Evaluating transcriptional tumour microenvironment response to immunotherapy using microarray analysis: From harvesting tumours to data analysis

In the recent years, a better understanding of the cellular and molecular processes that shape the dynamic balance of the immune system and the tumour has been gained. Accumulating evidence shows that cellular and acellular components in the tumour microenvironment (TME) can reprogram the response to immunotherapies. Transcriptome analyses of immunotherapy treatments have been invaluable for studying signalling pathways in cancer. Transcriptional characterization of tumours has allowed researchers to both predict the likely response to therapy as well as to evaluate the effect of therapy on tumours before any phenotypic changes are observed. Despite the rise of single-cell RNA sequencing (scRNAseq) it remains costly and technically challenging and, in many situations, unnecessarily detailed. Presented here is a protocol describing processing of tumours for microarray transcriptome analysis to evaluate the responses to therapy. This method has proven to be cost-effective in cases when broad transcriptional responses are being investigated.