Spatial Profiling of RNA and Protein with HCR Imaging

Introduction

Understanding the spatiotemporal patterns of gene expression is critical to decode complex biological events like disease and development. Digitally reconstructing the spatial patterns of expression in intact tissue paves the way for an unbiased and complete review of gene expression. This aids in understanding the molecular origin of developmental defect or disease pathogenesis for medical diagnostics. Visikol now offers next generation RNA and protein spatial profiling services powered by HCR RNA-FISH and IHC reagents from Molecular Instruments. HCR reagents enable multiplexed quantitative mapping of RNA and/or protein molecules with subcellular resolution and are rapidly becoming fundamental tools for drug discovery in gene therapy/RNA therapeutics.

Figure 1. 4X imaging of B-actin RNA with HCR RNA-FISH (red) and DAPI (blue).

Figure 2. 40X imaging of B-actin RNA with HCR RNA-FISH (red) and DAPI (blue).

How it works

Send Your Samples

After designing a statement of work and project scope with the Visikol team of experts, the tissue samples can be shipped to the Visikol lab.

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Choose Your Labels

HCR RNA-FISH is compatible with multiplex IHC such that we can combine 3+ IHC markers with multiple RNA targets on the same slide. We have panels of validated multiplex IHC antibodies here: Validated antibodies and Antibody Panels

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Visikol Executes Labeling and Imaging

Using its validated protocols, Visikol conducts tissue labeling and imaging. Multiple rounds of IHC labeling can be conducted prior to HCR RNA-FISH labeling using Visikol’s propriety multiplexing technique. Additionally, for low abundance or otherwise challenging protein targets, HCR IHC kits are compatible with Visikol’s Antibody Panels and can offer further signal amplification. The imaging can be conducted on a single region of interest to save cost or on an entire slide.

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Image Co-Registration

If multiple panels of IHC or RNA targets are utilized, the images are co-registered together to create one single image using elastic co-registration.

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Image Analysis, File Sharing and Reporting

Once the images are generated, Visikol can share these large files with clients easily using its BitSlide platform. The data then can be analyzed by the Visikol team to provide clients with actionable insights using its suite of digital pathology software.

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Background on Technology

The HCR imaging platform opens a new era for ISH and IHC, enabling multiplexed, quantitative, enzyme-free labeling of biomolecules in any sample type regardless of thickness or preparation. HCR RNA-FISH and HCR IHC allow simultaneous detection of up to 10 RNA and protein targets, respectively. Through this unique partnership, HCR RNA-FISH can be combined with Visikol’s wide array of in-house validated multiplex immunohistochemistry panels. This enables high-resolution co-detection of RNA and protein molecules with spatiotemporal and functional context in tissues. Furthermore, the technique is compatible with thick whole mount tissues in tandem with tissue clearing such that RNA can be imaged in large intact tissues using confocal or light sheet microscopy.