From CODEX user to Akoya Applications Scientist
I’ve spent the majority of my academic career in neuroscience. I received my doctorate from Dalhousie University and went on to complete postdocs at Yale and the Korea Institute of Science and Technology. During my postdoctoral appointments, I used state-of-the-art optical imaging and optogenetic tools to investigate the structure and function of the vertebrate nervous system.
In 2017, I became interested in translational research, so I joined the Nanomedicine Research Center at Cedars Sinai. In my time there, I worked on the development of novel nanodrugs that target Alzheimer’s disease and Glioblastoma. It was at Cedars Sinai that I was first exposed to techniques like gene sequencing, bioinformatic analyses and, later on, highly multiplexed imaging techniques like CODEX and MERFISH. I was giddy with excitement when I learned about the possibilities offered by these imaging tools. After all, I had spent much of my career conducting low-plex imaging experiments and lamenting that I couldn’t label my tissues with more markers. It was this excitement that eventually led me to join Akoya Biosciences.
Since joining Akoya, I have been focused on application development for the CODEX technology. I believe that this technology is deployable across many biological disciplines, including neuroscience. Adding to this excitement, Akoya’s portfolio contains two complementary imaging technologies, CODEX and the higher throughput mIF Phenoptics™ platform. These two technologies are tailormade to support neuroscience research across the continuum from biomarker discovery to validation.
Why use multiplex immunofluorescence for neuroscience research
Of all the organs in the body, the brain displays the most cellular and molecular heterogeneity. Although many neuronal cell types have been identified based on morphological or functional differences, we continue to discover heterogeneity among brain cells1. Techniques like single-cell transcriptome sequencing have proven to be incredibly powerful in this regard, and reports of previously unknown neuronal and glial subpopulations have become commonplace. However, single-cell sequencing does not allow us to resolve spatial relationships between cells, so we only know that cell populations exist, not how they combine and form spatial relationships with one another.
It is here that CODEX provides a good solution to further our research aspirations. CODEX provides an imaging-based, ultra-high plex immunohistochemistry platform through which it is possible to label tissues with 40+ antibodies. All the while, single-cell spatial resolution is retained and cells can be thoroughly phenotyped in their original environment.
There are many ways this technique can be used by neuroscientists, but let’s consider Alzheimer’s research as an example. Alzheimer’s pathology often features complex microenvironments in which heterogeneous protein aggregations and immune responses contribute to inflammation, damage and eventually the death of surrounding neurons and glia. In order to understand ‘who is who’ in Alzheimer’s pathology, one requires a multitude of markers plus good spatial resolution. This is what CODEX offers. In a single CODEX experiment it is now possible to label a tissue with 40+ biomarkers, which should allow us to dissect the composition of protein accumulations, identify nearby immune cells and also deploy some markers to identify neurons, glia and their activation states. Ultimately, we hope that this kind of research accelerates our understanding of Alzheimer’s biology and, hopefully, advances progress towards clinically useful therapeutic interventions for neurodegenerative disorders.
With that in mind, we’re happy to give a brief overview of two studies that we contributed to the FENS 2020 Virtual Forum.
Ultra-high plex immunohistochemistry meets neuroscience
The premise of this experiment was to tackle the very basic question: “Does CODEX work with brain tissues?” Sounds simple, but there is still little empirical evidence to support this answer, neither for CODEX nor other mIF technologies. We therefore designed a 22-antibody panel that contained markers for neurons, glia and the vasculature. This panel addressed the basic organizational principles of the brain and thus allowed us to simultaneously investigate distinct anatomical compartments in our tissues. The images below show a result from a formalin-fixed paraffin embedded (FFPE) human cerebral cortex. By clicking on the images, select markers can be viewed separately. It is evident from these data that the CODEX experiment worked very well.