High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor

• Published in: PLoS genetics Vol. 14; no. 7; p. e1007552
• Main Authors: Yamashita, Tetsuji, Zheng, Fei, Finkelstein, David, Kellard, Zoe, Carter, Robert, Rosencrance, Celeste D, Sugino, Ken, Easton, John, Gawad, Charles, Zuo, Jian
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 31.07.2018; Public Library of Science (PLoS)
• Subjects: Animals; Animals, Newborn; Basic Helix-Loop-Helix Transcription Factors - genetics; Basic Helix-Loop-Helix Transcription Factors - metabolism; Biology; Biology and Life Sciences; Cellular Reprogramming - genetics; Cochlea; Ears & hearing; Funding; Gene expression; Gene Expression Profiling - methods; Genetic aspects; Genetic research; Hair; Hair cells; Hair Cells, Auditory - physiology; Hearing loss; Islet-1 protein; LIM-Homeodomain Proteins - genetics; LIM-Homeodomain Proteins - metabolism; Math1 protein; Medicine and Health Sciences; Mice; Mice, Inbred C57BL; Mice, Transgenic; Neurobiology; Neurosciences; Nuclear reprogramming; Physical Sciences; Regeneration - genetics; Regenerative medicine; Research and Analysis Methods; Ribonucleic acid; RNA; RNA sequencing; Sequence Analysis, RNA - methods; Single-Cell Analysis - methods; Software; Transcription (Genetics); Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transgenic mice; United States > US; Tennessee
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1007552

In vivo direct conversion of differentiated cells holds promise for regenerative medicine; however, improving the conversion efficiency and producing functional target cells remain challenging. Ectopic Atoh1 expression in non-sensory supporting cells (SCs) in mouse cochleae induces their partial conversion to hair cells (HCs) at low efficiency. Here, we performed single-cell RNA sequencing of whole mouse sensory epithelia harvested at multiple time points after conditional overexpression of Atoh1. Pseudotemporal ordering revealed that converted HCs (cHCs) are present along a conversion continuum that correlates with both endogenous and exogenous Atoh1 expression. Bulk sequencing of isolated cell populations and single-cell qPCR confirmed 51 transcription factors, including Isl1, are differentially expressed among cHCs, SCs and HCs. In transgenic mice, co-overexpression of Atoh1 and Isl1 enhanced the HC conversion efficiency. Together, our study shows how high-resolution transcriptional profiling of direct cell conversion can identify co-reprogramming factors required for efficient conversion.