CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones

Danny Bavli; Xue Sun; Chen Kozulin; Dena Ennis; Alex Motzik; Alva Biran; Shlomi Brielle; Adi Alajem; Eran Meshorer; Amnon Buxboim; Oren Ram

doi:10.1016/j.devcel.2021.04.026

CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones

Danny Bavli, Xue Sun, Chen Kozulin, Dena Ennis, Alex Motzik, Alva Biran, Shlomi Brielle, Adi Alajem, Eran Meshorer, Amnon Buxboim, Oren Ram

The Hebrew University of Jerusalem

Research output: Contribution to journal › Article › peer-review

Abstract

Single-cell assays have revealed the importance of heterogeneity in many biological systems. However, limited sensitivity is a major hurdle for uncovering cellular variation. To overcome it, we developed CloneSeq, combining clonal expansion inside 3D hydrogel spheres and droplet-based RNA sequencing (RNA-seq). We show that clonal cells maintain similar transcriptional profiles and cell states. CloneSeq of lung cancer cells revealed cancer-specific subpopulations, including cancer stem-like cells, that were not revealed by scRNA-seq. Clonal expansion within 3D soft microenvironments supported cellular stemness of embryonic stem cells (ESCs) even without pluripotent media, and it improved epigenetic reprogramming efficiency of mouse embryonic fibroblasts. CloneSeq of ESCs revealed that the differentiation decision is made early during Oct4 downregulation and is maintained during early clonal expansion. Together, we show CloneSeq can be adapted to different biological systems to discover rare subpopulations by leveraging the enhanced sensitivity within clones.

Original language	English
Pages (from-to)	1804-1817.e7
Journal	Developmental Cell
Volume	56
Issue number	12
DOIs	https://doi.org/10.1016/j.devcel.2021.04.026
State	Published - 21 Jun 2021

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

3D culturing
CloneSeq technology
cancer clonal expansion
cancer heterogeneity
cellular stemness
clone-to-clone variation
drop-based microfluidics
early differentiation
embryonic stem cells
single-cell RNA-seq

All Science Journal Classification (ASJC) codes

Molecular Biology
General Biochemistry,Genetics and Molecular Biology
Developmental Biology
Cell Biology

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10.1016/j.devcel.2021.04.026

Cite this

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title = "CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones",

abstract = "Single-cell assays have revealed the importance of heterogeneity in many biological systems. However, limited sensitivity is a major hurdle for uncovering cellular variation. To overcome it, we developed CloneSeq, combining clonal expansion inside 3D hydrogel spheres and droplet-based RNA sequencing (RNA-seq). We show that clonal cells maintain similar transcriptional profiles and cell states. CloneSeq of lung cancer cells revealed cancer-specific subpopulations, including cancer stem-like cells, that were not revealed by scRNA-seq. Clonal expansion within 3D soft microenvironments supported cellular stemness of embryonic stem cells (ESCs) even without pluripotent media, and it improved epigenetic reprogramming efficiency of mouse embryonic fibroblasts. CloneSeq of ESCs revealed that the differentiation decision is made early during Oct4 downregulation and is maintained during early clonal expansion. Together, we show CloneSeq can be adapted to different biological systems to discover rare subpopulations by leveraging the enhanced sensitivity within clones.",

keywords = "3D culturing, CloneSeq technology, cancer clonal expansion, cancer heterogeneity, cellular stemness, clone-to-clone variation, drop-based microfluidics, early differentiation, embryonic stem cells, single-cell RNA-seq",

author = "Danny Bavli and Xue Sun and Chen Kozulin and Dena Ennis and Alex Motzik and Alva Biran and Shlomi Brielle and Adi Alajem and Eran Meshorer and Amnon Buxboim and Oren Ram",

note = "Publisher Copyright: {\textcopyright} 2021 Elsevier Inc.",

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doi = "10.1016/j.devcel.2021.04.026",

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AU - Bavli, Danny

AU - Sun, Xue

AU - Kozulin, Chen

AU - Ennis, Dena

AU - Motzik, Alex

AU - Biran, Alva

AU - Brielle, Shlomi

AU - Alajem, Adi

AU - Meshorer, Eran

AU - Buxboim, Amnon

AU - Ram, Oren

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AB - Single-cell assays have revealed the importance of heterogeneity in many biological systems. However, limited sensitivity is a major hurdle for uncovering cellular variation. To overcome it, we developed CloneSeq, combining clonal expansion inside 3D hydrogel spheres and droplet-based RNA sequencing (RNA-seq). We show that clonal cells maintain similar transcriptional profiles and cell states. CloneSeq of lung cancer cells revealed cancer-specific subpopulations, including cancer stem-like cells, that were not revealed by scRNA-seq. Clonal expansion within 3D soft microenvironments supported cellular stemness of embryonic stem cells (ESCs) even without pluripotent media, and it improved epigenetic reprogramming efficiency of mouse embryonic fibroblasts. CloneSeq of ESCs revealed that the differentiation decision is made early during Oct4 downregulation and is maintained during early clonal expansion. Together, we show CloneSeq can be adapted to different biological systems to discover rare subpopulations by leveraging the enhanced sensitivity within clones.

KW - 3D culturing

KW - CloneSeq technology

KW - cancer clonal expansion

KW - cancer heterogeneity

KW - cellular stemness

KW - clone-to-clone variation

KW - drop-based microfluidics

KW - early differentiation

KW - embryonic stem cells

KW - single-cell RNA-seq

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DO - 10.1016/j.devcel.2021.04.026

M3 - مقالة

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SN - 1534-5807

VL - 56

SP - 1804-1817.e7

JO - Developmental Cell

JF - Developmental Cell

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ER -

CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones

Abstract

UN SDGs

Keywords

All Science Journal Classification (ASJC) codes

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