Single-cell and spatially resolved omics: Advances and limitations

Abstract

Single-cell and spatially resolved omics: Advances and limitations Recent advances in experimental and computational single-cell and spatially resolved omics have opened new avenues for research in biology and medicine.These technologies allow for the study of individual cells in unprecedented detail, providing insights into the heterogeneity within tissues and organs, and how different cells interact with each other.Humans and other eukaryotes are composed of billions of cells, each with vastly heterogeneous cell types and functional cell states determined by intrinsic and extrinsic factors.Robust technologies for mono-omics measurements of individual cells have already revolutionized the discovery and understanding of various cell types, while multi-omics methodologies at single-cell and spatial resolution are necessary to develop fundamental understanding of the molecular hierarchy from genome to phenome in individual cells [1].Recent developments in single-cell and spatially resolved omics technologies enable investigation of intermolecular dynamics and the impact of genetic variation on cell function and tissue function.The field is rapidly advancing both technologically and computationally, enabling broad applications to understand cell biology.Recently, the throughput of single-cell RNA sequencing (scRNAseq) technology has rapidly increased, allowing for the analysis of hundreds of thousands of cells with a significant decrease in cost.Different technologies, such as microfluidics and microwells have enabled fast and accurate scRNA-seq.Thanks to the scRNA-seq technology, research has been able to establish the Human Cell Atlas since 2017 to map the characteristics of every cell type in the human body.The key steps involved in scRNA-seq include single-cell isolation and capture, cell lysis, reverse transcription, cDNA amplification, and library preparation.Advancements in microfluidics technology have led to more efficient and reliable methods for isolating single cells, including droplet and solid microfluidic techniques.The droplet microfluidic method separates individual cells using waterin-oil emulsions.The widely used 10X Genomics platform applies this technique in their kit.Alternatively, the solid microfluidic method uses physical partitions through diffusion and is often chosen for very limited clinical samples due to its lower throughput.Examples of solid microfluidic platforms include Fluidigm C1, which can capture a few hundred to around a thousand cells, and the higher throughput BD Rhapsody Single-Cell Analysis System, which uses a microwell technology to partition individual cells via diffusion.Recently, the scope of samples for scRNA-seq has been dramatically broadened.The 10X Chromium Gene Expression Flex platform, which is a probe-based method, can be applied to formalin-fixed paraffin-embedded (FFPE) tissues.M20 Genomics developed random primer based scRNA-seq platform that can be applied to FFPE tissues and bacteria [2].Metabolomics, the study of small molecules in cells, is now shifting towards the single-cell level.The single cell metabolomics

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