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Related Experiment Video

Updated: Jul 4, 2025

Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations
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3D Amplified Single-Cell RNA and Protein Imaging Identifies Oncogenic Transcript Subtypes in B-Cell Acute

Suyeon Shin1, Yoon-Jin Kim1, Hyo Geun Yun1

  • 1Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea.

ACS Nano
|February 6, 2024
PubMed
Summary

A new 3D imaging technique, 4DRCA, enables simultaneous single-cell RNA and protein quantification. This accessible method aids in understanding tumor heterogeneity and personalizing cancer treatments.

Keywords:
3D amplified cell imaging3D digital rolling circle amplificationB-cell acute lymphoblastic leukemiasimultaneous RNA and protein profilingsingle-cell analysis

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Area of Science:

  • Biotechnology
  • Molecular Biology
  • Cell Biology

Background:

  • Single-cell analysis of RNA and protein is crucial for understanding tumor heterogeneity and treatment response.
  • Current advanced 3D imaging techniques are often inaccessible, limiting their widespread adoption.

Purpose of the Study:

  • To introduce a novel, accessible 3D single-cell imaging technique for simultaneous RNA and protein quantification.
  • To demonstrate the utility of this technique in analyzing T-lymphocytes and leukemia cells.

Main Methods:

  • Developed 3D digital rolling circle amplification (4DRCA) for multiplexed, amplified digital quantification of single-cell RNA and proteins.
  • Integrated single-cell RNA and protein assays to generate spectrally distinguishable DNA amplicons.
  • Utilized open-source algorithms for 3D deconvolution and automatic gating for amplicon enumeration.

Main Results:

  • Successfully quantified surface protein markers and cytokine transcripts simultaneously in T-lymphocytes.
  • Differentiated BCR-ABL1 fusion transcript-positive B-cell acute lymphoblastic leukemia cells based on CD19 protein expression.
  • Demonstrated sensitive and accurate single-cell RNA and protein profiling.

Conclusions:

  • 4DRCA offers an accessible and extensible platform for multiplexed single-cell RNA and protein analysis.
  • This technique has broad applicability in cell-based diagnostic workflows.
  • Enables enhanced understanding of cellular heterogeneity and improved disease monitoring.