Abstract 1345: Advances in single cell whole transcriptome analysis: Single nucleus RNAseq and simultaneous protein and mRNA profiling using the BD RhapsodyTMSingle-Cell Analysis system and BD®AbSeq

Abstract Considerable evidence suggests that breast cancer development and metastasis are driven by cancer stem-like cells (CSCs). Due to their unique role in tumor initiation, the interaction between CSCs and stromal cells is especially critical. In this work, we developed a platform to reliably isolate single cells in suspension and grow single-cell-derived spheres for functional enrichment of CSCs. The platform also allows adherent culture of stromal cells for cancer-stromal interaction. As a proof of concept, we grew SUM149 breast cancer cells and successfully formed single-cell-derived spheres. Cancer-associated fibroblasts (CAFs) as stromal cells were found to significantly enhance the formation and growth of cancer spheres, indicating elevated tumor-initiation potential. After on-chip culture for 14 days, we retrieved single-cell derived spheres with and without CAF co-culture for single-cell transcriptome sequencing. Whole transcriptome analysis highlights that CAF co-culture can boost cancer stemness especially ALDHhigh CSCs and alter epithelial/mesenchymal status. Single-cell resolution allows identification of individual CSCs and investigation of cancer cellular heterogeneity. Incorporating whole transcriptome sequencing data with public patient database, we discovered novel genes associated with cancer-CAF interaction and critical to patient survival. The preliminary works demonstrated a reliable platform for enrichment of CSCs and studies of cancer-stromal interaction.

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Ribosomal RNA depletion for single-cell whole transcriptome analysis

The Proceedings of Mechanical Engineering Congress Japan ◽

10.1299/jsmemecj.2017.j0530202 ◽

2017 ◽

Vol 2017 (0) ◽

pp. J0530202

Author(s):

Arata TSUCHIDA ◽

Shota HATA ◽

Ryuzi YOKOKAWA ◽

Hidetoshi KOTERA ◽

Hirofumi SHINTAKU

Keyword(s):

Single Cell ◽

Ribosomal Rna ◽

Transcriptome Analysis ◽

Whole Transcriptome Analysis ◽

Whole Transcriptome ◽

Rna Depletion

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Faculty Opinions recommendation of mRNA-Seq whole-transcriptome analysis of a single cell.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1160539.620905 ◽

2009 ◽

Author(s):

Deyou Zheng

Keyword(s):

Single Cell ◽

Transcriptome Analysis ◽

Whole Transcriptome Analysis ◽

Whole Transcriptome

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mRNA-Seq whole-transcriptome analysis of a single cell

Nature Methods ◽

10.1038/nmeth.1315 ◽

2009 ◽

Vol 6 (5) ◽

pp. 377-382 ◽

Cited By ~ 1325

Author(s):

Fuchou Tang ◽

Catalin Barbacioru ◽

Yangzhou Wang ◽

Ellen Nordman ◽

Clarence Lee ◽

...

Keyword(s):

Single Cell ◽

Transcriptome Analysis ◽

Whole Transcriptome Analysis ◽

Whole Transcriptome

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Comparative whole transcriptome analysis ofLocusta migratoriarevealed differences in long-non-coding RNAs between segragation and gregarious phase locusts

10.1603/ice.2016.111798 ◽

2016 ◽

Author(s):

Young Ho Koh

Keyword(s):

Transcriptome Analysis ◽

Non Coding Rnas ◽

Whole Transcriptome Analysis ◽

Whole Transcriptome

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Single-Cell Transcriptome Analysis as a Promising Tool to Study Pluripotent Stem Cell Reprogramming

International Journal of Molecular Sciences ◽

10.3390/ijms22115988 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5988

Author(s):

Hyun Kyu Kim ◽

Tae Won Ha ◽

Man Ryul Lee

Keyword(s):

Stem Cells ◽

Single Cell ◽

Cell Fate ◽

Human Cell ◽

Transcriptome Analysis ◽

Single Cell Analysis ◽

Embryonic Stem ◽

Single Cell Level ◽

Cell Analysis ◽

Cell Level

Cells are the basic units of all organisms and are involved in all vital activities, such as proliferation, differentiation, senescence, and apoptosis. A human body consists of more than 30 trillion cells generated through repeated division and differentiation from a single-cell fertilized egg in a highly organized programmatic fashion. Since the recent formation of the Human Cell Atlas consortium, establishing the Human Cell Atlas at the single-cell level has been an ongoing activity with the goal of understanding the mechanisms underlying diseases and vital cellular activities at the level of the single cell. In particular, transcriptome analysis of embryonic stem cells at the single-cell level is of great importance, as these cells are responsible for determining cell fate. Here, we review single-cell analysis techniques that have been actively used in recent years, introduce the single-cell analysis studies currently in progress in pluripotent stem cells and reprogramming, and forecast future studies.

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