Cellular reprogramming with ATOH1, GFI1, and POU4F3 implicate epigenetic changes and cell-cell signaling as obstacles to hair cell regeneration in mature mammals
Amrita A Iyer,
Ishwar Hosamani,
John D Nguyen,
Tiantian Cai,
Sunita Singh,
Melissa M McGovern,
Lisa Beyer,
Hongyuan Zhang,
Hsin-I Jen,
Rizwan Yousaf,
Onur Birol,
Jenny J Sun,
Russell S Ray,
Yehoash Raphael,
Neil Segil,
Andrew K Groves
Affiliations
Amrita A Iyer
Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, United States
Ishwar Hosamani
Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, United States
John D Nguyen
Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at USC, Los Angeles, United States
Tiantian Cai
Program in Developmental Biology, Baylor College of Medicine, Houston, United States
Sunita Singh
Department of Neuroscience, Baylor College of Medicine, Houston, United States
Melissa M McGovern
Department of Neuroscience, Baylor College of Medicine, Houston, United States
Lisa Beyer
Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, United States
Hongyuan Zhang
Department of Neuroscience, Baylor College of Medicine, Houston, United States
Hsin-I Jen
Program in Developmental Biology, Baylor College of Medicine, Houston, United States; Department of Neuroscience, Baylor College of Medicine, Houston, United States
Rizwan Yousaf
Department of Neuroscience, Baylor College of Medicine, Houston, United States
Onur Birol
Program in Developmental Biology, Baylor College of Medicine, Houston, United States
Jenny J Sun
Department of Neuroscience, Baylor College of Medicine, Houston, United States
Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at USC, Los Angeles, United States; Caruso Department of Otolaryngology-Head and Neck Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, United States
Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, United States; Program in Developmental Biology, Baylor College of Medicine, Houston, United States; Department of Neuroscience, Baylor College of Medicine, Houston, United States
Reprogramming of the cochlea with hair-cell-specific transcription factors such as ATOH1 has been proposed as a potential therapeutic strategy for hearing loss. ATOH1 expression in the developing cochlea can efficiently induce hair cell regeneration but the efficiency of hair cell reprogramming declines rapidly as the cochlea matures. We developed Cre-inducible mice to compare hair cell reprogramming with ATOH1 alone or in combination with two other hair cell transcription factors, GFI1 and POU4F3. In newborn mice, all transcription factor combinations tested produced large numbers of cells with the morphology of hair cells and rudimentary mechanotransduction properties. However, 1 week later, only a combination of ATOH1, GFI1 and POU4F3 could reprogram non-sensory cells of the cochlea to a hair cell fate, and these new cells were less mature than cells generated by reprogramming 1 week earlier. We used scRNA-seq and combined scRNA-seq and ATAC-seq to suggest at least two impediments to hair cell reprogramming in older animals. First, hair cell gene loci become less epigenetically accessible in non-sensory cells of the cochlea with increasing age. Second, signaling from hair cells to supporting cells, including Notch signaling, can prevent reprogramming of many supporting cells to hair cells, even with three hair cell transcription factors. Our results shed light on the molecular barriers that must be overcome to promote hair cell regeneration in the adult cochlea.