration with our colleagues in clinical departments and also with the families and patients who are donors of brain tissue. These brain tissues will ultimately be used for many types of basic science investigations. Thus, many brain banks are as unique as the basic research programs that they serve. However, there are some commonalities in the field of brain banking. This paper represents a broad overview of brain banking and the issues that are common to all brain banks. Legal and ethical concerns regarding confidentiality of donor records and donor recruitment procedures, as well as safety precautions for technical staff, tissue banking methods and disbursement will be discussed. Finally, issues surrounding financial support for brain banks will be considered.

Biochemical and molecular studies using human autopsy brain tissue

The use of human brain tissue obtained at autopsy for neurochemical, pharmacological and physiological analyses is reviewed. RNA and protein samples have been found suitable for expression profiling by techniques that include RT-PCR, cDNA microarrays, western blotting, immunohistochemistry and proteomics. The rapid development of molecular biological techniques has increased the impetus for this work to be applied to studies of brain disease. It has been shown that most nucleic acids and proteins are reasonably stable post-mortem. However, their abundance and integrity can exhibit marked intra- and intercase variability, making comparisons between case-groups difficult. Variability can reveal important functional and biochemical information. The correct interpretation of neurochemical data must take into account such factors as age, gender, ethnicity, medicative history, immediate ante-mortem status, agonal state and post-mortem and post-autopsy intervals. Here we consider issues associated with the sampling of DNA, RNA and proteins using human autopsy brain tissue in relation to various ante- and post-mortem factors. We conclude that valid and practical measures of a variety of parameters may be made in human brain tissue, provided that specific factors are controlled.