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Semi-Quantitative Determination of Dopaminergic Neuron Density in the Substantia Nigra of Rodent Models using Automated Image Analysis

Published: February 2nd, 2021



1Krembil Research Institute, Toronto Western Hospital, University Health Network, 2Department of Laboratory Medicine and Pathobiology, University of Toronto, 3Department of Surgery, Division of Neurosurgery, University of Toronto, 4Department of Medicine, Division of Neurology, University of Toronto, 5Department of Medicine, Division of Neurology, Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, University Health Network, 6Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto

Here we present an automated method for semi-quantitative determination of dopaminergic neuron number in the rat substantia nigra pars compacta.

Estimation of the number of dopaminergic neurons in the substantia nigra is a key method in pre-clinical Parkinson's disease research. Currently, unbiased stereological counting is the standard for quantification of these cells, but it remains a laborious and time-consuming process, which may not be feasible for all projects. Here, we describe the use of an image analysis platform, which can accurately estimate the quantity of labeled cells in a pre-defined region of interest. We describe a step-by-step protocol for this method of analysis in rat brain and demonstrate it can identify a significant reduction in tyrosine hydroxylase positive neurons due to expression of mutant α-synuclein in the substantia nigra. We validated this methodology by comparing with results obtained by unbiased stereology. Taken together, this method provides a time-efficient and accurate process for detecting changes in dopaminergic neuron number, and thus is suitable for efficient determination of the effect of interventions on cell survival.

Parkinson's disease (PD) is a prevalent neurodegenerative movement disorder characterized by the presence of protein aggregates containing α-synuclein (α-syn) and the preferential loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc)1. Quantification of dopaminergic neuron number is a vital part of PD research as it permits the evaluation of the integrity of the nigrostriatal system, thus, providing an important endpoint to assess the effectiveness of potential disease-modifying therapeutics. Currently, the standard for quantification of cell number is unbiased stereological counting, which utilizes two-di....

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All procedures were approved by the University Health Network Animal Care Committee and performed in accordance with guidelines and regulations set by the Canadian Council on Animal Care.

1. Stereotactic injection

  1. Pair-house adult female Sprague-Dawley rats (250-280 g) in cages with wood bedding and ad lib access to food and water. Maintain the animal colony in a regular 12 h light/dark cycle (lights on 06:30) with constant temperature and humidity.
  2. Perform unilateral ste.......

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By applying the above methods to brain tissue collected 6 weeks after AAV injections, we demonstrated that stereotactic injection of AAV expressing mutant A53T α-syn (AAV-A53T) in the SNpc of rat brain results in a significant reduction in the density of dopaminergic neurons compared to injection of empty vector AAV (AAV-EV) as a control (Figure 5A,B). The mean number of TH-positive neurons/mm2 in the SNpc of rats injected with AAV-EV was 276.2 ± 34.7, a.......

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The reliable assessment of the integrity of the dopaminergic system in pre-clinical models of PD is critical to determine the effectiveness of potential disease-modifying therapeutics. Therefore, it is important to control and minimize potential confounds that may reduce the reliability and reproducibility of histopathological data. Careful quantitative outcomes can provide more information than qualitative or semi-quantitative descriptions alone. At the same time, we must recognize that constraints in time and resources.......

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The authors would like to thank all the staff at the Advanced Optical Microscopy Facility (AOMF) at University Health Network for their time and assistance in developing this protocol.


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Name Company Catalog Number Comments
A-Syn Antibody ThermoFisher Scientific 32-8100
ABC Elite Vector Labs PK-6102
Alexa Fluor 488 secondary antibody ThermoFisher Scientific A-11008
Alexa Fluor 555 secondary antibody ThermoFisher Scientific A-28180
Alkaline phosphatase-conjugated anti-rabbit igG Jackson Immuno 111-055-144
Biotinylated anti-mouse IgG Vector Labs BA-9200
Bovine Serum Albumin Sigma A2153
DAKO fluorescent mouting medium Agilent S3023
HALO™ Indica Labs
Histo-Clear II Diamed HS202
ImmPACT DAB Peroxidase substrate Vector Labs SK-4105
LSM880 Confocal Microscope Zeiss
NeuN Antibody Millipore MAB377
Normal Goat Serum Vector Labs S-1000-20
OCT Tissue-Tek
Paraformaldehyde BioShop PAR070.1
Sliding microtome Leica SM2010 R
Stereo Investigator MBF Bioscience
Sucrose BioShop SUC700
TH Antibody ThermoFisher Scientific P21962
VectaMount mounting medium Vector Labs H-5000
Vector Blue Alkaline Phosphatase substrate Vector Labs SK-5300
Zen Black Software Zeiss
Zen Blue Software Zeiss

  1. Kalia, L. V., Lang, A. E. Parkinson's disease. Lancet. 386 (9996), 896-912 (2015).
  2. West, M. J., Slomianka, L., Gundersen, H. J. Unbiased stereological estimation of the total number of neurons in thesubdivisions of the rat hippocampus using the optical fractionator. The Anatomical Record. 231 (4), 482-497 (1991).
  3. Nair-Roberts, R. G., et al. Stereological estimates of dopaminergic, GABAergic and glutamatergic neurons in the ventral tegmental area, substantia nigra and retrorubral field in the rat. Neuroscience. 152 (4), 1024-1031 (2008).
  4. Golub, V. M., et al. Neurostereology protocol for unbiased quantification of neuronal injury and neurodegeneration. Frontiers in Aging Neuroscience. 7, 196 (2015).
  5. Schmitz, C., Hof, P. R. Design-based stereology in neuroscience. Neuroscience. 130 (4), 813-831 (2005).
  6. Penttinen, A. M., et al. Implementation of deep neural networks to count dopamine neurons in substantia nigra. European Journal of Neuroscience. 48 (6), 2354-2361 (2018).
  7. Yousef, A., et al. Neuron loss and degeneration in the progression of TDP-43 in frontotemporal lobar degeneration. Acta Neuropathologica Communications. 5 (1), 68 (2017).
  8. Koprich, J. B., et al. Expression of human A53T alpha-synuclein in the rat substantia nigra using a novel AAV1/2 vector produces a rapidly evolving pathology with protein aggregation, dystrophic neurite architecture and nigrostriatal degeneration with potential to model the pathology of Parkinson's disease. Molecular Neurodegeneration. 5, 43 (2010).
  9. Koprich, J. B., et al. Progressive neurodegeneration or endogenous compensation in an animal model of Parkinson's disease produced by decreasing doses of alpha-synuclein. PLoS One. 6 (3), 17698 (2011).
  10. McKinnon, C., et al. Early-onset impairment of the ubiquitin-proteasome system in dopaminergic neurons caused by alpha-synuclein. Acta Neuropathologica Communications. 8 (1), 17 (2020).
  11. Henderson, M. X., et al. Spread of alpha-synuclein pathology through the brain connectome is modulated by selective vulnerability and predicted by network analysis. Nature Neuroscience. 22 (8), 1248-1257 (2019).
  12. Ip, C. W., et al. AAV1/2-induced overexpression of A53T-alpha-synuclein in the substantia nigra results in degeneration of the nigrostriatal system with Lewy-like pathology and motor impairment: a new mouse model for Parkinson's disease. Acta Neuropathologica Communications. 5 (1), 11 (2017).
  13. Webster, J. D., Dunstan, R. W. Whole-slide imaging and automated image analysis: considerations and opportunities in the practice of pathology. Veterinary Pathology. 51 (1), 211-223 (2014).

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