Laser Capture Microdissection for Gene Expression Analysis in Distinct Cell Populations

Knowledge in early phase cancer development to provide understanding of the mechanism of action of oncogenic mutations is constantly growing. A recent study carried out by Mo et al has highlighted several interesting results.

This study identifies the following:

Laser capture microdissection allows analysis of distinct transcriptional changes in discrete cell populations within preneoplastic lesions.

Genomic analysis of discrete lesions shows differential transcriptional disruption between mutation types.

Analysis of epithelium and stroma informs of interactions between tissues.

By comparing transcriptional profiles of AFC tissue compared to image analysis of immunostained adjacent AFC sections infers the contribution to differential expression is due to fibroblasts and infiltrating immune cells.

Differential expression analysis identified significant upregulation of TIMP-1 in AFC. TIMP-1 is a member of the matrix metalloproteinase inhibitor family. TIMP1 activity is associated with reduction in degradation of extracellular matrix and increase in cellular proliferation, potentially due to anti-apoptotic function. HRK, an apoptotic promoter, was heavily downregulated, and is known to be associated with chronic inflammation. BRAF/KRAS mutations significantly activated different gene sets compared to APC mutations, an analysis that would have been impossible to observe using whole tissue or macro-dissection of tissue. The value of laser capture microdissection to measure endpoint biomarkers to specific mutations in a heterogeneous neoplastic population is high, allowing biomarker identification in personalised medicine.

In this publication laser capture selection was based on tissue morphology, with further comparative image analysis performed on immunostained tissue. To directly correlate transcription profiles to cells of interest, direct capture of cells identified by immunostaining is preferred, however traditional IHC protocols result in heavily degraded RNA resulting in poor data quality in downstream analysis due to loss of sensitivity and extremely high variation.

At Epistem we offer optimised immunohistochemical staining and direct capture of immunolabelled cells of interest, resulting in the isolation of specific highly enriched populations of cells of interest for subsequent transcriptional profiling and mutation analysis. We have extensive experience in genomic analysis of ultralow RNA input, and routinely perform IHC in preclinical and clinical studies. Combining both methodologies, utilising Epistem's know-how to maximise RNA quality post immunostain, allows differential analysis between cells or cellular structures within the same tissue. This results in the ability to provide powerful analyses for preclinical target discovery or biomarker information in early phase clinical studies in our GCLP accredited laboratories.

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Mo et al. Distinct Transcriptional Changes and Epithelial–Stromal Interactions Are Altered in Early-Stage Colon Cancer Development. doi: 10.1158/1541-7786.MCR-16-0156. [Epub ahead of print]

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