Neuroinformatics to Visualize Brain Gene Expression

Client - Neurome, Inc.

 

(Circa 2002) Central nervous system diseases constitute a major target for drug development. Genes expressed by the nervous system may represent half or more of the mammalian genome, with literally tens of thousands of gene products. Better methods are therefore required to accelerate the pace of mapping gene expression patterns in the mouse brain and to evaluate the progressive phenotypic changes in genetic models of human brain diseases.  Recent studies of mouse models of Amyotrophic Lateral Sclerosis and Alzheimer’s disease illustrate how such data could be used for drug development.

In order for neuroscience to benefit from the application of the kinds of computer assisted searches that have empowered genomics research with rapid comparative analysis of nucleotide or amino acid sequence, the existing and future data must be organized into standardized databases. Some of the discrete aspects of neuroscience data that need to be incorporated into a broadly integrated database are:

• Molecular: data on neurotransmitters, their synthetic and catabolic enzymes, receptors and transductive mechanisms; their regulated ion channels; the sites and molecules to which drugs bind; other neuron-restricted molecular markers for structural, secretory and metabolic functions (e.g., all those properties recognized by gene markers or monoclonal antibodies).

• Cellular: attributes critical in categorizing specific categories of neurons and glial cells in specific brain locations (within nuclei or laminar brain macroregions) would include their functional classes, sizes, shapes, dendritic and axonal arbors; their developmental stage of origin; their survival during senescence. In general, this literature is highly descriptive and qualitative, but stereological methods of morphological assessment are gaining value.

• Circuitry: afferent and efferent connections between nuclear or laminar neuronal locations, their trajectories, their density; the forms of synaptic connections made and their relative numbers; the degree to which the projections are reciprocal, topographic, collateralized or specific; the methods by which the pathways were defined; the "functions" of such circuitry (excitatory, inhibitory or conditional), and the transmitter(s) and receptor(s) attributable to it. 

• Systems: The functional systems (e.g., sensory, motor, endocrine, visceral regulatory, emotion) to which a given set of cells and circuits has been attributed by physiological or behavioral experiments, the methods used.

• Behavioral: Relationships between nuclei or cortical regions and their circuits with distinctive forms and stages in behaviors, or of lesions that incapacitate certain forms of behaviors. Although relatively unimportant now for small experimental animals, non-invasive structural or functional imaging of the normal or diseased human subject performing higher order mental tasks identifies for databases the sites to which such operations can be attributed and may illuminate the alterations in specific pathologic states which may be shown to incapacitate such higher order functions.

Neuroinformatics tools were developed to support the production, collection and integration of accurate three-dimensional volumetric data on gene expression within the brain and to correlate that data with the developing wealth of learning on the architecture and functions of brain structures, circuits and cells. These toolsinclude:

1. MiceSlice - Ultra high-resolution digital brain sections for standardized preparation of brain section tissues. Microscope image tiles are seamlessly reassembled into one brain section and then rotated to perfect alignment. This provides the foundation material for development of standardized experimental protocols.
2. NeuroZoom Pro- Computerized microscopy analysis for precise, computer- aided extraction, analyses, and display of quantitative data from microscope images of the brain, including morphometrics, stereology and image processing.
3. BrainArchive - A comprehensive database of neuroinformation, BrainArchive is an electronic brain "atlas" for archiving, integration and comparison of brain structure and circuitry data.
4. BrainPrint - Digital profiles for comparison of quantitative, spatial and volumetric data from different transgenic models of mice.

With these tools applied to the study of certain central nervous system diseases, such as Alzheimer's Disease, high resolution digital images can be compared across mice of the same strain, age and gender in order to establish the inter-individual variations within the strain. The figure below shows the 3D surface reconstructions generated from image segmentation of the hippocampus (A), as well as the cerebellum (B) and whole brain (C). Figure D shows the 3D surface reconstructions within a 3D volumetric MRM file. Note the brain is undissected and still lies within the mouse head.

 

 

Using these digital atlases and databases, the expression of proteins in the brain, such as amyloid beta implicated in Alzheimer's Disease, can be followed and reconstructed, as shown in the next figure. 3D reconstruction of amyloid beta distribution. (A) Serial coronal sections immunostained with 3D6 were imaged and compiled into a 3D data file. A surface reconstruction of the hippocampus is shown in yellow. (B) Amyloid beta deposits were segmented by thresholding and are displayed as a 3D reconstruction (red). A surface reconstruction of the hippocampus (yellow) and a single coronal section are shown for orientation. (C) 3D reconstruction of amyloid beta (red) viewed from the posterior aspect of the brain with the hippocampus shown as transparent yellow. Note the extensive deposition in the neocortex and hippocampus, and the central lucency representing the midbrain and caudate-putamen with punctate amyloid beta visible in the frontal cortex and olfactory bulb. (D) Large lakes and ribbons of amyloid beta (cyan) were identified by automated detection of contiguous structures within the 3D reconstruction of amyloid beta (shown as transparent red; same angle of view as C). (E) Amyloid beta sheets (cyan) are visible in the rostral part of the dentate gyrus, shown against a single coronal section, with the surface reconstruction of the hippocampus in transparent yellow. (F) Magnified view of the amyloid beta lakes and ribbons (cyan) in the dentate gyrus (within the transparent yellow hippocampal surface) and extending into the retrosplenial cortex (above).

 

 

Studies performed with these tools suggest that in the case of amyloid beta distribution in the mice brain, there is pathology ongoing before tge amyloid deposits can be detected, and that this early pathology resulting from the mouse brain's overexpressing one of the protein abnormalities found in inheritable forms of Alzheimer's disease may set the stage for what has been regarded as the only pathology..