Technological advancements accelerating a paradigm shift towards single-cell analysis

Cell analysis encompasses a wide range of activities that help in understanding and predicting the dynamics that influence cell function, proliferation, growth and death. This is enabled through analysis of cell signalling mechanisms, elucidation of molecular function, study of cell behaviour, and correlating to multiple events with cell morphology, changes in biochemical constituents and cell health. Earlier, cell analysis was limited to population-level analysis, which represents the data of an average of the gene or protein expression patterns across thousands to millions of cells; this obscures biologically relevant differences between cells i.e. Cellular heterogeneity. Therefore, it was felt important to analyze individual/single cells to discover mechanisms which were not seen by studying a bulk population of cells, thus, the focus shifted towards the single-cell analysis.

For over the last two decades, technological advancements are disrupting the single cell analysis area by making possible of complete omics analysis of single cell which has significantly revealed cellular heterogeneity. Some of these advancements include development of droplet and nano well based microfluidic technologies, multiomics solutions, intelligent image-activated cell sorting or AI-driven cell isolation technologies and advanced spatial imaging technologies.

The microfluidic technologies such as droplet-based and nanowell based microfluidic technology platforms have opened a new avenue for single-cell isolation and omics analysis with particular emphasis on quantification and multiplicity that can perform measurements on single-cells. Companies are developing novel droplet or nonowell based platforms for high throughput analysis using unique barcode technology. For instance, ddSEQ -single-cell isolator (Ilumina, Bio-Rad), was developed to be used as microfluidic cartridges to encapsulate cells and barcodes into droplets containing single DNA/RNA which is further analyzed by sequencing technology. Similarly, 10x genomics’ chromium system and 1CellBio in-Drop system were introduced for scRNA-seq which has enabled high-throughput single-cell analysis of more than 10,000 cells.

Along with the development of single-cell genomics, transcriptomics and proteomics solutions separately, now the focus has shifted towards the development of multi-omics methods. For instance, in October 2020, Mission Bio, Inc. launched the complete Tapestri Single-cell Multi-omics Solution (instrument, single-cell multi-omics reagent kits, TotalSeq-D antibody content from BioLegend, and visualization software) a complete package that provides layered insight into multiple analytes across all blood cancers, reducing drug development time and cost by at least half. Mission Bio’s new solution can uniquely detect DNA and protein simultaneously from the same cell.

There is an increasing approach of integration of different analytical technologies, for high throughput single-cell analysis. For instance, intelligent image-activated cell sorting (iIACS) was developed by integrating machine-intelligence to performs real-time intelligent image-based sorting of single cells with high throughput. iIACS extends beyond the capabilities of fluorescence-activated cell sorting (FACS) from fluorescence intensity profiles of cells to multidimensional images, thereby enabling high-content sorting of cells or cell clusters with unique spatial chemical and morphological traits. ThinkCyte Company has developed Ghost Cytometry (image activated cell sorting) technology to achieve high-throughput and high-content single-cell sorting by combing microfluidics, imaging and machine learning.

The current single-cell technologies have drawbacks such as lacking the capacity to correlate the information of  genomes, transcriptomes, or proteomes of single cell with the phenotypes of adherent cells in situ (e.g., size, shape, intracellular marker expression, and distance to neighboring cells). Thus, single-cell spatial technology has been developed which give the information about a gene or protein expression in their natural context, Vizgen, company is developing a novel, next generation of single-cell spatial genomics profiling tools called MERFISH, which is quantitative; genome-scale multiplexed imaging technology for identifying nucleic acids in their native cellular and tissue environment. The technology leverages combinatorial labeling, sequential imaging, and error-tolerant barcoding schemes, to –produce massively multiplexed and accurate measurements of RNA expression.

Also, to bridge the gap between in situ microscopy and single-cell omics, the University of Toronto has developed a new tool called DISCO (digital microfluidic isolation of single cells for –omics), by combining cell microscopy with -omics technologies, to link cells’ physical parameters that are visible by eye—such as appearance, the presence of surface markers, or cell-cell contacts—to their molecular makeup. Specifically, DISCO combines digital microfluidics, laser cell lysis, and artificial intelligence-driven image processing to collect the contents of single cells from heterogeneous populations, followed by the analysis of single-cell genomes and transcriptomes by next-generation sequencing, and proteomes by nanoflow liquid chromatography and tandem mass spectrometry.

All these technological advancements will further accelerate the growth single-cell analysis arena and enhance their application in research, diagnosis and therapeutic development. Thus, pharma & biotech companies, academic and research institutions and CRO are collaborating to utilize these technologies. For instance, in July 2019, Celsius Therapeutics collaborated with Janssen Biotech, Inc. to apply its proprietary single-cell genomics and machine learning platform to identify predictive biomarkers of response from Janssen’s VEGA study, a Phase 2a clinical trial evaluating the efficacy and safety of combination therapy with guselkumab and golimumab in patients with ulcerative colitis. Similarly, in September 2020, IsoPlexis entered into a partnership with Yale University to use IsoPlexis' single-cell functional proteomics solutions to identify various predictive markers of the immune response to COVID-19. Overall, technological advancements are expanding the cell analysis market. According to IQ4I analysis, the cell analysis global market is expected to grow at mid-single digit CAGR from 2020 to 2027 to reach $33,542.0 million by 2027.

Major players in the cell analysis market include Agilent Technologies, Inc. (U.S.), Becton Dickinson and Company (U.S.), Illumina Inc. (U.S.), Bio-Rad Laboratories (U.S.), Danaher Corporation (U.S.), Merck KGaA (Germany), Olympus Corporation (Japan), PerkinElmer, Inc. (U.S.), Promega Corporation (U.S.), Qiagen N.V. (Netherlands), and Thermo Fisher Scientific, Inc. (U.S.).