Cochlear organoids reveal transcriptional programs of postnatal hair cell differentiation from supporting cells

Gurmannat Kalra; Danielle Lenz; Dunia Abdul-Aziz; Craig Hanna; Mahashweta Basu; Brian R Herb; Carlo Colantuoni; Beatrice Milon; Madhurima Saxena; Amol C Shetty; Ronna Hertzano; Ramesh A Shivdasani; Seth A Ament; Albert S B Edge

doi:10.1016/j.celrep.2023.113421

Cochlear organoids reveal transcriptional programs of postnatal hair cell differentiation from supporting cells

Cell Rep. 2023 Nov 28;42(11):113421. doi: 10.1016/j.celrep.2023.113421. Epub 2023 Nov 11.

Authors

Affiliations

¹ Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
² Department of Otolaryngology, Harvard Medical School, Boston, MA, USA; Eaton-Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA, USA.
³ Eaton-Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA, USA.
⁴ Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
⁵ Department of Otorhinolaryngology-Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA.
⁶ Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
⁷ National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA.
⁸ Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
⁹ Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Otorhinolaryngology-Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA.
¹⁰ Department of Otolaryngology, Harvard Medical School, Boston, MA, USA; Eaton-Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, USA. Electronic address: albert_edge@meei.harvard.edu.

Abstract

We explore the changes in chromatin accessibility and transcriptional programs for cochlear hair cell differentiation from postmitotic supporting cells using organoids from postnatal cochlea. The organoids contain cells with transcriptional signatures of differentiating vestibular and cochlear hair cells. Construction of trajectories identifies Lgr5+ cells as progenitors for hair cells, and the genomic data reveal gene regulatory networks leading to hair cells. We validate these networks, demonstrating dynamic changes both in expression and predicted binding sites of transcription factors (TFs) during organoid differentiation. We identify known regulators of hair cell development, Atoh1, Pou4f3, and Gfi1, and the analysis predicts the regulatory factors Tcf4, an E-protein and heterodimerization partner of Atoh1, and Ddit3, a CCAAT/enhancer-binding protein (C/EBP) that represses Hes1 and activates transcription of Wnt-signaling-related genes. Deciphering the signals for hair cell regeneration from mammalian cochlear supporting cells reveals candidates for hair cell (HC) regeneration, which is limited in the adult.

Keywords: ATAC sequencing; CP: Stem cell research; cochlea; gene expression analysis; sensory hair cells; single-cell RNA sequencing.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Basic Helix-Loop-Helix Transcription Factors* / metabolism
Cell Differentiation / genetics
Cochlea*
Mammals / metabolism
Organoids / metabolism
Transcription Factors / genetics
Transcription Factors / metabolism

Substances

Basic Helix-Loop-Helix Transcription Factors
Transcription Factors

Grants and funding

R01 DC014089/DC/NIDCD NIH HHS/United States