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Exploring personalized treatments for bladder cancer with scRNA-seq

A Dolomite Bio system is helping researchers in the Department of Molecular Medicine at Aarhus University Hospital in Denmark to explore the potential of single cell RNA sequencing for personalized treatment of bladder cancer. Associate Professor Iver Nordentoft explained: “Our focus is on translational research to obtain a deeper understanding of bladder cancer, identifying and validating molecular markers that could aid personalized medicine. In early stage bladder cancer, the main clinical challenge is to predict disease recurrence, aggressiveness and treatment response.”

“Previously, we used next generation sequencing (NGS, DNA- and RNA-Seq) for cancer genomics studies, but we are now moving into the single cell arena to delve further into tumor heterogeneity, clonality and the tumor microenvironment. NGS-based RNA analysis of bulk tumors identified three major molecular groups predicting different disease outcomes, and we are now using the scRNA-seq System to determine the specific cell type contribution of these molecular subgroups. In other words, are specific immune cells over- or under-represented in the aggressive tumors? Furthermore, characterization of cell type composition in apparently normal bladder tissue may also contribute to the development of molecular tools and clinically-applicable pipelines to predict the likely aggressiveness of the disease and the frequency of recurrence.”

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“We had been considering single cell sequencing for this application for a while, having realized the potential of the Drop-Seq protocol described in the Macosko paper1. I attended a demonstration of Dolomite Bio’s scRNA-seq System, thought it was very promising and liked the company, and so we purchased a system for our laboratory. Our research team decided to choose a platform that was as open as possible to accommodate new developments and changing laboratory needs, and this was one of the main reasons for selecting the Dolomite Bio system. The open design helps to futureproof the system, giving us the option to run emerging protocols – such as high throughput sequencing of single nuclei by DroNc-Seq – in the future. I am very pleased with the system and the support I receive from Dolomite Bio,” Iver concluded.

1.Macosko, E et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell, 2015, 161, 1202-1214