Design of a 770-plex Gene List for the Comprehensive Study of Neurodegeneration: The NanoString® Process

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Interested in performing comprehensive multiplex gene expression analysis covering six fundamental themes of neurodegeneration: neurotransmission, neuron-glia interaction, neuroplasticity, cell structure integrity, neuroinflammation and metabolism? Wondering how you can narrow down these complex processes into just 770 RNA targets? Read on to see how NanoString’s Bioinfomatics’ team, in collaboration with Key Opinion Leaders, developed the nCounter® Neuropathology Panels.

The content development process for the nCounter® Neuropathology Gene Expression Panels required a comprehensive review of the literature surrounding neurodegeneration and the basic biology of the nervous system. Diseases of the nervous system fundamentally disrupt the cells, processes, and structures unique to this differentiated tissue. As a result, great attention was given to both development and homeostasis of nervous system tissues. Examples include disruptions to axon or dendrite structure or loss of cell-cell interactions like myelin sheaths, which is particularly relevant in demyelinating diseases. Additionally, specific neuronal cell types, particularly microglia, have been implicated in driving disease progression. As in many contexts, tissue damage leads to cellular stress and re-activation of developmental processes, including growth factor secretion, angiogenesis, cell motility, and proliferation. Many reviews of neurodegenerative disease have been written which consistently point to key dysfunctions that span disease types. Perhaps most notable in these diseases is a loss of protein quality control, resulting in tangles or aggregates that are observed by pathologists. In recent years, however, many have also pointed to other basic homeostatic disruptions, including RNA processing, carbohydrate metabolism, mitochondrial function, and autophagy. Finally, one of the most intriguing and promising aspects of research into neurodegeneration focuses on the role of the immune system in disease. This is particularly fascinating as the CNS is considered an immune-privileged site. While resident macrophage-like immune cells, microglia, are involved in secreting cytokines and promoting inflammation, evidence is mounting that peripheral immune system involvement is also a factor in disease progression.

The pathways and processes described above provided a foundation for ensuring we captured the known biology using functional annotation information. Numerous datasets have uncovered novel genes associated with neurodegenerative diseases, whether via genetic association or gene expression alteration. We selected high-quality publications across disease areas to capture commonly disrupted genes in addition to the most commonly discovered genes in GWAS studies. Finally, to discover the most informative genes amongst the nearly 6,000 we had collected, we used the penalized PCA method on a dataset from Parkinson’s disease with over 70 samples, including normal controls. We included all genes that were in the first two principal components, and in most cases the first principal component covered >80% of the information in the data. In addition to the most informative genes from a data perspective, we included some of the most associated in the literature and other genes whose biological value to neurodegeneration was not well-reflected in the data-driven approach. Additionally, we utilized an RNAseq dataset from mouse to identify signatures that would quantify relative abundance of neuro-specific cell types. The content in the nCounter Neuropathology Panels thus represents a biologically curated and data-driven approach to find the most informative genes that comprehensively profile neurodegeneration in humans and mouse models. If we missed your favorite target, the nCounter Neuropathology Panels are compatible with the addition of up to 30 RNA targets.

Learn more about our Neuropathology Panels.

FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

Erin Piazza, Ph.D., Bioinformatics Scientist II at NanoString Technologies
By Erin Piazza
For research use only. Not for use in diagnostic procedures.