RNA sequencing data analysis on a mixture sample of human RNA and mouse RNA

NAISS 2023/22-223


NAISS Small Compute

Principal Investigator:

Andor Pivarcsi


Uppsala universitet

Start Date:


End Date:


Primary Classification:

30108: Cell and Molecular Biology




Cutaneous squamous cell carcinoma (cSCC) is a keratinocyte-derived skin cancer with an increasing incidence worldwide. Extracellular vesicles (EVs) are small membrane-bound vesicles that are present in all body fluids and are produced by virtually all cells of the human body. EVs play important roles in intercellular communication in particular in the tumor microenvironment (TME). Our results obtained with mouse xenograft model of cSCC revealed that suppression of EV-production by RAB27A-kncokdown resulted in altered cSCC tumor growth in vivo. We plan to analyse changes in the tumor composition as well as differences in the gene expression profile of tumor cells as well as in stromal cells by RNA-sequencing. To this end, we will analyse differential expression of transcripts in tumor xenografts formed by established cancer cell lines upon injection into mice. Mouse and human transcripts will be separated and differentially expression analysis will be performed. On the list of DEGs enrichment analyses will be performed.