Single Cell Genomics

Single-cell sequencing technologies provide insight into cellular processes at an unprecedented level of detail. They overcome the shortcomings of traditional bulk sequencing and enable the identification of individual cell types and dynamic states. The Máxima Single-Cell Genomics facility makes these technologies available to study pediatric tumors.

Purpose for research

Cancer cells do not exist in isolation but are embedded within a network of healthy ‘neighbors’. Blood vessels and stromal cells can support the disease via efficient nutrient delivery and cell-cell communication while immune cells can target malignant cells for destruction. Diseased cells also signal to their surrounding cells to promote cancer cell survival. Cancer cell heterogeneity makes some cells better able to survive under stressful conditions, such as nutrient deprivation, immune attack, or exposure to chemotherapy. Similarly, immune cells can either be ready to fight the disease or exhausted. Traditional bulk RNA-seq blends all these complex signals into an average that obscures the heterogeneity and interplay between cells.

Recent technological advances have made it possible to use single-cell sequencing to measure the activity of thousands of individual cells in parallel. This enables the investigation of several unexplored aspects of cancer biology such as tumor heterogeneity and clonality, niche-cancer crosstalk, and in-depth characterization of the immune microenvironment. Additionally, multiple modalities can be measured in parallel with RNA, such as open chromatin, cell surface markers, and VDJ rearrangements. All these possibilities lead to new insights into cancer biology, tumor composition, and treatment.

At the SCG facility single, cell genomics technologies are used to assist researchers in acquiring high-quality data to study pediatric cancer.

The facility provides support for single-cell data generation, including:

• Advice on experimental design, choosing the appropriate technique and optimizing sample preparation.
• Preparation of libraries and sequencing (10x Genomics, BD, and Illumina single cell preps).
• Analysis-ready processed data, including quality control reports.
• Expertise on single-cell data analysis and interpretation.
• We serve multiple Group Leaders in Utrecht Science Park, the Netherlands and abroad to fruitful outcomes, see “Publications”.