High-throughput single cell -omics using semi-permeable capsules

Area of Science:

• Biotechnology
• Genomics
• Cell Biology

Background:

• Biological systems exhibit complexity and heterogeneity, requiring advanced tools for phenotype and genotype analysis.
• Current single-cell omics assays face limitations in multi-step biochemical assays and analyte retention.
• Previous work established foundational technology for semi-permeable capsules (SPCs).

Purpose of the Study:

• To present a versatile SPC-based technology for high-throughput nucleic acid assays.
• To demonstrate the utility of SPCs for single-cell RNA sequencing (scRNA-Seq) and other applications.
• To overcome limitations of droplet microfluidics in cell cultivation and analyte retention.

Main Methods:

• Development of semi-permeable capsules (SPCs) for biochemical assays.
• Application of SPCs for digital PCR, genome sequencing, and scRNA-Seq.
• Performing scRNA-Seq on white blood cells from hematopoietic disorder patients using the capsule-based sequencing approach (CapSeq).

Main Results:

• SPCs support single-cell cultivation and clonal expansion, unlike droplet microfluidics.
• CapSeq demonstrated superior transcript capture, particularly for challenging cell types.
• Analysis of acute myeloid leukemia (AML) samples revealed significant transcriptome changes in mature granulocytes and monocytes.

Conclusions:

• SPC technology offers a customizable, sensitive, and broadly applicable tool for single-cell omics.
• CapSeq provides accurate representation of cellular heterogeneity, yielding insights into immune system dysfunction.
• The ability to clonally expand cells positions SPCs as valuable for scalable, easy-to-use single-cell analyses.