Single Cell Genomics

The last years have seen a rapid expansion of the field of single-cell genomics, which has allowed a progression in many fields of biological sciences, ranging from evolutionary biology over stem cell biology to cancer research.

Unlike bulk-cell analysis, single-cell approaches have the advantage of assessing cellular heterogeneity that governs key aspects of tumor biology. In fact the idea that every cell in a sample behaves exactly the same way is a dangerous evidence; taking averages of pooled cells can mask the dramatic variations in gene expression among cells. Single-cell sequencing significantly exceed previous sequencing technologies because it can investigate cellular and microenvironmental heterogeneity at single-cell resolution. This innovation has revolutionized the ability to interrogate the transcriptional, genomic, epigenomic and metabolic characteristics of thousands of individual cells in depth, thereby enabling an unbiased analysis of the cells within tumor lesions. It also provides molecular insights, including single-nucleotide variations (SNVs), copy number variations (CNVs) and structural variations (SVs). Recognizing cellular variations in what appear to be homogenous populations has become crucial to understand cancer cells and to study the effectiveness of biological therapies.

The Single Cell Genomics Lab research activity focuses on single-cell genomics. The main aim of our lab is developing and integrating techniques and tools for parallel genomics and transcriptomics characterisation from single cells for translational research. In our lab we are able to isolate and molecularly characterized single cells from tissues but also circulating tumor cells (CTCs) in blood.

Instruments

• Parsortix (ANGLE) – The Parsortix® PC1 Clinical System is a next generation liquid biopsy technology. Starting from a simple blood draw, which is non-invasive and can be repeated as often as needed, the system enriches to provide intact cancer cells, circulating tumor cells (CTCs) providing a real-time sample for subsequent analyses by common laboratory techniques, enabling a complete picture of the cancer.
• DEPArray (Menarini Silicon Byosistem) – DEPArray is an automated and versatile platform to sort pre-selected rare cell populations from a variety of sample types with single cell precision and 100% purity. DEPArray technology is based on the ability of a non-uniform electric field to exert forces on neutral, polarizable particles, such as cells, that are suspended in a liquid. This electro kinetic principle, called dielectrophoresis (DEP), can be used to trap cells in DEP “cages” by applying an appropriate pattern of Alternating Current voltages to the array of electodes. When a DEP cage is moved by a change in the electric field pattern, the trapped cell moves with it.
• Chromium Controller (10X Genomics) – The Chromium Controller uses advanced microfluidics to perform single cell partitioning and barcoding in a matter of minutes. Powered by Next GEM technology, the Chromium Controller enables integrated analysis of single cells at massive scale. Moreover, the Chromium Single Cell products can capture molecular readouts of cell activity in multiple dimensions, including gene expression, cell surface proteins, immune clonotype, antigen specificity, and chromatin accessibility. The key to this technology is its ability to generate tens of thousands of single cell partitions, each containing an identifying barcode for downstream analysis. This technology capture the full heterogeneity of a sample, in tens of thousands of cells. The Chromium Single Cell products has been validated on fixed, fresh, and frozen samples, as well as whole cells and nuclei.

In addition, the Single Cell Genomics Lab relies on the Genomics facility for all the NGS intruments (NextSeq2000 and Ion S5) and the Genetic Analyzer 3500.