CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones
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CloneSeq : A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones. / Bavli, Danny; Sun, Xue; Kozulin, Chen; Ennis, Dena; Motzik, Alex; Biran, Alva; Brielle, Shlomi; Alajem, Adi; Meshorer, Eran; Buxboim, Amnon; Ram, Oren.
In: Developmental Cell, Vol. 56, No. 12, 2021, p. 1804-1817.e7.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - CloneSeq
T2 - A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones
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
N1 - Publisher Copyright: © 2021 Elsevier Inc.
PY - 2021
Y1 - 2021
N2 - 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.
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 - cancer clonal expansion
KW - cancer heterogeneity
KW - cellular stemness
KW - clone-to-clone variation
KW - CloneSeq technology
KW - drop-based microfluidics
KW - early differentiation
KW - embryonic stem cells
KW - single-cell RNA-seq
U2 - 10.1016/j.devcel.2021.04.026
DO - 10.1016/j.devcel.2021.04.026
M3 - Journal article
C2 - 34010629
AN - SCOPUS:85107289236
VL - 56
SP - 1804-1817.e7
JO - Developmental Cell
JF - Developmental Cell
SN - 1534-5807
IS - 12
ER -
ID: 380216494