Neuropathology Panel
Human and Mouse
NanoString’s Neuropathology panels are designed to target and evaluate all aspects of neurodegeneration. The 770 gene panels target 6 fundamental themes: neurotransmission, neuron-glia interaction, neuroplasticity, cell structure integrity, neuroinflammation and metabolism. Each human or mouse panel provides an effective means to research the pathogenesis of all types of neurodegenerative diseases.
Benefits
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Details & data
Cell types and qualified gene content
Genes included in the Neuropathology Panels provide unique cell profiling data for measuring the abundance of five important cell types including neurons, astrocytes, microglia, oligodendrocytes and endothelial cells. The table below summarizes each cell type represented in the panels along with the gene content qualified through biostatistical approaches and selected literature in the field of neurodegenerative diseases.
| Cell Type | Cell Description | Associated Human Genes | Associated Mouse Gene |
|---|---|---|---|
| Neurons | Neuronal cell death and loss of function is a key driver of neurodegeneration. | DLX1, DLX2, GRM2, ISLR2, SLC17A6, TBR1 | Dix1, Dix2, Grm2, Isir2, Sic17a6, Tbr1 |
| Astrocytes | Astrocytes represent the most numerous and diverse glial cells in the brain, responsible for a wide variety of homeostatic functions including modulation of synaptic function, network regulation, energy metabolism, neurotransmitter synthesis, among others. The loss of normal homeostatic functions and gain of toxic functions is implicated in the onset and progression of neurodegeneration. | ALDH1L1, EGFR ENTPD2, GDPD2 ITGA7, KIAA1161 NWD1, SOX9 | Aldh1l1, Egfr, Entpd2, Gdpd2, Itga7, Al464131, Nwd1, Sox9 |
| Microglia | Microglia represent a CNS resident myeloid cell population ontologically distinct from peripheral macrophages/monocytes. Microglia act to maintain brain homeostasis, contribute to neuroplasticity, and serve as a first line of innate immune defense in the brain. Their activation may serve as an early indicator of pathology, while chronic microglia activation or dysfunction may contribute to disease pathogenesis. | GPR84, IRF8 LRRC25, NCF1 TLR2, TNF AIF1, TMEM119 ITGAM, CX3CR1 P2RY12, SPI1 | Gpr84, Irf8, Lrrc25, Ncf1, Tlr2, Aif1, Tmem119, Itgam, Cx3cr1, P2ry12, Spi1 |
| Oligodendrocytes | Oligodendrocytes are highly specialized glial cells that synthesize myelin to ensheath axons of the central nervous system. Injury to or loss of oligodendrocyte function puts neuronal network function and survival at risk. Oligondendrocyte injury and death and axonal demyelination are hallmarks of some devastating neurological diseases. | BCAS1, ERBB3 FA2H, GAL3ST1 GJB1, GSN MYRF, NINJ2 PLLP, PLXNB3 PRKCQ, SOX10 UGT8 | Bcas1, Erbb3 Fa2h, Gal3st1 Gjb1, Gsn Myrf, Ninj2 Pllp, Plxnb3 Prkcq, Sox10 Ugt8a |
| Endothelial Cells | Endothelial cells form the blood-brain barrier and play a critical role in protecting the central nervous system from dangerous pathogens. Endothelial cells are equipped with a defense system against oxidative stress and their dysfunction can release inflammatory and neurotoxic agents in the CNS. | CLDN5, EMCN ESAM, FLT1 ICAM2, LSR | Cldn5, Emcn Esam, Flt1 Icam2, Lsr |
Neuropathology Panel Functional Annotations
Functional annotations for 23 fundamental pathways and processes were assigned across all genes in the Neuropathology Panels. This allows for a practical view of important aspects of the onset and progression of neurodegenerative disease and the corresponding themes of neurodegeneration.
| Fundamental Themes of Neurodegeneration | Description | Annotation | Human Genes | Mouse Genes |
|---|---|---|---|---|
| Neurotransmission | Neurotransmission is the core function of the nervous system and is critically impaired in neurodegenerative disorders. | Transmitter Release | 165 | 164 |
| Vesicular Trafficking | 156 | 155 |
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| Transmitter Response/Reuptake | 148 | 147 |
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| Transmitter Synthesis & Storage | 59 | 59 |
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| Neuron-Glia Interaction | Glia protect neurons and maintain homeostasis within the CNS, making their function crucial to brain health and the prevention of neurodegenerative disorders. | Myelination | 47 | 47 |
| Secretion of Trophic Factors | 48 | 48 | ||
| Neuroplasticity, Development and Aging Neuroplasticity, Development and Aging | The ability of the nervous system to form new connections during development and throughout life in response to environmental changes or injury. The brain’s ability to repair itself declines with age and loss of plasticity is characteristic of neurodegenerative disorders. | Growth Factors | 150 | 149 |
| Angiogenesis | 78 | 82 | ||
| Chromatin Modification | 62 | 62 |
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| Apoptosis | 61 | 59 |
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| Compartmentalization and Structural Integrity | Neurodegenerative diseases are characterized by a relentlessly progressive loss of the functional and structural integrity of the nervous system. | Neuronal Cytoskeleton | 17 | 17 |
| Axon and Dendrite Structure | 160 | 159 | ||
| Inter-Neuron Connectivity | 166 | 166 | ||
| Tissue Integrity | 45 | 44 | ||
| Neuroinflammation | Inflammation within the central nervous system which may be initiated by neuronal death, aberrant protein aggregation, infection, traumatic brain injury, toxic metabolites or autoimmunity. | Activated Microglia | 92 | 97 |
| Matrix Remodeling | 5 | 7 | ||
| Pro-Inflammatory Cytokines | 52 | 50 | ||
| Metabolism | Impaired metabolic pathways, including RNA transcription/splicing, protein translation/ degradation, carbohydrate metabolism, lipid metabolism, autophagy, and oxidative stress are hallmarks and causative agents in neurodegenerative disorders. | Unfolded Protein Response | 48 | 47 |
| Oxidative Stress | 91 | 91 | ||
| Transcription of mRNA Splicing | 47 | 46 | ||
| Autophagy | 33 | 33 | ||
| Carbohydrate Metabolism | 44 | 44 | ||
| Lipid Metabolism | 41 | 41 |
Genes in panel
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References
Published use of this panel
Rosen, Ezra Y., Wexler, Eric M., Versano, R., Coppola, G., Gao, F., Winden, Kellen D., Oldham, Michael C., Martens, L., Zhou, P., Farese, Robert V., Geschwind, Daniel H. Functional Genomic Analyses Identify Pathways Dysregulated by Progranulin Deficiency, Implicating Wnt Signaling. Neuron 71, 1030-1042 (2011).
Chiu, Isaac M, Morimoto, Emiko T A, Goodarzi, Hani, Liao, Jennifer T, O’Keeffe, Sean, Phatnani, Hemali P, Muratet, Michael, Carroll, Michael C, Levy, Shawn, Tavazoie, Saeed, Myers, Richard M, Maniatis, Tom A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model. Cell Reports 4, 385-401 (2013).
Hickman Suzanne E, Kingery Nathan D, Ohsumi Toshiro K, Borowsky Mark L, Wang Li-chong, Means Terry K, El Khoury Joseph The microglial sensome revealed by direct RNA sequencing. Nature Neuroscience 16, 1896-1905 (2013).
Zhang, Gaiteri, Bodea, Wang, McElwee, Podtelezhnikov, Zhang, Xie, Tran, Dobrin, Fluder, Clurman, Melquist, Narayanan, Suver, Shah, Mahajan, Gillis, Mysore, MacDonald, Lamb, Bennett, Molony, Stone, Gudnason, Myers, Schadt, Neuma Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease. Cell 153, 707-720 (2013).
Scientific references informing panel creation
Twine, Natalie A, Janitz, Karolina, Wilkins, Marc R, Janitz, Michal Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer’s disease. PloS One 6, e16266 (2011).
