Faculty Collaboration Database

Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte. Nature 2017 Nov 02;551(7678):100-104

Date

10/27/2017

Pubmed ID

29072293

Pubmed Central ID

PMC5954984

DOI

10.1038/nature24454

Scopus ID

2-s2.0-85032797966 (requires institutional sign-in at Scopus site)   143 Citations

Abstract

Direct lineage conversion offers a new strategy for tissue regeneration and disease modelling. Despite recent success in directly reprogramming fibroblasts into various cell types, the precise changes that occur as fibroblasts progressively convert to the target cell fates remain unclear. The inherent heterogeneity and asynchronous nature of the reprogramming process renders it difficult to study this process using bulk genomic techniques. Here we used single-cell RNA sequencing to overcome this limitation and analysed global transcriptome changes at early stages during the reprogramming of mouse fibroblasts into induced cardiomyocytes (iCMs). Using unsupervised dimensionality reduction and clustering algorithms, we identified molecularly distinct subpopulations of cells during reprogramming. We also constructed routes of iCM formation, and delineated the relationship between cell proliferation and iCM induction. Further analysis of global gene expression changes during reprogramming revealed unexpected downregulation of factors involved in mRNA processing and splicing. Detailed functional analysis of the top candidate splicing factor, Ptbp1, revealed that it is a critical barrier for the acquisition of cardiomyocyte-specific splicing patterns in fibroblasts. Concomitantly, Ptbp1 depletion promoted cardiac transcriptome acquisition and increased iCM reprogramming efficiency. Additional quantitative analysis of our dataset revealed a strong correlation between the expression of each reprogramming factor and the progress of individual cells through the reprogramming process, and led to the discovery of new surface markers for the enrichment of iCMs. In summary, our single-cell transcriptomics approaches enabled us to reconstruct the reprogramming trajectory and to uncover intermediate cell populations, gene pathways and regulators involved in iCM induction.

Author List

Liu Z, Wang L, Welch JD, Ma H, Zhou Y, Vaseghi HR, Yu S, Wall JB, Alimohamadi S, Zheng M, Yin C, Shen W, Prins JF, Liu J, Qian L

Author

Ziqing Liu PhD Assistant Professor in the Physiology department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Algorithms
Animals
Cell Lineage
Cellular Reprogramming
Down-Regulation
Fibroblasts
GATA4 Transcription Factor
Heterogeneous-Nuclear Ribonucleoproteins
MEF2 Transcription Factors
Mice
Myocytes, Cardiac
Polypyrimidine Tract-Binding Protein
RNA Splicing
RNA, Messenger
Single-Cell Analysis
T-Box Domain Proteins
Transcriptome