Single Cell Omics

What are single cell omics?

Omics is a term summarizing different comprehensive molecular analyses, such as genomics, transcriptomics, proteomics, lipidomics or metabolomics. Transcriptomics for example does not only analyze the expression of a single gene, but investigates the expression pattern of many or even all genes. Omics analyses have been performed across whole tissues or organs. Today, with emerging technologies in single cell isolation and more sensitive molecular technologies, omics analyses can also be conducted at single cells resolution. These so called single cell omics analyses are providing unique insights into the heterogeneity of cells across tissues.

Why is single cell resolution important and what you should know about single cell omics?

Single cell omics have multiple advantages over bulk methods. Tissues consist of several different types of cells and even cells of the same type can differ significantly in their molecular state. Here are a few examples, where single cell omics have provided fundamental new insights: In developmental biology, cells are very differently regulated to be able to differentiate and form distinct tissue. Single cell omics and especially single cell transcriptomics provided novel insights into these regulation mechanisms on a molecular and cellular level.

In the recent years, tumor heterogeneity became one of the most important emerging research topics in oncology. Tumors do not only consist of tumor cells, but also comprise immune cells especially in their microenvironment. Single cell transcriptomics, in addition to other single cell omics analyses, revealed the complex interplay between these cell types. Single cell genomics helped to identify different tumor subclones which are crucial for diagnosis, to identify novel biomarkers and also to understand mechanisms of remission and relapse.

Very recently, single cells proteomics became available as chromatography and mass spectrometry technologies were optimized to become much more sensitive. As genes and transcripts are highly regulated and translated into proteins depending on a number of parameters, single cell proteomics adds new aspects to our knowledge based on single cell genomics and single cell transcriptomics. Combined with MALDI-Imaging, single cell proteomics is therefore a very powerful tool to investigate cells on a molecular level and to combine molecular with spatial data, thus providing comprehensive spatial omics data.

How much data is in a single cell?

Each cell contains a full set of genes. The transcription and translation of all genes is tightly regulated in each cell to be able to fulfill their specific tasks. Thus, all the omics data are present in each cell, but every cell harbors its individual omics data depending on differentiation state, cell type, age as well as infection processes, sickness and health. This makes single cell omics a very powerful tool to understand the molecular basis of cellular mechanisms. To understand cellular processes in tissues, single cell omics can be combined with spatial omics to uncover multi-dimensional effects. Spatial single cell transcriptomics can provide unique insights to understand highly complex mechanisms such as in embryonic development or cancer.

How do we identify a single cell?

Before we can isolate single cells for single cell omics analyses, we need to identify and select the target cells of interest. To be able to identify cells in tissue sections, typical histology stains such as Hematoxylin & Eosin stains are applied. In cytology, Giemsa is a well-known stain. For more specific identification, immunohistochemistry (IHC) or immunofluorescence (IF) are used to stain the cells using antibody-coupled reagents. The antibody recognizes specific structures on the surface of the cells, therefore only coloring the cells of interest. Intriguingly, several different antibodies can be combined for highly specific selection of cell types.
In addition to IHC and IF staining technologies, fluorescent proteins such as GFP can be co-expressed with marker proteins such as infection markers or transgenes. Several of these staining technologies can be combined to provide researchers with a comprehensive toolbox to identify and select cells for single cell isolation and single cell omics.

How do you isolate a single cell?

In the recent years, many technologies to isolate single cells have been developed to be able to perform single cell omics analyses. Fluorescence activated cell sorting (FACS) or magnetic activated cell sorting (MACS) are typically used to separate cell populations based on antibody-coupled fluorophores or magnetic beads. These technologies allow to sort thousands of cells at a time. However, the technologies are not suited to obtain individual single cells but to enrich cell populations which can further be applied in single cell technologies, such as microfluidics. Microfluidics technologies emerged in the recent years to combine single cell isolation with single cell sequencing thus enabling single cell genomics and single cell transcriptomics. Droplet technologies are able to perform sequencing reactions at single cell resolution within tiny droplets encapsulating one single cell including all required sequencing reagents. FACS, MACS and microfluidic technologies allow for the analyses of many cells at a time. However, these technologies require suspension cells for cell isolation and single cell omics. Tissue dissociation typically involves harsh treatments of the cells to destroy cell adhesion molecules and cell-cell interactions. In addition, the spatial information on the cells’ microenvironment is lost.
In contrast, laser microdissection is a powerful technology which is able to selectively isolate single cells from various origins, such as from tissue sections, from cytospins or smears, and from cell culture to perform single cell omics. With the MMI CellCut, MMI offers a laser microdissection system ideally suited to conduct single cell omics analyses and to combine these analyses with spatial information on tissue organization and cellular microenvironment thus providing multi-dimensional spatial single cell omics. The MMI CellCut employs a low-damage laser with a high-pulse frequency but low power to precisely cut single cells from tissue as well as living cells without impairing their molecular information. Thus, challenging single cell omics analyses, as well as single cell RNA sequencing or single cell transcriptomics are enabled. The patented ‘CapSure’ isolation technology ensures that target cells can reliably be isolated. Even rare cells can be extracted with highest confidence for meaningful single cell omics data.

With the MMI CellEctor, MMI also offers a system to isolate single cells from suspensions, such as circulating tumor cell (CTC) preparations from liquid biopsies or plant protoplasts. A microcapillary, controlled by a 3D micromanipulator and connected to a precise nanoliter pump, isolates individual cells manually or completely automated under full visual control. As the cells are not impaired by the isolation process with the MMI CellEctor, significant single cell omics can be performed.

Intriguingly, the two systems can be integrated on a single microscope platform to enable highly flexible and gentle single cell isolation on any kind of sample material. This is a crucial pre-requisite for reproducible and reliable single cell omics. In addition, the systems can be combined with the MMI CellScan system for 5D whole slide imaging, as well as the MMI CellManipulator Optical Tweezer for force spectroscopy. The MMI instruments therefore provide a complementary toolbox for single cell isolation and imaging to enable scientists to perform comprehensive single cell omics analyses.