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bioRxiv · 10.1101/2025.08.27.672653

Mapping Molecular Diversity in Prostate Cancer with a Combined Multiplex IHC and RNA-ISH Assay

Palanisamy, N.·Carskadon, S.·Jyothilingam, S.·Gupta, N.·Williamson, S.
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Abstract

Combining multiplex Immunohistochemistry (mIHC) and RNA in situ hybridization (RNA-ISH) in a single assay allows for the simultaneous detection of multiple markers in tissue sections. This approach can be a powerful tool for understanding the molecular landscape of tumors, such as prostate cancer, by providing information in the same tissue context. Studying the expression of multiple genes in the same tissue is often necessary. ERG, SPINK1, ETV1, and ETV4 are all relevant genes in the context of prostate cancer. ERG is a transcription factor, and its fusion with the TMPRSS2 gene is one of the most common genetic alterations in prostate cancer. Overexpression of the ERG protein due to this gene, involved in gene fusion with TMPRSS2 and rarely with other 5 partner genes, can be detected using Immunohistochemistry (IHC) due to the availability of a characterized antibody. SPINK1 (serine peptidase inhibitor, Kazal type 1) is an overexpressed protein in a subset of prostate cancers that do not harbor ERG rearrangements. High SPINK1 expression is known to be associated with a more aggressive tumor phenotype in some studies. SPINK1 expression can be detected using a well-characterized antibody by IHC. ETV1 and ETV4 are transcription factors that can also be involved in gene fusions in prostate cancer, albeit less frequently than ERG. There are no well-characterized antibodies for ETV1 and ETV4. Due to the mutually exclusive expression of ERG, SPINK1, ETV1, and ETV4, simultaneous evaluation of these genes can provide valuable information on the molecular subtype of prostate cancer, which can have implications for the assessment of inter- and intra-tumor heterogeneity, prognosis, and potential treatment. We describe a novel approach for the simultaneous evaluation of all four markers in prostate cancer tissues using a combined dual IHC and dual RNA-ISH method using validated antibodies for ERG, SPINK1, and RNAscope probes for ETV1 and ETV4.

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Palanisamy, N., Carskadon, S., Jyothilingam, S., Gupta, N., Williamson, S.. 2025-08-31. Mapping Molecular Diversity in Prostate Cancer with a Combined Multiplex IHC and RNA-ISH Assay. https://doi.org/10.1101/2025.08.27.672653

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